Figure 5.1 Giant panda (Ailuropoda melanoleuca)

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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
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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
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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)
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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
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Figure 5.10 Likelihood surfaces for the
migration rate parameter M ( 2Nm) for two
populations of sticklebacks from the Western and
Eastern Pacific Ocean
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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
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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)
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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)
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Figure 5.12 A star phylogeny the expected
average tree when many loci from a randomly
mating population are analyzed simultaneously
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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 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
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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 5.16 A PCA analysis of 3000 European
individuals, using 500,000 SNPs for each
individual (Part 1)
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Figure 5.16 A PCA analysis of 3000 European
individuals, using 500,000 SNPs for each
individual (Part 2)
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Equations 5.15.3
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Exercise 5.1, Table 1
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Exercise 5.2, Figure 1