Classification and Phylogenies Taxonomic categories and taxa Inferring phylogenies –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 –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 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 = 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