Exploring Evolutionary Patterns and Genetic Diversity

1. Figure 5.1 Giant panda (Ailuropoda melanoleuca)

2. Figure 5.2A coalescence tree with six leaf nodesrepresenting six DNA sequences

3. Figure 5.3A histogram showing the distribution of values of pin 100,000 coalescence simulations under the standard coalescence model with infinite sites mutation and q= 2.6

4. Figure 5.4A tree and a set of binary sequences, which together are not compatiblewith the infinite sites model

5. Figure 5.5Reciprocal monophyly (A) and incomplete lineage sorting (B)

6. Figure 5.5(A) Reciprocal monophyly

7. Figure 5.5(B)Incomplete lineage sorting

8. Figure 5.6The coalescence tree may (red) or may not (blue) match the structure of the species tree (black)

9. Figure 5.7 Human mtDNA tree

10. Figure 5.8Coalescence trees produced by different demographic and historical processes

11. Figure 5.8Coalescence trees produced by different demographic and historical processes(Part 1)

12. Figure 5.8Coalescence trees produced by different demographic and historical processes(Part 2)

13. Figure 5.8Coalescence trees produced by different demographic and historical processes(Part 3)

14. Figure 5.9The likelihood function for qunder the standard coalescence model with infinite sites mutation when n= 2 and the two sequencesdiffer by six nucleotide sites

15. Figure 5.10Likelihood surfaces for the migration rate parameter M(= 2Nm) for two populations of sticklebacks from the Western and Eastern Pacific Ocean

16. Figure 5.11Distribution of chimpanzee subspecies and the posterior distribution of the migration rates between Eastern, Central, and Western chimpanzees estimated using MCMC method

17. Figure 5.11Distribution of chimpanzee subspecies and posterior distribution of the migration rates between Eastern, Central, and Western chimpanzees estimated using MCMC method (Part 1)

18. Figure 5.11Distribution of chimpanzee subspecies and posterior distribution of the migration rates between Eastern, Central, and Western chimpanzees estimated using MCMC method (Part 2)

19. Figure 5.12A star phylogeny: the expected average tree when many loci from a randomly mating population are analyzed simultaneously

20. Figure 5.13The site frequency spectrum (SFS) for a sample of African Americans for 5982 SNPs

21. Figure 5.14The joint site frequency spectrum (SFS) for a Tibetan and a Han Chinese population estimated for a genome-wide data set of all protein-coding genes

22. Figure 5.15Admixture analysis of 1056 individuals from 52 populations for 377 microsatellite loci

23. Figure 5.16A PCA analysis of 3000 European individuals, using 500,000 SNPs for each individual

24. Figure 5.16A PCA analysis of 3000 European individuals, using 500,000 SNPs for each individual (Part 1)

25. Figure 5.16A PCA analysis of 3000 European individuals, using 500,000 SNPs for each individual(Part 2)

26. Equations 5.1–5.3

27. Exercise 5.1, Table 1

28. Exercise 5.2, Figure 1