1. Chapter 2 Opener How do we classify organisms?

2. Figure 2.1 Tracing the path of evolution to Homo sapiens from the universal ancestor of all life

3. Figure 2.2 The tree of life

4. Figure 2.3 Darwin’s representation of hypothetical phylogenetic relationships

5. Figure 2.4 A phylogenetic tree of human, chimpanzee, and bonobo taxa, illustrating major phylogenetic terms

6. Figure 2.5 Different representations of phylogenies

7. Figure 2.6 Phylogenetic analyses often use unrooted trees, which are converted to rooted trees

8. Figure 2.7 Phylogenetic analysis has revealed the relationships of some formerly puzzling organisms

9. Figure 2.8 Phylogenetically informative and uninformative similarities among species

10. Figure 2.9 Monophyletic groups whose members share derived character states that evolved only once

12. Figure 2.10 Two possible hypotheses for the phylogenetic relationships of humans

14. Figure 2.11 Steps in a phylogenetic analysis using the maximum parsimony method

15. Figure 2.12 Members of the primate superfamily Hominoidea

16. Figure 2.13 Evidence for phylogenetic relationships among primates

18. Table 2.1

19. Figure 2.14 How long branches can lead a parsimony analysis astray

20. Figure 2.14 How long branches can lead a parsimony analysis astray (Part 1)

21. Figure 2.14 How long branches can lead a parsimony analysis astray (Part 2)

22. Figure 2.15 A two-parameter model in which the rate of transition differs from the rate of transversion

23. Figure 2.16 Relationships among hominoid primates, based on a maximum likelihood analysis of sequences of two genes

24. Figure 2.17 The true phylogeny of the experimental populations of T7 bacteriophage studied by Hillis et al.

26. Figure 2.18 Relationships among vertebrates, as estimated from morphological characters and DNA sequences

27. Figure 2.19 Base pair differences  time since divergence suggests a fairly constant rate of sequence evolution

29. Figure 2.20 The relative rate test for constancy of the rate of molecular divergence

30. Figure 2.21 Proportions of base pairs at different codon positions in the DNA sequences of COI that differ between vertebrate species pairs, against time since their most recent common ancestor

32. Figure 2.22 Results of a study of divergence times for some lineages of primates

33. Figure 2.23 Relationships among haplotypes of the mitochondrial cytochrome b gene in MacGillivray’s warbler

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

36. Figure 2.25 A gene tree may or may not reflect the true phylogeny of the species from which the genes are sampled

38. Figure 2.25 A gene tree may or may not reflect the true phylogeny of the species from which the genes are sampled (Part 1)

39. Figure 2.25 A gene tree may or may not reflect the true phylogeny of the species from which the genes are sampled (Part 2)

40. Figure 2.25 A gene tree may or may not reflect the true phylogeny of the species from which the genes are sampled (Part 3)

41. Figure 2.26 Four species of grasshoppers inferred from multiple samples of each of six genes in each species

42. Figure 2.27 Relationships among 11 species of placental mammals, which represent four major clades

43. Figure 2.28 Rapid evolutionary radiation

45. Figure 2.29 Hybridization and reticulate evolution

46. Figure 2.30 Chimpanzees and gorillas carry several clades of the parasite Plasmodium, from which human P. falciparum is derived