title: Genetic depletion at adaptive but not neutral loci in an endangered bird species.
abstract: 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.
authors.affiliation: Wildlife Ecology and Management, Faculty of Environment and Natural Resources, University of Freiburg, Tennenbacher Straße 4, 79106, Freiburg, Germany; Department of Evolutionary Biology and Animal Ecology, Faculty of Biology, University of Freiburg, Hauptstr. 1, 79104, Freiburg, Germany.
authors.forename: Stefanie A
authors.initials: SA
authors.lastname: Hartmann
authors.forename: H Martin
authors.initials: HM
authors.lastname: Schaefer
authors.forename: Gernot
authors.initials: G
authors.lastname: Segelbacher
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D000818:Animals; D003247:Conservation of Natural Resources; D004484:Ecuador; D056727:Endangered Species; D046369:Finches / Q000235:genetics*; D056426:Genetic Loci; D014644:Genetic Variation; D005828:Genetics, Population; D018895:Microsatellite Repeats; D008957:Models, Genetic; D017422:Sequence Analysis, DNA; D051193:Toll-Like Receptors / Q000235:genetics
chemical_list: D051193:Toll-Like Receptors
keywords: Atlapetes pallidiceps; Toll-like receptors; bottleneck; conservation genetics; genetic diversity; microsatellites