Phylogeny and Classification

Phylogenetic Tree: • Shows evolutionary relationships • Branch lengths proportional to evolutionary change or time • Can show timing of divergence • Based on molecular or morphological data

Cladogram: • Type of phylogenetic tree • Branch lengths NOT meaningful (only topology matters) • Shows only branching order/pattern • Focus on shared derived characteristics

Key Features:

Branches: • Represent lineages evolving through time • Each branch = evolutionary path of a species or group • Tips = modern species or taxa

Nodes (branch points): • Represent common ancestors • Point where lineage splits (speciation event) • Most recent common ancestor (MRCA) of descendants

Root: • Common ancestor of all organisms in tree • Most ancient divergence shown

Sister taxa: • Groups that share an immediate common ancestor • More closely related to each other than to any other group

Key principle: Organisms sharing a more recent common ancestor are more closely related.

Principle of Parsimony: When constructing phylogenetic trees, choose the tree that requires the FEWEST evolutionary changes (mutations, character state changes) to explain the observed data.

Rationale: • Evolutionary changes are relatively rare events • Simplest explanation is usually best (Occam's Razor) • Minimizes assumptions about unseen evolutionary events

Example: Compare two possible trees for species A, B, C:

Tree 1: Requires 5 mutations Tree 2: Requires 3 mutations

→ Tree 2 is more parsimonious (preferred)

Limitations:

1. Evolution doesn't always take the simplest path
2. Convergent evolution can mislead parsimony analysis
3. Multiple mutations at same site can be missed
4. May not work well for rapidly evolving sequences

Alternative Methods: • Maximum likelihood (statistical approach) • Bayesian inference (probabilistic approach) • Molecular clock (assumes constant mutation rate)

When to use parsimony: • Works best for closely related species • Good for morphological data • Computationally simple • Standard in cladistics

Key insight: Parsimony helps us avoid over-complicated evolutionary scenarios, but it's not perfect!

Homologous Structures: • Similar due to SHARED ANCESTRY • May have different functions • Result from divergent evolution • Indicate evolutionary relationship

Example: Forelimbs of humans, whales, bats, horses • Same basic bone structure (humerus, radius, ulna, carpals, etc.) • Different functions (grasping, swimming, flying, running) • Inherited from common mammalian ancestor

Analogous Structures: • Similar FUNCTION but different evolutionary origin • Result from convergent evolution • Do NOT indicate close relationship • Similar environmental pressures lead to similar solutions

Example: Wings of birds vs. insects • Both used for flight • Completely different structure and development • Evolved independently

How they mislead phylogenetic analysis:

1. Analogous structures can make unrelated species appear related • Sharks and dolphins look similar (streamlined, fins) • But dolphins are mammals, sharks are fish • Convergent evolution for aquatic lifestyle

2. Morphological convergence • Succulent plants in deserts (cacti in Americas, euphorbs in Africa) • Similar appearance, different families • Similar adaptations to arid environments

3. Loss of homologous structures • Snakes lost legs (homologous to lizard legs) • Could mistakenly group snakes away from other reptiles

Solution: Use multiple characters • Molecular data less prone to convergence • Look for synapomorphies (shared derived traits) • Consider developmental biology • Use parsimony to minimize false homology

Three Domains (proposed by Carl Woese, 1990):

1. BACTERIA Characteristics: • Prokaryotic (no nucleus) • Peptidoglycan in cell walls • Unbranched membrane lipids (ester-linked) • Single circular chromosome • No histones (usually) • Simple RNA polymerase

Examples: E. coli, Streptococcus, cyanobacteria

1. ARCHAEA Characteristics: • Prokaryotic (no nucleus) • NO peptidoglycan in cell walls • Branched membrane lipids (ether-linked) • Single circular chromosome • Histones present (like eukaryotes) • Complex RNA polymerase (similar to eukaryotes)

Examples: Methanogens, halophiles, thermophiles

1. EUKARYA Characteristics: • Eukaryotic (membrane-bound nucleus) • No peptidoglycan • Unbranched membrane lipids (ester-linked) • Multiple linear chromosomes • Histones present • Complex RNA polymerases • Membrane-bound organelles

Examples: Protists, fungi, plants, animals

Key Evidence Supporting Three Domains:

1. rRNA sequence analysis • 16S/18S ribosomal RNA comparisons • Archaea as distinct from Bacteria • Molecular clock analysis

2. Membrane lipid chemistry • Bacteria/Eukarya: ester linkages • Archaea: ether linkages (unique) • Indicates ancient divergence

3. RNA polymerase structure • Archaea more similar to Eukarya than Bacteria • Suggests Archaea and Eukarya share more recent common ancestor

4. Translation machinery • Ribosome structure and function • Archaea and Eukarya similarities

Phylogenetic implications: • Archaea and Eukarya are sister groups • Bacteria branched off earliest • Eukaryotes may have evolved from archaeal host + bacterial endosymbiont

Step 1: Compare sequences and count differences

A: ATGCCG B: ATGCTG (differs from A at position 5: C→T) = 1 difference C: ATCCTG (differs from A at positions 3 and 5: G→C, C→T) = 2 differences D: TTCCTG (differs from A at positions 1 and 3: A→T, G→C) = 2 differences

B vs C: Position 3 (G→C) = 1 difference B vs D: Positions 1 and 3 (A→T, G→C) = 2 differences C vs D: Position 1 (A→T) = 1 difference

Step 2: Identify closest relationships • A and B differ by only 1 nucleotide → likely sister species • C and D differ by only 1 nucleotide → likely sister species • B and C differ by only 1 nucleotide → possible grouping

Step 3: Construct tree Most parsimonious tree:

   ┌─── A (ATGCCG)
┌──┤
│  └─── B (ATGCTG)  [mutation at position 5]

────┤ │ ┌─── C (ATCCTG) └──┤ └─── D (TTCCTG) [mutation at position 1]

Total mutations required: • Position 3: G→C (in ancestor of B, C, D) • Position 5: C→T (in ancestor of B, C, D) • Position 5: T→G (reversal in lineage to C and D) OR separate origin • Position 1: A→T (in lineage to D)

Minimum changes = 4 mutations

Step 4: Verify parsimony This tree requires the fewest evolutionary changes to explain the observed sequences.

Alternative trees would require more mutations, making them less parsimonious.