Recent genetic connectivity and clinal variation in chimpanzees

Abstract

Much like humans, chimpanzees occupy diverse habitats and exhibit extensive behavioural variability. However, chimpanzees are recognized as a discontinuous species, with four subspecies separated by historical geographic barriers. Nevertheless, their range-wide degree of genetic connectivity remains poorly resolved, mainly due to sampling limitations. By analyzing a geographically comprehensive sample set amplified at microsatellite markers that inform recent population history, we found that isolation by distance explains most of the range-wide genetic structure of chimpanzees. Furthermore, we did not identify spatial discontinuities corresponding with the recognized subspecies, suggesting that some of the subspecies-delineating geographic barriers were recently permeable to gene flow. Substantial range-wide genetic connectivity is consistent with the hypothesis that behavioural flexibility is a salient driver of chimpanzee responses to changing environmental conditions. Finally, our observation of strong local differentiation associated with recent anthropogenic pressures portends future loss of critical genetic diversity if habitat fragmentation and population isolation continue unabated.

Structure of Chimpanzee Gut Microbiomes across Tropical Africa

“…Furthermore, samples older than 3 days are highly degraded and generally do not yield viable DNA for reliable chimpanzee genotyping ( 108 ). DNA was extracted from the samples using the QIAamp 96 PowerFecal QIAcube HT robot and kit (Qiagen, Hilden, Germany) with a pretreatment step to improve DNA yield ( 40 ). Microsatellite genotypes were obtained for up to 15 microsatellite loci using a two-step multiplex PCR method ( 109 ) with slight modifications ( 40 ) and electrophoresing the amplicons using an ABI PRISM 3130 Genetic Analyser and GeneMapper v 3.7 software (Applied Biosystems, Foster City, CA, USA) to visualize and score the results manually.…”

“…DNA was extracted from the samples using the QIAamp 96 PowerFecal QIAcube HT robot and kit (Qiagen, Hilden, Germany) with a pretreatment step to improve DNA yield ( 40 ). Microsatellite genotypes were obtained for up to 15 microsatellite loci using a two-step multiplex PCR method ( 109 ) with slight modifications ( 40 ) and electrophoresing the amplicons using an ABI PRISM 3130 Genetic Analyser and GeneMapper v 3.7 software (Applied Biosystems, Foster City, CA, USA) to visualize and score the results manually. Individual identity was assigned based on matching genotypes at a minimum of seven loci ( 110 ) from at least three PCR replicates for homozygotes and at least two replicates for heterozygotes ( 40 ).…”

“…Until very recently, the idea of comparing the microbiome of chimpanzees across populations spanning the full extent of their extant geographic range was unfeasible. Recently, however, the “Pan African Programme: The Cultured Chimpanzee” (PanAf; http://panafrican.eva.mpg.de/ ) has studied the behavioral diversity of chimpanzees across Africa ( 39 ) and sampled chimpanzee feces across that same geographic range ( 40 ). Building on these data and samples, it is possible to disentangle the relative influence of host genetics (and evolutionary history), climate, vegetation composition, and tool use on chimpanzee microbiomes, including both prokaryotes (bacteria and archaea) as well as eukaryotic parasites (including protist and nematode parasites and note that we use a lenient definition of parasites to include organisms that may not be harmful to the host or were originally listed as parasites but are now known to operate on a spectrum).…”

Genetic diversity in chimpanzee transcriptomics does not represent wild populations

“…We consistently find that both in the number of samples and proportion of ancestry there is an overwhelming bias towards Western chimpanzees ( Pan troglodytes verus ) in public datasets. This is particularly noteworthy as, of the four extant chimpanzee subspecies, Western chimpanzees have the smallest effective population size, and show the highest amount of genetic drift [1,20]. All 40 studies we considered included at least one unadmixed individual of Western ancestry.…”

“…The first clade consists of the closely related Central (Pan troglodytes troglodytes) and Eastern chimpanzees (Pan troglodytes schweinfurthii), found in equatorial Africa, and the second clade is comprised of the Western chimpanzees (Pan troglodytes verus), found in upper Guinea and the recently designated Nigeria-Cameroon ( Pan troglodytes ellioti ) chimpanzees from the Gulf of Guinea [1,17,18]. Each subspecies has had a long separate history, and has been exposed to a wide range of ecological variation, such as incidence of pathogens, imposing different selective pressure [19], although evidence also points to considerable gene flow between subpopulations [14,20]. Pairwise F ST between Central and Eastern chimpanzees is estimated to be 0.09, similar to values seen between different populations of humans, but F ST between Western and Central chimpanzees is 0.29 and that between Western and Eastern is 0.32 – significantly higher values than typical human estimates [13].…”