1. 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

2. Taxonomic categories –Species –Genus –Family –Order –Class –Phylum –Division

3. Chapter 2 Opener How do we classify organisms? Morphological similarity occassionally obscurs relationships

4. Figure 2.2 Darwin’s representation of hypothetical phylogenetic relationships

5. Figure 2.1 The Tree of Life

6. 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

7. Figure 2.5 An example of phylogenetic analysis applied to three data sets (Part 2) Similarities can produce an incorrect phylogeny

8. Figure 2.5 An example of phylogenetic analysis applied to three data sets (Part 3) Homoplasies confound phylogeny reconstruction

9. Figure 2.6 Monophyletic groups whose members share derived character states that evolved only once Easy reconstruction

10. Figure 2.7 Two possible hypotheses for the phylogenetic relationships of humans Principle of parsimony: Okkam’s razor

11. Figure 2.9 Members of the primate superfamily Hominoidea Phenetic vs. cladistic classifications

12. Figure 2.10 Evidence for phylogenetic relationships among primates, based on the ψη-globin pseudogene

13. mtDNA 4,700 base sequence Genes for 11 tRNAs 6 proteins Human-chimpanzee relationship 10 23 more likely than Chimpanzee-gorilla relationship Y DNA Base sequence for Testis-specific protein Y Autosomal DNA Base sequence of Beta-globin gen cluster

14. Figure 2.11 Relationships among major groups of vertebrates Morphological and DNA sequences sometimes reveal the same phylogeny

15. 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

16. 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

17. Fruit fly divergence: Hawaiian Islands Results of speciation

18. Figure 2.15 The relative rate test for constancy of the rate of molecular divergence

19. 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

20. Figure 2.23 Hybridization and reticulate evolution

21. Figure 2.24 Phylogenies of some Old World monkeys and cats