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?

• 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.

• 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.

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.

• 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.

• 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.

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.

• 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

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.

• 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.

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