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: 4.87). 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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    ABSTRACT: The ancestral Pan and Homo lineages diverged about 6 million years ago, and Pan troglodytes (chimpanzee) and Pan paniscus (bonobo) diverged approximately 1-2 million years ago. The isolation of chimpanzee groups by changes in forest distribution and river topography over time resulted in the evolution of three widely recognized subspecies of P. troglodytes: P.t. schweinfurthii, P.t. troglodytes, and P.t. verus. Previous analyses of chimpanzee mitochondrial DNA (mtDNA) sequences have shown that each subspecies can be identified by specific mtDNA lineages. Through mtDNA hypervariable region I (HVI) sequencing, the subspecies of 239 individuals were identified through comparison to sequences of chimpanzees of known subspecies. HVI sequence analyses were used to study inter-and intra-subspecies relationships and population histories. Chimpanzees as a whole had greater mtDNA diversity (p = 0.078) than bonobos (p = 0.039) and humans (p = 0.026). P.t. schweinfurthii had lower levels of mtDNA diversity (p = 0.025) than the other two subspecies (P.t. troglodytes p = 0.045 and P.t. verus p = 0.051). The tentative subspecies P.t. vellerosus has a level of mtDNA diversity (p = 0.036) that falls within the range of the other subspecies. Recent analyses have shown that chimpanzees have lower levels of Y chromosome compared to mtDNA diversity. P.t. verus has the highest levels of mtDNA nucleotide diversity but lowest levels of Y chromosome diversity (based on previous studies) than the other subspecies, which suggests that demographic histories differ between subspecies.
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