Transcript Evolution, 2e

Classification and Phylogenies
• Taxonomic categories and taxa
• Inferring phylogenies
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The similarity vs. shared derived character states
Homoplasy
Maximum parsimony, maximum likelihood, and Baysian methods
An example of phylogenetic analysis
Molecular clocks and timing of branching events
Difficulties in Phylogenetic Analysis
• Taxonomic categories
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Species
Genus
Family
Order
Class
Phylum
Division
Chapter 2 Opener How do we classify organisms?
Morphological similarity occassionally obscurs relationships
Figure 2.2 Darwin’s representation of hypothetical phylogenetic relationships
Figure 2.1 The Tree of Life
Figure 2.5 An example of phylogenetic analysis applied to three data sets (Part 1)
Sometimes, phylogenies derived from similarities are congruent with
a phylogeny derived from synapomorphies
Figure 2.5 An example of phylogenetic analysis applied to three data sets (Part 2)
Similarities can produce an incorrect phylogeny
Figure 2.5 An example of phylogenetic analysis applied to three data sets (Part 3)
Homoplasies confound phylogeny reconstruction
Figure 2.6 Monophyletic groups whose members share derived character states that evolved only
once
Easy reconstruction
Figure 2.7 Two possible hypotheses for the phylogenetic relationships of humans
Principle of parsimony: Okkam’s
razor
Figure 2.9 Members of the primate superfamily Hominoidea
Phenetic vs. cladistic classifications
Figure 2.10 Evidence for phylogenetic relationships among primates, based on the ψη-globin
pseudogene
mtDNA
4,700 base sequence
Genes for 11 tRNAs
6 proteins
Human-chimpanzee relationship
1023 more likely than
Chimpanzee-gorilla relationship
Y DNA
Base sequence for
Testis-specific protein Y
Autosomal DNA
Base sequence of
Beta-globin gen cluster
Figure 2.11 Relationships among major groups of vertebrates
Morphological and DNA sequences sometimes reveal the same phylogeny
Figure 2.13 (A) If divergence occurred at a nearly constant rate, relative times of divergence of
lineages could be determined from differences/similarities between taxa and phylogeny of the taxa
could then be estimated. (B) Hypothetical phylogeny in which evolution occurs at a nearly constant
rate
Figure 2.14 Calibration of molecular clocks in Hawaiian organisms
Slope of regression reveals the
rate of evolution
Y = a + bX
b = 0.016
b = 0.019
Fruit fly divergence: Hawaiian Islands
Results of speciation
Figure 2.15 The relative rate test for constancy of the rate of molecular divergence
Difficulties in phylogenetic reconstruction
• 1. Scoring characters
• 2. Homoplasy
• 3. Past evolutionary events may be obscured by recent
evolution.
• 4. Polytomy
• 5. Gene trees and character trees can be incongruent
• 6. ± hybridization and horizontal allele transfer
Figure 2.23 Hybridization and reticulate evolution
Figure 2.24 Phylogenies of some Old World monkeys and cats