Low nucleotide diversity in chimpanzees and bonobos

Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA.
Genetics (Impact Factor: 5.96). 09/2003; 164(4):1511-8.
Source: PubMed

ABSTRACT Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (pi) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the pi value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The pi values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (N(e)) in the human lineage after the human-chimpanzee divergence, because a reduction in N(e) has a stronger effect on mtDNA diversity than on nuclear DNA diversity. Sequence data from this article have been deposited with the GenBank Data libraries under accession nos. AY 275957-AY 277244.

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    • "Alternatively, the northern range expansion hypothesis predicts that U. scoparia should exhibit low genetic diversity compared with the U. notata complex due to a bottleneck event associated with the LGM (Norris 1958). Indeed, the nucleotide diversity of U. scoparia is not only low compared with the U. notata complex, but is on par with that of mammals such as chimpanzees (Yu et al. 2003) and southern elephant seals (Slade et al. 1998) that are regarded to have low genetic diversity. However, determining the underlying process explaining this pattern proved to be elusive. "
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    Ecology and Evolution 06/2014; 4(12). DOI:10.1002/ece3.1111 · 2.32 Impact Factor
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    • "V. Pilbrow, C. Groves could be divergent from other bonobo populations (Pilbrow 2006), but there is need for further study. Early studies of genetic variability, albeit from captive individuals of unknown geographic origin or individuals from a single wild locality, highlighted low levels of genetic diversity in bonobos compared to chimpanzees (Fischer et al. 2011; Gerloff et al. 1999; Hashimoto et al. 1996; Reinartz et al. 2000; Yu et al. 2003). More recent population genetic studies using a greater sampling of bonobos from across their distribution in the wild show significant differences among populations (Eriksson et al. 2004, 2006; Kawamoto et al. 2013). "
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    International Journal of Primatology 12/2013; 34(6). DOI:10.1007/s10764-013-9737-1 · 1.99 Impact Factor
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    • "It should be noted, however, that these previous studies were conducted on a sampling of captive individuals from varied geographic origins within the distribution of each subspecies . At least one study employing sequencing of autosomal DNA segments from individuals of captive origin found very similar nucleotide diversity (p) in eastern and western chimpanzee populations (0.08 vs. 0.09 %, respectively) (Yu et al. 2003). These results were further corroborated by findings of similar effective population sizes (N e ) for the two subspecies (Hey 2010), and evidence that both eastern and western chimpanzee populations experienced population bottlenecks prior to expansion to their current ranges (Wegmann and Excoffier 2010). "
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