Evidence of genetic erosion in a peripheral population of a North American game bird: the Montezuma quail (Cyrtonyx montezumae)

Population extirpations are often precursors to species extinctions. Anthropogenic activities often lead to smaller populations that are more prone to extirpations and advocates for active conservation management have recently called for the preservation and monitoring of genetic diversity, particularly with regard to the adaptive potential of vulnerable populations. We used genomics and curated arrays of molecular markers, including those expected to impact key fitness traits, to quantify evidence of genomic erosion in core and peripheral populations of a gallinaceous bird. The Montezuma quail (Cyrtonyx montezumae) is a game species considered vulnerable to extirpation in Texas, but core populations in Arizona and New Mexico are robust and have the potential to serve as genetic reservoirs. We sequenced the Montezuma quail genome then developed a single nucleotide polymorphism (SNP) assay to quantify genetic variation, effective population sizes, signatures of natural selection, and population structure. We genotyped SNPs from gene deserts and from genes associated with fitness traits and found the isolated Texas population exhibits an extremely small effective population size, is genetically distinct from our Arizona and New Mexico samples, and has reduced heterozygosity at the fitness-related markers. Thus, our samples from Texas exhibit symptoms of genetic erosion that could exacerbate future risk of local extirpation. Management agencies must decide if active conservation efforts such as assisted gene flow or genetic rescue are now warranted. This decision may not be straightforward because the current conservation status of the Texas population reflects its isolated geographic locale on the periphery of the species’ range.

种群局部灭绝往往是物种全域灭绝的前兆。人类活动常导致种群规模缩小，使种群更易发生局部灭绝；积极保护管理的倡导者近期呼吁开展遗传多样性的保护与监测工作，尤其应聚焦弱势种群的适应性演化潜力。本研究针对一种鸡形目鸟类的核心种群与边缘种群，采用基因组学手段与经过精心筛选的分子标记阵列（包括预期会影响关键适合度性状的标记），量化基因组侵蚀的相关证据。蒙特祖马鹌鹑（Cyrtonyx montezumae）是一种猎用物种，在得克萨斯州被认为面临局部灭绝风险，但其在亚利桑那州与新墨西哥州的核心种群规模稳定，具备作为遗传储备库的潜力。本研究对蒙特祖马鹌鹑的基因组进行测序，随后开发了单核苷酸多态性（Single Nucleotide Polymorphism, SNP）分型技术，以量化遗传变异、有效种群大小、自然选择信号以及种群结构。本研究对基因荒漠区域以及与适合度性状相关基因区域的SNP进行基因分型，结果发现孤立的得克萨斯州种群有效种群规模极小，在遗传上与亚利桑那州和新墨西哥州的样本存在显著分化，且其与适合度相关的标记位点的杂合度有所降低。因此，本研究采集的得克萨斯州样本表现出基因组侵蚀的特征，这可能加剧其未来发生局部灭绝的风险。管理机构亟需决策，是否应立即开展辅助基因流、遗传救援等积极保护措施。该决策并非易事，因为得克萨斯州种群当前的保护现状，恰恰反映出其地处物种分布范围边缘的孤立地理区位特征。