Evidence for a Complex Demographic History of Chimpanzees

Abstract

To characterize patterns of genomic variation in central chimpanzees (Pan troglodytes troglodytes) and gain insight into their evolution, we sequenced nine unlinked, intergenic regions, representing a total of 19,000 base pairs, in 14 individuals. When these DNA sequences are compared with homologous sequences previously collected in humans and in western chimpanzees (Pan troglodytes verus), nucleotide diversity is higher in central chimpanzees than in western chimpanzees or in humans. Consistent with a larger effective population size of central chimpanzees, levels of linkage disequilibrium are lower than in humans. Patterns of linkage disequilibrium further suggest that homologous gene conversion may be an important contributor to genetic exchange at short distances, in agreement with a previous study of the same DNA sequences in humans. In central chimpanzees, but not in western chimpanzees, the allele frequency spectrum is significantly skewed towards rare alleles, pointing to population size changes or fine-scale population structure. Strikingly, the extent of genetic differentiation between western and central chimpanzees is much stronger than what is seen between human populations. This suggests that careful attention should be paid to geographic sampling in studies of chimpanzee genetic variation.

Combining Sperm Typing and Linkage Disequilibrium Analyses Reveals Differences in Selective Pressures or Recombination Rates Across Human Populations

“…The chimpanzees show two-to threefold lower polymorphism levels compared to humans and a slight skew toward rare variants. Both polymorphism levels and the frequency spectrum are within the range of previous polymorphism surveys in this chimpanzee subspecies (Yu et al 2003;Fischer et al 2004). Moreover, a sliding-window analysis of u W in the chimpanzee and human population samples shows distinct patterns of variation, with no prominent peak of polymorphism in the chimpanzees (data not shown).…”

“…Here, we have collected resequencing data for an orthologous subsegment of 10,268 bp, centered on the peak, in 15 Western chimpanzees (P. troglodytes verus). This subspecies was chosen because a previous analysis of noncoding regions showed that patterns of variation are in rough accordance with the expectation of a standard neutral model (Fischer et al 2004). Summary statistics of the polymorphism data in each sample are shown in Table 1.…”

Implications of biogeography of human populations for 'race' and medicine

“…This degree of diversity is less than what typically exists among chimpanzees [23][24][25] . Current estimates of how much variation occurs specieswide indicates that all H. sapiens are ∼99.6-99.8% identical at the nucleotide sequence level.…”

Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons

“…It is also possible that one or several biological processes are responsible for these differences. For example, assuming that full-length or relatively long L1 elements are more deleterious than severely truncated elements (Boissinot et al, 2001), the size differences observed between chimpanzee and human L1 elements could be explained by a higher efficiency of selection in chimpanzees than in humans, given that the chimpanzee effective population size is higher than that of humans (Graur and Li, 2000;Fischer et al, 2004) and that the efficiency of selection theoretically increases with effective population size (Graur and Li, 2000). An alternative explanation might be that, due to innovations in the host or L1 biology, L1 elements have become less adept at integrating themselves into the chimpanzee genome.…”