Large-scale recombination rate patterns are conserved among human populations

Abstract

In humans, most recombination events occur in a small fraction of the genome. These hotspots of recombination show considerable variation in intensity and/or location across species and, potentially, across human populations. On a larger scale, the patterns of recombination rates have been mostly investigated in individuals of European ancestry, and it remains unknown whether the results obtained can be directly applied to other human populations. Here, we investigate this question using genome-wide polymorphism data. We show that population recombination rates recapitulate a large part of the genetic map information, regardless of the population considered. We also show that the ratio of the population recombination rate estimate of two populations is overall constant along the chromosomes. These two observations support the hypothesis that large-scale recombination patterns are conserved across human populations. Local deviations from the overall pattern of conservation of the recombination rates can be used to select candidate regions with large polymorphic inversions or under local selection.

Figure 1.

Average value of in each population for, respectively, telomeric regions, centromeric regions, and the rest of the genome. The mean values of the European-American population are in blue, of the Han Chinese in pink, and of the African-Americans in green. The bars represent two standard errors from the mean.

Figure 2.

Plot of the recombination rate estimates for 2609 windows of the human genome. Each point represents a 1-Mb window displayed according to the value of the DeCode recombination rate c_map (on the x-axis) and to the population recombination rate calculated using 23 unrelated individuals from the Perlegen data set (on the y-axis). The estimates for the Han Chinese population are in pink, for the African-Americans in green, and for the European-Americans in blue. The straight lines are the regression lines obtained for each population.

Figure 3.

Variation of the log₁₀ ratio along Chromosome 1. Each point of the figure represents one window of 1 Mb displayed according to its position on the chromosome (x-axis) and the value of the log ratios . (A) The log ratios are shown in blue; (B) the log ratios are shown in pink; and (C) the log ratios are shown in red. See also Supplemental Figures S2 to S22 online for the variation along Chromosomes 2 to 22.

Figure 4.

Position of the windows with the 5% most extreme log ratios . The chromosomes are organized according to their number from 1 (lowest y-axis coordinate) to 22 (on top). Each gray point represents the value of the log ratio for one 1-Mb window and is displayed according to its position on the chromosome (on the x-axis). The 5% most extreme log ratios are shown in blue and in pink. See also Supplemental Figure S23 for a blowup of Chromosomes 1 to 5 and Supplemental Figure S24 for the 5% most extreme log ratios .

Figure 5.

Variation of the log ratios along the chromosomal arm 8p. The position of the polymorphic inversion at 8p23 is shown by the red bar on the chromosome picture.