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The structure of the DNA double helix (type B-DNA). The atoms in the structure are colour-coded by element and the detailed structures of two base pairs are shown in the bottom right.

Simplified diagram

Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids. Alongside proteins, lipids and complex carbohydrates ( polysaccharides), nucleic acids are one of the four major types of macromolecules that are essential for all known forms of life.

The two DNA strands are known as polynucleotides as they are composed of simpler monomeric units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases ( cytosine [C], guanine [G], adenine [A] or thymine [T]), a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds (known as the phosphodiester linkage) between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. The nitrogenous bases of the two separate polynucleotide strands are bound together, according to base pairing rules (A with T and C with G), with hydrogen bonds to make double-stranded DNA. The complementary nitrogenous bases are divided into two groups, the single-ringed pyrimidines and the double-ringed purines. In DNA, the pyrimidines are thymine and cytosine; the purines are adenine and guanine.

Both strands of double-stranded DNA store the same biological information. This information is replicated when the two strands separate. A large part of DNA (more than 98% for humans) is non-coding, meaning that these sections do not serve as patterns for protein sequences. The two strands of DNA run in opposite directions to each other and are thus antiparallel. Attached to each sugar is one of four types of nucleobases (or bases). It is the sequence of these four nucleobases along the backbone that encodes genetic information. RNA strands are created using DNA strands as a template in a process called transcription, where DNA bases are exchanged for their corresponding bases except in the case of thymine (T), for which RNA substitutes uracil (U). Under the genetic code, these RNA strands specify the sequence of amino acids within proteins in a process called translation.

Within eukaryotic cells, DNA is organized into long structures called chromosomes. Before typical cell division, these chromosomes are duplicated in the process of DNA replication, providing a complete set of chromosomes for each daughter cell. Eukaryotic organisms ( animals, plants, fungi and protists) store most of their DNA inside the cell nucleus as nuclear DNA, and some in the mitochondria as mitochondrial DNA or in chloroplasts as chloroplast DNA. In contrast, prokaryotes ( bacteria and archaea) store their DNA only in the cytoplasm, in circular chromosomes. Within eukaryotic chromosomes, chromatin proteins, such as histones, compact and organize DNA. These compacting structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.

Properties

Chemical structure of DNA; hydrogen bonds shown as dotted lines. Each end of the double helix has an exposed 5' phosphate on one strand and an exposed 3′ hydroxyl group (-OH) on the other.

DNA is a long polymer made from repeating units called nucleotides. The structure of DNA is dynamic along its length, being capable of coiling into tight loops and other shapes. In all species it is composed of two helical chains, bound to each other by hydrogen bonds. Both chains are coiled around the same axis, and have the same pitch of 34 ångströms (3.4 nm). The pair of chains have a radius of 10 Å (1.0 nm). According to another study, when measured in a different solution, the DNA chain measured 22-26 Å (2.2-2.6 nm) wide, and one nucleotide unit measured 3.3 Å (0.33 nm) long. The buoyant density of most DNA is 1.7g/cm ³.

DNA does not usually exist as a single strand, but instead as a pair of strands that are held tightly together. These two long strands coil around each other, in the shape of a double helix. The nucleotide contains both a segment of the backbone of the molecule (which holds the chain together) and a nucleobase (which interacts with the other DNA strand in the helix). A nucleobase linked to a sugar is called a nucleoside, and a base linked to a sugar and to one or more phosphate groups is called a nucleotide. A biopolymer comprising multiple linked nucleotides (as in DNA) is called a polynucleotide.

The backbone of the DNA strand is made from alternating phosphate and sugar groups. The sugar in DNA is 2-deoxyribose, which is a pentose (five- carbon) sugar. The sugars are joined by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings. These are known as the 3′-end (three prime end), and 5′-end (five prime end) carbons, the prime symbol being used to distinguish these carbon atoms from those of the base to which the deoxyribose forms a glycosidic bond.

Therefore, any DNA strand normally has one end at which there is a phosphate group attached to the 5′ carbon of a ribose (the 5′ phosphoryl) and another end at which there is a free hydroxyl group attached to the 3′ carbon of a ribose (the 3′ hydroxyl). The orientation of the 3′ and 5′ carbons along the sugar-phosphate backbone confers directionality (sometimes called polarity) to each DNA strand. In a nucleic acid double helix, the direction of the nucleotides in one strand is opposite to their direction in the other strand: the strands are antiparallel. The asymmetric ends of DNA strands are said to have a directionality of five prime end (5′ ), and three prime end (3′), with the 5′ end having a terminal phosphate group and the 3′ end a terminal hydroxyl group. One major difference between DNA and RNA is the sugar, with the 2-deoxyribose in DNA being replaced by the related pentose sugar ribose in RNA.

A section of DNA. The bases lie horizontally between the two spiraling strands[15] (animated version).

The DNA double helix is stabilized primarily by two forces: hydrogen bonds between nucleotides and base-stacking interactions among aromatic nucleobases. The four bases found in DNA are adenine (A), cytosine (C), guanine (G) and thymine (T). These four bases are attached to the sugar-phosphate to form the complete nucleotide, as shown for adenosine monophosphate. Adenine pairs with thymine and guanine pairs with cytosine, forming A-T and G-C base pairs.

Nucleobase classification

The nucleobases are classified into two types: the purines, A and G, which are fused five- and six-membered heterocyclic compounds, and the pyrimidines, the six-membered rings C and T. A fifth pyrimidine nucleobase, uracil (U), usually takes the place of thymine in RNA and differs from thymine by lacking a methyl group on its ring. In addition to RNA and DNA, many artificial nucleic acid analogues have been created to study the properties of nucleic acids, or for use in biotechnology.

Non-canonical bases

Modified bases occur in DNA. The first of these recognized was 5-methylcytosine, which was found in the genome of Mycobacterium tuberculosis in 1925. The reason for the presence of these noncanonical bases in bacterial viruses ( bacteriophages) is to avoid the restriction enzymes present in bacteria. This enzyme system acts at least in part as a molecular immune system protecting bacteria from infection by viruses. Modifications of the bases cytosine and adenine, the more common and modified DNA bases, play vital roles in the epigenetic control of gene expression in plants and animals.

A number of noncanonical bases are known to occur in DNA. Most of these are modifications of the canonical bases plus uracil.

Modified Adenine

N6-carbamoyl-methyladenine

N6-methyadenine

Modified Guanine

7-Deazaguanine

7-Methylguanine

Modified Cytosine

N4-Methylcytosine

5-Carboxylcytosine

5-Formylcytosine

5-Glycosylhydroxymethylcytosine

5-Hydroxycytosine

5-Methylcytosine

Modified Thymidine

α-Glutamythymidine

α-Putrescinylthymine

Uracil and modifications

Base J

Uracil

5-Dihydroxypentauracil

5-Hydroxymethyldeoxyuracil

Others

Deoxyarchaeosine

2,6-Diaminopurine (2-Aminoadenine)

DNA major and minor grooves. The latter is a binding site for the Hoechst stain dye 33258.

Twin helical strands form the DNA backbone. Another double helix may be found tracing the spaces, or grooves, between the strands. These voids are adjacent to the base pairs and may provide a binding site. As the strands are not symmetrically located with respect to each other, the grooves are unequally sized. The major groove is 22 ångströms (2.2 nm) wide, while the minor groove is 12 Å (1.2 nm) in width. Due to the larger width of the major groove, the edges of the bases are more accessible in the major groove than in the minor groove. As a result, proteins such as transcription factors that can bind to specific sequences in double-stranded DNA usually make contact with the sides of the bases exposed in the major groove. This situation varies in unusual conformations of DNA within the cell (see below), but the major and minor grooves are always named to reflect the differences in width that would be seen if the DNA was twisted back into the ordinary B form.

Base pairing

In a DNA double helix, each type of nucleobase on one strand bonds with just one type of nucleobase on the other strand. This is called complementary base pairing. Purines form hydrogen bonds to pyrimidines, with adenine bonding only to thymine in two hydrogen bonds, and cytosine bonding only to guanine in three hydrogen bonds. This arrangement of two nucleotides binding together across the double helix (from six-carbon ring to six-carbon ring) is called a Watson-Crick base pair. DNA with high GC-content is more stable than DNA with low GC-content. A Hoogsteen base pair (hydrogen bonding the 6-carbon ring to the 5-carbon ring) is a rare variation of base-pairing. As hydrogen bonds are not covalent, they can be broken and rejoined relatively easily. The two strands of DNA in a double helix can thus be pulled apart like a zipper, either by a mechanical force or high temperature. As a result of this base pair complementarity, all the information in the double-stranded sequence of a DNA helix is duplicated on each strand, which is vital in DNA replication. This reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in organisms.

ssDNA vs. dsDNA

Most DNA molecules are actually two polymer strands, bound together in a helical fashion by noncovalent bonds; this double-stranded (dsDNA) structure is maintained largely by the intrastrand base stacking interactions, which are strongest for G,C stacks. The two strands can come apart-a process known as melting-to form two single-stranded DNA (ssDNA) molecules. Melting occurs at high temperatures, low salt and high pH (low pH also melts DNA, but since DNA is unstable due to acid depurination, low pH is rarely used).

The stability of the dsDNA form depends not only on the GC-content (% G,C basepairs) but also on sequence (since stacking is sequence specific) and also length (longer molecules are more stable). The stability can be measured in various ways; a common way is the melting temperature (also called value), which is the temperature at which 50% of the double-strand molecules are converted to single-strand molecules; melting temperature is dependent on ionic strength and the concentration of DNA. As a result, it is both the percentage of GC base pairs and the overall length of a DNA double helix that determines the strength of the association between the two strands of DNA. Long DNA helices with a high GC-content have more strongly interacting strands, while short helices with high AT content have more weakly interacting strands. In biology, parts of the DNA double helix that need to separate easily, such as the TATAAT Pribnow box in some promoters, tend to have a high AT content, making the strands easier to pull apart.

In the laboratory, the strength of this interaction can be measured by finding the melting temperature necessary to break half of the hydrogen bonds. When all the base pairs in a DNA double helix melt, the strands separate and exist in solution as two entirely independent molecules. These single-stranded DNA molecules have no single common shape, but some conformations are more stable than others.

Schematic karyogram of a human. It shows 22 homologous chromosomes, both the female (XX) and male (XY) versions of the sex chromosome (bottom right), as well as the mitochondrial genome (to scale at bottom left). The blue scale to the left of each chromosome pair (and the mitochondrial genome) shows its length in terms of millions of DNA base pairs.

In humans, the total female diploid nuclear genome per cell extends for 6.37 Gigabase pairs (Gbp), is 208.23 cm long and weighs 6.51 picograms (pg). Male values are 6.27 Gbp, 205.00 cm, 6.41 pg. Each DNA polymer can contain hundreds of millions of nucleotides, such as in chromosome 1. Chromosome 1 is the largest human chromosome with approximately 220 million base pairs, and would be 85 mm long if straightened.

In eukaryotes, in addition to nuclear DNA, there is also mitochondrial DNA (mtDNA) which encodes certain proteins used by the mitochondria. The mtDNA is usually relatively small in comparison to the nuclear DNA. For example, the human mitochondrial DNA forms closed circular molecules, each of which contains 16,569 DNA base pairs, with each such molecule normally containing a full set of the mitochondrial genes. Each human mitochondrion contains, on average, approximately 5 such mtDNA molecules. Each human cell contains approximately 100 mitochondria, giving a total number of mtDNA molecules per human cell of approximately 500. However, the amount of mitochondria per cell also varies by cell type, and an egg cell can contain 100,000 mitochondria, corresponding to up to 1,500,000 copies of the mitochondrial genome (constituting up to 90% of the DNA of the cell).

Sense and antisense

A DNA sequence is called a "sense" sequence if it is the same as that of a messenger RNA copy that is translated into protein. The sequence on the opposite strand is called the "antisense" sequence. Both sense and antisense sequences can exist on different parts of the same strand of DNA (i.e. both strands can contain both sense and antisense sequences). In both prokaryotes and eukaryotes, antisense RNA sequences are produced, but the functions of these RNAs are not entirely clear. One proposal is that antisense RNAs are involved in regulating gene expression through RNA-RNA base pairing.

A few DNA sequences in prokaryotes and eukaryotes, and more in plasmids and viruses, blur the distinction between sense and antisense strands by having overlapping genes. In these cases, some DNA sequences do double duty, encoding one protein when read along one strand, and a second protein when read in the opposite direction along the other strand. In bacteria, this overlap may be involved in the regulation of gene transcription, while in viruses, overlapping genes increase the amount of information that can be encoded within the small viral genome.

Supercoiling

DNA can be twisted like a rope in a process called DNA supercoiling. With DNA in its "relaxed" state, a strand usually circles the axis of the double helix once every 10.4 base pairs, but if the DNA is twisted the strands become more tightly or more loosely wound. If the DNA is twisted in the direction of the helix, this is positive supercoiling, and the bases are held more tightly together. If they are twisted in the opposite direction, this is negative supercoiling, and the bases come apart more easily. In nature, most DNA has slight negative supercoiling that is introduced by enzymes called topoisomerases. These enzymes are also needed to relieve the twisting stresses introduced into DNA strands during processes such as transcription and DNA replication.

Alternative DNA structures

From left to right, the structures of A, B and Z-DNA

DNA exists in many possible conformations that include A-DNA, B-DNA, and Z-DNA forms, although only B-DNA and Z-DNA have been directly observed in functional organisms. The conformation that DNA adopts depends on the hydration level, DNA sequence, the amount and direction of supercoiling, chemical modifications of the bases, the type and concentration of metal ions, and the presence of polyamines in solution.

The first published reports of A-DNA X-ray diffraction patterns-and also B-DNA-used analyses based on Patterson functions that provided only a limited amount of structural information for oriented fibers of DNA. An alternative analysis was proposed by Wilkins et al. in 1953 for the B-DNA X-ray diffraction-scattering patterns of highly hydrated DNA fibers in terms of squares of Bessel functions. In the same journal, James Watson and Francis Crick presented their molecular modeling analysis of the DNA X-ray diffraction patterns to suggest that the structure was a double helix.

Although the B-DNA form is most common under the conditions found in cells, it is not a well-defined conformation but a family of related DNA conformations that occur at the high hydration levels present in cells. Their corresponding X-ray diffraction and scattering patterns are characteristic of molecular paracrystals with a significant degree of disorder.

Compared to B-DNA, the A-DNA form is a wider right-handed spiral, with a shallow, wide minor groove and a narrower, deeper major groove. The A form occurs under non-physiological conditions in partly dehydrated samples of DNA, while in the cell it may be produced in hybrid pairings of DNA and RNA strands, and in enzyme-DNA complexes. Segments of DNA where the bases have been chemically modified by methylation may undergo a larger change in conformation and adopt the Z form. Here, the strands turn about the helical axis in a left-handed spiral, the opposite of the more common B form. These unusual structures can be recognized by specific Z-DNA binding proteins and may be involved in the regulation of transcription.

Alternative DNA chemistry

For many years, exobiologists have proposed the existence of a shadow biosphere, a postulated microbial biosphere of Earth that uses radically different biochemical and molecular processes than currently known life. One of the proposals was the existence of lifeforms that use arsenic instead of phosphorus in DNA. A report in 2010 of the possibility in the bacterium GFAJ-1 was announced, though the research was disputed, and evidence suggests the bacterium actively prevents the incorporation of arsenic into the DNA backbone and other biomolecules.

Quadruplex structures

DNA quadruplex formed by telomere repeats. The looped conformation of the DNA backbone is very different from the typical DNA helix. The green spheres in the center represent potassium ions.[62]

At the ends of the linear chromosomes are specialized regions of DNA called telomeres. The main function of these regions is to allow the cell to replicate chromosome ends using the enzyme telomerase, as the enzymes that normally replicate DNA cannot copy the extreme 3′ ends of chromosomes. These specialized chromosome caps also help protect the DNA ends, and stop the DNA repair systems in the cell from treating them as damage to be corrected. In human cells, telomeres are usually lengths of single-stranded DNA containing several thousand repeats of a simple TTAGGG sequence.

These guanine-rich sequences may stabilize chromosome ends by forming structures of stacked sets of four-base units, rather than the usual base pairs found in other DNA molecules. Here, four guanine bases, known as a guanine tetrad, form a flat plate. These flat four-base units then stack on top of each other to form a stable G-quadruplex structure. These structures are stabilized by hydrogen bonding between the edges of the bases and chelation of a metal ion in the centre of each four-base unit. Other structures can also be formed, with the central set of four bases coming from either a single strand folded around the bases, or several different parallel strands, each contributing one base to the central structure.

In addition to these stacked structures, telomeres also form large loop structures called telomere loops, or T-loops. Here, the single-stranded DNA curls around in a long circle stabilized by telomere-binding proteins. At the very end of the T-loop, the single-stranded telomere DNA is held onto a region of double-stranded DNA by the telomere strand disrupting the double-helical DNA and base pairing to one of the two strands. This triple-stranded structure is called a displacement loop or D-loop.

Branched DNA

In DNA, fraying occurs when non-complementary regions exist at the end of an otherwise complementary double-strand of DNA. However, branched DNA can occur if a third strand of DNA is introduced and contains adjoining regions able to hybridize with the frayed regions of the pre-existing double-strand. Although the simplest example of branched DNA involves only three strands of DNA, complexes involving additional strands and multiple branches are also possible. Branched DNA can be used in nanotechnology to construct geometric shapes, see the section on uses in technology below.

Artificial bases

Several artificial nucleobases have been synthesized, and successfully incorporated in the eight-base DNA analogue named Hachimoji DNA. Dubbed S, B, P, and Z, these artificial bases are capable of bonding with each other in a predictable way (S-B and P-Z), maintain the double helix structure of DNA, and be transcribed to RNA. Their existence could be seen as an indication that there is nothing special about the four natural nucleobases that evolved on Earth. On the other hand, DNA is tightly related to RNA which does not only act as a transcript of DNA but also performs as molecular machines many tasks in cells. For this purpose it has to fold into a structure. It has been shown that to allow to create all possible structures at least four bases are required for the corresponding RNA, while a higher number is also possible but this would be against the natural principle of least effort.

The phosphate groups of DNA give it similar acidic properties to phosphoric acid and it can be considered as a strong acid. It will be fully ionized at a normal cellular pH, releasing protons which leave behind negative charges on the phosphate groups. These negative charges protect DNA from breakdown by hydrolysis by repelling nucleophiles which could hydrolyze it.

Macroscopic appearance

Impure DNA extracted from an orange

Pure DNA extracted from cells forms white, stringy clumps.

Chemical modifications and altered DNA packaging

Base modifications and DNA packaging

The expression of genes is influenced by how the DNA is packaged in chromosomes, in a structure called chromatin. Base modifications can be involved in packaging, with regions that have low or no gene expression usually containing high levels of methylation of cytosine bases. DNA packaging and its influence on gene expression can also occur by covalent modifications of the histone protein core around which DNA is wrapped in the chromatin structure or else by remodeling carried out by chromatin remodeling complexes (see Chromatin remodeling). There is, further, crosstalk between DNA methylation and histone modification, so they can coordinately affect chromatin and gene expression.

For one example, cytosine methylation produces 5-methylcytosine, which is important for X-inactivation of chromosomes. The average level of methylation varies between organisms-the worm Caenorhabditis elegans lacks cytosine methylation, while vertebrates have higher levels, with up to 1% of their DNA containing 5-methylcytosine. Despite the importance of 5-methylcytosine, it can deaminate to leave a thymine base, so methylated cytosines are particularly prone to mutations. Other base modifications include adenine methylation in bacteria, the presence of 5-hydroxymethylcytosine in the brain, and the glycosylation of uracil to produce the "J-base" in kinetoplastids.

A covalent adduct between a metabolically activated form of benzo[a]pyrene, the major mutagen in tobacco smoke, and DNA[82]

DNA can be damaged by many sorts of mutagens, which change the DNA sequence. Mutagens include oxidizing agents, alkylating agents and also high-energy electromagnetic radiation such as ultraviolet light and X-rays. The type of DNA damage produced depends on the type of mutagen. For example, UV light can damage DNA by producing thymine dimers, which are cross-links between pyrimidine bases. On the other hand, oxidants such as free radicals or hydrogen peroxide produce multiple forms of damage, including base modifications, particularly of guanosine, and double-strand breaks. A typical human cell contains about 150,000 bases that have suffered oxidative damage. Of these oxidative lesions, the most dangerous are double-strand breaks, as these are difficult to repair and can produce point mutations, insertions, deletions from the DNA sequence, and chromosomal translocations. These mutations can cause cancer. Because of inherent limits in the DNA repair mechanisms, if humans lived long enough, they would all eventually develop cancer. DNA damages that are naturally occurring, due to normal cellular processes that produce reactive oxygen species, the hydrolytic activities of cellular water, etc., also occur frequently. Although most of these damages are repaired, in any cell some DNA damage may remain despite the action of repair processes. These remaining DNA damages accumulate with age in mammalian postmitotic tissues. This accumulation appears to be an important underlying cause of aging.

Many mutagens fit into the space between two adjacent base pairs, this is called intercalation. Most intercalators are aromatic and planar molecules; examples include ethidium bromide, acridines, daunomycin, and doxorubicin. For an intercalator to fit between base pairs, the bases must separate, distorting the DNA strands by unwinding of the double helix. This inhibits both transcription and DNA replication, causing toxicity and mutations. As a result, DNA intercalators may be carcinogens, and in the case of thalidomide, a teratogen. Others such as benzo[a]pyrene diol epoxide and aflatoxin form DNA adducts that induce errors in replication. Nevertheless, due to their ability to inhibit DNA transcription and replication, other similar toxins are also used in chemotherapy to inhibit rapidly growing cancer cells.

Biological functions

Location of eukaryote nuclear DNA within the chromosomes

DNA usually occurs as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. The set of chromosomes in a cell makes up its genome; the human genome has approximately 3 billion base pairs of DNA arranged into 46 chromosomes. The information carried by DNA is held in the sequence of pieces of DNA called genes. Transmission of genetic information in genes is achieved via complementary base pairing. For example, in transcription, when a cell uses the information in a gene, the DNA sequence is copied into a complementary RNA sequence through the attraction between the DNA and the correct RNA nucleotides. Usually, this RNA copy is then used to make a matching protein sequence in a process called translation, which depends on the same interaction between RNA nucleotides. In an alternative fashion, a cell may copy its genetic information in a process called DNA replication. The details of these functions are covered in other articles; here the focus is on the interactions between DNA and other molecules that mediate the function of the genome.

Genes and genomes

Genomic DNA is tightly and orderly packed in the process called DNA condensation, to fit the small available volumes of the cell. In eukaryotes, DNA is located in the cell nucleus, with small amounts in mitochondria and chloroplasts. In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the nucleoid. The genetic information in a genome is held within genes, and the complete set of this information in an organism is called its genotype. A gene is a unit of heredity and is a region of DNA that influences a particular characteristic in an organism. Genes contain an open reading frame that can be transcribed, and regulatory sequences such as promoters and enhancers, which control transcription of the open reading frame.

In many species, only a small fraction of the total sequence of the genome encodes protein. For example, only about 1.5% of the human genome consists of protein-coding exons, with over 50% of human DNA consisting of non-coding repetitive sequences. The reasons for the presence of so much noncoding DNA in eukaryotic genomes and the extraordinary differences in genome size, or , among species, represent a long-standing puzzle known as the " C-value enigma". However, some DNA sequences that do not code protein may still encode functional non-coding RNA molecules, which are involved in the regulation of gene expression.

T7 RNA polymerase (blue) producing an mRNA (green) from a DNA template (orange)[101]

Some noncoding DNA sequences play structural roles in chromosomes. Telomeres and centromeres typically contain few genes but are important for the function and stability of chromosomes. An abundant form of noncoding DNA in humans are pseudogenes, which are copies of genes that have been disabled by mutation. These sequences are usually just molecular fossils, although they can occasionally serve as raw genetic material for the creation of new genes through the process of gene duplication and divergence.

Transcription and translation

A gene is a sequence of DNA that contains genetic information and can influence the phenotype of an organism. Within a gene, the sequence of bases along a DNA strand defines a messenger RNA sequence, which then defines one or more protein sequences. The relationship between the nucleotide sequences of genes and the amino-acid sequences of proteins is determined by the rules of translation, known collectively as the genetic code. The genetic code consists of three-letter 'words' called codons formed from a sequence of three nucleotides (e.g. ACT, CAG, TTT).

In transcription, the codons of a gene are copied into messenger RNA by RNA polymerase. This RNA copy is then decoded by a ribosome that reads the RNA sequence by base-pairing the messenger RNA to transfer RNA, which carries amino acids. Since there are 4 bases in 3-letter combinations, there are 64 possible codons (4 ³ combinations). These encode the twenty standard amino acids, giving most amino acids more than one possible codon. There are also three 'stop' or 'nonsense' codons signifying the end of the coding region; these are the TAG, TAA, and TGA codons, (UAG, UAA, and UGA on the mRNA).

DNA replication: The double helix is unwound by a helicase and topoisomerase. Next, one DNA polymerase produces the leading strand copy. Another DNA polymerase binds to the lagging strand. This enzyme makes discontinuous segments (called Okazaki fragments) before DNA ligase joins them together.

Replication

Cell division is essential for an organism to grow, but, when a cell divides, it must replicate the DNA in its genome so that the two daughter cells have the same genetic information as their parent. The double-stranded structure of DNA provides a simple mechanism for DNA replication. Here, the two strands are separated and then each strand's complementary DNA sequence is recreated by an enzyme called DNA polymerase. This enzyme makes the complementary strand by finding the correct base through complementary base pairing and bonding it onto the original strand. As DNA polymerases can only extend a DNA strand in a 5′ to 3′ direction, different mechanisms are used to copy the antiparallel strands of the double helix. In this way, the base on the old strand dictates which base appears on the new strand, and the cell ends up with a perfect copy of its DNA.

Extracellular nucleic acids

Naked extracellular DNA (eDNA), most of it released by cell death, is nearly ubiquitous in the environment. Its concentration in soil may be as high as 2 μg/L, and its concentration in natural aquatic environments may be as high at 88 μg/L. Various possible functions have been proposed for eDNA: it may be involved in horizontal gene transfer; it may provide nutrients; and it may act as a buffer to recruit or titrate ions or antibiotics. Extracellular DNA acts as a functional extracellular matrix component in the biofilms of several bacterial species. It may act as a recognition factor to regulate the attachment and dispersal of specific cell types in the biofilm; it may contribute to biofilm formation; and it may contribute to the biofilm's physical strength and resistance to biological stress.

Cell-free fetal DNA is found in the blood of the mother, and can be sequenced to determine a great deal of information about the developing fetus.

Under the name of environmental DNA eDNA has seen increased use in the natural sciences as a survey tool for ecology, monitoring the movements and presence of species in water, air, or on land, and assessing an area's biodiversity.

Neutrophil extracellular traps

Neutrophil extracellular traps (NETs) are networks of extracellular fibers, primarily composed of DNA, which allow neutrophils, a type of white blood cell, to kill extracellular pathogens while minimizing damage to the host cells.

Interactions with proteins

All the functions of DNA depend on interactions with proteins. These protein interactions can be non-specific, or the protein can bind specifically to a single DNA sequence. Enzymes can also bind to DNA and of these, the polymerases that copy the DNA base sequence in transcription and DNA replication are particularly important.

DNA-binding proteins

Interaction of DNA (in orange) with histones (in blue). These proteins' basic amino acids bind to the acidic phosphate groups on DNA.

Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. Within chromosomes, DNA is held in complexes with structural proteins. These proteins organize the DNA into a compact structure called chromatin. In eukaryotes, this structure involves DNA binding to a complex of small basic proteins called histones, while in prokaryotes multiple types of proteins are involved. The histones form a disk-shaped complex called a nucleosome, which contains two complete turns of double-stranded DNA wrapped around its surface. These non-specific interactions are formed through basic residues in the histones, making ionic bonds to the acidic sugar-phosphate backbone of the DNA, and are thus largely independent of the base sequence. Chemical modifications of these basic amino acid residues include methylation, phosphorylation, and acetylation. These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription. Other non-specific DNA-binding proteins in chromatin include the high-mobility group proteins, which bind to bent or distorted DNA. These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that make up chromosomes.

A distinct group of DNA-binding proteins is the DNA-binding proteins that specifically bind single-stranded DNA. In humans, replication protein A is the best-understood member of this family and is used in processes where the double helix is separated, including DNA replication, recombination, and DNA repair. These binding proteins seem to stabilize single-stranded DNA and protect it from forming stem-loops or being degraded by nucleases.

The lambda repressor helix-turn-helix transcription factor bound to its DNA target[124]

In contrast, other proteins have evolved to bind to particular DNA sequences. The most intensively studied of these are the various transcription factors, which are proteins that regulate transcription. Each transcription factor binds to one particular set of DNA sequences and activates or inhibits the transcription of genes that have these sequences close to their promoters. The transcription factors do this in two ways. Firstly, they can bind the RNA polymerase responsible for transcription, either directly or through other mediator proteins; this locates the polymerase at the promoter and allows it to begin transcription. Alternatively, transcription factors can bind enzymes that modify the histones at the promoter. This changes the accessibility of the DNA template to the polymerase.

As these DNA targets can occur throughout an organism's genome, changes in the activity of one type of transcription factor can affect thousands of genes. Consequently, these proteins are often the targets of the signal transduction processes that control responses to environmental changes or cellular differentiation and development. The specificity of these transcription factors' interactions with DNA come from the proteins making multiple contacts to the edges of the DNA bases, allowing them to "read" the DNA sequence. Most of these base-interactions are made in the major groove, where the bases are most accessible.

The restriction enzyme EcoRV (green) in a complex with its substrate DNA[128]

DNA-modifying enzymes

Nucleases and ligases

Nucleases are enzymes that cut DNA strands by catalyzing the hydrolysis of the phosphodiester bonds. Nucleases that hydrolyse nucleotides from the ends of DNA strands are called exonucleases, while endonucleases cut within strands. The most frequently used nucleases in molecular biology are the restriction endonucleases, which cut DNA at specific sequences. For instance, the EcoRV enzyme shown to the left recognizes the 6-base sequence 5′-GATATC-3′ and makes a cut at the horizontal line. In nature, these enzymes protect bacteria against phage infection by digesting the phage DNA when it enters the bacterial cell, acting as part of the restriction modification system. In technology, these sequence-specific nucleases are used in molecular cloning and DNA fingerprinting.

Enzymes called DNA ligases can rejoin cut or broken DNA strands. Ligases are particularly important in lagging strand DNA replication, as they join the short segments of DNA produced at the replication fork into a complete copy of the DNA template. They are also used in DNA repair and genetic recombination.

Topoisomerases and helicases

Topoisomerases are enzymes with both nuclease and ligase activity. These proteins change the amount of supercoiling in DNA. Some of these enzymes work by cutting the DNA helix and allowing one section to rotate, thereby reducing its level of supercoiling; the enzyme then seals the DNA break. Other types of these enzymes are capable of cutting one DNA helix and then passing a second strand of DNA through this break, before rejoining the helix. Topoisomerases are required for many processes involving DNA, such as DNA replication and transcription.

Helicases are proteins that are a type of molecular motor. They use the chemical energy in nucleoside triphosphates, predominantly adenosine triphosphate (ATP), to break hydrogen bonds between bases and unwind the DNA double helix into single strands. These enzymes are essential for most processes where enzymes need to access the DNA bases.

Polymerases

Polymerases are enzymes that synthesize polynucleotide chains from nucleoside triphosphates. The sequence of their products is created based on existing polynucleotide chains-which are called templates. These enzymes function by repeatedly adding a nucleotide to the 3′ hydroxyl group at the end of the growing polynucleotide chain. As a consequence, all polymerases work in a 5′ to 3′ direction. In the active site of these enzymes, the incoming nucleoside triphosphate base-pairs to the template: this allows polymerases to accurately synthesize the complementary strand of their template. Polymerases are classified according to the type of template that they use.

In DNA replication, DNA-dependent DNA polymerases make copies of DNA polynucleotide chains. To preserve biological information, it is essential that the sequence of bases in each copy are precisely complementary to the sequence of bases in the template strand. Many DNA polymerases have a proofreading activity. Here, the polymerase recognizes the occasional mistakes in the synthesis reaction by the lack of base pairing between the mismatched nucleotides. If a mismatch is detected, a 3′ to 5′ exonuclease activity is activated and the incorrect base removed. In most organisms, DNA polymerases function in a large complex called the replisome that contains multiple accessory subunits, such as the DNA clamp or helicases.

RNA-dependent DNA polymerases are a specialized class of polymerases that copy the sequence of an RNA strand into DNA. They include reverse transcriptase, which is a viral enzyme involved in the infection of cells by retroviruses, and telomerase, which is required for the replication of telomeres. For example, HIV reverse transcriptase is an enzyme for AIDS virus replication. Telomerase is an unusual polymerase because it contains its own RNA template as part of its structure. It synthesizes telomeres at the ends of chromosomes. Telomeres prevent fusion of the ends of neighboring chromosomes and protect chromosome ends from damage.

Transcription is carried out by a DNA-dependent RNA polymerase that copies the sequence of a DNA strand into RNA. To begin transcribing a gene, the RNA polymerase binds to a sequence of DNA called a promoter and separates the DNA strands. It then copies the gene sequence into a messenger RNA transcript until it reaches a region of DNA called the terminator, where it halts and detaches from the DNA. As with human DNA-dependent DNA polymerases, RNA polymerase II, the enzyme that transcribes most of the genes in the human genome, operates as part of a large protein complex with multiple regulatory and accessory subunits.

Genetic recombination

A current model of meiotic recombination, initiated by a double-strand break or gap, followed by pairing with an homologous chromosome and strand invasion to initiate the recombinational repair process. Repair of the gap can lead to crossover (CO) or non-crossover (NCO) of the flanking regions. CO recombination is thought to occur by the Double Holliday Junction (DHJ) model, illustrated on the right, above. NCO recombinants are thought to occur primarily by the Synthesis Dependent Strand Annealing (SDSA) model, illustrated on the left, above. Most recombination events appear to be the SDSA type.

A DNA helix usually does not interact with other segments of DNA, and in human cells, the different chromosomes even occupy separate areas in the nucleus called " chromosome territories". This physical separation of different chromosomes is important for the ability of DNA to function as a stable repository for information, as one of the few times chromosomes interact is in chromosomal crossover which occurs during sexual reproduction, when genetic recombination occurs. Chromosomal crossover is when two DNA helices break, swap a section and then rejoin.

Recombination allows chromosomes to exchange genetic information and produces new combinations of genes, which increases the efficiency of natural selection and can be important in the rapid evolution of new proteins. Genetic recombination can also be involved in DNA repair, particularly in the cell's response to double-strand breaks.

The most common form of chromosomal crossover is homologous recombination, where the two chromosomes involved share very similar sequences. Non-homologous recombination can be damaging to cells, as it can produce chromosomal translocations and genetic abnormalities. The recombination reaction is catalyzed by enzymes known as recombinases, such as RAD51. The first step in recombination is a double-stranded break caused by either an endonuclease or damage to the DNA. A series of steps catalyzed in part by the recombinase then leads to joining of the two helices by at least one Holliday junction, in which a segment of a single strand in each helix is annealed to the complementary strand in the other helix. The Holliday junction is a tetrahedral junction structure that can be moved along the pair of chromosomes, swapping one strand for another. The recombination reaction is then halted by cleavage of the junction and re-ligation of the released DNA. Only strands of like polarity exchange DNA during recombination. There are two types of cleavage: east-west cleavage and north-south cleavage. The north-south cleavage nicks both strands of DNA, while the east-west cleavage has one strand of DNA intact. The formation of a Holliday junction during recombination makes it possible for genetic diversity, genes to exchange on chromosomes, and expression of wild-type viral genomes.

DNA contains the genetic information that allows all forms of life to function, grow and reproduce. However, it is unclear how long in the 4-billion-year history of life DNA has performed this function, as it has been proposed that the earliest forms of life may have used RNA as their genetic material. RNA may have acted as the central part of early cell metabolism as it can both transmit genetic information and carry out catalysis as part of ribozymes. This ancient RNA world where nucleic acid would have been used for both catalysis and genetics may have influenced the evolution of the current genetic code based on four nucleotide bases. This would occur, since the number of different bases in such an organism is a trade-off between a small number of bases increasing replication accuracy and a large number of bases increasing the catalytic efficiency of ribozymes. However, there is no direct evidence of ancient genetic systems, as recovery of DNA from most fossils is impossible because DNA survives in the environment for less than one million years, and slowly degrades into short fragments in solution. Claims for older DNA have been made, most notably a report of the isolation of a viable bacterium from a salt crystal 250 million years old, but these claims are controversial.

Building blocks of DNA ( adenine, guanine, and related organic molecules) may have been formed extraterrestrially in outer space. Complex DNA and RNA organic compounds of life, including uracil, cytosine, and thymine, have also been formed in the laboratory under conditions mimicking those found in outer space, using starting chemicals, such as pyrimidine, found in meteorites. Pyrimidine, like polycyclic aromatic hydrocarbons (PAHs), the most carbon-rich chemical found in the universe, may have been formed in red giants or in interstellar cosmic dust and gas clouds.

Ancient DNA has been recovered from ancient organisms at a timescale where genome evolution can be directly observed, including from extinct organisms up to millions of years old, such as the woolly mammoth.

Uses in technology

Genetic engineering

Methods have been developed to purify DNA from organisms, such as phenol-chloroform extraction, and to manipulate it in the laboratory, such as restriction digests and the polymerase chain reaction. Modern biology and biochemistry make intensive use of these techniques in recombinant DNA technology. Recombinant DNA is a man-made DNA sequence that has been assembled from other DNA sequences. They can be transformed into organisms in the form of plasmids or in the appropriate format, by using a viral vector. The genetically modified organisms produced can be used to produce products such as recombinant proteins, used in medical research, or be grown in agriculture.

DNA profiling

Forensic scientists can use DNA in blood, semen, skin, saliva or hair found at a crime scene to identify a matching DNA of an individual, such as a perpetrator. This process is formally termed DNA profiling, also called DNA fingerprinting. In DNA profiling, the lengths of variable sections of repetitive DNA, such as short tandem repeats and minisatellites, are compared between people. This method is usually an extremely reliable technique for identifying a matching DNA. However, identification can be complicated if the scene is contaminated with DNA from several people. DNA profiling was developed in 1984 by British geneticist Sir Alec Jeffreys, and first used in forensic science to convict Colin Pitchfork in the 1988 Enderby murders case.

The development of forensic science and the ability to now obtain genetic matching on minute samples of blood, skin, saliva, or hair has led to re-examining many cases. Evidence can now be uncovered that was scientifically impossible at the time of the original examination. Combined with the removal of the double jeopardy law in some places, this can allow cases to be reopened where prior trials have failed to produce sufficient evidence to convince a jury. People charged with serious crimes may be required to provide a sample of DNA for matching purposes. The most obvious defense to DNA matches obtained forensically is to claim that cross-contamination of evidence has occurred. This has resulted in meticulous strict handling procedures with new cases of serious crime.

DNA profiling is also used successfully to positively identify victims of mass casualty incidents, bodies or body parts in serious accidents, and individual victims in mass war graves, via matching to family members.

DNA profiling is also used in DNA paternity testing to determine if someone is the biological parent or grandparent of a child with the probability of parentage is typically 99.99% when the alleged parent is biologically related to the child. Normal DNA sequencing methods happen after birth, but there are new methods to test paternity while a mother is still pregnant.

DNA enzymes or catalytic DNA

Deoxyribozymes, also called DNAzymes or catalytic DNA, were first discovered in 1994. They are mostly single stranded DNA sequences isolated from a large pool of random DNA sequences through a combinatorial approach called in vitro selection or systematic evolution of ligands by exponential enrichment (SELEX). DNAzymes catalyze variety of chemical reactions including RNA-DNA cleavage, RNA-DNA ligation, amino acids phosphorylation-dephosphorylation, carbon-carbon bond formation, etc. DNAzymes can enhance catalytic rate of chemical reactions up to 100,000,000,000-fold over the uncatalyzed reaction. The most extensively studied class of DNAzymes is RNA-cleaving types which have been used to detect different metal ions and designing therapeutic agents. Several metal-specific DNAzymes have been reported including the GR-5 DNAzyme (lead-specific), the CA1-3 DNAzymes (copper-specific), the 39E DNAzyme (uranyl-specific) and the NaA43 DNAzyme (sodium-specific). The NaA43 DNAzyme, which is reported to be more than 10,000-fold selective for sodium over other metal ions, was used to make a real-time sodium sensor in cells.

Bioinformatics

Bioinformatics involves the development of techniques to store, data mine, search and manipulate biological data, including DNA nucleic acid sequence data. These have led to widely applied advances in computer science, especially string searching algorithms, machine learning, and database theory. String searching or matching algorithms, which find an occurrence of a sequence of letters inside a larger sequence of letters, were developed to search for specific sequences of nucleotides. The DNA sequence may be aligned with other DNA sequences to identify homologous sequences and locate the specific mutations that make them distinct. These techniques, especially multiple sequence alignment, are used in studying phylogenetic relationships and protein function. Data sets representing entire genomes' worth of DNA sequences, such as those produced by the Human Genome Project, are difficult to use without the annotations that identify the locations of genes and regulatory elements on each chromosome. Regions of DNA sequence that have the characteristic patterns associated with protein- or RNA-coding genes can be identified by gene finding algorithms, which allow researchers to predict the presence of particular gene products and their possible functions in an organism even before they have been isolated experimentally. Entire genomes may also be compared, which can shed light on the evolutionary history of particular organism and permit the examination of complex evolutionary events.

DNA nanotechnology

The DNA structure at left (schematic shown) will self-assemble into the structure visualized by atomic force microscopy at right. DNA nanotechnology is the field that seeks to design nanoscale structures using the molecular recognition properties of DNA molecules.[178]

DNA nanotechnology uses the unique molecular recognition properties of DNA and other nucleic acids to create self-assembling branched DNA complexes with useful properties. DNA is thus used as a structural material rather than as a carrier of biological information. This has led to the creation of two-dimensional periodic lattices (both tile-based and using the DNA origami method) and three-dimensional structures in the shapes of polyhedra. Nanomechanical devices and algorithmic self-assembly have also been demonstrated, and these DNA structures have been used to template the arrangement of other molecules such as gold nanoparticles and streptavidin proteins. DNA and other nucleic acids are the basis of aptamers, synthetic oligonucleotide ligands for specific target molecules used in a range of biotechnology and biomedical applications.

History and anthropology

Because DNA collects mutations over time, which are then inherited, it contains historical information, and, by comparing DNA sequences, geneticists can infer the evolutionary history of organisms, their phylogeny. This field of phylogenetics is a powerful tool in evolutionary biology. If DNA sequences within a species are compared, population geneticists can learn the history of particular populations. This can be used in studies ranging from ecological genetics to anthropology.

Information storage

DNA as a storage device for information has enormous potential since it has much higher storage density compared to electronic devices. However, high costs, slow read and write times ( memory latency), and insufficient reliability has prevented its practical use.

Maclyn McCarty (left) shakes hands with Francis Crick and James Watson, co-originators of the double-helix model based on the X-ray diffraction data and insights of Rosalind Franklin and Raymond Gosling.

DNA was first isolated by the Swiss physician Friedrich Miescher who, in 1869, discovered a microscopic substance in the pus of discarded surgical bandages. As it resided in the nuclei of cells, he called it "nuclein". In 1878, Albrecht Kossel isolated the non-protein component of "nuclein", nucleic acid, and later isolated its five primary nucleobases.

In 1909, Phoebus Levene identified the base, sugar, and phosphate nucleotide unit of RNA (then named "yeast nucleic acid"). In 1929, Levene identified deoxyribose sugar in "thymus nucleic acid" (DNA). Levene suggested that DNA consisted of a string of four nucleotide units linked together through the phosphate groups ("tetranucleotide hypothesis"). Levene thought the chain was short and the bases repeated in a fixed order. In 1927, Nikolai Koltsov proposed that inherited traits would be inherited via a "giant hereditary molecule" made up of "two mirror strands that would replicate in a semi-conservative fashion using each strand as a template". In 1928, Frederick Griffith in his experiment discovered that traits of the "smooth" form of Pneumococcus could be transferred to the "rough" form of the same bacteria by mixing killed "smooth" bacteria with the live "rough" form. This system provided the first clear suggestion that DNA carries genetic information.

In 1933, while studying virgin sea urchin eggs, Jean Brachet suggested that DNA is found in the cell nucleus and that RNA is present exclusively in the cytoplasm. At the time, "yeast nucleic acid" (RNA) was thought to occur only in plants, while "thymus nucleic acid" (DNA) only in animals. The latter was thought to be a tetramer, with the function of buffering cellular pH.

In 1937, William Astbury produced the first X-ray diffraction patterns that showed that DNA had a regular structure.

In 1943, Oswald Avery, along with co-workers Colin MacLeod and Maclyn McCarty, identified DNA as the transforming principle, supporting Griffith's suggestion ( Avery-MacLeod-McCarty experiment). Erwin Chargaff developed and published observations now known as Chargaff's rules, stating that in DNA from any species of any organism, the amount of guanine should be equal to cytosine and the amount of adenine should be equal to thymine.

A blue plaque outside The Eagle pub in Cambridge, England commemorating Crick and Watson

Late in 1951, Francis Crick started working with James Watson at the Cavendish Laboratory within the University of Cambridge. DNA's role in heredity was confirmed in 1952 when Alfred Hershey and Martha Chase in the Hershey-Chase experiment showed that DNA is the genetic material of the enterobacteria phage T2.

In May 1952, Raymond Gosling, a graduate student working under the supervision of Rosalind Franklin, took an X-ray diffraction image, labeled as " Photo 51", at high hydration levels of DNA. This photo was given to Watson and Crick by Maurice Wilkins and was critical to their obtaining the correct structure of DNA. Franklin told Crick and Watson that the backbones had to be on the outside. Before then, Linus Pauling, and Watson and Crick, had erroneous models with the chains inside and the bases pointing outwards. Franklin's identification of the space group for DNA crystals revealed to Crick that the two DNA strands were antiparallel. In February 1953, Linus Pauling and Robert Corey proposed a model for nucleic acids containing three intertwined chains, with the phosphates near the axis, and the bases on the outside. Watson and Crick completed their model, which is now accepted as the first correct model of the double helix of DNA. On 28 February 1953 Crick interrupted patrons' lunchtime at The Eagle pub in Cambridge, England to announce that he and Watson had "discovered the secret of life".

Pencil sketch of the DNA double helix by Francis Crick in 1953

The 25 April 1953 issue of the journal published a series of five articles giving the Watson and Crick double-helix structure DNA and evidence supporting it. The structure was reported in a letter titled " MOLECULAR STRUCTURE OF NUCLEIC ACIDS A Structure for Deoxyribose Nucleic Acid", in which they said, "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." This letter was followed by a letter from Franklin and Gosling, which was the first publication of their own X-ray diffraction data and of their original analysis method. Then followed a letter by Wilkins and two of his colleagues, which contained an analysis of in vivo B-DNA X-ray patterns, and which supported the presence in vivo of the Watson and Crick structure.

In April 2023, scientists, based on new evidence, concluded that Rosalind Franklin was a contributor and "equal player" in the discovery process of DNA, rather than otherwise, as may have been presented subsequently after the time of the discovery.

In 1962, after Franklin's death, Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine. Nobel Prizes are awarded only to living recipients. A debate continues about who should receive credit for the discovery.

In an influential presentation in 1957, Crick laid out the central dogma of molecular biology, which foretold the relationship between DNA, RNA, and proteins, and articulated the "adaptor hypothesis". Final confirmation of the replication mechanism that was implied by the double-helical structure followed in 1958 through the Meselson-Stahl experiment. Further work by Crick and co-workers showed that the genetic code was based on non-overlapping triplets of bases, called codons, allowing Har Gobind Khorana, Robert W. Holley, and Marshall Warren Nirenberg to decipher the genetic code. These findings represent the birth of molecular biology.

In 1986, DNA analysis was first used for criminal investigative purposes when police in the UK requested Alec Jeffreys of the University of Leicester to verify or disprove a suspect's rape-murder "confession". In this particular case, the suspect had confessed to two rape-murders, but had later retracted his confession. DNA testing at the university labs soon disproved the veracity of the suspect's original "confession", and the suspect was exonerated from the murder-rape charges.

References

Further reading

External links

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Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids.

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Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes that are passed on from parent to offspring during reproduction. Different characteristics tend to exist within any given population as a result of mutation, genetic recombination and other sources of genetic variation. Evolution occurs when evolutionary processes such as natural selection (including sexual selection) and genetic drift act on this variation, resulting in certain characteristics becoming more common or rare within a population. The circumstances that determine whether a characteristic should be common or rare within a population constantly change, resulting in the change in heritable characteristics arising over successive generations. It is this process of evolution that has given rise to biodiversity at every level of biological organisation, including the levels of species, individual organisms and molecules.

The scientific theory of evolution by natural selection was conceived independently by Charles Darwin and Alfred Russel Wallace in the mid-19th century and was set out in detail in Darwin's book On the Origin of Species. Evolution by natural selection was first demonstrated by the observation that more offspring are often produced than can possibly survive. This is followed by three observable facts about living organisms: (1) traits vary among individuals with respect to their morphology, physiology and behaviour ( phenotypic variation), (2) different traits confer different rates of survival and reproduction (differential fitness) and (3) traits can be passed from generation to generation ( heritability of fitness). Thus, in successive generations members of a population are more likely to be replaced by the progenies of parents with favourable characteristics that have enabled them to survive and reproduce in their respective environments. In the early 20th century, other competing ideas of evolution such as mutationism and orthogenesis were refuted as the modern synthesis reconciled Darwinian evolution with classical genetics, which established adaptive evolution as being caused by natural selection acting on Mendelian genetic variation.

All life on Earth shares a last universal common ancestor (LUCA) that lived approximately 3.5-3.8 billion years ago. The fossil record includes a progression from early biogenic graphite, to microbial mat fossils, to fossilised multicellular organisms. Existing patterns of biodiversity have been shaped by repeated formations of new species ( speciation), changes within species ( anagenesis) and loss of species ( extinction) throughout the evolutionary history of life on Earth. Morphological and biochemical traits are more similar among species that share a more recent common ancestor, and can be used to reconstruct phylogenetic trees.

Evolutionary biologists have continued to study various aspects of evolution by forming and testing hypotheses as well as constructing theories based on evidence from the field or laboratory and on data generated by the methods of mathematical and theoretical biology. Their discoveries have influenced not just the development of biology but numerous other scientific and industrial fields, including agriculture, medicine and computer science.

History of evolutionary thought

Classical antiquity

The proposal that one type of organism could descend from another type goes back to some of the first pre-Socratic Greek philosophers, such as Anaximander and Empedocles. Such proposals survived into Roman times. The poet and philosopher Lucretius followed Empedocles in his masterwork De rerum natura ( On the Nature of Things).

Middle Ages

In contrast to these materialistic views, Aristotelianism considered all natural things as actualisations of fixed natural possibilities, known as forms. This was part of a medieval teleological understanding of nature in which all things have an intended role to play in a divine cosmic order. Variations of this idea became the standard understanding of the Middle Ages and were integrated into Christian learning, but Aristotle did not demand that real types of organisms always correspond one-for-one with exact metaphysical forms and specifically gave examples of how new types of living things could come to be.

Pre-Darwinian

In the 17th century, the new method of modern science rejected the Aristotelian approach. It sought explanations of natural phenomena in terms of physical laws that were the same for all visible things and that did not require the existence of any fixed natural categories or divine cosmic order. However, this new approach was slow to take root in the biological sciences, the last bastion of the concept of fixed natural types. John Ray applied one of the previously more general terms for fixed natural types, "species", to plant and animal types, but he strictly identified each type of living thing as a species and proposed that each species could be defined by the features that perpetuated themselves generation after generation. The biological classification introduced by Carl Linnaeus in 1735 explicitly recognised the hierarchical nature of species relationships, but still viewed species as fixed according to a divine plan.

Other naturalists of this time speculated on the evolutionary change of species over time according to natural laws. In 1751, Pierre Louis Maupertuis wrote of natural modifications occurring during reproduction and accumulating over many generations to produce new species. Georges-Louis Leclerc, Comte de Buffon, suggested that species could degenerate into different organisms, and Erasmus Darwin proposed that all warm-blooded animals could have descended from a single microorganism (or "filament"). The first full-fledged evolutionary scheme was Jean-Baptiste Lamarck's "transmutation" theory of 1809, which envisaged spontaneous generation continually producing simple forms of life that developed greater complexity in parallel lineages with an inherent progressive tendency, and postulated that on a local level, these lineages adapted to the environment by inheriting changes caused by their use or disuse in parents. (The latter process was later called Lamarckism.) These ideas were condemned by established naturalists as speculation lacking empirical support. In particular, Georges Cuvier insisted that species were unrelated and fixed, their similarities reflecting divine design for functional needs. In the meantime, Ray's ideas of benevolent design had been developed by William Paley into the Natural Theology or Evidences of the Existence and Attributes of the Deity (1802), which proposed complex adaptations as evidence of divine design and which was admired by Charles Darwin.

Darwinian revolution

The crucial break from the concept of constant typological classes or types in biology came with the theory of evolution through natural selection, which was formulated by Charles Darwin in terms of variable populations. Darwin used the expression " descent with modification" rather than "evolution". Partly influenced by An Essay on the Principle of Population (1798) by Thomas Robert Malthus, Darwin noted that population growth would lead to a "struggle for existence" in which favourable variations prevailed as others perished. In each generation, many offspring fail to survive to an age of reproduction because of limited resources. This could explain the diversity of plants and animals from a common ancestry through the working of natural laws in the same way for all types of organism. Darwin developed his theory of "natural selection" from 1838 onwards and was writing up his "big book" on the subject when Alfred Russel Wallace sent him a version of virtually the same theory in 1858. Their separate papers were presented together at an 1858 meeting of the Linnean Society of London. At the end of 1859, Darwin's publication of his "abstract" as On the Origin of Species explained natural selection in detail and in a way that led to an increasingly wide acceptance of Darwin's concepts of evolution at the expense of alternative theories. Thomas Henry Huxley applied Darwin's ideas to humans, using paleontology and comparative anatomy to provide strong evidence that humans and apes shared a common ancestry. Some were disturbed by this since it implied that humans did not have a special place in the universe.

Pangenesis and heredity

The mechanisms of reproductive heritability and the origin of new traits remained a mystery. Towards this end, Darwin developed his provisional theory of pangenesis. In 1865, Gregor Mendel reported that traits were inherited in a predictable manner through the independent assortment and segregation of elements (later known as genes). Mendel's laws of inheritance eventually supplanted most of Darwin's pangenesis theory. August Weismann made the important distinction between germ cells that give rise to gametes (such as sperm and egg cells) and the somatic cells of the body, demonstrating that heredity passes through the germ line only. Hugo de Vries connected Darwin's pangenesis theory to Weismann's germ/soma cell distinction and proposed that Darwin's pangenes were concentrated in the cell nucleus and when expressed they could move into the cytoplasm to change the cell's structure. De Vries was also one of the researchers who made Mendel's work well known, believing that Mendelian traits corresponded to the transfer of heritable variations along the germline. To explain how new variants originate, de Vries developed a mutation theory that led to a temporary rift between those who accepted Darwinian evolution and biometricians who allied with de Vries. In the 1930s, pioneers in the field of population genetics, such as Ronald Fisher, Sewall Wright and J. B. S. Haldane set the foundations of evolution onto a robust statistical philosophy. The false contradiction between Darwin's theory, genetic mutations, and Mendelian inheritance was thus reconciled.

The 'modern synthesis'

In the 1920s and 1930s, the so-called modern synthesis connected natural selection and population genetics, based on Mendelian inheritance, into a unified theory that applied generally to any branch of biology. The modern synthesis explained patterns observed across species in populations, through fossil transitions in palaeontology.

Further syntheses

Since then, the modern synthesis has been further extended in the light of numerous discoveries, to explain biological phenomena across the full and integrative scale of the biological hierarchy, from genes to populations.

The publication of the structure of DNA by James Watson and Francis Crick with contribution of Rosalind Franklin in 1953 demonstrated a physical mechanism for inheritance. Molecular biology improved understanding of the relationship between genotype and phenotype. Advances were also made in phylogenetic systematics, mapping the transition of traits into a comparative and testable framework through the publication and use of evolutionary trees. In 1973, evolutionary biologist Theodosius Dobzhansky penned that " nothing in biology makes sense except in the light of evolution," because it has brought to light the relations of what first seemed disjointed facts in natural history into a coherent explanatory body of knowledge that describes and predicts many observable facts about life on this planet.

One extension, known as evolutionary developmental biology and informally called "evo-devo," emphasises how changes between generations (evolution) acts on patterns of change within individual organisms ( development). Since the beginning of the 21st century and in light of discoveries made in recent decades, some biologists have argued for an extended evolutionary synthesis, which would account for the effects of non-genetic inheritance modes, such as epigenetics, parental effects, ecological inheritance and cultural inheritance, and evolvability.

Evolution in organisms occurs through changes in heritable traits-the inherited characteristics of an organism. In humans, for example, eye colour is an inherited characteristic and an individual might inherit the "brown-eye trait" from one of their parents. Inherited traits are controlled by genes and the complete set of genes within an organism's genome (genetic material) is called its genotype.

The complete set of observable traits that make up the structure and behaviour of an organism is called its phenotype. These traits come from the interaction of its genotype with the environment. As a result, many aspects of an organism's phenotype are not inherited. For example, suntanned skin comes from the interaction between a person's genotype and sunlight; thus, suntans are not passed on to people's children. However, some people tan more easily than others, due to differences in genotypic variation; a striking example are people with the inherited trait of albinism, who do not tan at all and are very sensitive to sunburn.

Heritable traits are passed from one generation to the next via DNA, a molecule that encodes genetic information. DNA is a long biopolymer composed of four types of bases. The sequence of bases along a particular DNA molecule specify the genetic information, in a manner similar to a sequence of letters spelling out a sentence. Before a cell divides, the DNA is copied, so that each of the resulting two cells will inherit the DNA sequence. Portions of a DNA molecule that specify a single functional unit are called genes; different genes have different sequences of bases. Within cells, the long strands of DNA form condensed structures called chromosomes. The specific location of a DNA sequence within a chromosome is known as a locus. If the DNA sequence at a locus varies between individuals, the different forms of this sequence are called alleles. DNA sequences can change through mutations, producing new alleles. If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the organism. However, while this simple correspondence between an allele and a trait works in some cases, most traits are more complex and are controlled by quantitative trait loci (multiple interacting genes).

Recent findings have confirmed important examples of heritable changes that cannot be explained by changes to the sequence of nucleotides in the DNA. These phenomena are classed as epigenetic inheritance systems. DNA methylation marking chromatin, self-sustaining metabolic loops, gene silencing by RNA interference and the three-dimensional conformation of proteins (such as prions) are areas where epigenetic inheritance systems have been discovered at the organismic level. Developmental biologists suggest that complex interactions in genetic networks and communication among cells can lead to heritable variations that may underlay some of the mechanics in developmental plasticity and canalisation. Heritability may also occur at even larger scales. For example, ecological inheritance through the process of niche construction is defined by the regular and repeated activities of organisms in their environment. This generates a legacy of effects that modify and feed back into the selection regime of subsequent generations. Descendants inherit genes plus environmental characteristics generated by the ecological actions of ancestors. Other examples of heritability in evolution that are not under the direct control of genes include the inheritance of cultural traits and symbiogenesis.

Sources of variation

Evolution can occur if there is genetic variation within a population. Variation comes from mutations in the genome, reshuffling of genes through sexual reproduction and migration between populations ( gene flow). Despite the constant introduction of new variation through mutation and gene flow, most of the genome of a species is identical in all individuals of that species. However, even relatively small differences in genotype can lead to dramatic differences in phenotype: for example, chimpanzees and humans differ in only about 5% of their genomes.

An individual organism's phenotype results from both its genotype and the influence of the environment it has lived in. A substantial part of the phenotypic variation in a population is caused by genotypic variation. The modern evolutionary synthesis defines evolution as the change over time in this genetic variation. The frequency of one particular allele will become more or less prevalent relative to other forms of that gene. Variation disappears when a new allele reaches the point of fixation -when it either disappears from the population or replaces the ancestral allele entirely.

Before the discovery of Mendelian genetics, one common hypothesis was blending inheritance. But with blending inheritance, genetic variation would be rapidly lost, making evolution by natural selection implausible. The Hardy-Weinberg principle provides the solution to how variation is maintained in a population with Mendelian inheritance. The frequencies of alleles (variations in a gene) will remain constant in the absence of selection, mutation, migration and genetic drift.

Mutations are changes in the DNA sequence of a cell's genome and are the ultimate source of genetic variation in all organisms. When mutations occur, they may alter the product of a gene, or prevent the gene from functioning, or have no effect. Based on studies in the fly Drosophila melanogaster, it has been suggested that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70% of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial.

Mutations can involve large sections of a chromosome becoming duplicated (usually by genetic recombination), which can introduce extra copies of a gene into a genome. Extra copies of genes are a major source of the raw material needed for new genes to evolve. This is important because most new genes evolve within gene families from pre-existing genes that share common ancestors. For example, the human eye uses four genes to make structures that sense light: three for colour vision and one for night vision; all four are descended from a single ancestral gene.

New genes can be generated from an ancestral gene when a duplicate copy mutates and acquires a new function. This process is easier once a gene has been duplicated because it increases the redundancy of the system; one gene in the pair can acquire a new function while the other copy continues to perform its original function. Other types of mutations can even generate entirely new genes from previously noncoding DNA, a phenomenon termed de novo gene birth.

The generation of new genes can also involve small parts of several genes being duplicated, with these fragments then recombining to form new combinations with new functions ( exon shuffling). When new genes are assembled from shuffling pre-existing parts, domains act as modules with simple independent functions, which can be mixed together to produce new combinations with new and complex functions. For example, polyketide synthases are large enzymes that make antibiotics; they contain up to one hundred independent domains that each catalyse one step in the overall process, like a step in an assembly line.

Sex and recombination

In asexual organisms, genes are inherited together, or linked, as they cannot mix with genes of other organisms during reproduction. In contrast, the offspring of sexual organisms contain random mixtures of their parents' chromosomes that are produced through independent assortment. In a related process called homologous recombination, sexual organisms exchange DNA between two matching chromosomes. Recombination and reassortment do not alter allele frequencies, but instead change which alleles are associated with each other, producing offspring with new combinations of alleles. Sex usually increases genetic variation and may increase the rate of evolution.

The two-fold cost of sex was first described by John Maynard Smith. The first cost is that in sexually dimorphic species only one of the two sexes can bear young. This cost does not apply to hermaphroditic species, like most plants and many invertebrates. The second cost is that any individual who reproduces sexually can only pass on 50% of its genes to any individual offspring, with even less passed on as each new generation passes. Yet sexual reproduction is the more common means of reproduction among eukaryotes and multicellular organisms. The Red Queen hypothesis has been used to explain the significance of sexual reproduction as a means to enable continual evolution and adaptation in response to coevolution with other species in an ever-changing environment. Another hypothesis is that sexual reproduction is primarily an adaptation for promoting accurate recombinational repair of damage in germline DNA, and that increased diversity is a byproduct of this process that may sometimes be adaptively beneficial.

Gene flow is the exchange of genes between populations and between species. It can therefore be a source of variation that is new to a population or to a species. Gene flow can be caused by the movement of individuals between separate populations of organisms, as might be caused by the movement of mice between inland and coastal populations, or the movement of pollen between heavy-metal-tolerant and heavy-metal-sensitive populations of grasses.

Gene transfer between species includes the formation of hybrid organisms and horizontal gene transfer. Horizontal gene transfer is the transfer of genetic material from one organism to another organism that is not its offspring; this is most common among bacteria. In medicine, this contributes to the spread of antibiotic resistance, as when one bacteria acquires resistance genes it can rapidly transfer them to other species. Horizontal transfer of genes from bacteria to eukaryotes such as the yeast Saccharomyces cerevisiae and the adzuki bean weevil Callosobruchus chinensis has occurred. An example of larger-scale transfers are the eukaryotic bdelloid rotifers, which have received a range of genes from bacteria, fungi and plants. Viruses can also carry DNA between organisms, allowing transfer of genes even across biological domains.

Large-scale gene transfer has also occurred between the ancestors of eukaryotic cells and bacteria, during the acquisition of chloroplasts and mitochondria. It is possible that eukaryotes themselves originated from horizontal gene transfers between bacteria and archaea.

Evolutionary processes

From a neo-Darwinian perspective, evolution occurs when there are changes in the frequencies of alleles within a population of interbreeding organisms, for example, the allele for black colour in a population of moths becoming more common. Mechanisms that can lead to changes in allele frequencies include natural selection, genetic drift, gene flow and mutation bias.

Natural selection

Evolution by natural selection is the process by which traits that enhance survival and reproduction become more common in successive generations of a population. It embodies three principles:

Variation exists within populations of organisms with respect to morphology, physiology and behaviour (phenotypic variation).

Different traits confer different rates of survival and reproduction (differential fitness).

These traits can be passed from generation to generation (heritability of fitness).

More offspring are produced than can possibly survive, and these conditions produce competition between organisms for survival and reproduction. Consequently, organisms with traits that give them an advantage over their competitors are more likely to pass on their traits to the next generation than those with traits that do not confer an advantage. This teleonomy is the quality whereby the process of natural selection creates and preserves traits that are seemingly fitted for the functional roles they perform. Consequences of selection include nonrandom mating and genetic hitchhiking.

The central concept of natural selection is the evolutionary fitness of an organism. Fitness is measured by an organism's ability to survive and reproduce, which determines the size of its genetic contribution to the next generation. However, fitness is not the same as the total number of offspring: instead fitness is indicated by the proportion of subsequent generations that carry an organism's genes. For example, if an organism could survive well and reproduce rapidly, but its offspring were all too small and weak to survive, this organism would make little genetic contribution to future generations and would thus have low fitness.

If an allele increases fitness more than the other alleles of that gene, then with each generation this allele will become more common within the population. These traits are said to be "selected for." Examples of traits that can increase fitness are enhanced survival and increased fecundity. Conversely, the lower fitness caused by having a less beneficial or deleterious allele results in this allele becoming rarer-they are "selected against." Importantly, the fitness of an allele is not a fixed characteristic; if the environment changes, previously neutral or harmful traits may become beneficial and previously beneficial traits become harmful. However, even if the direction of selection does reverse in this way, traits that were lost in the past may not re-evolve in an identical form (see Dollo's law). However, a re-activation of dormant genes, as long as they have not been eliminated from the genome and were only suppressed perhaps for hundreds of generations, can lead to the re-occurrence of traits thought to be lost like hindlegs in dolphins, teeth in chickens, wings in wingless stick insects, tails and additional nipples in humans etc. "Throwbacks" such as these are known as atavisms.

Natural selection within a population for a trait that can vary across a range of values, such as height, can be categorised into three different types. The first is directional selection, which is a shift in the average value of a trait over time-for example, organisms slowly getting taller. Secondly, disruptive selection is selection for extreme trait values and often results in two different values becoming most common, with selection against the average value. This would be when either short or tall organisms had an advantage, but not those of medium height. Finally, in stabilising selection there is selection against extreme trait values on both ends, which causes a decrease in variance around the average value and less diversity. This would, for example, cause organisms to eventually have a similar height.

Natural selection most generally makes nature the measure against which individuals and individual traits, are more or less likely to survive. "Nature" in this sense refers to an ecosystem, that is, a system in which organisms interact with every other element, physical as well as biological, in their local environment. Eugene Odum, a founder of ecology, defined an ecosystem as: "Any unit that includes all of the organisms...in a given area interacting with the physical environment so that a flow of energy leads to clearly defined trophic structure, biotic diversity, and material cycles (i.e., exchange of materials between living and nonliving parts) within the system...." Each population within an ecosystem occupies a distinct niche, or position, with distinct relationships to other parts of the system. These relationships involve the life history of the organism, its position in the food chain and its geographic range. This broad understanding of nature enables scientists to delineate specific forces which, together, comprise natural selection.

Natural selection can act at different levels of organisation, such as genes, cells, individual organisms, groups of organisms and species. Selection can act at multiple levels simultaneously. An example of selection occurring below the level of the individual organism are genes called transposons, which can replicate and spread throughout a genome. Selection at a level above the individual, such as group selection, may allow the evolution of cooperation.

Genetic hitchhiking

Recombination allows alleles on the same strand of DNA to become separated. However, the rate of recombination is low (approximately two events per chromosome per generation). As a result, genes close together on a chromosome may not always be shuffled away from each other and genes that are close together tend to be inherited together, a phenomenon known as linkage. This tendency is measured by finding how often two alleles occur together on a single chromosome compared to expectations, which is called their linkage disequilibrium. A set of alleles that is usually inherited in a group is called a haplotype. This can be important when one allele in a particular haplotype is strongly beneficial: natural selection can drive a selective sweep that will also cause the other alleles in the haplotype to become more common in the population; this effect is called genetic hitchhiking or genetic draft. Genetic draft caused by the fact that some neutral genes are genetically linked to others that are under selection can be partially captured by an appropriate effective population size.

Sexual selection

A special case of natural selection is sexual selection, which is selection for any trait that increases mating success by increasing the attractiveness of an organism to potential mates. Traits that evolved through sexual selection are particularly prominent among males of several animal species. Although sexually favoured, traits such as cumbersome antlers, mating calls, large body size and bright colours often attract predation, which compromises the survival of individual males. This survival disadvantage is balanced by higher reproductive success in males that show these hard-to-fake, sexually selected traits.

Genetic drift

Genetic drift is the random fluctuations of allele frequencies within a population from one generation to the next. When selective forces are absent or relatively weak, allele frequencies are equally likely to drift upward or downward at each successive generation because the alleles are subject to sampling error. This drift halts when an allele eventually becomes fixed, either by disappearing from the population or replacing the other alleles entirely. Genetic drift may therefore eliminate some alleles from a population due to chance alone. Even in the absence of selective forces, genetic drift can cause two separate populations that began with the same genetic structure to drift apart into two divergent populations with different sets of alleles.

The neutral theory of molecular evolution proposed that most evolutionary changes are the result of the fixation of neutral mutations by genetic drift. Hence, in this model, most genetic changes in a population are the result of constant mutation pressure and genetic drift. This form of the neutral theory is now largely abandoned, since it does not seem to fit the genetic variation seen in nature. However, a more recent and better-supported version of this model is the nearly neutral theory, where a mutation that would be effectively neutral in a small population is not necessarily neutral in a large population. Other alternative theories propose that genetic drift is dwarfed by other stochastic forces in evolution, such as genetic hitchhiking, also known as genetic draft. Another concept is constructive neutral evolution (CNE), which explains that complex systems can emerge and spread into a population through neutral transitions with the principles of excess capacity, presuppression, and ratcheting, and it has been applied in areas ranging from the origins of the spliceosome to the complex interdependence of microbial communities.

The time for a neutral allele to become fixed by genetic drift depends on population size, with fixation occurring more rapidly in smaller populations. The number of individuals in a population is not critical, but instead a measure known as the effective population size. The effective population is usually smaller than the total population since it takes into account factors such as the level of inbreeding and the stage of the lifecycle in which the population is the smallest. The effective population size may not be the same for every gene in the same population.

It is usually difficult to measure the relative importance of selection and neutral processes, including drift. The comparative importance of adaptive and non-adaptive forces in driving evolutionary change is an area of current research.

Gene flow involves the exchange of genes between populations and between species. The presence or absence of gene flow fundamentally changes the course of evolution. Due to the complexity of organisms, any two completely isolated populations will eventually evolve genetic incompatibilities through neutral processes, as in the Bateson-Dobzhansky-Muller model, even if both populations remain essentially identical in terms of their adaptation to the environment.

If genetic differentiation between populations develops, gene flow between populations can introduce traits or alleles which are disadvantageous in the local population and this may lead to organisms within these populations evolving mechanisms that prevent mating with genetically distant populations, eventually resulting in the appearance of new species. Thus, exchange of genetic information between individuals is fundamentally important for the development of the Biological Species Concept.

During the development of the modern synthesis, Sewall Wright developed his shifting balance theory, which regarded gene flow between partially isolated populations as an important aspect of adaptive evolution. However, recently there has been substantial criticism of the importance of the shifting balance theory.

Mutation bias

Mutation bias is usually conceived as a difference in expected rates for two different kinds of mutation, e.g., transition-transversion bias, GC-AT bias, deletion-insertion bias. This is related to the idea of developmental bias.

Haldane and Fisher argued that, because mutation is a weak pressure easily overcome by selection, tendencies of mutation would be ineffectual except under conditions of neutral evolution or extraordinarily high mutation rates. This opposing-pressures argument was long used to dismiss the possibility of internal tendencies in evolution, until the molecular era prompted renewed interest in neutral evolution.

Noboru Sueoka and Ernst Freese proposed that systematic biases in mutation might be responsible for systematic differences in genomic GC composition between species. The identification of a GC-biased E. coli mutator strain in 1967, along with the proposal of the neutral theory, established the plausibility of mutational explanations for molecular patterns, which are now common in the molecular evolution literature.

For instance, mutation biases are frequently invoked in models of codon usage. Such models also include effects of selection, following the mutation-selection-drift model, which allows both for mutation biases and differential selection based on effects on translation. Hypotheses of mutation bias have played an important role in the development of thinking about the evolution of genome composition, including isochores. Different insertion vs. deletion biases in different taxa can lead to the evolution of different genome sizes. The hypothesis of Lynch regarding genome size relies on mutational biases toward increase or decrease in genome size.

However, mutational hypotheses for the evolution of composition suffered a reduction in scope when it was discovered that (1) GC-biased gene conversion makes an important contribution to composition in diploid organisms such as mammals and (2) bacterial genomes frequently have AT-biased mutation.

Contemporary thinking about the role of mutation biases reflects a different theory from that of Haldane and Fisher. More recent work showed that the original "pressures" theory assumes that evolution is based on standing variation: when evolution depends on the introduction of new alleles, mutational and developmental biases in the introduction can impose biases on evolution without requiring neutral evolution or high mutation rates.

Several recent studies report that the mutations implicated in adaptation reflect common mutation biases though others dispute this interpretation.

Evolution influences every aspect of the form and behaviour of organisms. Most prominent are the specific behavioural and physical adaptations that are the outcome of natural selection. These adaptations increase fitness by aiding activities such as finding food, avoiding predators or attracting mates. Organisms can also respond to selection by cooperating with each other, usually by aiding their relatives or engaging in mutually beneficial symbiosis. In the longer term, evolution produces new species through splitting ancestral populations of organisms into new groups that cannot or will not interbreed.

These outcomes of evolution are distinguished based on time scale as macroevolution versus microevolution. Macroevolution refers to evolution that occurs at or above the level of species, in particular speciation and extinction; whereas microevolution refers to smaller evolutionary changes within a species or population, in particular shifts in allele frequency and adaptation. In general, macroevolution is regarded as the outcome of long periods of microevolution. Thus, the distinction between micro- and macroevolution is not a fundamental one-the difference is simply the time involved. However, in macroevolution, the traits of the entire species may be important. For instance, a large amount of variation among individuals allows a species to rapidly adapt to new habitats, lessening the chance of it going extinct, while a wide geographic range increases the chance of speciation, by making it more likely that part of the population will become isolated. In this sense, microevolution and macroevolution might involve selection at different levels-with microevolution acting on genes and organisms, versus macroevolutionary processes such as species selection acting on entire species and affecting their rates of speciation and extinction.

A common misconception is that evolution has goals, long-term plans, or an innate tendency for "progress", as expressed in beliefs such as orthogenesis and evolutionism; realistically however, evolution has no long-term goal and does not necessarily produce greater complexity. Although complex species have evolved, they occur as a side effect of the overall number of organisms increasing and simple forms of life still remain more common in the biosphere. For example, the overwhelming majority of species are microscopic prokaryotes, which form about half the world's biomass despite their small size, and constitute the vast majority of Earth's biodiversity. Simple organisms have therefore been the dominant form of life on Earth throughout its history and continue to be the main form of life up to the present day, with complex life only appearing more diverse because it is more noticeable. Indeed, the evolution of microorganisms is particularly important to modern evolutionary research, since their rapid reproduction allows the study of experimental evolution and the observation of evolution and adaptation in real time.

Adaptation

Adaptation is the process that makes organisms better suited to their habitat. Also, the term adaptation may refer to a trait that is important for an organism's survival. For example, the adaptation of horses' teeth to the grinding of grass. By using the term adaptation for the evolutionary process and adaptive trait for the product (the bodily part or function), the two senses of the word may be distinguished. Adaptations are produced by natural selection. The following definitions are due to Theodosius Dobzhansky:

1. Adaptation is the evolutionary process whereby an organism becomes better able to live in its habitat or habitats.

2. Adaptedness is the state of being adapted: the degree to which an organism is able to live and reproduce in a given set of habitats.

3. An adaptive trait is an aspect of the developmental pattern of the organism which enables or enhances the probability of that organism surviving and reproducing.

Adaptation may cause either the gain of a new feature, or the loss of an ancestral feature. An example that shows both types of change is bacterial adaptation to antibiotic selection, with genetic changes causing antibiotic resistance by both modifying the target of the drug, or increasing the activity of transporters that pump the drug out of the cell. Other striking examples are the bacteria Escherichia coli evolving the ability to use citric acid as a nutrient in a long-term laboratory experiment, Flavobacterium evolving a novel enzyme that allows these bacteria to grow on the by-products of nylon manufacturing, and the soil bacterium Sphingobium evolving an entirely new metabolic pathway that degrades the synthetic pesticide pentachlorophenol. An interesting but still controversial idea is that some adaptations might increase the ability of organisms to generate genetic diversity and adapt by natural selection (increasing organisms' evolvability).[excessive citations ]

Adaptation occurs through the gradual modification of existing structures. Consequently, structures with similar internal organisation may have different functions in related organisms. This is the result of a single ancestral structure being adapted to function in different ways. The bones within bat wings, for example, are very similar to those in mice feet and primate hands, due to the descent of all these structures from a common mammalian ancestor. However, since all living organisms are related to some extent, even organs that appear to have little or no structural similarity, such as arthropod, squid and vertebrate eyes, or the limbs and wings of arthropods and vertebrates, can depend on a common set of homologous genes that control their assembly and function; this is called deep homology.

During evolution, some structures may lose their original function and become vestigial structures. Such structures may have little or no function in a current species, yet have a clear function in ancestral species, or other closely related species. Examples include pseudogenes, the non-functional remains of eyes in blind cave-dwelling fish, wings in flightless birds, the presence of hip bones in whales and snakes, and sexual traits in organisms that reproduce via asexual reproduction. Examples of vestigial structures in humans include wisdom teeth, the coccyx, the vermiform appendix, and other behavioural vestiges such as goose bumps and primitive reflexes.

However, many traits that appear to be simple adaptations are in fact exaptations: structures originally adapted for one function, but which coincidentally became somewhat useful for some other function in the process. One example is the African lizard Holaspis guentheri, which developed an extremely flat head for hiding in crevices, as can be seen by looking at its near relatives. However, in this species, the head has become so flattened that it assists in gliding from tree to tree-an exaptation. Within cells, molecular machines such as the bacterial flagella and protein sorting machinery evolved by the recruitment of several pre-existing proteins that previously had different functions. Another example is the recruitment of enzymes from glycolysis and xenobiotic metabolism to serve as structural proteins called crystallins within the lenses of organisms' eyes.

An area of current investigation in evolutionary developmental biology is the developmental basis of adaptations and exaptations. This research addresses the origin and evolution of embryonic development and how modifications of development and developmental processes produce novel features. These studies have shown that evolution can alter development to produce new structures, such as embryonic bone structures that develop into the jaw in other animals instead forming part of the middle ear in mammals. It is also possible for structures that have been lost in evolution to reappear due to changes in developmental genes, such as a mutation in chickens causing embryos to grow teeth similar to those of crocodiles. It is now becoming clear that most alterations in the form of organisms are due to changes in a small set of conserved genes.

Coevolution

Interactions between organisms can produce both conflict and cooperation. When the interaction is between pairs of species, such as a pathogen and a host, or a predator and its prey, these species can develop matched sets of adaptations. Here, the evolution of one species causes adaptations in a second species. These changes in the second species then, in turn, cause new adaptations in the first species. This cycle of selection and response is called coevolution. An example is the production of tetrodotoxin in the rough-skinned newt and the evolution of tetrodotoxin resistance in its predator, the common garter snake. In this predator-prey pair, an evolutionary arms race has produced high levels of toxin in the newt and correspondingly high levels of toxin resistance in the snake.

Cooperation

Not all co-evolved interactions between species involve conflict. Many cases of mutually beneficial interactions have evolved. For instance, an extreme cooperation exists between plants and the mycorrhizal fungi that grow on their roots and aid the plant in absorbing nutrients from the soil. This is a reciprocal relationship as the plants provide the fungi with sugars from photosynthesis. Here, the fungi actually grow inside plant cells, allowing them to exchange nutrients with their hosts, while sending signals that suppress the plant immune system.

Coalitions between organisms of the same species have also evolved. An extreme case is the eusociality found in social insects, such as bees, termites and ants, where sterile insects feed and guard the small number of organisms in a colony that are able to reproduce. On an even smaller scale, the somatic cells that make up the body of an animal limit their reproduction so they can maintain a stable organism, which then supports a small number of the animal's germ cells to produce offspring. Here, somatic cells respond to specific signals that instruct them whether to grow, remain as they are, or die. If cells ignore these signals and multiply inappropriately, their uncontrolled growth causes cancer.

Such cooperation within species may have evolved through the process of kin selection, which is where one organism acts to help raise a relative's offspring. This activity is selected for because if the helping individual contains alleles which promote the helping activity, it is likely that its kin will also contain these alleles and thus those alleles will be passed on. Other processes that may promote cooperation include group selection, where cooperation provides benefits to a group of organisms.

Speciation

Speciation is the process where a species diverges into two or more descendant species.

There are multiple ways to define the concept of "species." The choice of definition is dependent on the particularities of the species concerned. For example, some species concepts apply more readily toward sexually reproducing organisms while others lend themselves better toward asexual organisms. Despite the diversity of various species concepts, these various concepts can be placed into one of three broad philosophical approaches: interbreeding, ecological and phylogenetic. The Biological Species Concept is a classic example of the interbreeding approach. Defined by evolutionary biologist Ernst Mayr in 1942, the BSC states that "species are groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups." Despite its wide and long-term use, the BSC like others is not without controversy, for example because these concepts cannot be applied to prokaryotes, and this is called the species problem. Some researchers have attempted a unifying monistic definition of species, while others adopt a pluralistic approach and suggest that there may be different ways to logically interpret the definition of a species.

Barriers to reproduction between two diverging sexual populations are required for the populations to become new species. Gene flow may slow this process by spreading the new genetic variants also to the other populations. Depending on how far two species have diverged since their most recent common ancestor, it may still be possible for them to produce offspring, as with horses and donkeys mating to produce mules. Such hybrids are generally infertile. In this case, closely related species may regularly interbreed, but hybrids will be selected against and the species will remain distinct. However, viable hybrids are occasionally formed and these new species can either have properties intermediate between their parent species, or possess a totally new phenotype. The importance of hybridisation in producing new species of animals is unclear, although cases have been seen in many types of animals, with the gray tree frog being a particularly well-studied example.

Speciation has been observed multiple times under both controlled laboratory conditions (see laboratory experiments of speciation) and in nature. In sexually reproducing organisms, speciation results from reproductive isolation followed by genealogical divergence. There are four primary geographic modes of speciation. The most common in animals is allopatric speciation, which occurs in populations initially isolated geographically, such as by habitat fragmentation or migration. Selection under these conditions can produce very rapid changes in the appearance and behaviour of organisms. As selection and drift act independently on populations isolated from the rest of their species, separation may eventually produce organisms that cannot interbreed.

The second mode of speciation is peripatric speciation, which occurs when small populations of organisms become isolated in a new environment. This differs from allopatric speciation in that the isolated populations are numerically much smaller than the parental population. Here, the founder effect causes rapid speciation after an increase in inbreeding increases selection on homozygotes, leading to rapid genetic change.

The third mode is parapatric speciation. This is similar to peripatric speciation in that a small population enters a new habitat, but differs in that there is no physical separation between these two populations. Instead, speciation results from the evolution of mechanisms that reduce gene flow between the two populations. Generally this occurs when there has been a drastic change in the environment within the parental species' habitat. One example is the grass Anthoxanthum odoratum, which can undergo parapatric speciation in response to localised metal pollution from mines. Here, plants evolve that have resistance to high levels of metals in the soil. Selection against interbreeding with the metal-sensitive parental population produced a gradual change in the flowering time of the metal-resistant plants, which eventually produced complete reproductive isolation. Selection against hybrids between the two populations may cause reinforcement, which is the evolution of traits that promote mating within a species, as well as character displacement, which is when two species become more distinct in appearance.

Finally, in sympatric speciation species diverge without geographic isolation or changes in habitat. This form is rare since even a small amount of gene flow may remove genetic differences between parts of a population. Generally, sympatric speciation in animals requires the evolution of both genetic differences and nonrandom mating, to allow reproductive isolation to evolve.

One type of sympatric speciation involves crossbreeding of two related species to produce a new hybrid species. This is not common in animals as animal hybrids are usually sterile. This is because during meiosis the homologous chromosomes from each parent are from different species and cannot successfully pair. However, it is more common in plants because plants often double their number of chromosomes, to form polyploids. This allows the chromosomes from each parental species to form matching pairs during meiosis, since each parent's chromosomes are represented by a pair already. An example of such a speciation event is when the plant species Arabidopsis thaliana and Arabidopsis arenosa crossbred to give the new species Arabidopsis suecica. This happened about 20,000 years ago, and the speciation process has been repeated in the laboratory, which allows the study of the genetic mechanisms involved in this process. Indeed, chromosome doubling within a species may be a common cause of reproductive isolation, as half the doubled chromosomes will be unmatched when breeding with undoubled organisms.

Speciation events are important in the theory of punctuated equilibrium, which accounts for the pattern in the fossil record of short "bursts" of evolution interspersed with relatively long periods of stasis, where species remain relatively unchanged. In this theory, speciation and rapid evolution are linked, with natural selection and genetic drift acting most strongly on organisms undergoing speciation in novel habitats or small populations. As a result, the periods of stasis in the fossil record correspond to the parental population and the organisms undergoing speciation and rapid evolution are found in small populations or geographically restricted habitats and therefore rarely being preserved as fossils.

Extinction

Extinction is the disappearance of an entire species. Extinction is not an unusual event, as species regularly appear through speciation and disappear through extinction. Nearly all animal and plant species that have lived on Earth are now extinct, and extinction appears to be the ultimate fate of all species. These extinctions have happened continuously throughout the history of life, although the rate of extinction spikes in occasional mass extinction events. The Cretaceous-Paleogene extinction event, during which the non-avian dinosaurs became extinct, is the most well-known, but the earlier Permian-Triassic extinction event was even more severe, with approximately 96% of all marine species driven to extinction. The Holocene extinction event is an ongoing mass extinction associated with humanity's expansion across the globe over the past few thousand years. Present-day extinction rates are 100-1000 times greater than the background rate and up to 30% of current species may be extinct by the mid 21st century. Human activities are now the primary cause of the ongoing extinction event; global warming may further accelerate it in the future. Despite the estimated extinction of more than 99 percent of all species that ever lived on Earth, about 1 trillion species are estimated to be on Earth currently with only one-thousandth of one percent described.

The role of extinction in evolution is not very well understood and may depend on which type of extinction is considered. The causes of the continuous "low-level" extinction events, which form the majority of extinctions, may be the result of competition between species for limited resources (the competitive exclusion principle). If one species can out-compete another, this could produce species selection, with the fitter species surviving and the other species being driven to extinction. The intermittent mass extinctions are also important, but instead of acting as a selective force, they drastically reduce diversity in a nonspecific manner and promote bursts of rapid evolution and speciation in survivors.

Evolutionary history of life

Origin of life

The Earth is about 4.54 billion years old. The earliest undisputed evidence of life on Earth dates from at least 3.5 billion years ago, during the Eoarchean Era after a geological crust started to solidify following the earlier molten Hadean Eon. Microbial mat fossils have been found in 3.48 billion-year-old sandstone in Western Australia. Other early physical evidence of a biogenic substance is graphite in 3.7 billion-year-old metasedimentary rocks discovered in Western Greenland as well as "remains of biotic life" found in 4.1 billion-year-old rocks in Western Australia. Commenting on the Australian findings, Stephen Blair Hedges wrote, "If life arose relatively quickly on Earth, then it could be common in the universe." In July 2016, scientists reported identifying a set of 355 genes from the last universal common ancestor (LUCA) of all organisms living on Earth.

More than 99 percent of all species, amounting to over five billion species, that ever lived on Earth are estimated to be extinct. Estimates on the number of Earth's current species range from 10 million to 14 million, of which about 1.9 million are estimated to have been named and 1.6 million documented in a central database to date, leaving at least 80 percent not yet described.

Highly energetic chemistry is thought to have produced a self-replicating molecule around 4 billion years ago, and half a billion years later the last common ancestor of all life existed. The current scientific consensus is that the complex biochemistry that makes up life came from simpler chemical reactions. The beginning of life may have included self-replicating molecules such as RNA and the assembly of simple cells.

Common descent

All organisms on Earth are descended from a common ancestor or ancestral gene pool. Current species are a stage in the process of evolution, with their diversity the product of a long series of speciation and extinction events. The common descent of organisms was first deduced from four simple facts about organisms: First, they have geographic distributions that cannot be explained by local adaptation. Second, the diversity of life is not a set of completely unique organisms, but organisms that share morphological similarities. Third, vestigial traits with no clear purpose resemble functional ancestral traits. Fourth, organisms can be classified using these similarities into a hierarchy of nested groups, similar to a family tree.

Modern research has suggested that, due to horizontal gene transfer, this "tree of life" may be more complicated than a simple branching tree since some genes have spread independently between distantly related species. To solve this problem and others, some authors prefer to use the " Coral of life" as a metaphor or a mathematical model to illustrate the evolution of life. This view dates back to an idea briefly mentioned by Darwin but later abandoned.

Past species have also left records of their evolutionary history. Fossils, along with the comparative anatomy of present-day organisms, constitute the morphological, or anatomical, record. By comparing the anatomies of both modern and extinct species, palaeontologists can infer the lineages of those species. However, this approach is most successful for organisms that had hard body parts, such as shells, bones or teeth. Further, as prokaryotes such as bacteria and archaea share a limited set of common morphologies, their fossils do not provide information on their ancestry.

More recently, evidence for common descent has come from the study of biochemical similarities between organisms. For example, all living cells use the same basic set of nucleotides and amino acids. The development of molecular genetics has revealed the record of evolution left in organisms' genomes: dating when species diverged through the molecular clock produced by mutations. For example, these DNA sequence comparisons have revealed that humans and chimpanzees share 98% of their genomes and analysing the few areas where they differ helps shed light on when the common ancestor of these species existed.

Evolution of life

Prokaryotes inhabited the Earth from approximately 3-4 billion years ago. No obvious changes in morphology or cellular organisation occurred in these organisms over the next few billion years. The eukaryotic cells emerged between 1.6 and 2.7 billion years ago. The next major change in cell structure came when bacteria were engulfed by eukaryotic cells, in a cooperative association called endosymbiosis. The engulfed bacteria and the host cell then underwent coevolution, with the bacteria evolving into either mitochondria or hydrogenosomes. Another engulfment of cyanobacterial-like organisms led to the formation of chloroplasts in algae and plants.

The history of life was that of the unicellular eukaryotes, prokaryotes and archaea until about 610 million years ago when multicellular organisms began to appear in the oceans in the Ediacaran period. The evolution of multicellularity occurred in multiple independent events, in organisms as diverse as sponges, brown algae, cyanobacteria, slime moulds and myxobacteria. In January 2016, scientists reported that, about 800 million years ago, a minor genetic change in a single molecule called GK-PID may have allowed organisms to go from a single cell organism to one of many cells.

Soon after the emergence of these first multicellular organisms, a remarkable amount of biological diversity appeared over approximately 10 million years, in an event called the Cambrian explosion. Here, the majority of types of modern animals appeared in the fossil record, as well as unique lineages that subsequently became extinct. Various triggers for the Cambrian explosion have been proposed, including the accumulation of oxygen in the atmosphere from photosynthesis.

About 500 million years ago, plants and fungi colonised the land and were soon followed by arthropods and other animals. Insects were particularly successful and even today make up the majority of animal species. Amphibians first appeared around 364 million years ago, followed by early amniotes and birds around 155 million years ago (both from " reptile"-like lineages), mammals around 129 million years ago, Homininae around 10 million years ago and modern humans around 250,000 years ago. However, despite the evolution of these large animals, smaller organisms similar to the types that evolved early in this process continue to be highly successful and dominate the Earth, with the majority of both biomass and species being prokaryotes.

Applications

Concepts and models used in evolutionary biology, such as natural selection, have many applications.

Artificial selection is the intentional selection of traits in a population of organisms. This has been used for thousands of years in the domestication of plants and animals. More recently, such selection has become a vital part of genetic engineering, with selectable markers such as antibiotic resistance genes being used to manipulate DNA. Proteins with valuable properties have evolved by repeated rounds of mutation and selection (for example modified enzymes and new antibodies) in a process called directed evolution.

Understanding the changes that have occurred during an organism's evolution can reveal the genes needed to construct parts of the body, genes which may be involved in human genetic disorders. For example, the Mexican tetra is an albino cavefish that lost its eyesight during evolution. Breeding together different populations of this blind fish produced some offspring with functional eyes, since different mutations had occurred in the isolated populations that had evolved in different caves. This helped identify genes required for vision and pigmentation.

Evolutionary theory has many applications in medicine. Many human diseases are not static phenomena, but capable of evolution. Viruses, bacteria, fungi and cancers evolve to be resistant to host immune defences, as well as pharmaceutical drugs. These same problems occur in agriculture with pesticide and herbicide resistance. It is possible that we are facing the end of the effective life of most of available antibiotics and predicting the evolution and evolvability of our pathogens and devising strategies to slow or circumvent it is requiring deeper knowledge of the complex forces driving evolution at the molecular level.

In computer science, simulations of evolution using evolutionary algorithms and artificial life started in the 1960s and were extended with simulation of artificial selection. Artificial evolution became a widely recognised optimisation method as a result of the work of Ingo Rechenberg in the 1960s. He used evolution strategies to solve complex engineering problems. Genetic algorithms in particular became popular through the writing of John Henry Holland. Practical applications also include automatic evolution of computer programmes. Evolutionary algorithms are now used to solve multi-dimensional problems more efficiently than software produced by human designers and also to optimise the design of systems.

Social and cultural responses

In the 19th century, particularly after the publication of On the Origin of Species in 1859, the idea that life had evolved was an active source of academic debate centred on the philosophical, social and religious implications of evolution. Today, the modern evolutionary synthesis is accepted by a vast majority of scientists. However, evolution remains a contentious concept for some theists.

While various religions and denominations have reconciled their beliefs with evolution through concepts such as theistic evolution, there are creationists who believe that evolution is contradicted by the creation myths found in their religions and who raise various objections to evolution. As had been demonstrated by responses to the publication of Vestiges of the Natural History of Creation in 1844, the most controversial aspect of evolutionary biology is the implication of human evolution that humans share common ancestry with apes and that the mental and moral faculties of humanity have the same types of natural causes as other inherited traits in animals. In some countries, notably the United States, these tensions between science and religion have fuelled the current creation-evolution controversy, a religious conflict focusing on politics and public education. While other scientific fields such as cosmology and Earth science also conflict with literal interpretations of many religious texts, evolutionary biology experiences significantly more opposition from religious literalists.

The teaching of evolution in American secondary school biology classes was uncommon in most of the first half of the 20th century. The Scopes Trial decision of 1925 caused the subject to become very rare in American secondary biology textbooks for a generation, but it was gradually re-introduced later and became legally protected with the 1968 Epperson v. Arkansas decision. Since then, the competing religious belief of creationism was legally disallowed in secondary school curricula in various decisions in the 1970s and 1980s, but it returned in pseudoscientific form as intelligent design (ID), to be excluded once again in the 2005 Kitzmiller v. Dover Area School District case. The debate over Darwin's ideas did not generate significant controversy in China.

References

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Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes that are passed on from parent to offspring during reproduction. Different characteristics tend to exist within any given population as a result of mutation, genetic recombination and other sources of genetic variation.

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The Black Forest ( German: Schwarzwald [ˈʃvaʁt͡svalt] ) is a large forested mountain range in the state of Baden-Württemberg in southwest Germany, bounded by the Rhine Valley to the west and south and close to the borders with France and Switzerland. It is the source of the Danube and Neckar rivers.

Its highest peak is the Feldberg with an elevation of 1,493 metres (4,898 ft) above sea level. Roughly oblong in shape, with a length of 160 kilometres (100 miles) and breadth of up to 50 km (30 mi), it has an area of about 6,009 km ² (2,320 sq mi).

Historically, the area was known for forestry and the mining of ore deposits, but tourism has now become the primary industry, accounting for around 300,000 jobs. There are several ruined military fortifications dating back to the 17th century.

The Black Forest on the Tabula Peutingeriana: a mountain chain with fantastically formed trees as a symbol of an unsettled and virtually inaccessible terrain

An unmarried Black Forest woman wearing a red Bollenhut, 1898

In ancient times, the Black Forest was known as Abnoba mons, after the Celtic deity, Abnoba. In Roman times ( Late antiquity), it was given the name Silva Marciana ("Marcynian Forest", from the Germanic word marka = "border"). The Black Forest probably represented the border area of the Marcomanni ("border people") who were settled east of the Roman limes. They, in turn, were part of the Germanic tribe of Suebi, who subsequently gave their name to the historic state of Swabia. With the exception of Roman settlements on the perimeter (e.g. the baths in Badenweiler, and mines near Badenweiler and Sulzburg) and the construction of the Roman road of Kinzigtalstraße, the colonization of the Black Forest was not carried out by the Romans but by the Alemanni. They settled and first colonized the valleys, crossing the old settlement boundary, the so-called "red sandstone border", for example, from the region of Baar. Soon afterwards, increasingly higher areas and adjacent forests were colonized, so that by the end of the 10th century, the first settlements could be found in the red (bunter) sandstone region. These include, for example, Rötenbach, which was first mentioned in 819.

Remnants of military fortifications dating from the 17th and 18th centuries can be found in the Black Forest, especially on the mountain passes. Examples include the multiple baroque fieldworks of Margrave Louis William of Baden-Baden or individual defensive positions such as the Alexanderschanze (Alexander's Redoubt), the Röschenschanze and the Schwedenschanze ( Swedish Redoubt).

Originally, the Black Forest was a mixed forest of deciduous trees and firs. At the higher elevations spruce also grew. In the middle of the 19th century, the Black Forest was almost completely deforested by intensive forestry and was subsequently replanted, mostly with spruce monocultures.

In 1990, extensive damage to the forest was caused by a series of windstorms. On 26 December 1999, Cyclone Lothar raged across the Black Forest and caused even greater damage, especially to the spruce monocultures. As had happened following the 1990 storms, large quantities of fallen logs were kept in provisional wet-storage areas for years. The effects of the storm are demonstrated by the Lothar Path, a forest educational and adventure trail at the nature centre in Ruhestein on a highland timber forest of about 10 hectares that was destroyed by a hurricane. Several areas of storm damage, both large and small, were left to nature and have developed today into a natural mixed forest again.

The Black Forest stretches from the High Rhine in the south to the Kraichgau in the north. In the west it is bounded by the Upper Rhine Plain (which, from a natural region perspective, also includes the low chain of foothills); in the east it transitions to the Gäu, Baar and hill country west of the Klettgau. From north to south, the Black Forest extends for over 160 km (100 mi), attaining a width of up to 50 km (30 mi) in the south and 30 km (20 mi) in the north. The Black Forest is the highest part of the South German Scarplands, and much of it is densely wooded, a fragment of the Hercynian Forest of antiquity.

Administratively, the Black Forest belongs completely to the state of Baden-Württemberg and comprises the cities of Freiburg, Pforzheim and Baden-Baden as well as the following districts (). In the north: Enz, Rastatt and Calw; in the middle: Freudenstadt, Ortenaukreis and Rottweil; in the south: Emmendingen, Schwarzwald-Baar, Breisgau-Hochschwarzwald, Lörrach and Waldshut.

The natural regions of the Black Forest are separated by various features.

Geomorphologically, the main division is between the gentle eastern slopes with their mostly rounded hills and broad plateaux (so-called Danubian relief, especially prominent in the north and east on the Bunter Sandstone) and the deeply incised, steeply falling terrain in the west that drops into the Upper Rhine Graben; the so-called Valley Black Forest () with its Rhenanian relief. It is here, in the west, where the highest mountains and the greatest local differences in height (of up to 1000 metres) are found. The valleys are often narrow and ravine-like. The summits are rounded, and there are remnants of plateaux and arête-like landforms.

Geologically the clearest division is also between east and west. Large areas of the eastern Black Forest, the lowest layer of the South German Scarplands composed of Bunter Sandstone, are covered by seemingly endless coniferous forest with their island clearings. The exposed basement in the west, predominantly made up of metamorphic rocks and granites, was, despite its rugged topography, easier to settle and appears much more open and inviting today with its varied meadow valleys.

The most common way of dividing the regions of the Black Forest is, however, from north to south. Until the 1930s, the Black Forest was divided into the Northern and Southern Black Forest, the boundary being the line of the Kinzig valley. Later the Black Forest was divided into the heavily forested Northern Black Forest, the lower, central section, predominantly used for agriculture in the valleys, was the Central Black Forest and the much higher Southern Black Forest with its distinctive highland economy and ice age glacial relief. The term High Black Forest referred to the highest areas of the South and southern Central Black Forest.

The boundaries drawn were, however, quite varied. In 1931, Robert Gradmann called the Central Black Forest the catchment area of the Kinzig and in the west the section up to the lower Elz and Kinzig tributary of the Gutach. A pragmatic division, which is oriented not just on natural and cultural regions, uses the most important transverse valleys. Based on that, the Central Black Forest is bounded by the Kinzig in the north and the line from Dreisam to Gutach in the south, corresponding to the Bonndorf Graben zone and the course of the present day B 31.

In 1959, Rudolf Metz combined the earlier divisions and proposed a modified tripartite division, which combined natural and cultural regional approaches and was widely used. His Central Black Forest is bounded in the north by the watershed between the Acher and Rench and subsequently between the Murg and Kinzig or Forbach and Kinzig, in the south by the Bonndorf Graben zone, which restricts the Black Forest in the east as does the Freudenstadt Graben further north by its transition into the Northern Black Forest.

The Handbook of the Natural Region Divisions of Germany published by the Federal Office of Regional Geography (Bundesanstalt für Landeskunde ) since the early 1950s names the Black Forest as one of six tertiary-level major landscape regions within the secondary-level region of the South German Scarplands and, at the same time, one of nine new major landscape unit groups. It is divided into six so-called major units (level 4 landscapes). This division was refined and modified in several successor publications (1:200,000 individual map sheets) up to 1967, each covering individual sections of the map. The mountain range was also divided into three regions. The northern boundary of the Central Black Forest in this classification runs south of the Rench Valley and the Kniebis to near Freudenstadt. Its southern boundary varied with each edition.

In 1998, the Baden-Württemberg State Department for Environmental Protection (today the Baden-Württemberg State Department for the Environment, Survey and Nature Conservation) published a reworked Natural Region Division of Baden-Württemberg. It is restricted to the level of the natural regional major units and has been used since for the state's administration of nature conservation:

The Black Forest Foothills (Schwarzwald-Randplatten , 150) geomorphologically form plateaux on the north and northeast periphery of the mountain range that descend to the Kraichgau in the north and the Heckengäu landscapes in the east. They are incised by valleys, especially those of the Nagold river system, into individual interfluves; a narrow northwestern finger extends to beyond the Enz near Neuenbürg and also borders the middle reaches of the Alb to the west as far as a point immediately above Ettlingen. To the southwest it is adjoined by the Black Forest Grinden and Enz Hills ( Grindenschwarzwald und Enzhöhen, 151), along the upper reaches of the Enz and Murg, forming the heart of the Northern Black Forest. The west of the Northern Black Forest is formed by the Northern Black Forest Valleys ( Nördliche Talschwarzwald, 152) with the middle reaches of the Murg around Gernsbach, the middle course of the Oos to Baden-Baden, the middle reaches of the Bühlot above Bühls and the upper reaches of the Rench around Oppenau. Their exit valleys from the mountain range are all oriented towards the northwest.

The Southeastern Black Forest ( Südöstliche Schwarzwald, 154) consists mainly of the catchment areas of the upper reaches of the Danube headstreams, the Brigach and Breg as well as the left side valleys of the Wutach north of Neustadt - and thus draining from the northeast of the Southern Black Forest. To the south and west it is adjoined by the High Black Forest ( Hochschwarzwald, 155) with the highest summits in the whole range around the Feldberg and the Belchen. Its eastern part, the Southern Black Forest Plateau, is oriented towards the Danube, but drained over the Wutach and the Alb into the Rhine. The southern crest of the Black Forest in the west is deeply incised by the Rhine into numerous ridges. Immediately right of the Wiese above Lörrach rises the relatively small Bunter Sandstone- Rotliegendes table of the Weintenau Uplands ( Weitenauer Bergland) in the extreme southwest of the Black Forest; morphologically, geologically and climatically it is separate from the other parts of the Southern Black Forest and, in this classification, is also counted as part of the High Black Forest.

At 1,493 m above sea level (NHN) the Feldberg in the Southern Black Forest is the range's highest summit. Also in the same area are the Herzogenhorn (1,415 m) and the Belchen (1,414 m). In general the mountains of the Southern or High Black Forest are higher than those in the Northern Black Forest. The highest Black Forest peak north of the Freiburg-Höllental-Neustadt line is the Kandel (1,241.4 m). Like the highest point of the Northern Black Forest, the Hornisgrinde (1,163 m), or the Southern Black Forest lookout mountains, the Schauinsland (1,284.4 m) and Blauen (1,164.7 m) it lies near the western rim of the range.

The longest Black Forest rivers are (length includes stretches outside the Black Forest):

Enz (105 kilometres; 65 mi)

Kinzig (93 kilometres; 58 mi)

Elz (90 kilometres; 56 mi)

Wutach (91 kilometres; 57 mi)

Nagold (90 kilometres; 56 mi), hydrological main artery of the Nagold-Enz systems

Danube (86 kilometres; 53 mi), headstreams:

Breg (46 kilometres; 29 mi)

Brigach (40 kilometres; 25 mi)

Murg (79 kilometres; 49 mi)

Rench (57 kilometres; 35 mi)

Schutter (56 kilometres; 35 mi)

Wiese (55 kilometres; 34 mi)

Acher (54 kilometres; 34 mi)

Dreisam (incl. Rotbach 49 kilometres; 30 mi)

Alb (incl. Menzenschwander Alb 43 kilometres; 27 mi)

Glatt (37 kilometres; 23 mi)

Möhlin (32 kilometres; 20 mi)

Wolf (31 kilometres; 19 mi)

Schiltach (30 kilometres; 19 mi)

Wehra (incl. Rüttebach 28 kilometres; 17 mi)

Oos (25 kilometres; 16 mi)

Glasbach (18 kilometres; 11 mi), hydrological main artery of the Neckar system

Important lakes of natural, glacial origin in the Black Forest include the Titisee, the Mummelsee and the Feldsee. Especially in the Northern Black Forest are a number of other, smaller tarns. Numerous reservoirs like the - formerly natural but much smaller - Schluchsee with the other lakes of the Schluchseewerk, the Schwarzenbach Reservoir, the Kleine Kinzig Reservoir or the Nagold Reservoir are used for electricity generation, flood protection or drinking water supply.

The Black Forest consists of a cover of sandstone on top of a core of gneiss and granite. Formerly it shared tectonic evolution with the nearby Vosges Mountains. Later during the Middle Eocene a rifting period affected the area and caused formation of the Upper Rhine Plain. During the last glacial period of the Würm glaciation, the Black Forest was covered by glaciers; several tarns (or lakes) such as the Mummelsee are remains of this period.

Since the downfaulting of the Upper Rhine Graben during the Eocene epoch, the two shoulders on either side have been uplifted: the Black Forest to the east and the Vosges to the west. In the centre lies the Kaiserstuhl volcano, which dates to the Miocene. In the times that followed, the Mesozoic platform on the uplands was largely eroded, apart from remains of Bunter Sandstone and Rotliegend Group, but it has survived within the graben itself. During the Pliocene a pronounced but uneven bulge especially affected the southern Black Forest, including the Feldberg. As a result, the upper surface of the basement in the northern part of the forest around the Hornisgrinde is considerably lower. In the central Black Forest, the tectonic syncline of the Kinzig and Murg emerged.

Geomorphologist Walther Penck regarded the Black Forest as an uplifted geologic dome and modeled his theory of piedmonttreppen (piedmont benchlands) on it.

Above the crystalline basement of the Northern Black Forest and the adjacent parts of the Central Black Forest, the bunter sandstone platforms rise in prominent steps. The most resistant surface strata on the stepped terrain of the grinden uplands and the heights around the upper reaches of the Enz, which have been heavily eroded by the tributaries of the Murg, is the silicified main conglomerate (Middle Bunter). To the east and north are the nappes of the Upper Bunter (platten sandstones and red clays). South of the Kinzig the Bunter Sandstone zone narrows to a fringe in the east of the mountain range.

It is considered proven that the Black Forest was heavily glaciated during the peak periods of at least the Riss and Würm glaciations (up to about 10,000 years ago). This glacial geomorphology characterizes almost all of the High Black Forest as well as the main ridge of the Northern Black Forest. Apart from that, it is only discernible from a large number of cirques mainly facing northeast. Especially in this direction snow accumulated on the shaded and leeward slopes of the summit plateau to form short cirque glaciers that made the sides of these funnel-shaped depressions. There are still tarns in some of these old cirques, partly a result of the anthropogenic elevation of the low-side lip of the cirque, such as the Mummelsee, Wildsee, Schurmsee, Glaswaldsee, Buhlbachsee, Nonnenmattweiher, and Feldsee. The Titisee formed as glacial lake behind a glacial moraine.

The Black Forest is mainly rural, with many scattered villages and a few large towns. Tradition and custom are celebrated in many places in the form of annual festivities. The main dialect spoken in the Black Forest area is Alemannic. The forest is best known for its typical farmhouses with their sweeping half-hipped roofs, its Black Forest gâteaus, Black Forest ham, Black Forest gnomes, Kirschwasser and the cuckoo clock.

Traditional costume or Tracht is still sometimes worn today, usually at festive occasions. The appearance of such costume varies from region to region, sometimes markedly. One of the best-known Black Forest costumes is that of the villages of Kirnbach, Reichenbach and Gutach im Kinzigtal with the characteristic headdress. Unmarried women wear the hats with red bobbles or Bollen; married women wear black. Engaged women sometimes wear a bridal crown ( Schäppel) before and on the day of their wedding, whose largest examples from the town of St. Georgen weigh up to 5 kilograms.

Traditionally, the Bollenhut is worn by unmarried women as part of the tracht.

Its rural beauty as well as the sense of tradition of its inhabitants attracted many artists in the 19th and early 20th centuries, whose works made the Black Forest famous the world over. Notable were Hans Thoma from Bernau and his fellow student, Rudolf Epp, who was sponsored by the Grand Duke of Baden, Frederick I. Both artists painted motifs from the Black Forest throughout their lives. Artist J. Metzler from Düsseldorf travelled through the Black Forest to paint his landscapes. The works of the Gutach artist colony around Wilhelm Hasemann were widely admired, their landscape and genre motifs capturing the character of the Black Forest. Like local author Heinrich Hansjakob, they were part of a Baden folk costume movement.

Glassblowing is another notable craft of the Black Forest region. At the beginning of the 15th century, the art of glassmaking took hold in the Bavarian-Bohemian border mountains, especially since the necessary raw materials such as quartz and wood were abundant here. With the permission of the manor, glassblowers operated simple glass production facilities as "wandering huts" ( Wanderhütten), the locations of which were relocated when the local resources were available. They needed huge amounts of firewood and wood for potash. In the second half of the 18th century, the huts had to close due to a shortage of wood and sales difficulties. Only after 1800, when the demand for luxury glass increased enormously, when a few decades of regulated forestry had ensured the regrowth of the raw material wood and when the forest-destroying potash extraction had become unnecessary due to the new glass flux soda, some glass huts ( Glashütten) revived. Some glassblowing factories still testify to this today, for example in Höllental, near Todtnau and in Wolfach.

Black Forest ham originated from this region, as did the Black Forest gâteau, which is also known as "Black Forest Cherry Cake" or "Black Forest Cake" and is made with chocolate cake, cream, sour cherries and Kirsch. The Black Forest variety of Flammekueche is a Baden specialty made with ham, cheese and cream. Pfannkuchen, a crêpe or crêpe-like (Eierkuchen or Palatschinken) pastry, is also common.

The Black Forest is known for its long tradition in gourmet cuisine. No fewer than 17 Michelin starred restaurants are located in the region, among them two restaurants with three stars (Restaurants Bareiss and Schwarzwaldstube in Baiersbronn) as well as the only restaurant in Germany that has been awarded a Michelin star every year since 1966. At Schwarzwald Hotel Adler in Häusern, three generations of chefs from the same family have defended the award from the first year the Michelin Guide selected restaurants in Germany until today.

The German holiday of Fastnacht, or Fasnet, as it is known in the Black Forest region, occurs in the time leading up to Lent. On Fasnetmendig, or the Monday before Ash Wednesday, crowds of people line the streets, wearing wooden, mostly hand-carved masks. One prominent style of mask is called the Black Forest Style, originating from the Black Forest Region.

The Black Forest is home to an unusual tarot card game called Cego, that is part of the region's cultural heritage. After the defeat of Further Austria in 1805, much of its territory was allocated to the Grand Duchy of Baden. During the ensuing Napoleonic Wars, soldiers from Baden deployed with Napoleon's troops to Spain where, among other things, they learned a new card game, Ombre. They took this back to Baden and adapted it to be played with Tarot cards which were then in common use in southern Germany.

Cego soon developed into the national game of Baden and Hohenzollern, and these are the only regions of Germany where tarot cards are still used for playing games. The game has grown organically, and there are many regional variations, but in recent years the establishment of a Cego Black Forest Championship has led to official tournament rules being defined. In addition, regular courses and local tournaments are held and it is a permanent feature of Alemannic Week, held annually in the Black Forest at the end of September.

There are two nature parks and one national park named after the Black Forest that cover the region: the Southern Black Forest Nature Park, the Central/North Black Forest and the Black Forest National Park. The difference between a nature park and a national park is that a nature park's aim is to strive for environmentally sustainable land use, to preserve the countryside as a cultural landscape, to market local produce more effectively, to make the area more suitable for sustainable tourism and to practice environmental education. A national park's aims are to protect the country's natural heritage, to practice environmental education, to serve purposes of scientific environmental observation and to prevent the area from being commercially exploited.

The Southern Black Forest Nature Park ( Naturpark Südschwarzwald) was founded in 1999. It comprises 394,000 ha and is therefore Germany's largest nature park (as of 2020). It encloses the southern part of the Central Black Forest, the Southern Black Forest and adjacent areas.

The Central/North Black Forest Nature Park ( Naturpark Schwarzwald Mitte/Nord) was founded in 2000. It covers 375,000 ha and is thus the second-largest in Germany (as of 2020). It begins in the southern part of the Central Black Forest, bordering on the Southern Black Forest Nature Park and covers the rest of the Black Forest to the north.

The Black Forest National Park, established in 2014, is the first national park in Baden-Württemberg. It lies completely within the Central/North Black Forest Nature Park between the cities of Freudenstadt and Baden-Baden and covers an area of 10,062 ha. Its motto is "Natur Natur sein lassen" (let nature be nature).

In addition to the characteristic range of fauna found in Central European forests, the following less common animals may be observed in the Black Forest:

The mountain range has lower temperatures and higher rainfall than its surrounding countryside. The highlands of the Black Forest are characterized by regular rainfall throughout the year. However, temperatures do not fall evenly with increasing elevation, nor does the rainfall increase uniformly. Rather, the precipitation rises quickly even in the lower regions and is disproportionately heavy on the rainier western side of the mountains.

The wettest areas are the highlands around the Hornisgrinde in the north and around the Belchen and Feldberg in the south, where annual rainfall reaches 1,800-2,100 mm. Moisture-laden Atlantic westerlies dump about as much rain in the Northern Black Forest, despite its lower elevation, than in the higher area of the Southern Black Forest. There, the Vosges act as a rain shield in the face of the prevailing winds. On the exposed east side of the Central Black Forest, it is much drier; the annual rainfall there is about 750 L/m ².

The higher elevations of the Black Forest are characterized by relatively small annual fluctuations and steamed extreme values. This is the result of the frequent light winds and greater cloud cover in summer. During the winter months, frequent high pressure means that the summits are often bathed in sunshine, while the valleys disappear under a thick blanket of fog as a result of pockets of cold air ( temperature inversion).

The main industry of the Black Forest is tourism. Black Forest Tourism ( Schwarzwald Tourismus) assesses that there are around 140,000 direct full-time jobs in the tourist sector and around 34.8 million tourist overnight stays in 2009. In spring, summer and autumn an extensive network of hiking trails and mountain bike routes enable different groups of people to use the natural region. In winter, it is the various types of winter sport that come to the fore. There are facilities for both downhill and Nordic skiing in many places.

The Altstadt of Altensteig in the Northern Black Forest

The most heavily frequented tourist destinations and resorts in the Black Forest are the Titisee and the Schluchsee. Both lakes offer opportunities for water sports like diving and windsurfing. The Mummelsee is a recreational lake and a starting point for a number of hiking trails including the Kunstpfad am Mummelsee ("sculpture trail at the Mummelsee"). The Murg valley, the Kinzig valley, the Triberg Waterfalls and the Open Air Museum at Vogtsbauernhof are also popular. Lookout mountains include the Feldberg, the Belchen, the Kandel and the Schauinsland in the Southern Black Forest; and the Hornisgrinde, the Schliffkopf, the Hohloh, the Merkur and the Teufelsmühle in the Northern Black Forest. The height differences in the mountains are used in many places for hang gliding and paragliding.

One oft-visited town is Baden-Baden with its thermal baths and festival hall. Other thermal baths are found in the spa resorts of Badenweiler, Bad Herrenalb, Bad Wildbad, Bad Krozingen, Bad Liebenzell and Bad Bellingen. From the beginning of the 19th century, the desire for spa and bathing resorts arose in all of Central Europe because of the increasing economic potential, increasing mobility and the use of advertising. The Neo-renaissance style Friedrichsbad and the Palais Thermal are examples for spas built in this era.

There are well known winter sports areas around the Feldberg, near Todtnau with its FIS downhill ski run of Fahler Loch and in Hinterzarten, a centre and talent forge for German ski jumpers. In the Northern Black Forest, the winter-sports areas are concentrated along the Black Forest High Road and on the ridge between the Murg and Enz rivers around Kaltenbronn.

The Black Forest has a great number of very varied trails; some of pan-regional significance. The European long-distance path E1 crosses the Black Forest following the routes of some of the local long-distance paths. Their framework is a network of long-distance paths with main routes and side branches, many of which were laid out in the early 20th century by the Black Forest Club (Schwarzwaldverein). The best known of these is the challenging West Way ( Westweg) with its many steep inclines. After 1950, circular walks were constructed to meet the changing demand, initially from the relatively dense railway network and, later, mainly from locally established hiking car parks. Currently, special, more experience-oriented themed paths are being laid out, such as the Dornstetten Barefoot Park (Barfußpark Dornstetten), the Park of All Senses ( Park mit allen Sinnen) in Gutach ( Black Forest Railway), as well as those designed to bring the walker more directly in contact with nature (e.g. the Schluchtensteig). Roads and wide forest tracks are thus less often used than hitherto.

There are numerous shorter paths suitable for day walks, as well as mountain biking and cross-country skiing trails. The total network of tracks amounts to around 23,000 kilometres (14,000 mi), and is maintained and overseen by volunteers of the Black Forest Club (figures from Bremke, 1999, p. 9), which is the second largest German hiking association. As of 2021, the club counts 65,000 members.

The Vogtsbauernhof (1612) of the Black Forest Open Air Museum in the Gutach valley

The Black Forest Open Air Museum at the Vogtsbauernhof farm in Gutach has original Black Forest houses offering insights into farming life of the 16th and 17th centuries. The buildings were dismantled at their original sites, the individual pieces numbered and then re-erected to exactly the same plan in the museum. The open-air museum shows the life of 16th and 17th century farmers in the region featuring the Vogtsbauernhof which dates back to 1612.

From this early precision engineering a formerly important phonographic industry developed in the 20th century; the history of leisure electronics is presented in the German Phono Museum in St. Georgen.

The Black Forest Costume Museum in Haslach im Kinzigtal offers an overview of the traditional costume of the whole of the Black Forest and its peripheral regions. Also located in Haslach: the Hansjakob Museum and the Hansjakob Archive with numerous works of the writer, priest, politician, historian and chronicler, Heinrich Hansjakob.

The MiMa Mineralogy and Mathematics Museum in Oberwolfach houses minerals and mining exhibits from the whole of the Black Forest and links them to mathematical explanations.

Several tourist routes run through the Black Forest. Well known holiday routes are the Black Forest High Road ( B 500) and the German Clock Road.

Thanks to its winding country roads, the Black Forest is a popular destination for motorcyclists. This arm of tourism is controversial due to the high number of accidents and the wide-ranging noise pollution and has been restricted through the introduction of speed limits and by placing certain roads out of bounds. For example, since 1984, motorcyclists have been banned from using the mountain-racing route on the Schauinsland during summer weekends.

The whole of the Black Forest was once linked by railway. In the eastern part of the Northern Black Forest by the Enz Valley Railway from Pforzheim to Bad Wildbad, by the Nagold Valley Railway from Pforzheim via Calw and Nagold to Horb am Neckar, by the Württemberg Black Forest Railway from Stuttgart to Calw and the Gäu Railway from Stuttgart to Freudenstadt or its present-day section from Eutingen to Freudenstadt.

The Three Lakes Railway branches off at the Titisee from the Höllental Railway and runs to the Windgfällweiher and the Schluchsee. The Wutach Valley Railway runs along the border between Baden-Württemberg and Switzerland, linking Waldshut-Tiengen with Immendingen on the Black Forest Railway.

Most of these routes are still busy today, whilst some are popular heritage lines.

Since January 2006, the Black Forest Tourist organisation, Schwarzwald Tourismus, whose head office is in Freiburg, has been responsible for the administration of tourism in the 320 municipalities of the region. Hitherto there had been four separate tourist associations.

For drivers, the main route through the region is the fast A 5 (E35) motorway, but a variety of signposted scenic routes such as the Schwarzwaldhochstraße (60 km (37 mi), Baden-Baden to Freudenstadt), Schwarzwald Tälerstraße (100 km (62 mi), the Murg and Kinzig valleys) or Badische Weinstraße (Baden Wine Street, 160 km (99 mi), a wine route from Baden-Baden to Weil am Rhein) offers calmer driving along high roads. The last is a picturesque trip starting in the south of the Black Forest going north and includes numerous old wineries and tiny villages. Another, more specialized route is the German Clock Route, a circular route that traces the horological history of the region.

Due to the rich mining history dating from medieval times (the Black Forest was one of the most important mining regions of Europe c.  1100) there are many mines re-opened to the public. Such mines may be visited in the Kinzig valley, the Suggental, the Muenster valley, and around Todtmoos.

The Black Forest was visited on several occasions by Count Otto von Bismarck during his years as Prussian and later German chancellor (1862-1890). Allegedly, he was especially interested in the Triberg Waterfalls. There is now a monument in Triberg dedicated to Bismarck, who apparently enjoyed the tranquility of the region as an escape from his day-to-day political duties in Berlin.

The Black Forest featured in the philosophical development of Martin Heidegger. Heidegger wrote and edited some of his philosophical works in a small hut in the Black Forest, and would receive visitors there for walks, including his former pupil Hannah Arendt. This hut features explicitly in his essay Building, Dwelling, Thinking. His walks in the Black Forest are supposed to have inspired the title of his collection of essays Holzwege, translated as Off The Beaten Track.

An important mining area was the Kinzig valley and its side valleys. The small mining settlement of Wittichen near Schenkenzell in the upper Kinzig valley had many pits from which miners dug baryte, cobalt and silver of many kinds. A circular, geological footpath runs today past the old pits and tips.

Another boom began in the early 18th century after the loss of the Alsace to France. It lasted until the 19th century. Many pits from this period may be visited today as show mines; for example the Teufelsgrund Pit ( Münstertal), the Finstergrund Pit near Wieden, the Hoffnungsstollen ("Hope Gallery") at Todtmoos, the mine in the Schauinsland, the formerly especially silver-rich Wenzel Pit in Oberwolfach and Gr. Segen Gottes ("God's Great Blessing") in Haslach-Schnellingen.

Compared with the Harz and Ore Mountains the quantities of silver extracted in the Black Forest were rather modest and reached only about ten percent of that produced in the other silver-mining regions.

Trunks of White Fir from Gersbach hold up the largest unsupported wooden roof in the world at Expo 2000.

For several centuries logs from the Black Forest were rafted down the Enz, Kinzig, Murg, Nagold and Rhine rivers for use in the shipping industry, as construction timber and for other purposes. This branch of industry boomed in the 18th century and led to large-scale clearances. As most of the long, straight pine logs were transported downriver for shipbuilding in the Netherlands, they were referred to as "Dutchmen". The logs were used in the Netherlands, above all, as piles for house construction in the sandy and wet ground. Even today in Amsterdam large numbers of historic building are built on these posts and the reforestation of the Black Forest with spruce monocultures testifies to the destruction of the original mixed forest. With the expansion of the railway and road network as alternative transportation, rafting largely came to an end in the late 19th century.

Today, loggers harvest fir trees-especially very tall and branchless ones-mainly to ship to Japan. The global advertising impact of Expo 2000 fuelled a resurgence of timber exports. The importance of the timber resources of the Black Forest has also increased sharply recently due to the increasing demand for wood pellets for heating.

Glass-making, charcoal-burning and potash-mining

The timber resources of the Black Forest provided the basis for other sectors of the economy that have now largely disappeared. Charcoal burners ( Köhler) built their wood piles ( Meiler) in the woods and produced charcoal, which, like the products of the potash boilers-further processed inter alia for the glassmaking industry. The Black Forest supplied raw materials and energy for the manufacture of forest glass. This is evidenced today by a number of glassblowing houses e.g. in the Hoellental in Todtnau and Wolfach and the Forest Glass Centre in Gersbach (Schopfheim), which is open to visitors.

Precision-engineering, clock and jewellery manufacture

In the relatively inaccessible Black Forest valleys, industrialization did not arrive until late in the day. In winter, many farmers made wooden cuckoo clocks to supplement their income. This developed in the 19th century into the precision engineering and watch industry, which boomed with the arrival of the railway in many of the Black Forest valleys. The initial disadvantage of their remote location, which led to the development of precision-engineered wooden handicrafts, became a competitive advantage because of their access to raw materials: timber from the forest and metal from the mines. As part of a structural support programme the Baden State Government founded the first clockmaking school in 1850 in Furtwangen to ensure that small artisans were given good training and thus better sales opportunities. Due to the increasing demand for mechanical devices, large companies such as Junghans and Kienzle became established. In the 20th century, the production of consumer electronics was developed by companies such as SABA, Dual and Becker. In the 1970s, the industry declined due to Far Eastern competition. Nevertheless, the Black Forest remains a centre for the metalworking industry and is home to many high-tech companies.

Since the start of industrialisation there have been numerous firms in Pforzheim that manufacture jewellery and work with precious metals and stones. There is also a goldsmith's school in Pforzheim.

The Hornberg Basin near Herrischried, upper reservoir of the Wehr pumped storage station (emptied, May 2008)

Since the 20th century, the Black Forest has seen the large-scale generation of electrical power using run-of-the-river power plants and pumped storage power stations. From 1914 to 1926, the Rudolf Fettweis Company was established in the Murg valley in the Northern Black Forest with the construction of the Schwarzenbach Dam. In 1932, the Schluchsee reservoir, with its new dam, became the upper basin of a pumped-storage power plant. In 2013 the association of the Southern Black Forest's Schluchseewerk owned five power plants with 14 storage tanks. At the Hornberg Basin topographical conditions allow an average head of water of 625 m to drive the turbines before it flows into the Wehra Reservoir.

In the 21st century, in the wake of the Renewable Energy Sources Act, numerous smaller run-of-the-river power stations were re-opened or newly constructed.

Hans Jakob Christoffel von Grimmelshausen (1621/22-1676), German novelist; in 1665-67, he kept an inn in Gaisbach in the Black Forest while writing his famous picaresque novel Simplicius Simplicissimus (1669)

Hans Thoma, born in Bernau (1839-1924), German painter

Hermann Hesse, born in Calw (1877-1962), German poet and novelist

Jürgen Klopp, football manager, who grew up in village of Glatten

Martin Heidegger, German philosopher, who spent much of his time in Todtnauberg, where he wrote most of Being and Time.

1. Chilcoat, Loretta and Rueben Acciano, ^ Western Europe, Lonely Planet: 2005, p. 480.

2. ^ Information Service for Agriculture, Nutrition and Regional Planning Archived 10 February 2012 at the Wayback Machine at the Ministry for Regional Planning, Nutrition and Consumer Protection in Baden-Württemberg

3. Robert Gradmann: ^ Süddeutschland. Engelhorn, Stuttgart 1931. Reprint: Wissenschaftliche Buchgesellschaft Darmstadt, ISBN 3-534-00124-9. Vol. 2: The einzelnen Landschaften, p. 85.

4. c.f. ^ Das Land Baden-Württemberg - Amtliche Beschreibung nach Kreisen und Gemeinden. Vol. 1: Allgemeiner Teil. Kohlhammer Verlag, Stuttgart 1974, ISBN 3-17-001835-3, p. 32, or: Christoph Borcherdt (ed.): Geographische Landeskunde von Baden-Württemberg. 3rd edition, Kohlhammer, Stuttgart, 1993, pp. 169 f.

5. Rudolf Metz: ^ Zur naturräumlichen Gliederung des Schwarzwalds In: Alemannisches Institut (ed.): Alemannisches Jahrbuch 1959, Schauenburg, Lahr 1959, pp. 1-33

6. Emil Meynen, Josef Schmithüsen: ^ Handbuch der naturräumlichen Gliederung Deutschlands. Bundesanstalt für Landeskunde, Remagen/Bad Godesberg 1953-1962 (nine instalments in eight books, updated 1:1,000,000 map with major units, 1960).

7. Emil Meynen, Josef Schmithüsen (editors: ^ Handbuch der naturräumlichen Gliederung Deutschlands. Bundesanstalt für Landeskunde, Remagen/Bad Godesberg, 1953-1962 (9 issues in 8 books, updated map, 1:1,000,000 with major units, 1960).

8. ^ Major natural region units, Baden-Württemberg State Office for the Environment, Survey and Conservation (Landesanstalt für Umwelt, Messungen und Naturschutz Baden-Württemberg) (pdf, 3.1 MB)

9. ^ Harris, Stuart A. (1968). "Treppen concept (penck)". Geomorphology. Encyclopedia of Earth Science. ISBN 978-3-540-31060-0.

10. ^ Spreitzer, H. (1951). "Die Piedmonttreppen in der regionalen Geomorphologie". (in German). 5 (4): 294-305. JSTOR 25635740.

11. Brigitte Heck: ^ Ein Hut macht Karriere.. In: Badisches Landesmuseum Karlsruhe (publ.): Baden! 900 Jahre - Geschichten eines Landes. Info-Verlag, Karlsruhe 2012, ISBN 978-3-937345-56-7, p. 256 (Katalog zur Großen Landesausstellung)

12. ^ "Possibly Germany's most famous cake: Schwarzwalder Kirschtorte (Black Forest Cake)". European Cuisines. Archived from the original on 1 February 2018.

13. ^ Michelin Restaurants Archived 23 June 2011 at the Wayback Machine. Via Michelin. Retrieved 18 June 2011

14. "^ The Archived 21 June 2011 at the Wayback Machine Michelin Guide and the Zumkeller Chefs". Schwarzwald Hotel Adler. Retrieved 18 June 2011

15. ^ Enjoy nature with all the senses / Nature / Home / Inhalte - Schwarzwald Tourismus GmbH

16. ^ Liehl, Ekkehard; Sick, Wolf Dieter, eds. (1984), "Der Schwarzwald. Beiträge zur Landeskunde", Veröffentlichung des Alemannischen Instituts Freiburg I. Br. (in German) (3 ed.), Bühl: Konkordia, vol. 47, p. 70, ISBN 3-7826-0047-9

17. ^ LUBW, Deutscher Wetterdienst: Klimaatlas Baden-Württemberg, Jahresniederschläge 1971-2000: Kartenbeschreibung Archived 20 May 2008 at the Wayback Machine, Karte Archived 11 November 2013 at the Wayback Machine, retrieved 3 September 2013

18. ^ Bachmann, Günther (1996). Denkmalpflege in Baden-Württemberg. Baden-Württemberg: Nachrichtenblatt des Landesdenkmalamtes. pp. 47-56.

19. ^ Parallelus. "On the trail of the Black Forest Cuckooclock " Black Forest Clock Association". Archived from the original on 8 May 2021.

20. ^ Baden-Württemberg: Landesregierung will Motorradlärm eindämmen. Archived 1 June 2022 at the Wayback Machine In: Spiegel Online date 24 July 2012

21. ^ Schauinsland: Motorradfahrer ignorieren Fahrverbot - Radler in Angst. Archived 2 April 2015 at the Wayback Machine In: Badische Zeitung dated 28 June 2010

22. ^ Apropos Werbung, Telefon 07721-98770. "German Clock Route Location". Deutsche Uhrenstrasse. Archived from the original on 9 February 2006.

23. ^ Ken Barnes (2007). A Rough Passage, Volume II: Memories of Empire. The Radcliffe Press. ISBN 9781845112646. Archived from the original on 1 June 2022.

24. ^ Sharr, Adam (27 October 2006). Heidegger's Hut | The MIT Press. Mitpress.mit.edu. ISBN 9780262195515. Archived from the original on 10 May 2015.

25. ^ "Heidegger's Aesthetics (Stanford Encyclopedia of Philosophy)". Plato.stanford.edu. Archived from the original on 11 December 2015.

26. ^ Heidegger, Martin (2002). Heidegger: Off the Beaten Track - Martin Heidegger, Julian Young, Kenneth Haynes. ISBN 9780521805070. Archived from the original on 21 December 2019.

Economy, geology and mining

Eberhard Gothein: Wirtschaftsgeschichte des Schwarzwaldes und der angrenzenden Landschaften. Erster Band: Städte- und Gewerbegeschichte, Verlag Karl J. Trübner, Strassburg 1892 (digitalised).

Georg Sawatzki, Horst Peter Hann (2003), "Badenweiler-Lenzkirch-Zone (Südschwarzwald): Erläuterungen mit Hinweisen für Exkursionen", Geologische Karte von Baden-Württemberg 1:50000 (in German), Freiburg im Breisgau: Landesamt für Geologie, Rohstoffe und Bergbau Baden-Württemberg.

Wolfgang Werner, Volker Dennert (2004), Lagerstätten und Bergbau im Schwarzwald (in German), Freiburg im Breisgau: Landesamt für Geologie, Rohstoffe und Bergbau Baden-Württemberg.

Richard Schmidt: Schwarzwald (Deutsche Lande - Deutsche Kunst). Munich/Berlin, 1965.

Adolf Hanle: Nordschwarzwald (Meyers Naturführer). Mannheim/Vienna/Zurich, 1989.

Adolf Hanle: Südschwarzwald (Meyers Naturführer). Mannheim/Vienna/Zurich, 1989.

Ulrike Klugmann (Hrsg.): Südschwarzwald, Feldberg und Wutachschlucht (Naturmagazin Draußen). Hamburg, 1983.

Hans-Peter Schaub: Der Schwarzwald. Naturvielfalt in einer alten Kulturlandschaft. Mannheim, 2001.

Jürgen Lodemann (ed.): Schwarzwaldgeschichten. Klöpfer & Mayer, Tübingen, 2007, ISBN 978-3-940086-04-4.

Herbert Schnierle-Lutz (ed.): Schwarzwald-Lesebuch. Geschichten aus 6 Jahrhunderten mit zahlreichen Bildern, 224 pages, Hohenheim Verlag, Stuttgart, 2011, ISBN 978-3-89850-213-9.

Bremke, N. (1999). Schwarzwald quer. Karlsruhe: Braun. ISBN 3-7650-8228-7.

Lamparski, F. (1985). Der Einfluß der Regenwurmart Lumbricus badensis auf Waldböden im Südschwarzwald. Schriftenreihe des Institut für Bodenkunde und Waldernährungslehre der Albert-Ludwigs-Universität Freiburg i. Br., 15. ISSN 0344-2691. English summary

Barnes, K. J. (2007). A Rough Passage: Memories of an Empire

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The Black Forest ( German: Schwarzwald [ˈʃvaʁt͡svalt] ) is a large forested mountain range in the state of Baden-Württemberg in southwest Germany, bounded by the Rhine Valley to the west and south and close to the borders with France and Switzerland. It is the source of the Danube and Neckar rivers.

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Meaning of 🌞 Sun With Face Emoji

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🌞 Sun With Face Emoji - Dictionary of Emoji, Copy & Paste

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Sun With Face emoji represents the with a human face - the way we normally see it in the illustrations to some tales or myths. It is used mostly in the meanings the "ordinary" sun would be used.

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The Parthenon was built in thanksgiving for the Hellenic victory over Persian Empire invaders during the Greco-Persian Wars. Like most Greek temples, the Parthenon also served as the city treasury.

Construction started in 447 BC when the Delian League was at the peak of its power. It was completed in 438 BC; work on the decoration continued until 432 BC. For a time, it served as the treasury of the Delian League, which later became the Athenian Empire. In the final decade of the 6th century AD, the Parthenon was converted into a Christian church dedicated to the Virgin Mary. After the Ottoman conquest in the mid-fifteenth century, it became a mosque. In the Morean War, a Venetian bomb landed on the Parthenon, which the Ottomans had used as a munitions dump, during the 1687 siege of the Acropolis. The resulting explosion severely damaged the Parthenon. From 1800 to 1803, the 7th Earl of Elgin took down some of the surviving sculptures, now known as the Elgin Marbles, in an act widely considered, both in its time and subsequently, to constitute vandalism and looting.

The Parthenon replaced an older temple of Athena, which historians call the Pre-Parthenon or Older Parthenon, that was demolished in the Persian invasion of 480 BC.

Since 1975, numerous large-scale restoration projects have been undertaken to preserve remaining artifacts and ensure its structural integrity.

The origin of the word "Parthenon" comes from the Greek word parthénos (), meaning "maiden, girl" as well as "virgin, unmarried woman." The Liddell-Scott-Jones Greek-English Lexicon states that it may have referred to the "unmarried women's apartments" in a house, but that in the Parthenon it seems to have been used for a particular room of the temple. There is some debate as to which room that was. The lexicon states that this room was the western cella of the Parthenon. This has also been suggested by J.B. Bury. Jamauri D. Green claims that the Parthenon was the room where the arrephoroi, a group of four young girls chosen to serve Athena each year, wove a peplos that was presented to Athena during Panathenaic Festivals. Christopher Pelling asserts that the name "Parthenon" means the "temple of the virgin goddess," referring to the cult of Athena Parthenos that was associated with the temple. It has also been suggested that the name of the temple alludes to the maidens ( parthénoi), whose supreme sacrifice guaranteed the safety of the city. In that case, the room originally known as the Parthenon could have been a part of the temple known today as the Erechtheion.

In 5th-century BC accounts of the building, the structure is simply called ( ho naos; lit. "the temple"). Douglas Frame writes that the name "Parthenon" was a nickname related to the statue of Athena Parthenos, and only appeared a century after construction. He contends that "Athena's temple was never officially called the Parthenon and she herself most likely never had the cult title parthénos." The ancient architects Iktinos and Callicrates appear to have called the building Ἑκατόμπεδος ( Hekatómpedos; lit. "the hundred footer") in their lost treatise on Athenian architecture. Harpocration wrote that some people used to call the Parthenon the " Hekatompedos", not due to its size but because of its beauty and fine proportions. The first instance in which Parthenon definitely refers to the entire building comes from the fourth century BC orator Demosthenes. In the 4th century BC and later, the building was referred to as the or the Hekatompedon as well as the Parthenon. Plutarch referred to the building during the first century AD as the Hekatompedos Parthenon .

A 2020 study by Janric van Rookhuijzen supports the idea that the building known today as the Parthenon was originally called the Hekatompedon. Based on literary and historical research, he proposes that "the treasury called the Parthenon should be recognized as the west part of the building now conventionally known as the Erechtheion."

Because the Parthenon was dedicated to the Greek goddess Athena it has sometimes been referred to as the Temple of Minerva, the Roman name for Athena, particularly during the 19th century.

Parthénos was also applied to the Virgin Mary ( Parthénos Maria) when the Parthenon was converted to a Christian church dedicated to the Virgin Mary in the final decade of the 6th century.

The Doric order of the Parthenon

Although the Parthenon is architecturally a temple and is usually called so, some scholars have argued that it is not really a temple in the conventional sense of the word. A small shrine has been excavated within the building, on the site of an older sanctuary probably dedicated to Athena as a way to get closer to the goddess, but the Parthenon apparently never hosted the official cult of Athena Polias, patron of Athens. The cult image of Athena Polias, which was bathed in the sea and to which was presented the , was an olive-wood , located in another temple on the northern side of the Acropolis, more closely associated with the Great Altar of Athena. The High Priestess of Athena Polias supervised the city cult of Athena based in the Akropolis, and was the chief of the lesser officials, such as the plyntrides, arrephoroi and kanephoroi.

The colossal statue of Athena by Phidias was not specifically related to any cult attested by ancient authors and is not known to have inspired any religious fervour. Preserved ancient sources do not associate it with any priestess, altar or cult name.

According to Thucydides, during the Peloponnesian War when Sparta's forces were first preparing to invade Attica, Pericles, in an address to the Athenian people, said that the statue could be used as a gold reserve if that was necessary to preserve Athens, stressing that it "contained forty talents of pure gold and it was all removable," but adding that the gold would afterward have to be restored. The Athenian statesman thus implies that the metal, obtained from contemporary coinage, could be used again if absolutely necessary without any impiety. According to Aristotle, the building also contained golden figures that he described as "Victories." The classicist Harris Rackham noted that eight of those figures were melted down for coinage during the Peloponnesian War. Other Greek writers have claimed that treasures such as Persian swords were also stored inside the temple.[citation needed ] Some scholars, therefore, argue that the Parthenon should be viewed as a grand setting for a monumental votive statue rather than as a cult site.

Archaeologist Joan Breton Connelly has recently argued for the coherency of the Parthenon's sculptural programme in presenting a succession of genealogical narratives that track Athenian identity through the ages: from the birth of Athena, through cosmic and epic battles, to the final great event of the Athenian Bronze Age, the war of Erechtheus and Eumolpos. She argues a pedagogical function for the Parthenon's sculptured decoration, one that establishes and perpetuates Athenian foundation myth, memory, values and identity. While some classicists, including Mary Beard, Peter Green, and Garry Wills have doubted or rejected Connelly's thesis, an increasing number of historians, archaeologists, and classical scholars support her work. They include: J.J. Pollitt, Brunilde Ridgway, Nigel Spivey, Caroline Alexander, and A. E. Stallings.

The Older Parthenon (in black) was destroyed by the Achaemenids during the Destruction of Athens in 480-479 BC, and then rebuilt by Pericles (in grey).

The first endeavour to build a sanctuary for Athena Parthenos on the site of the present Parthenon was begun shortly after the Battle of Marathon (c. 490-488 BC) upon a solid limestone foundation that extended and levelled the southern part of the Acropolis summit. This building replaced a Hekatompedon temple ("hundred-footer") and would have stood beside the archaic temple dedicated to Athena Polias ("of the city"). The Older or Pre-Parthenon, as it is frequently referred to, was still under construction when the Persians sacked the city in 480 BC razing the Acropolis.

The existence of both the proto-Parthenon and its destruction were known from Herodotus, and the drums of its columns were visibly built into the curtain wall north of the Erechtheion. Further physical evidence of this structure was revealed with the excavations of Panagiotis Kavvadias of 1885-1890. The findings of this dig allowed Wilhelm Dörpfeld, then director of the German Archaeological Institute, to assert that there existed a distinct substructure to the original Parthenon, called Parthenon I by Dörpfeld, not immediately below the present edifice as previously assumed. Dörpfeld's observation was that the three steps of the first Parthenon consisted of two steps of Poros limestone, the same as the foundations, and a top step of Karrha limestone that was covered by the lowest step of the Periclean Parthenon. This platform was smaller and slightly to the north of the final Parthenon, indicating that it was built for a different building, now completely covered over. This picture was somewhat complicated by the publication of the final report on the 1885-1890 excavations, indicating that the substructure was contemporary with the Kimonian walls, and implying a later date for the first temple.

Part of the archaeological remains called Perserschutt, or "Persian rubble": remnants of the destruction of Athens by the armies of Xerxes I. Photographed in 1866, just after excavation.

If the original Parthenon was indeed destroyed in 480, it invites the question of why the site was left as a ruin for thirty-three years. One argument involves the oath sworn by the Greek allies before the Battle of Plataea in 479 BC declaring that the sanctuaries destroyed by the Persians would not be rebuilt, an oath from which the Athenians were only absolved with the Peace of Callias in 450. The cost of reconstructing Athens after the Persian sack is at least as likely a cause. The excavations of Bert Hodge Hill led him to propose the existence of a second Parthenon, begun in the period of Kimon after 468. Hill claimed that the Karrha limestone step Dörpfeld thought was the highest of Parthenon I was the lowest of the three steps of Parthenon II, whose stylobate dimensions Hill calculated at 23.51 by 66.888 metres (77.13 ft × 219.45 ft).

One difficulty in dating the proto-Parthenon is that at the time of the 1885 excavation, the archaeological method of seriation was not fully developed; the careless digging and refilling of the site led to a loss of much valuable information. An attempt to make sense of the potsherds found on the Acropolis came with the two-volume study by Graef and Langlotz published in 1925-1933. This inspired American archaeologist William Bell Dinsmoor to give limiting dates for the temple platform and the five walls hidden under the re-terracing of the Acropolis. Dinsmoor concluded that the latest possible date for Parthenon I was no earlier than 495 BC, contradicting the early date given by Dörpfeld. He denied that there were two proto-Parthenons, and held that the only pre-Periclean temple was what Dörpfeld referred to as Parthenon II. Dinsmoor and Dörpfeld exchanged views in the American Journal of Archaeology in 1935.

In the mid-5th century BC, when the Athenian Acropolis became the seat of the Delian League and Athens was the greatest cultural centre of its time, Pericles initiated an ambitious building project that lasted the entire second half of the century. The most important buildings visible on the Acropolis today - the Parthenon, the Propylaia, the Erechtheion and the temple of Athena Nike - were erected during this period. The Parthenon was built under the general supervision of Phidias, who also had charge of the sculptural decoration. The architects Ictinos and Callicrates began their work in 447, and the building was substantially completed by 432. Work on the decorations continued until at least 431.[citation needed ]

The Parthenon was built primarily by men who knew how to work marble. These quarrymen had exceptional skills and were able to cut the blocks of marble to very specific measurements. The quarrymen also knew how to avoid the faults, which were numerous in the Pentelic marble. If the marble blocks were not up to standard, the architects would reject them. The marble was worked with iron tools - picks, points, punches, chisels, and drills. The quarrymen would hold their tools against the marble block and firmly tap the surface of the rock.

A big project like the Parthenon attracted stonemasons from far and wide who travelled to Athens to assist in the project. Slaves and foreigners worked together with the Athenian citizens in the building of the Parthenon, doing the same jobs for the same pay. Temple building was a specialized craft, and there were not many men in Greece qualified to build temples like the Parthenon, so these men would travel and work where they were needed.

Other craftsmen were necessary for the building of the Parthenon, specifically carpenters and metalworkers. Unskilled labourers also had key roles in the building of the Parthenon. They loaded and unloaded the marble blocks and moved the blocks from place to place. In order to complete a project like the Parthenon, many different labourers were needed.

The Parthenon is a peripteral octastyle Doric temple with Ionic architectural features. It stands on a platform or stylobate of three steps. In common with other Greek temples, it is of post and lintel construction and is surrounded by columns ('peripteral') carrying an entablature. There are eight columns at either end ('octastyle') and seventeen on the sides. There is a double row of columns at either end. The colonnade surrounds an inner masonry structure, the which is divided into two compartments. The opisthodomos (the back room of the cella) contained the monetary contributions of the Delian League. At either end of the building, the gable is finished with a triangular pediment originally occupied by sculpted figures.

The Parthenon has been described as "the culmination of the development of the Doric order." The Doric columns, for example, have simple capitals, fluted shafts, and no bases. Above the architrave of the entablature is a frieze of carved pictorial panels ( metopes), separated by formal architectural triglyphs, also typical of the Doric order. The continuous frieze in low relief around the cella and across the lintels of the inner columns, in contrast, reflects the Ionic order. Architectural historian John R. Senseney suggests that this unexpected switch between orders was due to an aesthetic choice on the part of builders during construction, and was likely not part of the original plan of the Parthenon.

Measured at the stylobate, the dimensions of the base of the Parthenon are 69.5 by 30.9 metres (228 by 101 ft). The cella was 29.8 metres long by 19.2 metres wide (97.8 × 63.0 ft). On the exterior, the Doric columns measure 1.9 metres (6.2 ft) in diameter and are 10.4 metres (34 ft) high. The corner columns are slightly larger in diameter. The Parthenon had 46 outer columns and 23 inner columns in total, each column having 20 flutes. (A flute is the concave shaft carved into the column form.) The roof was covered with large overlapping marble tiles known as imbrices and tegulae.

The Parthenon is regarded as the finest example of Greek architecture. John Julius Cooper wrote that "even in antiquity, its architectural refinements were legendary, especially the subtle correspondence between the curvature of the stylobate, the taper of the naos walls, and the entasis of the columns." Entasis refers to the slight swelling, of 4 centimetres (1.6 in), in the center of the columns to counteract the appearance of columns having a waist, as the swelling makes them look straight from a distance. The stylobate is the platform on which the columns stand. As in many other classical Greek temples, it has a slight parabolic upward curvature intended to shed rainwater and reinforce the building against earthquakes. The columns might therefore be supposed to lean outward, but they actually lean slightly inward so that if they carried on, they would meet almost exactly 2,400 metres (1.5 mi) above the centre of the Parthenon. Since they are all the same height, the curvature of the outer stylobate edge is transmitted to the architrave and roof above: "All follow the rule of being built to delicate curves", Gorham Stevens observed when pointing out that, in addition, the west front was built at a slightly higher level than that of the east front.

It is not universally agreed what the intended effect of these "optical refinements" was. They may serve as a sort of "reverse optical illusion." As the Greeks may have been aware, two parallel lines appear to bow, or curve outward, when intersected by converging lines. In this case, the ceiling and floor of the temple may seem to bow in the presence of the surrounding angles of the building. Striving for perfection, the designers may have added these curves, compensating for the illusion by creating their own curves, thus negating this effect and allowing the temple to be seen as they intended. It is also suggested that it was to enliven what might have appeared an inert mass in the case of a building without curves. But the comparison ought to be, according to Smithsonian historian Evan Hadingham, with the Parthenon's more obviously curved predecessors than with a notional rectilinear temple.

Some studies of the Acropolis, including of the Parthenon and its facade, have conjectured that many of its proportions approximate the golden ratio. More recent studies have shown that the proportions of the Parthenon do not match the golden proportion.

Group from the east pediment, British Museum

The cella of the Parthenon housed the chryselephantine statue of Athena Parthenos sculpted by Phidias and dedicated in 439 or 438 BC. The appearance of this is known from other images. The decorative stonework was originally highly coloured. The temple was dedicated to Athena at that time, though construction continued until almost the beginning of the Peloponnesian War in 432. By the year 438, the Doric metopes on the frieze above the exterior colonnade and the Ionic frieze around the upper portion of the walls of the cella had been completed.[citation needed ]

Only a small number of the original sculptures remain Most of the surviving sculptures are at the Acropolis Museum in Athens and (controversially) at the British Museum in London (see Elgin Marbles). Additional pieces are at the Louvre, the National Museum of Denmark, and museums in Rome, Vienna, and Palermo.

In March 2022, the Acropolis Museum launched a new website with "photographs of all the frieze blocks preserved today in the Acropolis Museum, the British Museum and the Louvre."

The frieze of the Parthenon's entablature contained 92 metopes, 14 each on the east and west sides, 32 each on the north and south sides. They were carved in high relief, a practice employed until then only in treasuries (buildings used to keep votive gifts to the gods). According to the building records, the metope sculptures date to the years 446-440. The metopes of the east side of the Parthenon, above the main entrance, depict the Gigantomachy (the mythical battle between the Olympian gods and the Giants). The metopes of the west end show the Amazonomachy (the mythical battle of the Athenians against the Amazons). The metopes of the south side show the Thessalian Centauromachy (battle of the Lapiths aided by Theseus against the half-man, half-horse Centaurs). Metopes 13-21 are missing, but drawings from 1674 attributed to Jaques Carrey indicate a series of humans; these have been variously interpreted as scenes from the Lapith wedding, scenes from the early history of Athens, and various myths. On the north side of the Parthenon, the metopes are poorly preserved, but the subject seems to be the sack of Troy.

The mythological figures of the metopes of the East, North, and West sides of the Parthenon had been deliberately mutilated by Christian iconoclasts in late antiquity.

The metopes present examples of the Severe Style in the anatomy of the figures' heads, in the limitation of the corporal movements to the contours and not to the muscles, and in the presence of pronounced veins in the figures of the Centauromachy. Several of the metopes still remain on the building, but, with the exception of those on the northern side, they are severely damaged. Some of them are located at the Acropolis Museum, others are in the British Museum, and one is at the Louvre museum.

In March 2011, archaeologists announced that they had discovered five metopes of the Parthenon in the south wall of the Acropolis, which had been extended when the Acropolis was used as a fortress. According to Eleftherotypia daily, the archaeologists claimed the metopes had been placed there in the 18th century when the Acropolis wall was being repaired. The experts discovered the metopes while processing 2,250 photos with modern photographic methods, as the white Pentelic marble they are made of differed from the other stone of the wall. It was previously presumed that the missing metopes were destroyed during the Morosini explosion of the Parthenon in 1687.

Phidias Showing the Frieze of the Parthenon to his Friends, 1868 painting by Lawrence Alma-Tadema

The most characteristic feature in the architecture and decoration of the temple is the Ionic frieze running around the exterior of the cella walls. The bas-relief frieze was carved in situ and is dated to 442-438.[citation needed ]

One interpretation is that it depicts an idealized version of the Panathenaic procession from the Dipylon Gate in the Kerameikos to the Acropolis. In this procession held every year, with a special procession taking place every four years, Athenians and foreigners participated in honouring the goddess Athena by offering her sacrifices and a new peplos dress, woven by selected noble Athenian girls called ergastines. The procession is more crowded (appearing to slow in pace) as it nears the gods on the eastern side of the temple.

Joan Breton Connelly offers a mythological interpretation for the frieze, one that is in harmony with the rest of the temple's sculptural programme which shows Athenian genealogy through a series of succession myths set in the remote past. She identifies the central panel above the door of the Parthenon as the pre-battle sacrifice of the daughter of the king Erechtheus, a sacrifice that ensured Athenian victory over Eumolpos and his Thracian army. The great procession marching toward the east end of the Parthenon shows the post-battle thanksgiving sacrifice of cattle and sheep, honey and water, followed by the triumphant army of Erechtheus returning from their victory. This represents the first Panathenaia set in mythical times, the model on which historic Panathenaic processions were based. This interpretation has been rejected by William St Clair, who considers that the frieze shows the celebration of the birth of Ion, who was a descendant of Erechtheus.

Two pediments rise above the portals of the Parthenon, one on the east front, one on the west. The triangular sections once contained massive sculptures that, according to the second-century geographer Pausanias, recounted the birth of Athena and the mythological battle between Athena and Poseidon for control of Athens.

East pediment

The east pediment originally contained 10 to 12 sculptures depicting the Birth of Athena. Most of those pieces were removed and lost during renovations in either the eighth or the twelfth century. Only two corners remain today with figures depicting the passage of time over the course of a full day. Tethrippa of Helios is in the left corner and Selene is on the right. The horses of Helios's chariot are shown with livid expressions as they ascend into the sky at the start of the day. Selene's horses struggle to stay on the pediment scene as the day comes to an end.

West pediment

The supporters of Athena are extensively illustrated at the back of the left chariot, while the defenders of Poseidon are shown trailing behind the right chariot. It is believed that the corners of the pediment are filled by Athenian water deities, such as the Kephisos river, the Ilissos river, and nymph Kallirhoe. This belief emerges from the fluid character of the sculptures' body position which represents the effort of the artist to give the impression of a flowing river. Next to the left river god, there are the sculptures of the mythical king of Athens ( Cecrops or Kekrops) with his daughters ( Aglaurus, Pandrosos, Herse). The statue of Poseidon was the largest sculpture in the pediment until it broke into pieces during Francesco Morosini's effort to remove it in 1688. The posterior piece of the torso was found by Lusieri in the groundwork of a Turkish house in 1801 and is currently held in the British Museum. The anterior portion was revealed by Ross in 1835 and is now held in the Acropolis Museum of Athens.

Every statue on the west pediment has a fully completed back, which would have been impossible to see when the sculpture was on the temple; this indicates that the sculptors put great effort into accurately portraying the human body.

The only piece of sculpture from the Parthenon known to be from the hand of Phidias was the statue of Athena housed in the naos. This massive chryselephantine sculpture is now lost and known only from copies, vase painting, gems, literary descriptions and coins.

A major fire broke out in the Parthenon shortly after the middle of the third century AD. which destroyed the roof and much of the sanctuary's interior. Heruli pirates sacked Athens in 276, and destroyed most of the public buildings there, including the Parthenon. Repairs were made in the fourth century AD, possibly during the reign of Julian the Apostate. A new wooden roof overlaid with clay tiles was installed to cover the sanctuary. It sloped at a greater angle than the original roof and left the building's wings exposed.

The Parthenon survived as a temple dedicated to Athena for nearly 1,000 years until Theodosius II, during the Persecution of pagans in the late Roman Empire, decreed in 435 that all pagan temples in the Eastern Roman Empire be closed. It is debated exactly when during the 5th century that the closure of the Parthenon as a temple was put into practice. It is suggested to have occurred in c. 481-484, on the order of Emperor Zeno, because the temple had been the focus of Pagan Hellenic opposition against Zeno in Athens in support of Illus, who had promised to restore Hellenic rites to the temples that were still standing.

At some point in the fifth century, Athena's great cult image was looted by one of the emperors and taken to Constantinople, where it was later destroyed, possibly during the siege and sack of Constantinople during the Fourth Crusade in 1204 AD.

The Parthenon was converted into a Christian church in the final decades of the fifth century to become the Church of the Parthenos Maria (Virgin Mary) or the Church of the Theotokos ( Mother of God). The orientation of the building was changed to face towards the east; the main entrance was placed at the building's western end, and the Christian altar and iconostasis were situated towards the building's eastern side adjacent to an apse built where the temple's pronaos was formerly located. A large central portal with surrounding side-doors was made in the wall dividing the cella, which became the church's nave, and from the rear chamber, the church's narthex. The spaces between the columns of the opisthodomos and the peristyle were walled up, though a number of doorways still permitted access. Icons were painted on the walls, and many Christian inscriptions were carved into the Parthenon's columns. These renovations inevitably led to the removal and dispersal of some of the sculptures.

The Parthenon became the fourth most important Christian pilgrimage destination in the Eastern Roman Empire after Constantinople, Ephesos, and Thessaloniki. In 1018, the emperor Basil II went on a pilgrimage to Athens after his final victory over the First Bulgarian Empire for the sole purpose of worshipping at the Parthenon. In medieval Greek accounts it is called the Temple of Theotokos Atheniotissa and often indirectly referred to as famous without explaining exactly which temple they were referring to, thus establishing that it was indeed well known.

At the time of the Latin occupation, it became for about 250 years a Roman Catholic church of Our Lady. During this period a tower, used either as a watchtower or bell tower and containing a spiral staircase, was constructed at the southwest corner of the cella, and vaulted tombs were built beneath the Parthenon's floor.

The rediscovery of the Parthenon as an ancient monument dates back to the period of Humanism; Cyriacus of Ancona was the first after antiquity to describe the Parthenon, of which he had read many times in ancient texts. Thanks to him, Western Europe was able to have the first design of the monument, which Ciriaco called "temple of the goddess Athena", unlike previous travellers, who had called it "church of Virgin Mary":

...mirabile Palladis Divae marmoreum templum, divum quippe opus Phidiae ("...the wonderful temple of the goddess Athena, a divine work of Phidias").

Drawing of the Parthenon by James Skene, 1838

In 1456, Ottoman Turkish forces invaded Athens and laid siege to a Florentine army defending the Acropolis until June 1458, when it surrendered to the Turks. The Turks may have briefly restored the Parthenon to the Greek Orthodox Christians for continued use as a church. Some time before the end of the fifteenth century, the Parthenon became a mosque.

The precise circumstances under which the Turks appropriated it for use as a mosque are unclear; one account states that Mehmed II ordered its conversion as punishment for an Athenian plot against Ottoman rule. The apse was repurposed into a mihrab, the tower previously constructed during the Roman Catholic occupation of the Parthenon was extended upwards to become a minaret, a minbar was installed, the Christian altar and iconostasis were removed, and the walls were whitewashed to cover icons of Christian saints and other Christian imagery.

Despite the alterations accompanying the Parthenon's conversion into a church and subsequently a mosque, its structure had remained basically intact. In 1667, the Turkish traveller Evliya Çelebi expressed marvel at the Parthenon's sculptures and figuratively described the building as "like some impregnable fortress not made by human agency". He composed a poetic supplication stating that, as "a work less of human hands than of Heaven itself, [it] should remain standing for all time". The French artist Jacques Carrey in 1674 visited the Acropolis and sketched the Parthenon's sculptural decorations. Early in 1687, an engineer named Plantier sketched the Parthenon for the Frenchman Graviers d'Ortières. These depictions, particularly Carrey's, provide important, and sometimes the only, evidence of the condition of the Parthenon and its various sculptures prior to the devastation it suffered in late 1687 and the subsequent looting of its art objects.

As part of the Morean War (1684-1699), the Venetians sent an expedition led by Francesco Morosini to attack Athens and capture the Acropolis. The Ottoman Turks fortified the Acropolis and used the Parthenon as a gunpowder magazine - despite having been forewarned of the dangers of this use by the 1656 explosion that severely damaged the Propylaea - and as a shelter for members of the local Turkish community.

On 26 September 1687 a Venetian mortar round, fired from the Hill of Philopappos, blew up the magazine. The explosion blew out the building's central portion and caused the cella's walls to crumble into rubble. According to Greek architect and archaeologist Kornilia Chatziaslani:

...three of the sanctuary's four walls nearly collapsed and three-fifths of the sculptures from the frieze fell. Nothing of the roof apparently remained in place. Six columns from the south side fell, eight from the north, as well as whatever remained from the eastern porch, except for one column. The columns brought down with them the enormous marble architraves, triglyphs, and metopes.

About three hundred people were killed in the explosion, which showered marble fragments over nearby Turkish defenders and sparked fires that destroyed many homes.

Accounts written at the time conflict over whether this destruction was deliberate or accidental; one such account, written by the German officer Sobievolski, states that a Turkish deserter revealed to Morosini the use to which the Turks had put the Parthenon; expecting that the Venetians would not target a building of such historic importance. Morosini was said to have responded by directing his artillery to aim at the Parthenon. Subsequently, Morosini sought to loot sculptures from the ruin and caused further damage in the process. Sculptures of Poseidon and Athena's horses fell to the ground and smashed as his soldiers tried to detach them from the building's west pediment.

In 1688 the Venetians abandoned Athens to avoid a confrontation with a large force the Turks had assembled at Chalcis; at that time, the Venetians had considered blowing up what remained of the Parthenon along with the rest of the Acropolis to deny its further use as a fortification to the Turks, but that idea was not pursued.

Once the Turks had recaptured the Acropolis, they used some of the rubble produced by this explosion to erect a smaller mosque within the shell of the ruined Parthenon. For the next century and a half, parts of the remaining structure were looted for building material and especially valuable objects.

The 18th century was a period of Ottoman stagnation-so that many more Europeans found access to Athens, and the picturesque ruins of the Parthenon were much drawn and painted, spurring a rise in philhellenism and helping to arouse sympathy in Britain and France for Greek independence. Amongst those early travellers and archaeologists were James Stuart and Nicholas Revett, who were commissioned by the Society of Dilettanti to survey the ruins of classical Athens. They produced the first measured drawings of the Parthenon, published in 1787 in the second volume of Antiquities of Athens Measured and Delineated. In 1801, the British Ambassador at Constantinople, the Earl of Elgin, claimed that he obtained a firman (edict) from the kaymakam, whose existence or legitimacy has not been proved to this day, to make casts and drawings of the antiquities on the Acropolis, and to remove sculptures that were lying on the ground.

When independent Greece gained control of Athens in 1832, the visible section of the minaret was demolished; only its base and spiral staircase up to the level of the architrave remain intact. Soon all the medieval and Ottoman buildings on the Acropolis were destroyed. The image of the small mosque within the Parthenon's cella has been preserved in Joly de Lotbinière's photograph, published in Lerebours's Excursions Daguerriennes in 1842: the first photograph of the Acropolis. The area became a historical precinct controlled by the Greek government. In the later 19th century, the Parthenon was widely considered by Americans and Europeans to be the pinnacle of human architectural achievement, and became a popular destination and subject of artists, including Frederic Edwin Church and Sanford Robinson Gifford. Today it attracts millions of tourists every year, who travel up the path at the western end of the Acropolis, through the restored Propylaea, and up the Panathenaic Way to the Parthenon, which is surrounded by a low fence to prevent damage.[citation needed ]

The dispute centres around those of the Parthenon Marbles removed by Thomas Bruce, 7th Earl of Elgin, from 1801 to 1803, which are in the British Museum. A few sculptures from the Parthenon are also in the Louvre in Paris, in Copenhagen, and elsewhere, while more than half are in the Acropolis Museum in Athens. A few can still be seen on the building itself. The Greek government has campaigned since 1983 for the British Museum to return the sculptures to Greece. The British Museum has consistently refused to return the sculptures, and successive British governments have been unwilling to force the museum to do so (which would require legislation). Talks between senior representatives from Greek and British cultural ministries and their legal advisors took place in London on 4 May 2007. These were the first serious negotiations for several years, and there were hopes that the two sides might move a step closer to a resolution.

In December 2022, the British newspaper The Guardian published a story with quotes from Greek government officials that suggested negotiations to return the marbles were underway and a "credible" solution was being discussed.

Four pieces of the sculptures have been repatriated to Greece: 3 from the Vatican, and 1 from a museum in Sicily.

An organized effort to preserve and restore buildings on the Acropolis began in 1975, when the Greek government established the Committee for the Conservation of the Acropolis Monuments (ESMA). That group of interdisciplinary specialist scholars oversees the academic understanding of the site to guide restoration efforts. The project later attracted funding and technical assistance from the European Union. An archaeological committee thoroughly documented every artefact remaining on the site, and architects assisted with computer models to determine their original locations. Particularly important and fragile sculptures were transferred to the Acropolis Museum.

A crane was installed for moving marble blocks; the crane was designed to fold away beneath the roofline when not in use. In some cases, prior re-constructions were found to be incorrect. These were dismantled, and a careful process of restoration began.

Originally, various blocks were held together by elongated iron H pins that were completely coated in lead, which protected the iron from corrosion. Stabilizing pins added in the 19th century were not so coated, and corroded. Since the corrosion product (rust) is expansive, the expansion caused further damage by cracking the marble.

In 2019, Greece's Central Archaeological Council approved a restoration of the interior cella's north wall (along with parts of others). The project will reinstate as many as 360 ancient stones, and install 90 new pieces of Pentelic marble, minimizing the use of new material as much as possible. The eventual result of these restorations will be a partial restoration of some or most of each wall of the interior cella.

Beard, Mary. The Parthenon. Harvard University: 2003. ISBN 0-674-01085-X.

Vinzenz Brinkmann (ed.): Athen. Triumph der Bilder. Exhibition catalogue Liebieghaus Skulpturensammlung, Frankfurt, 2016, ISBN 978-3-7319-0300-0.

Connelly, Joan Breton Connelly. "The Parthenon Enigma: A New Understanding of the West's Most Iconic Building and the People Who Made It." Archived 28 July 2020 at the Wayback Machine Knopf: 2014. ISBN 0-307-47659-6.

Cosmopoulos, Michael (editor). The Parthenon and its Sculptures. Cambridge University: 2004. ISBN 0-521-83673-5.

King, Dorothy "The Elgin Marbles" Hutchinson / Random House, 2006. ISBN 0-09-180013-7

Osada, T. (ed.) The Parthenon Frieze. The Ritual Communication between the Goddess and the Polis. Parthenon Project Japan 2011-2014 Phoibos Verlag, Wien 2016, ISBN 978-3-85161-124-3.

Papachatzis, Nikolaos D. Pausaniou Ellados Periegesis - Attika Athens, 1974.

Tournikio, Panayotis. Parthenon. Abrams: 1996. ISBN 0-8109-6314-0.

Traulos, Ioannis N. I Poleodomike ekselikses ton Athinon Athens, 1960 ISBN 960-7254-01-5

Woodford, Susan. The Parthenon. Cambridge University, 1981. ISBN 0-521-22629-5

Catharine Titi, The Parthenon Marbles and International Law, Springer, 2023, ISBN 978-3-031-26356-9.

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The Parthenon was built in thanksgiving for the Hellenic victory over Persian Empire invaders during the Greco-Persian Wars. Like most Greek temples, the Parthenon also served as the city treasury. Construction started in 447 BC when the Delian League was at the peak of its power.

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