Data from: Consequences for conservation: population density and genetic effects on reproduction of an endangered lagomorph

Understanding reproduction and mating systems is important for managers tasked with conserving vulnerable species. Genetic tools allow biologists to investigate reproduction and mating systems with high resolution and are particularly useful for species that are otherwise difficult to study in their natural environments. We conducted parentage analyses using 19 nuclear DNA microsatellite loci to assess the influence of population density, genetic diversity, and ancestry on reproduction, and to examine the mating system of pygmy rabbits (Brachylagus idahoensis) bred in large naturalized enclosures for the reintroduction and recovery of the endangered distinct population in central Washington, USA. Reproductive output for females and males decreased as population density and individual homozygosity increased. We identified an interaction indicating that male reproductive output decreased as genetic diversity declined at high population densities, but there was no effect at low densities. Males with high amounts (>50%) of Washington ancestry had higher reproductive output than the other ancestry groups, while reproductive output was decreased for males with high northern Utah/Wyoming ancestry and females with high Oregon/Nevada ancestry. Females and males bred with an average of 3.8 and 3.6 mates per year, respectively, and we found no evidence of positive or negative assortative mating with regards to ancestry. Multiple paternity was confirmed in 81% of litters, and we report the first documented cases of juvenile breeding by pygmy rabbits. This study demonstrates how variation in population density, genetic diversity, and ancestry impact fitness for an endangered species being bred for conservation. Our results advance understanding of basic life history characteristics for a cryptic species that is difficult to study in the wild, and provide lessons for managing populations of vulnerable species in captive and free-ranging populations.

明晰繁殖与交配系统，对于负责保护弱势物种的管理者而言至关重要。遗传工具能够让生物学家以高分辨率开展繁殖与交配系统的研究，对于那些难以在自然环境中开展研究的物种而言尤为实用。本研究采用19个核DNA微卫星位点开展亲权分析（parentage analyses），旨在评估种群密度、遗传多样性及祖先血统对繁殖的影响，并探究在美国华盛顿州中部圈养于大型天然化圈舍、用于该濒危独特种群再引入与恢复的侏兔（Brachylagus idahoensis）的交配系统。随着种群密度与个体纯合度（homozygosity）升高，雌性与雄性的繁殖产出均有所下降。本研究发现了一项交互效应：在高种群密度条件下，雄性繁殖产出随遗传多样性降低而下降，但在低密度条件下并无此类效应。拥有超过50%华盛顿血统的雄性，其繁殖产出高于其他血统类群的雄性；而携带高比例犹他州北部/怀俄明州血统的雄性，以及携带高比例俄勒冈州/内华达州血统的雌性，其繁殖产出则有所降低。雌性与雄性每年的平均配偶数量分别为3.8只与3.6只，未发现任何基于祖先血统的正选型交配（positive assortative mating）与负选型交配（negative assortative mating）证据。81%的幼崽窝被证实存在多父本现象（multiple paternity），本研究还报告了侏兔幼体繁殖的首个记录案例。本研究阐明了种群密度、遗传多样性及祖先血统的变异，如何影响用于保护繁育的濒危物种的适合度（fitness）。本研究结果增进了人们对这类难以在野外开展研究的隐蔽性物种的基础生活史特征的认知，并为弱势物种的圈养种群与野生种群的管理提供了参考依据。