Data from: Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus)

Deciphering patterns of genetic variation within a species is essential
for understanding population structure, local adaptation and differences
in diversity between populations. Whilst neutrally evolving genetic
markers can be used to elucidate demographic processes and genetic
structure, they are not subject to selection and therefore are not
informative about patterns of adaptive variation. As such, assessments of
pertinent adaptive loci, such as the immunity genes of the Major
Histocompatibility Complex (MHC), are increasingly being incorporated into
genetic studies. In this study we combined neutral (microsatellite, mtDNA)
and adaptive (MHC class II DLA-DRB1 locus) markers to elucidate the
factors influencing patterns of genetic variation in the African wild dog
(Lycaon pictus); an endangered canid that has suffered extensive declines
in distribution and abundance. Our genetic analyses found all extant wild
dog populations to be relatively small (Ne < 30). Furthermore,
through coalescent modelling, we detected a genetic signature of a recent
and substantial demographic decline, which correlates with human
expansion, but contrasts with findings in some other African mammals. We
found strong structure of wild dog populations, indicating the negative
influence of extensive habitat fragmentation and loss of gene flow between
habitat patches. Across populations we found that the spatial and temporal
structure of microsatellite and MHC diversity were correlated, and
strongly influenced by demographic stability and population size,
indicating the effects of genetic drift in these small populations.
Despite this correlation, we detected signatures of selection at the MHC,
implying that selection has not been completely overwhelmed by genetic
drift.