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The site covers international issues such as Kosovo, Russia, and China. The site also covers issues. Great ape genetic diversity and population history : Nature : Nature Research. We sequenced great ape genomes to a mean of 2. Table 1, Supplementary Information and Supplementary Table 1) sampling natural diversity by selecting captive individuals of known wild- born origin as well as individuals from protected areas in Africa (Fig. We also included nine human genomes—three African and six non- African individuals. Variants were called using the software package GATK (ref. Methods), applying several quality filters, including conservative allele balance filters, and requiring that genomes showed < 2% contamination between samples (Methods and Supplementary Information). In order to assess the quality of single nucleotide variant (SNV) calls, we performed three sets of independent validation experiments with concordance rates ranging from 8. Supplementary Information and Supplementary Table 2). In total, we discovered 8. Table 1 and Supplementary Table 3), providing the most comprehensive catalogue of great ape genetic diversity to date. From these variants we also constructed a list of potentially ancestry- informative markers (AIMs) for each of the surveyed populations, although a larger sampling of some subspecies is still required (Supplementary Information). The formation of the islands of Borneo and Sumatra resulted in the speciation of the two corresponding orangutan populations. The Sanaga River forms a natural boundary between Nigeria–Cameroon and central chimpanzee populations whereas the Congo River separates the bonobo population from the central and eastern chimpanzees. Eastern lowland and western lowland gorillas are both separated by a large geographical distance. Arrows indicate heterozygosities previously reported. The relationship between the coefficient of inbreeding (FROH) and the number of autozygous > 1 megabase segments is shown. Bonobos and eastern lowland gorillas show an excess of inbreeding compared to the other great apes, suggesting small population sizes or a fragmented population. All individuals (columns) are grouped into different clusters (K = 2 to K = 6, rows) coloured by species and according to their common genetic structure. Most captive individuals, labelled on top, show a complex admixture from different wild populations. A signature of admixture, for example, is clearly observed in the known hybrid Donald, a second- generation captive predicted to be a 1. A grey line at the bottom denotes new groups at K = 6 in agreement with the location of origin or ancestral admixture. We initially explored the genetic relationships between individuals by constructing neighbour- joining phylogenetic trees from both autosomal and mitochondrial genomes (Supplementary Information). The autosomal tree identified separate monophyletic groupings for each species or subspecies designation (Supplementary Fig. Nigeria–Cameroon and western chimpanzees form a monophyletic clade (> 9. Genome- wide patterns of heterozygosity (Fig. SNP) diversity. Non- African humans, eastern lowland gorillas, bonobos and western chimpanzees show the lowest genetic diversity (~0. In contrast, central chimpanzees, western lowland gorillas and both orangutan species show the greatest genetic diversity (1. These differences are also reflected by measures of inbreeding from runs of homozygosity. Fig. 1c and Supplementary Information). Bonobos and western lowland gorillas, for example, have similar distributions of tracts of homozygosity as human populations that have experienced strong genetic bottlenecks (Karitiana and Papuan). Eastern lowland gorillas appear to represent the most inbred population, with evidence that they have been subjected to both recent and ancient inbreeding. To examine the level of genetic differentiation between individuals we performed a principal component analysis (PCA) of SNP genotypes (Supplementary Information). Chimpanzees were stratified between subspecies with PC1 separating western and Nigeria–Cameroon chimpanzees from the eastern and central chimpanzees and PC2 separating western and Nigeria–Cameroon chimpanzees. In gorillas, PC1 clearly separates eastern and western gorillas, whereas the western lowland gorillas are distributed along a gradient of PC2, with individuals from the Congo and western Cameroon positioning in opposite directions along the axis. The isolated Cross River gorilla is genetically more similar to Cameroon western lowland gorillas and can be clearly differentiated with PC3 (Supplementary Fig. We explored the level of shared ancestry among individuals within each group. FRAPPE). In chimpanzees, the four known subspecies are clearly distinguished when fitting the model using four ancestry components (K = 4) (Fig. Additional substructure is identified among the eastern chimpanzees Vincent and Andromeda (K = 6), who hail from the most eastern sample site (Gombe National Park, Tanzania). As in Gonder et al. Nigeria–Cameroon samples (Julie, Tobi and Banyo, K = 3–5) with components of central chimpanzee ancestry. However, taking central chimpanzees and the remaining Nigeria–Cameroon chimpanzees as ancestral populations shows no evidence of gene flow by either the F3 statistic or Hap. Mix. This indicates that these three samples are not the result of a recent admixture and may represent a genetically distinct population (Supplementary Information). In gorillas, following the separation of eastern and western lowland species (K = 2), an increasing number of components further subdivide western lowland populations distinguishing Congolese and Cameroonian gorillas—a pattern consistent with the structure observed in the PCA analysis (Supplementary Fig. One striking observation is the extent of admixed ancestry predicted for captive individuals when compared to wild- born. Our analysis suggests that most captive individuals included in this study are admixed from two or more genetically distinct wild- born populations leading to an erosion of phylogeographic signal. This finding is consistent with microsatellite analyses of captive gorillas. As great apes have been evolving on separate lineages since the middle Miocene, we attempted to reconstruct the history of these various species and subspecies by applying methods sensitive to branching processes, changes in effective population size (Ne), and gene flow occurring at different time scales. Using a combination of speciation times inferred from a haploid pairwise sequential Markovian coalescent (PSMC) analysis. Markov model (Coal. HMM)3 and incomplete lineage sorting approaches, we were able to estimate the most ancient split times and effective population sizes among the great ape species. By combining these estimates with an approximate Bayesian computation (ABC)1. Fig. This model presents a complete overview of great ape divergence and speciation events in the context of historical effective population sizes. Split times (dark brown) and divergence times (light brown) are plotted as a function of divergence (d) on the bottom and time on top. Time is estimated using a single mutation rate (. The ancestral and current effective population sizes are also estimated using this mutation rate. The results from several methods used to estimate Ne (COALHMM, ILS COALHMM, PSMC and ABC) are coloured in orange, purple, blue and green, respectively. The chimpanzee split times are estimated using the ABC method. The x axis is rescaled for divergences larger than 2 . All the values used in this figure can be found in Supplementary Table 5. The terminal Ne correspond to the effective population size after the last split event. PSMC analyses of historical Ne (Fig. Pan lineage had the largest effective population size of all lineages > 3 million years ago (Myr), after which time the population of the common ancestor of both bonobos and chimpanzees experienced a dramatic decline. Both PSMC and ABC analyses support a model of subsequent increase in chimpanzee Ne starting ~1 Myr, before their divergence into separate subspecies. Following an eastern chimpanzee increase in Ne (~5. Although the PSMC profiles of the two subspecies within each of the major chimpanzee clades (eastern/central and Nigeria–Cameroon/western) closely shadow each other between 1. Myr, the western chimpanzee PSMC profile is notable for its initial separation from that of the other chimpanzees, followed by its sudden rise and decline (Fig. Supplementary Information). The different gorilla species also show variable demographic histories over the past ~2. Eastern lowland gorillas have the smallest historical Ne, consistent with smaller present- day populations and a history of inbreeding (Fig. A comparison of effective population sizes with the ratio of non- synonymous to synonymous substitutions finds that selection has acted more efficiently in populations with higher Ne, consistent with neutral theory (Supplementary Information). The lower x axis gives time measured by pairwise sequence divergence and the y axis gives the effective population size measured by the scaled mutation rate. The upper x axis indicates scaling in years, assuming a mutation rate ranging from 1. The top left panel shows the inference for modern human populations. In the rest of the three panels, thin light lines of the same colour correspond to PSMC inferences on 1. Although the phylogeny of bonobos and western, central and eastern common chimpanzees has been well established based on genetic data. Nigeria–Cameroon chimpanzees. Regional neighbour- joining trees and a maximum- likelihood tree estimated from allele frequencies both show that Nigeria–Cameroon and western chimpanzees form a clade. A complex demographic history has been previously reported for chimpanzees with evidence of asymmetrical gene flow among different subspecies. For instance, migration has been identified from western into eastern chimpanzees.
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