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Traditional classification systems have recognized two major categories of organisms based on cell types: eukaryotes and prokaryotes.

But in 1977, microbiologist Carl Woese and colleagues compared rRNA base sequences from different prokaryotes.

The results revealed two fundamentally distinct groups of prokaryotes:

1. Eubacteria (true bacteria)

2. Archaea (a separate lineage, more closely related to eukaryotes than to bacteria).

This led to a paradigm shift in biology: the recognition of new three major categories of organism, Eubacteria, Archaea and Eukaryota. These categories would later be called as domains

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1. Ensures that groups of organisms are close evolutionary relatives rather than arbitrary groups that happen to look similar

2. The use of DNA sequencing has allowed some organisms to be reclassified into more accurate groups

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1. RNA is a key component of ribosomes, the cellular machinery for protein synthesis.

2. It's found in all living organisms, making it a universal molecular marker.

3. Ribosomal RNA (rRNA) is essential for protein synthesis in all organisms, making it universal.

4. It has conserved regions that change very little over evolutionary time, allowing comparisons across distant groups.

5. It also has variable regions, which accumulate mutations at a steady rate, providing useful evidence for divergence.

Also using rRNA, scientists discovered that "prokaryotes" consisted of two fundamentally distinct groups.

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All The Domains Explained: Domain Archaea

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All The Domains Explained: Domain Archaea

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Prokaryotic, but distinct from bacteria.

Often live in extreme environments (thermophiles, halophiles, methanogens).

Key features:

1. Circular chromosomes.

2. Cell wall without peptidoglycan (unlike bacteria).

3. Glycerol-ether lipids in cell membranes (unique).

4. 70S ribosomes, but with a small subunit more similar to eukaryotes.

5. Histone-like proteins present.

6. Introns present in some genes.

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All The Domains Explained: Domain Eubacteria (Bacteria)

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All The Domains Explained: Domain Eubacteria (Bacteria)

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True bacteria; unicellular prokaryotes.

Found in almost all environments.

Key features:

1. Circular chromosomes.

2. Cell walls with peptidoglycan.

3. Glycerol-ester membrane lipids.

4. 70S ribosomes, distinct from archaeal and eukaryotic ribosomes.

5. No histones, introns extremely rare.

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All The Domain Explained: Domain Eukaryota

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All The Domain Explained: Domain Eukaryota

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Includes animals, plants, fungi, and protists.

Key features:

1. Linear chromosomes within a nucleus.

2. 80S ribosomes in the cytoplasm (70S in mitochondria and chloroplasts).

3. Histones present.

4. Introns common in genes.

Complex cells with membrane-bound organelles.

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was the first formal system of grouping organisms. In this system, organisms are grouped and subdivided into smaller and smaller categories of organisms (taxon), with species as the smallest, most exclusive grouping

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The traditional hierarchy of kingdom, phylum , class, order, family, genus, and species does not always correspond to patterns of divergence generated by evolution.

1. Unclear and subjective when two populations should be grouped as separate species (A3.1). Ultimately contrived and does not always reflect evolutionary history and divergence

-> Introgression: transfer of genetic material between species following hybridization and backcrossing to the parental species. Demonstrates difficulty in species classification as the resulting offspring after several generations do not fit completely into either species, but neither does it seem to make sense to classify them as a new species

2. A fixed ranking of taxa is arbitrary – one taxonomist might argue traits in a group of species are similar enough to form a genus; another may think them different enough to form a family

3. Distinct taxa does not reflect gradation of variation and gradual divergence of species and larger groups over time. As species in a genus diverge from each other, there will eventally be sufficient diversity for the genus to split into two or more separate ones.

4. The instant in time when these separations occurred cannot be determined objectively

Hirearchy poses issues in re-classification: if an organism is moved from one taxon to another, does this mean all other members of that taxon should be moved as well?

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This diagram illustrates the nested hierarchy used in a traditional biological classification system with a set number of taxonomic levels.  Organisms are usually grouped together based on their shared characteristics.  Moving down through each level of classification, the number of types of organisms in the group decreases until there is only a single species remaining.

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Cladistics is a method of classifying organisms into groups of species called clades.

(from Greek ‘klados' = branch)

Each clade (branched out group) consists of an ancestral organism and all of its evolutionary descendants.

Clades are organised according to evolutionary relationships - the branches show common evolutionary lineage.

Each branch point (node) represents a speciation event by which distinct species are formed via

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A cladogram is a diagram that shows the evolutionary relationships between species. It is constructed based on shared characteristics, such as similarities and differences in DNA base sequences or amino acid sequences of proteins.

1. Cladograms are branching diagrams that represent hypotheses about evolutionary relationships.

2. They are constructed using evidence from DNA base sequences or amino acid sequences of proteins, which provide objective data about shared ancestry.

3. The more similar two sequences are, the more recently the species diverged.

4. Conversely, species with greater sequence differences likely diverged further back in evolutionary time.

The fewer the differences between sequences, the more closely related the species are, and the more recent their common ancestor.

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The superseding of the Linnaeus system by a cladistics approach to the classification of life is an example of a paradigm shift in science.  A paradigm shift is a fundamental change in the understanding of a phenomena.

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1. DNA and proteins accumulate changes over time as a result of mutations.

2. These changes occur at a roughly measurable rate, allowing scientists to infer how long ago two species diverged.

3. The fewer the sequence differences, the more recently the species shared a common ancestor.

4. The greater the sequence differences, the longer the evolutionary separation.

5. Amino acid sequences are derived from DNA sequences and can also be used to determine evolutionary relationships.

6. They are useful when DNA sequences are unavailable or when studying ancient relationships.

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A case study of transfer of plant species between families could be used to develop understanding, for example the reclassification of the figwort family (Scrophulariaceae).

- Plants commonly known as figworts used to be classified in the family Scrophulariacee, and many of them have been used in herbal medicine. The name Scrophulariacee, sometimes affectionately referred to by botanists as "scrophs".

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There are millions of species on Earth, and new ones are being discovered every day. With such a vast variety of organisms, it becomes very difficult to manage and study them without a proper system.

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Classification makes it easier for biologists to organize information about organisms. It groups living things according to their traits or evolutionary origins, helping with:

Storing information

Retrieving knowledge

Identifying unknown species

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1. DNA encodes proteins, so changes in DNA often result in changes in amino acid sequences.

2. The greater the number of differences in homologous DNA or protein sequences between two species, the longer the time since they diverged.

3. These differences arise through mutations: base substitutions, insertions, or deletions.

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1. Identify the roots or base which is the common ancestor of all of the organisms.

2. Looking at the branches, each split shows a divergence event (when a common ancestor has two or more descendant groups). The more recent the node, the organisms are more closely related.

3. Check for shared derived traits. Ex: feathers appear before the branch leading to birds meaning all birds share feathers.

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1. a particular sequence variation/trait will (likely) occur/evolve once rather than independently

2. provides the criteria for the construction of cladograms

3. choose the simplest explanation that can account for our observations. i.e. choose the tree that requires the fewest independent genetic events (appearances or disappearances of traits) to take place.

Limitations of Parsimony

Evolution doesn’t always follow the simplest path.

A base might mutate to a different base and then revert to the original.

Such events can complicate the analysis and lead to misleading conclusions if parsimony is applied rigidly.

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What is a Clade?

A clade is a group of organisms that comes from one common ancestor and includes all of its descendants.

Members of a clade usually share similar traits, inherited from that ancestor.

Clades can be nested inside each other, like boxes within boxes.

The study of these evolutionary relationships is called Cladistics.

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How to determine a clade in phylogenetic tree??

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How to determine a clade in phylogenetic tree??

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If you cut a branch of the tree at one point, all organisms above that cut belong to one clade.

Examples:

Green box and blue box = these are clades (they include the ancestor and all descendants).

Red box and orange box = not clades (they leave out some descendants of the ancestor).

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1. Mutations introduce changes in nucleotide base sequences of DNA.

2. Over time, differences accumulate in genomes between lineages that no longer interbreed.

3. The greater the number of sequence differences, the longer ago the species diverged.

4. These differences can be quantified and used as an approximate measure of evolutionary time.

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How Do We Measure the Past Without a Time Machine?

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How Do We Measure the Past Without a Time Machine?

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1. Scientists estimate evolutionary timelines by examining changes in DNA sequences.

2. This technique is called the molecular clock.

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Factors Affecting the Rate of Accumulation

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Factors Affecting the Rate of Accumulation

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1. Generation time: species with shorter generations (e.g., bacteria, viruses) accumulate mutations faster due to more replication cycles.

2. Population size: large populations retain more genetic variants, while small populations may lose mutations due to genetic drift.

3. Selective pressure: harmful mutations are often removed, while neutral mutations accumulate.

4. DNA repair mechanisms: species with efficient repair enzymes accumulate fewer mutations; those lacking proofreading accumulate more.

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Morphological traits (body form, structure) can be used, but they can be misleading because unrelated organisms might look similar due to adaptation.

The most reliable method is genetic and molecular data, such as:

DNA sequences of genes

RNA sequences (mRNA, rRNA)

Amino acid sequences in proteins

Mitochondrial DNA (mtDNA)

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Organisms are arranged in a hierarchy: Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species. The species is the smallest and most basic unit.

For example, the organism in the picture. We can obviously see that it is eukaryotic (domain) and an animal (kingdom), but there is still a million possible species.

We can see hair and mammary glands, so we can deduce that the organism is one of the 6,500 species of mammals. Other traits show that it belongs to the order Carnivora, which narrows the possibilities to about 270 species. Further classification places it in the Mustelid family, which contains around 60 species. From there, it becomes relatively easy to identify the genus and species as Pekania pennanti, commonly known as the fisher.

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Correct classification helps scientists to:

Count and record species accurately

Understand evolutionary relationships

Support conservation efforts

Speed up medical research

Identify and respond to new diseases, such as COVID-19

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Constructing Cladogram Using  Amino Acid Sequences

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Constructing Cladogram Using  Amino Acid Sequences

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Constructing Cladogram Using DNA Base Sequences

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Constructing Cladogram Using DNA Base Sequences

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-> a monophyletic group (or clade) includes a common ancestor and ALL of its descendants, forming a complete evolutionary lineage.

-> In contrast, a paraphyletic group are ones that includes a common ancestor and some of its descendants but excludes other descendants

Think of a monophyletic group as a complete family tree, while a paraphyletic group is a family tree that has some branches intentionally cut off.

so we now know that the old family Scrophulariacee was paraphyletic. Plants that were the scrophulariacee family have been given new families to belong to, such plantaginaceae, which is where we now find foxgloves. Foxgloves are no longe

considered to be figworts.

Moving the branches of the tree of life around and reclassifying a taxon in a new

branch in this manner means changing the species' circumscription.

Circumscription:

process of placing taxa where they clearly show monophyletic groups, indicating

that they all share a recent common ancestor.

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- Before mid-1990s, the family Scrophulariaceae was characterized by morphological features such as how the flower petals are arranged in the bud before the flower opens.

- Called aestivation, and botanists look for whether the flower petals overlap with each other or whether they are arranged in a spiral. Another characteristic that was used was the morphology of the nectaries, the parts of the flower that make nectar.

- Since the mid-1990s, DNA analysis of the plants within this taxon has led botanists to rethink their classification.

Analysis of zones of DNA markers, such as the nuclear

ribosomal internal transcribed spacer (ITS) region, has revealed old classification was monophyletic, meaning the taxa didn't share a recent common ancestor. Rather, the old system was grouping together plants that

belonged to separate branches, making it impossible to fit them into a cladogram attempting to show their evolutionary relationships.

WHY RE-CLASS??

lack of uniquely defining traits raises the possibility that the figwort family are not part of the same family.

Analysis of ribosomal (ITS) regions DNA sequencing of three chloroplast genes revealed taxa didn't share recent common ancestor->previous classification was paraphyletic and not monophyletic

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If you want to identify the clades (a common ancestor and all its descendants):

1. Cut one branch and circle everything that follows that clade.

2. Closer branches means closer relatives. So that if any organism shares recent common ancestor, they are more closely related than those that split earlier.

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1. Do not assume more evolved, since cladograms does not show progress and only relationships.

2. Branch does not matter left to right, only the branching points matter.

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1. Reliance of data avilability

2. Varius divergence

3. Difficulty with extinct species

4. Interpretation limitations

5. Not really applicable to prokaryote since they do horizontal gene transfer (ex: asexual reproduction)

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The development of DNA sequencing technology means that classification can now be carried out based on evolutionary relationship

Clades are organisms grouped based on the development of the DNA sequence and carried out based on evolutionary relationships.

Every member of a clade shares a recent common ancestor

Clades are monophyletic groups, meaning that they contain all of the descendants of a common ancestor

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Ideally, classification should follow evolutionary relationships, so all members of a taxonomic group have evolved from a common ancestor. This shows unbroken lines of evolutionary descent = Clade.

Two Criteria:

1. Every organism that has evolved from a common ancestor is included in the same taxonomic group

2. In each taxonomic group, all the species evolved from the same common ancestor

Advantages of classification corresponding to evolutionary relationships:

All members of a clade will share characteristics inherited from a common ancestor (synapomorphies)

Can be used to predict characteristics