Data and R script for: Barriers to chimpanzee gene flow at the south‐east edge of their distribution

Populations on the edge of a species' distribution may represent an
important source of adaptive diversity, yet these populations tend to be
more fragmented and are more likely to be geographically isolated. Lack of
genetic exchanges between such populations, due to barriers to animal
movement, can not only compromise adaptive potential but also lead to the
fixation of deleterious alleles. The south‐eastern edge of chimpanzee
distribution is particularly fragmented, and conflicting hypotheses have
been proposed about population connectivity and viability. To address this
uncertainty, we generated both mitochondrial and MiSeq‐based
microsatellite genotypes for 290 individuals ranging across western
Tanzania. While shared mitochondrial haplotypes confirmed historical gene
flow, our microsatellite analyses revealed two distinct clusters,
suggesting two populations currently isolated from one another. However,
we found evidence of high levels of gene flow maintained within each of
these clusters, one of which covers an 18,000 km2 ecosystem.
Landscape genetic analyses confirmed the presence of barriers to gene flow
with rivers and bare habitats highly restricting chimpanzee movement. Our
study demonstrates how advances in sequencing technologies, combined with
the development of landscape genetics approaches, can resolve ambiguities
in the genetic history of critical populations and better inform
conservation efforts of endangered species.