A decision-making framework to maximize the evolutionary potential of populations: Genetic and genomic insights from the common midwife toad (Alytes obstetricans) at its range limits

Anthropogenic habitat modification and climate change are fundamental drivers of biodiversity declines, reducing the evolutionary potential of species, particularly at their distributional limits. Supportive breeding or reintroductions of individuals are often made to replenish declining populations, sometimes informed by genetic analysis. However, most approaches utilised (i.e. single locus markers) do not have the resolution to account for local adaptation to environmental conditions, a crucial aspect to consider when selecting donor and recipient populations. Here, we incorporate genetic (microsatellite) and genome-wide SNP (ddRAD-seq) markers, accounting for both neutral and putative adaptive genetic diversity, to inform the conservation management of the threatened common midwife toad, Alytes obstetricans at the northern and eastern edges of its range in Europe. We find geographically structured populations (n=4), weak genetic differentiation and fairly consistent levels of genetic diversity across localities (observed heterozygosity and allelic richness). Categorising individuals based on putatively adaptive regions of the genome showed that the majority of localities are not strongly locally adapted. However, several localities present high numbers of private alleles in tandem with local adaptation to warmer conditions and rough topography. Combining genetic diversity and local adaptations with estimates of migration rates, we develop a decision-making framework for selecting donor and recipient populations which maximises the geographic dispersal of neutral and putatively adaptive genetic diversity. Our framework is generally applicable to any species, but especially to amphibians, so armed with this information, conservationists may avoid the reintroduction of unsuitable/maladapted individuals to new sites and increase the evolutionary potential of populations within species.

Methods
This is a novel dataset generated form sampling Alytes obstetricans across its northern and Eastern range limits in Germany and Belgium. Our dataset represents 38 unique localities and contains 467 individuals genotyped at up to 9 microsatelite loci, and 70 individuals with ddRAD-seq data (our analyses are based on 8650 SNPs.

人为生境改造与气候变化是生物多样性下降的核心驱动因素，会降低物种的进化潜力，尤其是在物种分布边界区域。辅助繁育或个体放归常被用于补充衰退种群，此类工作有时会借助遗传分析作为依据。然而，当前多数使用的分析方法（即单位点标记）无法精准解析物种对环境的局部适应性，而这正是筛选供体与受体种群时需考量的关键要素。本研究整合了遗传（微卫星（microsatellite））标记与基于双酶切简化基因组测序（ddRAD-seq）获得的全基因组单核苷酸多态性（single nucleotide polymorphism, SNP）标记，同时考量中性遗传多样性与推定的适应性遗传多样性，以此为欧洲分布北缘与东缘的受胁物种普通助产蟾（Alytes obstetricans）的保护管理提供依据。研究发现存在地理结构的种群（n=4），种群间遗传分化较弱，且各采样点的遗传多样性水平（观测杂合度与等位基因丰富度）较为一致。基于基因组推定的适应性区域对个体进行分类的结果显示，多数采样点的种群未表现出强烈的局部适应性。但部分采样点存在大量私有等位基因，且其种群对温暖生境与复杂地形具备局部适应性。结合遗传多样性、局部适应性与迁移率估算结果，我们构建了一套供体与受体种群筛选决策框架，该框架可最大化中性与推定适应性遗传多样性的地理扩散范围。本决策框架可普遍适用于多数物种，尤其适用于两栖类；借此研究结果，保护工作者可避免将不适配/适应性不良的个体放归至新栖息地，并提升物种种群的进化潜力。

方法
本数据集为全新生成，采样范围覆盖普通助产蟾（Alytes obstetricans）在德国与比利时的分布北缘及东缘区域。本数据集共包含38个独立采样点，其中467个个体经至多9个微卫星位点基因分型，另有70个个体获得了ddRAD-seq测序数据（本研究的分析基于8650个SNP位点）。