Ch 20.3 Phylogeny - Phylogenetic Systematics

Systematists gather extensive data on organisms to infer phylogeny, focusing on features resulting from common ancestry.
Molecular genetic sequences are widely used today.

Phylogenies help differentiate between homologous (shared ancestry) and analogous (independent evolution) similarities.
Homologies are phenotypic and genetic similarities due to shared ancestry.
- Example: Bone arrangement in mammal limbs.
Genes or DNA sequences are homologous if descended from common ancestor sequences.
Closely related organisms share similar morphologies or DNA sequences.
Morphological divergence can be great with small genetic divergence, or vice versa.
- Example: Hawaiian silverzord plants with varying morphologies but similar genes.
- Divergence estimated at five million years based on molecular data correlating with the formation of the Hawaiian Islands.

Analogy results from convergent evolution, where similar environments lead to similar adaptations in different lineages.
- Example: Mole-like animals with similar external appearance but different internal anatomy.
- Common ancestor lived 160 million years ago and was not mole-like.
Complex characters suggest homology.
- Example: Human and chimpanzee skulls sharing many bones.
Computer technology and genetic sequencing have revolutionized phylogenetic inference.

Genes are sequences of nucleotides (A, G, C, T).
Homologous genes share portions of nucleotide sequences.
Comparing DNA molecules poses challenges.
The first step is to align comparable sequences.
Closely related species have sequences differing at few sites.
Distantly related species have different bases and lengths due to insertions and deletions.

Computer programs identify matches by testing possible alignments for DNA segments of different lengths.
Molecular comparisons reveal base substitutions in Australian and golden moles, indicating distant relation.
Silver sword plants show high gene sequence similarity despite morphological differences.
It is necessary to distinguish homology from analogy in evaluating molecular similarities.
Similar sequences are likely homologous.
Coincidental matches may occur in distantly related organisms.
*Scientists have developed statistical tools to distinguish distant homologies from coincidental matches in divergent sequences.

Branch lengths can represent evolutionary change or time.
In some trees, branch lengths are proportional to the amount of evolutionary change in a DNA sequence.
The total length of horizontal lines from the base of a tree to the mouse is less than that of the line leading to the outgroup species, the fruit fly drosophila.
More genetic changes have occurred in the drosophila lineage than the mouse lineage.
All lineages from a common ancestor have survived for the same time.
- Example: Humans and bacteria share a single-celled prokaryote ancestor from three billion years ago.
Trees can represent chronological time using fossil data.
Branch points can be labeled with rates of genetic change or dates of divergence.

As the database of DNA sequences grows, building phylogenetic trees becomes more difficult.
For 50 species, there are $3 \times 10^{76}$ possible tree arrangements.
Maximum parsimony is used to narrow possibilities.
The principle of maximum parsimony holds that we should first investigate the simplest explanation that is consistent with the facts.
Also known as Occam's razor.
For morphology-based trees, the most parsimonious tree requires the fewest evolutionary events.
For DNA-based phylogenies, the most parsimonious tree requires the fewest base changes.
Computer programs use parsimony to estimate phylogenies.

Systematists compare molecular data and identify the most parsimonious hypothesis.
Step 1: Draw possible trees.
- Three species have three possible trees.
- Four species have 15 trees.
- Ten species have 34,459,425 trees.
Step 2: Tabulate molecular data (DNA sequence).
Step 3: Focus on a single site in the DNA sequence.
Step 4: Compare bases at sites II, III, and IV.
Results: Identify the most parsimonious tree by totaling base change events.

Analogy vs. Homology:
- A. Porcupine quills and cactus spines: Analogy (convergent evolution due to similar environmental pressures).
- B. Cat's paw and human's hand: Homology (shared ancestry and bone structure).
- C. Owl's wing and hornet's wing: Analogy (wings serving the same function but evolved independently).
What if: Suppose that two species, a and b, have similar appearances, very divergent gene sequences, while species b and c have very different appearances.
Species A and B's similar appearances are likely due to convergent evolution (analogy) driven by similar environmental conditions or lifestyles. Species B and C, despite their different appearances, may share a more recent common ancestor and retain more similar genetic information.