Genetic diversity at the edge: comparative assessment of Y-chromosome and autosomal diversity in eastern chimpanzees (Pan troglodytes schweinfurthii) of Ugalla, Tanzania

Population dynamics and genetic connectivity in recent chimpanzee history

Knowledge on the population history of endangered species is critical for conservation, but whole-genome data on chimpanzees (Pan troglodytes) is geographically sparse. Here, we produced the first non-invasive geolocalized catalog of genomic diversity by capturing chromosome 21 from 828 non-invasive samples collected at 48 sampling sites across Africa. The four recognized subspecies show clear genetic differentiation correlating with known barriers, while previously undescribed genetic exchange suggests that these have been permeable on a local scale. We obtained a detailed reconstruction of population stratification and fine-scale patterns of isolation, migration, and connectivity, including a comprehensive picture of admixture with bonobos (Pan paniscus). Unlike humans, chimpanzees did not experience extended episodes of long-distance migrations, which might have limited cultural transmission. Finally, based on local rare variation, we implement a fine-grained geolocalization approach demonstrating improved precision in determining the origin of confiscated chimpanzees.

Genetic censusing identifies an unexpectedly sizeable population of an endangered large mammal in a fragmented forest landscape

Background

As habitat degradation and fragmentation continue to impact wildlife populations around the world, it is critical to understand the behavioral flexibility of species in these environments. In Uganda, the mostly unprotected forest fragment landscape between the Budongo and Bugoma Forests is a potential corridor for chimpanzees, yet little is known about the status of chimpanzee populations in these fragments.

Results

From 2011 through 2013, we noninvasively collected 865 chimpanzee fecal samples across 633 km² and successfully genotyped 662 (77%) at up to 14 microsatellite loci. These genotypes corresponded to 182 chimpanzees, with a mean of 3.5 captures per individual. We obtained population size estimates of 256 (95% confidence interval 246–321) and 319 (288–357) chimpanzees using capture-with-replacement and spatially explicit capture–recapture models, respectively. The spatial clustering of associated genotypes suggests the presence of at least nine communities containing a minimum of 8–33 individuals each. Putative community distributions defined by the locations of associated genotypes correspond well with the distribution of 14 Y-chromosome haplotypes.

Conclusions

These census figures are more than three times greater than a previous estimate based on an extrapolation from small-scale nest count surveys that tend to underestimate population size. The distribution of genotype clusters and Y-chromosome haplotypes together indicate the presence of numerous male philopatric chimpanzee communities throughout the corridor habitat. Our findings demonstrate that, despite extensive habitat loss and fragmentation, chimpanzees remain widely distributed and exhibit distinct community home ranges. Our results further imply that elusive and rare species may adapt to degraded habitats more successfully than previously believed. Their long-term persistence is unlikely, however, if protection is not afforded to them and habitat loss continues unabated.

Electronic supplementary material

The online version of this article (doi:10.1186/s12898-015-0052-x) contains supplementary material, which is available to authorized users.

Estimation of chimpanzee community size and genetic diversity in Kahuzi-Biega National Park, Democratic Republic of Congo

A small chimpanzee habitat in the montane forest of Kahuzi-Biega National Park, Democratic Republic of Congo, is connected with the lowland forest of this park through a corridor, which is affected by human encroachment. To assess the conservation status of the chimpanzee population in this small habitat, we estimated the size of the community and evaluated its genetic diversity by using 279 fecal samples collected in the montane forest of Kahuzi. Using autosomal microsatellite (or short tandem repeat, STR) loci, we identified 32 individuals, comprising 19 females and 13 males. Samples from 24 individuals were collected at least twice and a genetic mark-recapture analysis estimated that the community size was 36 (range: 32-42). Data on nest site sharing confirmed that all the samples belonged to the same community. Nest site sharing information may be useful in population studies of unhabituated chimpanzees. The genetic structure and diversity of the 32 genotyped individuals was assessed using Y-chromosomal short tandem repeat (Y-STR) loci and mitochondrial D-loops. One dominant Y-STR haplotype was found, whereas there was no dominant haplotype in the mitochondrial region, reflecting a female-biased dispersal pattern, which is typical of chimpanzees. The genetic diversity for three markers in Kahuzi chimpanzees was comparable to that in other eastern chimpanzee populations. A relatively high heterozygosity and negative inbreeding coefficient (F_IS ) for STR loci suggests that the study community belongs to an outbreeding chimpanzee population. These findings suggest that individuals of the study community may have reproductive contact with other chimpanzee individuals from neighboring communities in Kahuzi-Biega National Park, at least in the recent past. Am. J. Primatol. 77:1015-1025, 2015. © 2015 Wiley Periodicals, Inc.