Data from: Genetic depletion at adaptive but not neutral loci in an endangered bird species

Many endangered species suffer from the loss of genetic diversity, but
some populations may be able to thrive even if genetically depleted. To
investigate the underlying genetic processes of population bottlenecks, we
apply an innovative approach for assessing genetic diversity in the last
known population of the endangered Pale-headed Brushfinch (Atlapetes
pallidiceps) in Ecuador. First, we measure genetic diversity at eleven
neutral microsatellite loci and adaptive SNP variation in five Toll-like
receptor (TLR) immune system genes. Bottleneck tests confirm genetic drift
as the main force shaping genetic diversity in this species and indicate a
99 % reduction in population size dating back several hundred years.
Second, we compare contemporary microsatellite diversity with historic
museum samples of A. pallidiceps, finding no change in genetic diversity.
Third, we compare genetic diversity in the Pale-headed Brushfinch with two
co-occurring-related brushfinch species (Atlapetes latinuchus, Buarremon
torquatus), finding a reduction of up to 91% diversity in the immune
system genes but not in microsatellites. High TLR diversity is linked to
decreased survival probabilities in A. pallidiceps. Low TLR diversity is
thus probably an adaptation to the specific selection regime within its
currently very restricted distribution (approximately 200 ha), but could
severely restrict the adaptive potential of the species in the long run.
Our study illustrates the importance of investigating both neutral and
adaptive markers to assess the effect of population bottlenecks and for
recommending specific management plans in endangered species.