Figure 5.1 Giant panda (Ailuropoda melanoleuca) IntroPopGen-Fig-05-01-0.jpg

Figure 5.2 A coalescence tree with six leaf nodes representing six DNA sequences IntroPopGen-Fig-05-02-0.jpg

Figure 5.3 A histogram showing the distribution of values of p in 100,000 coalescence simulations under the standard coalescence model with infinite sites mutation and q = 2.6 IntroPopGen-Fig-05-03-0.jpg

Figure 5.4 A tree and a set of binary sequences, which together are not compatible with the infinite sites model IntroPopGen-Fig-05-04-0.jpg

Figure 5.5 Reciprocal monophyly (A) and incomplete lineage sorting (B) IntroPopGen-Fig-05-05-0.jpg

Figure 5.5 (A) Reciprocal monophyly IntroPopGen-Fig-05-05-1R.jpg

Figure 5.5 (B) Incomplete lineage sorting IntroPopGen-Fig-05-05-2R.jpg

Figure 5.6 The coalescence tree may (red) or may not (blue) match the structure of the species tree (black) IntroPopGen-Fig-05-06-0.jpg

Figure 5.7 Human mtDNA tree IntroPopGen-Fig-05-07-0.jpg

Figure 5.8 Coalescence trees produced by different demographic and historical processes IntroPopGen-Fig-05-08-0.jpg

Figure 5.8 Coalescence trees produced by different demographic and historical processes (Part 1) IntroPopGen-Fig-05-08-1R.jpg

Figure 5.8 Coalescence trees produced by different demographic and historical processes (Part 2) IntroPopGen-Fig-05-08-2R.jpg

Figure 5.8 Coalescence trees produced by different demographic and historical processes (Part 3) IntroPopGen-Fig-05-08-3R.jpg

Figure 5.9 The likelihood function for q under the standard coalescence model with infinite sites mutation when n = 2 and the two sequences differ by six nucleotide sites IntroPopGen-Fig-05-09-0.jpg

Figure 5.10 Likelihood surfaces for the migration rate parameter M (= 2Nm) for two populations of sticklebacks from the Western and Eastern Pacific Ocean IntroPopGen-Fig-05-10-0.jpg

Figure 5.11 Distribution of chimpanzee subspecies and the posterior distribution of the migration rates between Eastern, Central, and Western chimpanzees estimated using MCMC method IntroPopGen-Fig-05-11-0.jpg

Figure 5.11 Distribution of chimpanzee subspecies and posterior distribution of the migration rates between Eastern, Central, and Western chimpanzees estimated using MCMC method (Part 1) IntroPopGen-Fig-05-11-1R.jpg

Figure 5.11 Distribution of chimpanzee subspecies and posterior distribution of the migration rates between Eastern, Central, and Western chimpanzees estimated using MCMC method (Part 2) IntroPopGen-Fig-05-11-2R.jpg

Figure 5.12 A star phylogeny: the expected average tree when many loci from a randomly mating population are analyzed simultaneously IntroPopGen-Fig-05-12-0.jpg

Figure 5.13 The site frequency spectrum (SFS) for a sample of African Americans for 5982 SNPs IntroPopGen-Fig-05-13-0.jpg

Figure 5.14 The 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 IntroPopGen-Fig-05-14-0.jpg

Figure 5.15 Admixture analysis of 1056 individuals from 52 populations for 377 microsatellite loci IntroPopGen-Fig-05-15-0.jpg

Figure 5.16 A PCA analysis of 3000 European individuals, using 500,000 SNPs for each individual IntroPopGen-Fig-05-16-0.jpg

Figure 5.16 A PCA analysis of 3000 European individuals, using 500,000 SNPs for each individual (Part 1) IntroPopGen-Fig-05-16-1R.jpg

Figure 5.16 A PCA analysis of 3000 European individuals, using 500,000 SNPs for each individual (Part 2) IntroPopGen-Fig-05-16-2R.jpg

Equations 5.1–5.3 IntroPopGen-Eq-05_01-03.jpg

Exercise 5.1, Table 1 IntroPopGen-Eq-05_01-03.jpg

Exercise 5.2, Figure 1 IntroPopGen-Eq-05_01-03.jpg