The Impact of Linked Selection in Chimpanzees: A Comparative Study

Abstract

Levels of nucleotide diversity vary greatly across the genomes of most species owing to multiple factors. These include variation in the underlying mutation rates, as well as the effects of both direct and linked selection. Fundamental to interpreting the relative importance of these forces is the common observation of a strong positive correlation between nucleotide diversity and recombination rate. While indeed observed in humans, the interpretation of this pattern has been difficult in the absence of high-quality polymorphism data and recombination maps in closely related species. Here, we characterize genetic features driving nucleotide diversity in Western chimpanzees using a recently generated whole genome polymorphism data set. Our results suggest that recombination rate is the primary predictor of nucleotide variation with a strongly positive correlation. In addition, telomeric distance, regional GC-content, and regional CpG-island content are strongly negatively correlated with variation. These results are compared with humans, with both similarities and differences interpreted in the light of the estimated effective population sizes of the two species as well as their strongly differing recent demographic histories.

Direct estimate of the spontaneous germ line mutation rate in African green monkeys

“…). It is important to note the assumption of neutrality in the above estimates, and the potential reduction in N e owing to linked selection in these species (see Pfeifer and Jensen ).…”

“…Levels of autosomal nucleotide diversity in the noncoding, nonrepetitive parts of the genome range from intergenic = 3.2 × 10 −4 − 4.7 × 10 −4 in the different African green monkey populations (Pfeifer 2017b), corresponding to estimated effective population sizes N e of ß8500-12,500 under the assumption of neutrality-in the range of the effective population sizes N e = 11,000 for western chimpanzees and N e = 18,000 for humans (assuming an underlying mutation rate of 1.8 × 10 −8 and diversity levels between human individuals from Yoruba (Africa) and western chimpanzees; Fischer et al 2006;Hernandez et al 2011). It is important to note the assumption of neutrality in the above estimates, and the potential reduction in N e owing to linked selection in these species (see Pfeifer and Jensen 2016).…”

Impact of demography on linked selection in two outcrossing Brassicaceae species

“…Furthermore, a difference in the pattern and magnitude of linked selection is expected in populations with different demographic histories, as for instance in humans and chimpanzees (Pfeifer & Jensen, 2016). At equilibrium, the rate of random loss of variation due to genetic drift is lower in populations with a large N e , and hence, they can carry more variation (Wright, 1931).…”

What can be learned by scanning the genome for molecular convergence in wild populations?

“…This reduction in linked positive selection and background selection (BGS) 96,97 in areas of high recombination is predicted to drive positive correlations between recombination rate and nucleotide diversity genome-wide. Indeed, a positive relationship between recombination and nucleotide diversity has been observed in several species, including chimpanzees 98 and Drosophila, 99,100 but its ubiquity among taxa is questionable. 101,102 Given that these features of the genomic landscape are important for promoting or limiting adaptation, if they are consistent across lineages, then we would predict some degree of convergence at the genome level.…”

“…This reduction in linked positive selection and background selection (BGS) in areas of high recombination is predicted to drive positive correlations between recombination rate and nucleotide diversity genome‐wide. Indeed, a positive relationship between recombination and nucleotide diversity has been observed in several species, including chimpanzees and Drosophila , but its ubiquity among taxa is questionable …”