Accepted Article

Received Date : 09-Jul-2014 Revised Date : 09-Oct-2014 Accepted Date : 17-Oct-2014 Article type

: Original Article

Genetic depletion at adaptive but not neutral loci in an endangered bird species Stefanie A. Hartmann1,2 · H. Martin Schaefer2 · Gernot Segelbacher1 1 Wildlife Ecology and Management, Faculty of Environment and Natural Resources, University of Freiburg, Tennenbacher Straße 4, 79106 Freiburg, Germany

2 Department of Evolutionary Biology and Animal Ecology, Faculty of Biology, University of Freiburg, Hauptstr. 1, 79104 Freiburg, Germany

Corresponding author: Stefanie A. Hartmann Email address: [email protected] Fax number: 49 (0)761 203 3661

This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/mec.12975 This article is protected by copyright. All rights reserved.

Accepted Article

Abstract Many endangered species suffer from the loss of genetic diversity, but some populations may be able to thrive even if genetically depleted. In order 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 (approx. 200ha), 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.

Keywords (4-6): Atlapetes pallidiceps, Toll-like Receptors, bottleneck, genetic diversity, microsatellites, conservation genetics

This article is protected by copyright. All rights reserved.

Accepted Article

Introduction The role of genetic diversity for the long term sustainability of small and endangered populations has been widely accepted (Frankham 2005). This is especially true for populations which have undergone a severe bottleneck in their history. Populations with low numbers of individuals can display low genetic diversity (Greenwald 2010; Wang et al. 2014), e.g. reduced heterozygosity (Madsen et al. 1996), allelic richness (Darvill et al. 2006) or immune system variation (Miller & Lambert 2004). Low genetic diversity can limit the potential of small populations to adapt to changing environments and can lower both indirect and direct fitness components (Willi et al. 2006), e.g. when genetic drift leads to fixation of deleterious alleles (Lande 1998). Thus, mutual feedback loops between a reduction in population size and a reduction in genetic diversity may finally lead to extinction (O'Grady et al. 2006; Westemeier et al. 1998).

Although the erosion of genetic diversity generally decreases population viability (Kvist et al. 2011; Reed & Frankham 2003), genetic diversity is not necessarily per se a good predictor of population trends. The most famous conservation success stories highlight that species can recover from very low numbers (e.g.,

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 investi...
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