Genetic diversity in humans and non-human primates and its evolutionary consequences

Abstract

Genetic diversity is a key parameter in population genetics and is important for understanding the process of evolution and for the development of appropriate conservation strategies. Recent advances in sequencing technology have enabled the measurement of genetic diversity of various organisms at the nucleotide level and on a genome-wide scale, yielding more precise estimates than were previously achievable. In this review, I have compiled and summarized the estimates of genetic diversity in humans and non-human primates based on recent genome-wide studies. Although studies on population genetics demonstrated fluctuations in population sizes over time, general patterns have emerged. As shown previously, genetic diversity in humans is one of the lowest among primates; however, certain other primate species exhibit genetic diversity that is comparable to or even lower than that in humans. There exists greater than 10-fold variation in genetic diversity among primate species, and I found weak correlation with species fecundity but not with body or propagule size. I further discuss the potential evolutionary consequences of population size decline on the evolution of primate species. The level of genetic diversity negatively correlates with the ratio of non-synonymous to synonymous polymorphisms in a population, suggesting that proportionally greater numbers of slightly deleterious mutations segregate in small rather than large populations. Although population size decline is likely to promote the fixation of slightly deleterious mutations, there are molecular mechanisms, such as compensatory mutations at various molecular levels, which may prevent fitness decline at the population level. The effects of slightly deleterious mutations from theoretical and empirical studies and their relevance to conservation biology are also discussed in this review.

Structure and Diversity of the Rhesus Macaque Immunoglobulin Loci through Multiple De Novo Genome Assemblies

“…Our results are consistent with those of several other studies showing that genetic diversity is substantially lower generally in humans compared with other primates ( 44 ). This conclusion has substantial consequences for the interpretation of immunological experiments with rhesus macaques.…”

Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution

“…We estimated the effective population size of each species in the 36 mammalian species tree based on neutral genetic diversity and body weight. First, we collected estimates of synonymous genetic diversity from the literature (Osada 2015;Leffler et al 2012) . For species where we did not find an estimate of synonymous diversity, we predicted diversity from its body weight from a linear regression model of log(bodyweight) on log(diversity) ( Figure S5).…”

Medaka population genome structure and demographic history described via genotyping-by-sequencing

“…Wright-Fisher populations of a constant size, a rough value of Ne was estimated using the 264 relationship π = 4Neµ (Tajima 1983), where π is genome-wide nucleotide diversity and µ is 265 the mutation rate per site per generation (Osada 2015). We calculated Ne using the above 266 formula with the following values: µ = 10 -9 /site/generation; generation = 1 year, which 267 resulted in a mean effective population size from all presented demes in northern Kyushu of 268 1,275,000.…”