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The Earth, as we all know, is a huge planet covered with land and ocean. Being a habitable planet, Earth has been home to many living organisms. Not only humans, or rice, but things like dragons and reptiles, too. The diversity of life on Earth is vast, and the total number of species that we have found now might be limited by our current technology.

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a. Common ancestor: Two species start from a common ancestor with identical DNA at a particular gene or sequence.

b. Mutations occur over time: As the species evolve independently, mutations slowly accumulate in their DNA.

c. More time = more differences: The longer two species have been separated, the more mutations will have built up in their DNA.

d. Compare DNA or protein sequences: Scientists compare the same gene in two species and count the differences.

e. Use the molecular clock: If you know the rate of mutation (e.g., 1 change per 10 million years), you can estimate how long ago the species diverged.

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Over time, mutations accumulate in the DNA sequences of organisms. These mutations happen at a relatively constant rate (this is called the molecular clock). By comparing DNA or amino acid sequences between different species or clades, scientists can estimate how long ago they shared a common ancestor.

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Cladistics investigates evolutionary relationships by organizing organisms into hierarchical groups called clades, each containing an ancestor and all of its descendants, based on shared derived characteristics (synapomorphies) found in anatomical, physiological, or genetic data. These relationships are visualized in cladograms, which are branching diagrams that represent a hypothesis of evolutionary history, allowing scientists to infer common ancestry and refine traditional biological classifications.

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As you move down from domain, taxa ( taxonomy rank) will be smaller and share more characteritics

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Base sequences of genes or amino acid sequences of proteins can be used as the basis for constructing cladograms.

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Base sequences of genes or amino acid sequences of proteins can be used as the basis for constructing cladograms.

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Cladograms are diagrams that show how species are related based on common ancestry (like a family tree of organisms).

To build these trees, scientists need evidence of relatedness.

Two main kinds of evidence can be used:

DNA base sequences (e.g., A, T, G, C order in a gene).

Amino acid sequences in proteins (which come from the DNA code).

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✖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

✖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

✖Distinct taxa (taxonomy rank) 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. The instant in time when these separations occurred cannot be determined objectively

✖Hirearchy poses issues in reclassification: 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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When interbreeding between 2 different species (Example: polar bear and black bear)

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When interbreeding between 2 different species (Example: polar bear and black bear)

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Both of them have same amount of chromosomes (74 chromosomes) and have a intermediate phenotype will makes different phenotype and species

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All living organisms use the same genetic code, so their DNA/proteins are comparable.

If two species have similar sequences, it suggests they share a recent common ancestor.

If the sequences are very different, they are less closely related.

DNA (base) sequences give more detailed data (exact codons, including silent mutations).

Amino acid sequences are useful when comparing distant organisms, since proteins are more conserved (don’t change as quickly).

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WELCOME TO: Advantages of Classification Corresponding to Evolutionary Relationship

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WELCOME TO: Advantages of Classification Corresponding to Evolutionary Relationship

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When reading cladograms, we have to focus on the branching, not the order:

The order of taxa (left-to-right) doesn’t matter.

Only the branching pattern shows relationships.

Example: Whether WXYZ or ZYXW, the evolutionary story is the same.

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Proximity on the diagram doesn’t matter. The true measure is the age of the most recent common ancestor (MRCA).

Taxa with a younger MRCA are more closely related than those with an older MRCA.

The number of nodes separating taxa isn’t important, it changes depending on how many species are included in the tree.

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Each “end point” (terminal taxon) represents a unique evolutionary lineage.

No taxon at the tip is the ancestor of another tip, instead, they share an ancestor further back in time.

Example: humans, chimpanzees, and gorillas are evolutionary cousins, not descendants of one another.

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Modern biological classification is ideally phylogenetic, it reflects evolutionary relationships rather than superficial similarities.

Organisms should be grouped into clades, which include a common ancestor and all of its descendants.

This ensures that the classification represents unbroken evolutionary lineages.

There are two criterias:

1. Every organism descended from a common ancestor belongs in the same taxonomic group.

2. All species in a taxonomic group must share that same ancestor (no “outsiders”).

This is stricter than traditional classification, which sometimes grouped organisms by morphology rather than ancestry.

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A true clade is a monophyletic group.

But “Reptiles” (snakes, lizards, turtles, crocodiles) is paraphyletic if birds are excluded.
Why? Birds and crocodiles share a more recent ancestor with each other than either does with lizards.

This forces two choices in taxonomy:

Reject “reptiles” as a valid clade

Or redefine reptiles to include birds (making them feathered reptiles).

This illustrates how phylogenetic classification can overturn traditional terms when they don’t reflect ancestry.

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Using clades offers powerful predictive and explanatory value:

Synapomorphies: Members of a clade share derived traits from their common ancestor.

Example: All mammals have mammary glands, hair, and a four-chambered heart.

Predictive power: When a new species is discovered, classification allows biologists to predict its traits with confidence.

Example: If a new bat species is found, we can reasonably infer mammalian features like placenta, endothermy, and mammary glands.

Consistency with evolutionary theory: Classification by clades ensures taxonomic systems match the reality of descent with modification.

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Revolutionary way to classify using rRNA base sequence

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Revolutionary way to classify using rRNA base sequence

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Classification of Organisms into Three Domains (1977, rRNA evidence)

Traditional classification:

Two groups → Prokaryotes and Eukaryotes.

In 1977, rRNA base sequences were compared → revealed three domains:

Eubacteria (true bacteria)

Archaea

Eukaryotes

Why Archaea are Separate from Eubacteria

Differences in small ribosomal subunit rRNA sequences.

Unique metabolic reactions in archaea (e.g., methanogenesis).

Transcription & translation in archaea are more similar to eukaryotes than eubacteria.

Some structural features in archaea resemble eukaryotes more than bacteria.

rRNA Sequence Evidence

Certain sequences found in archaea (methanogens) but never or only sometimes in typical bacteria.

Confirms distinct evolutionary lineage.

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Archaeal membranes:

Ether linkages (more stable in extreme conditions).

Can form monolayers instead of bilayers.

Histones in Archaea: structurally different but similar function to eukaryotic histones.

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Let's take a whale as an example. Even a type of animal will have many species. There is not only one whale species but dozens of them. This is where classification is essential for us to understand their evolutionary pathway and similarities. Classification is the process of putting organisms into groups, and yes, it is a branch of science called taxonomy.

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Cladistics is a way of classifying organisms based on DNA evidence to show how they are related through evolution. This is more reliable than looking only at physical features.

The Figwort family (Scrophulariaceae) was originally a big group of plants that looked similar. But DNA studies showed they were not all closely related. This meant the old group was polyphyletic (included species from different ancestors). The similarities were caused by convergent evolution—plants evolving similar traits even though they were not closely related.

Scientists then reclassified the figworts into smaller, correct groups called monophyletic clades (plants that share one ancestor). After this, many plants were moved into new families such as Orobanchaceae, Stilbaceae, Veronicaceae, and Calceolariaceae.

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What is the benefit of classifiying those organisms?

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What is the benefit of classifiying those organisms?

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Correct classification allows scientists to:

Accurately determine the number of known species

Without classification, there would be a risk of recording species more than once or incorrectly grouping multiple species together as one

Learn about the evolution of species

Accurate classification allows scientists to determine the evolutionary relationships between species, i.e. which species share common ancestry, and how recently

Ensure that conservation is carried out when needed

It is not possible to conserve a species if we don't know that it exists, e.g. if several species are incorrectly classified as one species, then the extinction of what might be thought of as one local population could actually result in the extinction of an entire species

Carry out medical research more quickly

E.g. if one plant species is known to have medicinal properties, then it is possible to quickly identify others by looking at its close relatives; this is much faster than just selecting plants at random for research

Identify and treat new diseases more quickly

E.g. the virus that causes COVID-19 was quickly classified as being a coronavirus, providing medics with information about how it might affect the body, and how to go about developing a vaccine

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Cladistics

Cladistics is the branch of science in which scientists put organisms into clades

The term clade can be defined as

A group of organisms that have all descended from a common ancestor

Clades can include both living and extinct species

Some of the descendants of a common ancestor may have gone extinct

The common ancestor species itself may have gone extinct

Clades can be large or small, depending on the common ancestor being studied

While taxonomy is about classifying and then naming organisms, cladistics is about identifying evolutionary relationships between organisms

A taxon is a group of organisms that has been given a group name by taxonomists based on its shared features

A clade is a group of organisms classified together based on their shared descent from a common ancestor

If taxonomy is carried out correctly, then all of the members of a taxon should form a clade, but due to historical error, this is not always the case

In cladistics, species must be placed into true clades; this avoids mistakes such as:

Some descendants of a common ancestor being placed in different clades from each other

Some organisms that descend from a different ancestor being included in the same clade

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Parsimony means simplicity.

In cladistics, the principle of parsimony says:

"The best cladogram is the one that requires the fewest evolutionary changes (mutations, gains, losses of traits)."

Evolution could, in theory, explain relationships in many complicated ways.

But scientists assume that the simplest explanation (least number of steps) is the most likely to be correct.

This avoids making unnecessary assumptions about multiple independent mutations happening when one change could explain it.