Monday, September 30, 2013

African Ape Demographic History Using Whole Genome Sequences

Hara et al.'s (2012) paper represents the latest study of population history in the Gorilla-Chimpanzee-Human lineage. Thanks to the recent sequencing of the gorilla and orangutan genomes (Locke et al., 2011; Scally et al., 2012) in addition to the chimp and human, Hara et al. were able to utilize whole genome sequences in a Bayesian MCMC framework developed by Rannala & Yang (2003). This paper is nice because they first perform a simulation study to estimate the optimal, recombination-free size block of genome to use. By also paying extra attention to orthology, Hara et al. undertake a robust inference based on many, many independently evolving loci throughout the genome and ultimately estimate the following divergence dates and ancestral effective population sizes:
·      6.0–7.6 Ma human lineage split from chimpanzee lineage with Ne of 75,600
·      7.6–9.7 Ma human + chimpanzee lineage split from gorilla lineage with Ne of 65,500
·      15–19 Ma African ape lineage split from orangutan lineage with Ne of 203,000
Interestingly, Hara et al. also report variation in mutation rates among lineages and chromosomes. This evidence refutes prior claims of ongoing hybridization between humans and chimpanzees after their lineages’ initial split, based on the younger divergence date of the X chromosome (Patterson et al., 2006).


Hara, Y. et al (2012). Reconstructing the Demographic History of the Human Lineage Using Whole-Genome Sequences from Human and Three Great Apes. Genome Biol Evol 4(11):1133-1145. 

Locke, D et al (2011). Comparative and demographic analysis of orang-utan genomes. Nature 269: 529-533. 

Patterson, N et al (2006). Genetic evidence for complex speciation of humans and chimpanzees. Nature 441: 1103-1108.

Rannala, B & Yang, Z (2003). Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164: 1645-1656.

Scally, C et al (2012). Insights into hominid evolution from the gorilla genome sequence. Nature 483: 169-175. 

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