Reduced meiotic recombination in rhesus macaques and the origin of the human recombination landscape

Abstract

Characterizing meiotic recombination rates across the genomes of nonhuman primates is important for understanding the genetics of primate populations, performing genetic analyses of phenotypic variation and reconstructing the evolution of human recombination. Rhesus macaques (Macaca mulatta) are the most widely used nonhuman primates in biomedical research. We constructed a high-resolution genetic map of the rhesus genome based on whole genome sequence data from Indian-origin rhesus macaques. The genetic markers used were approximately 18 million SNPs, with marker density 6.93 per kb across the autosomes. We report that the genome-wide recombination rate in rhesus macaques is significantly lower than rates observed in apes or humans, while the distribution of recombination across the macaque genome is more uniform. These observations provide new comparative information regarding the evolution of recombination in primates.

Taking identity-by-descent analysis into the wild: Estimating realized relatedness in free-ranging macaques

“…Importantly, although linkage disequilibrium-based methods like LDhelmet are known to produce some errors [90][91][92][93] , the resulting recombination map is well-correlated with a previous map generated for rheMac8, an older version of the rhesus macaque reference genome (Fig. S6) 88 .…”

“…M 88 . This discrepancy might be due to 1) IBD detection errors, for example, occasional false positives and the break-up of long, continuous IBD segments into several adjacent shorter ones; 2) Xue et al 88 based their estimate on an older assembly than the Mmul10 assembly used here, which is less complete. However, we note that the discrepancy of estimated genetic length is unlikely to substantially bias the estimated female-to-male recombination rate ratio because the IBD detection error rates are expected to be similar across maternal and paternal dyads and therefore the relative ratio of the number of segments of maternal dyads to that of paternal dyads is expected to remain the same.…”

Recombination map tailored to Native Hawaiians improves robustness of genomic scans for positive selection

“…Next, each chromosome was split into windows of 4000 SNPs with 200 overlapping SNPs between windows. Finally, per previous studies (Auton et al, 2015; Xue et al, 2020; Zhou et al, 2020), the interval program from LDhat was run with the following settings: 30 million iterations, sampling set to every 15,000 iterations, 7.5 million iterations used for burn-in, and a block penalty of 5. The resulting estimates were integrated by removing the distal half of each overlapping region for each window and combining all windows for each chromosome.…”

“…Native Hawaiian-specific recombination map using LDhat and IBDrecomb Recombination maps were inferred using LDhat (Auton & McVean, 2007) with data ascertained on the MEGA array. We modeled the analytic pipeline using LDhat after previously published descriptions on similar efforts to infer the recombination landscape in humans and primates (Spence & Song, 2019a;Xue et al, 2020;Zhou et al, 2020). LDhat relies on lookup tables to allow for tractable computation.…”

Genomic resources for rhesus macaques (Macaca mulatta)

“…The first linkage studies using polymorphisms known at the time were published in the mid-1980’s (Ferrell et al 1985 ). Investigators subsequently produced a whole genome pedigree-based linkage map using microsatellite loci (Rogers et al 2006 ) and then later a higher-resolution recombination map using SNV genotypes (Xue et al 2016 , 2020 ). Variation in mitochondrial DNA sequences have also received substantial attention.…”