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Figure 5.1 Giant panda (Ailuropoda melanoleuca)
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Figure 5.2 A coalescence tree with six leaf nodes representing six DNA sequences
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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 jpg
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Figure 5.4 A tree and a set of binary sequences, which together are not compatible with the infinite sites model IntroPopGen-Fig jpg
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Figure 5.5 Reciprocal monophyly (A) and incomplete lineage sorting (B)
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Figure 5.5 (A) Reciprocal monophyly
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Figure 5.5 (B) Incomplete lineage sorting
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Figure 5.6 The coalescence tree may (red) or may not (blue) match the structure of the species tree (black) IntroPopGen-Fig jpg
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Figure 5.7 Human mtDNA tree
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Figure 5.8 Coalescence trees produced by different demographic and historical processes
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Figure 5.8 Coalescence trees produced by different demographic and historical processes (Part 1)
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Figure 5.8 Coalescence trees produced by different demographic and historical processes (Part 2)
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Figure 5.8 Coalescence trees produced by different demographic and historical processes (Part 3)
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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 jpg
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Figure Likelihood surfaces for the migration rate parameter M (= 2Nm) for two populations of sticklebacks from the Western and Eastern Pacific Ocean IntroPopGen-Fig jpg
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Figure Distribution of chimpanzee subspecies and the posterior distribution of the migration rates between Eastern, Central, and Western chimpanzees estimated using MCMC method IntroPopGen-Fig jpg
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Figure 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 R.jpg
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Figure 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 R.jpg
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Figure A star phylogeny: the expected average tree when many loci from a randomly mating population are analyzed simultaneously IntroPopGen-Fig jpg
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Figure 5.13 The site frequency spectrum (SFS) for a sample of African Americans for 5982 SNPs
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Figure 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 jpg
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Figure 5.15 Admixture analysis of 1056 individuals from 52 populations for 377 microsatellite loci
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Figure 5.16 A PCA analysis of 3000 European individuals, using 500,000 SNPs for each individual
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Figure A PCA analysis of 3000 European individuals, using 500,000 SNPs for each individual (Part 1) IntroPopGen-Fig R.jpg
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Figure A PCA analysis of 3000 European individuals, using 500,000 SNPs for each individual (Part 2) IntroPopGen-Fig R.jpg
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Equations 5.1–5.3 IntroPopGen-Eq-05_01-03.jpg
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Exercise 5.1, Table 1 IntroPopGen-Eq-05_01-03.jpg
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Exercise 5.2, Figure 1 IntroPopGen-Eq-05_01-03.jpg
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