Article

Analysis of Chimpanzee History Based on Genome Sequence Alignments

Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America.
PLoS Genetics (Impact Factor: 8.17). 05/2008; 4(4):e1000057. DOI: 10.1371/journal.pgen.1000057
Source: PubMed

ABSTRACT Population geneticists often study small numbers of carefully chosen loci, but it has become possible to obtain orders of magnitude for more data from overlaps of genome sequences. Here, we generate tens of millions of base pairs of multiple sequence alignments from combinations of three western chimpanzees, three central chimpanzees, an eastern chimpanzee, a bonobo, a human, an orangutan, and a macaque. Analysis provides a more precise understanding of demographic history than was previously available. We show that bonobos and common chimpanzees were separated approximately 1,290,000 years ago, western and other common chimpanzees approximately 510,000 years ago, and eastern and central chimpanzees at least 50,000 years ago. We infer that the central chimpanzee population size increased by at least a factor of 4 since its separation from western chimpanzees, while the western chimpanzee effective population size decreased. Surprisingly, in about one percent of the genome, the genetic relationships between humans, chimpanzees, and bonobos appear to be different from the species relationships. We used PCR-based resequencing to confirm 11 regions where chimpanzees and bonobos are not most closely related. Study of such loci should provide information about the period of time 5-7 million years ago when the ancestors of humans separated from those of the chimpanzees.

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Available from: Christine Schirmer, Aug 29, 2015
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    • "Chimpanzees and bonobos are the closest living relatives of humans. Population genetic data from chimpanzee subspecies have until recently been scarce and mainly based on either mitogenomes (Stone et al. 2010; Hvilsom et al. 2014), microsatellite markers (Becquet et al. 2007; Wegmann and Excoffier 2010; Gonder et al. 2011; Hvilsom et al. 2013) or on nuclear fragments (Fischer et al. 2004; Caswell et al. 2008). "
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    • "The timing and magnitude of past demographic events were inferred through Bayesian Markov chain Monte Carlo (MCMC) coalescent-based analysis of the mitogenomes using the program BEAST v.1.6.1 (Drummond and Rambaut 2007). As dates are completely dependent on the substitution rates used, we inferred the rates (see Online Resources 3 and 6 in the ESM), using a root time calibration with a normally distributed prior mean of 1.2 million years (My), and with 95 % of the density between 0.87 and 1.53 My ago, on the basis of the earliest well-supported date for Pan divergence (Won and Hey 2005; Becquet and Przeworski 2007; Becquet et al. 2007; Caswell et al. 2008; Hey 2010; Wegmann and Excoffier 2010; Stone et al. 2010). Subsequently, the substitution rates were used to estimate changes in population size over time for the four chimpanzee subspecies and the bonobo using a separate concatenated partition, comprising rRNA, CDS, and D-loop to permit a separate evolutionary model for each partition and allow for different patterns of rate heterogeneity. "
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