Most great ape genetic variation remains uncharacterized; however,\ud its study is critical for understanding population history, recombination,\ud selection and susceptibility to disease.Herewe sequence\ud to high coverage a total of 79 wild- and captive-born individuals\ud representing all six great ape species and seven subspecies and report\ud 88.8 million single nucleotide polymorphisms. Our analysis provides\ud support for genetically distinct populations within each species,\ud signals of gene flow, and the split of common chimpanzees\ud into two distinct groups: Nigeria–Cameroon/western and central/\ud eastern populations.We find extensive inbreeding in almost all wild\ud populations, with eastern gorillas being the most extreme. Inferred\ud effective population sizes have varied radically over timein different\ud lineages and this appears to have a profound effect on the genetic\ud diversity at, or close to, genes in almost all species. We discover and\ud assign 1,982 loss-of-function variants throughout the human and\ud great ape lineages, determining that the rate of gene loss has not\ud been different in the human branch compared to other internal\ud branches in the great ape phylogeny. This comprehensive catalogue\ud of great ape genomediversity provides a framework for understanding\ud evolution and a resource for more effective management of wild\ud and captive great ape populations

No abstract

Recently developed methods of individual-based analysis of genetic data allow an unprecedented opportunity to understand the relationships among fragmented populations. By defining population structure and identifying migrant individuals, such analyses can provide a framework to aid in evaluating the threats posed by inbreeding and reduced genetic variability as a consequence of limited gene flow among fragments. Here we investigate population structure in the critically endangered Cross River gorilla (Gorilla gorilla diehli) by applying a suite of individual-based analyses to data obtained from between one-quarter and one-third of the estimated total population through the use of noninvasively collected DNA samples. The population structure inferred using data from 11 autosomal microsatellite loci was broadly consistent with geography and habitat fragmentation, but showed no simple isolation-by-distance effects. In contrast to previous field surveys, which suggested that all gorilla localities were isolated from one another, we infer low levels of gene flow and identify migrants between habitat fragments as well as individuals of admixed ancestry, suggesting persistent recent reproductive contact between many of the localities. These results are encouraging for the conservation of the Cross River gorilla population. Conservation efforts should strive to maintain connectivity between subpopulations that are still in migratory contact and attempt to restore connectivity where it has been lost.

No abstract

Human adenoviruses (HAdV; species HAdV-A to -G) are highly prevalent in the human population, and represent an important cause of morbidity and, to a lesser extent, mortality. Recent studies have identified close relatives of these viruses in African great apes, suggesting that some HAdV may be of zoonotic origin. We analyzed more than 800 fecal samples from wild African great apes and humans to further investigate the evolutionary history and zoonotic potential of hominine HAdV. HAdV-B and -E were frequently detected in wild gorillas (55%) and chimpanzees (25%), respectively. Bayesian ancestral host reconstruction under discrete diffusion models supported a gorilla and chimpanzee origin for these viral species. Host switches were relatively rare along HAdV evolution, with about ten events recorded in 4.5 My. Despite presumably rare direct contact between sympatric populations of the two species, transmission events from gorillas to chimpanzees were observed, suggesting that habitat and dietary overlap may lead to fecal-oral cross-hominine transmission of HAdV. Finally, we determined that two independent HAdV-B transmission events to humans occurred more than 100,000 years ago. We conclude that HAdV-B circulating in humans are of zoonotic origin and have probably affected global human health for most of our species lifetime.

The unique inheritance pattern of the X chromosome exposes it to natural selection in a way that is different from that of the autosomes, potentially resulting in accelerated evolution. We perform a comparative analysis of X chromosome polymorphism in 10 great ape species, including humans. In most species, we identify striking megabase-wide regions, where nucleotide diversity is less than 20% of the chromosomal average. Such regions are found exclusively on the X chromosome. The regions overlap partially among species, suggesting that the underlying targets are partly shared among species. The regions have higher proportions of singleton SNPs, higher levels of population differentiation, and a higher nonsynonymous-to-synonymous substitution ratio than the rest of the X chromosome. We show that the extent to which diversity is reduced is incompatible with direct selection or the action of background selection and soft selective sweeps alone, and therefore, we suggest that very strong selective sweeps have independently targeted these specific regions in several species. The only genomic feature that we can identify as strongly associated with loss of diversity is the location of testis-expressed ampliconic genes, which also have reduced diversity around them. We hypothesize that these genes may be responsible for selective sweeps in the form of meiotic drive caused by an intragenomic conflict in male meiosis. X-chromosome evolution | great apes | selective sweeps | ampliconic genes | meiotic drive

In small and fragmented populations, genetic diversity may be reduced owing to increased levels of drift and inbreeding. This reduced diversity is often associated with decreased fitness and a higher threat of extinction. However, it is difficult to determine when a population has low diversity except in a comparative context. We assessed genetic variability in the critically endangered Cross River gorilla (Gorilla gorilla diehli), a small and fragmented population, using 11 autosomal microsatellite loci. We show that levels of diversity in the Cross River population are not evenly distributed across the three genetically identified subpopulations, and that one centrally located subpopulation has higher levels of variability than the others. All measures of genetic variability in the Cross River population were comparable to those of the similarly small mountain gorilla (G. beringei beringei) populations (Bwindi and Virunga). However, for some measures both the Cross River and mountain gorilla populations show lower levels of diversity than a sample from a large, continuous western gorilla population (Mondika, G. gorilla gorilla). Finally, we tested for the genetic signature of a bottleneck in each of the four populations. Only Cross River showed strong evidence of a reduction in population size, suggesting that the reduction in size of this population was more recent or abrupt than in the two mountain gorilla populations. These results emphasize the need for maintaining connectivity in fragmented populations and highlight the importance of allowing small populations to expand.

No abstract