Data from: Isolation by distance, resistance and/or clusters? Lessons learned from a forest-dwelling carnivore inhabiting a heterogeneous landscape

Landscape genetics provides a valuable framework to understand how landscape features influence gene flow and to disentangle the factors that lead to discrete and/or clinal population structure. Here, we attempt to differentiate between these processes in a forest-dwelling small carnivore [European pine marten (Martes martes)]. Specifically, we used complementary analytical approaches to quantify the spatially explicit genetic structure and diversity and analyse patterns of gene flow for 140 individuals genotyped at 15 microsatellite loci. We first used spatially explicit and nonspatial Bayesian clustering algorithms to partition the sample into discrete clusters and evaluate hypotheses of ‘isolation by barriers’ (IBB). We further characterized the relationships between genetic distance and geographical (‘isolation by distance’, IBD) and ecological distances (‘isolation by resistance’, IBR) obtained from optimized landscape models. Using a reciprocal causal modelling approach, we competed the IBD, IBR and IBB hypotheses with each other to unravel factors driving population genetic structure. Additionally, we further assessed spatially explicit indices of genetic diversity using sGD across potentially overlapping genetic neighbourhoods that matched the inferred population structure. Our results revealed a complex spatial genetic cline that appears to be driven jointly by IBD and partial barriers to gene flow (IBB) associated with poor habitat and interspecific competition. Habitat loss and fragmentation, in synergy with past overharvesting and possible interspecific competition with sympatric stone marten (Martes foina), are likely the main factors responsible for the spatial genetic structure we observed. These results emphasize the need for a more thorough evaluation of discrete and clinal hypotheses governing gene flow in landscape genetic studies, and the potential influence of different limiting factors affecting genetic structure at different spatial scales.

景观遗传学（Landscape genetics）为解析景观特征如何影响基因流（gene flow）、厘清导致离散/渐变式种群结构的因素提供了极具价值的研究框架。本研究以栖息于森林的小型食肉动物——欧洲松貂（Martes martes）为研究对象，尝试区分这两类种群结构形成过程。具体而言，我们采用互补分析方法，对140个在15个微卫星位点（microsatellite loci）上完成基因分型的个体开展空间显性遗传结构与遗传多样性的定量分析，并解析其基因流模式。首先，我们利用空间显性与非空间贝叶斯聚类算法（Bayesian clustering algorithms）将样本划分为离散集群，并验证障碍隔离（IBB）假说。随后，我们基于优化后的景观模型，对遗传距离（genetic distance）与地理距离（即距离隔离，IBD）、生态距离（即抗性隔离，IBR）之间的关联进行了表征。通过互作因果建模方法（reciprocal causal modelling approach），我们对IBD、IBR与IBB假说进行两两比较，以解析驱动种群遗传结构的核心因子。此外，我们还针对与推断种群结构匹配的潜在重叠遗传邻域，利用sGD评估了空间显性遗传多样性指数。研究结果揭示了一个复杂的空间遗传渐变群，其形成似乎由距离隔离（IBD）以及与劣质生境和种间竞争（interspecific competition）相关的基因流部分障碍（IBB）共同驱动。生境丧失与片段化（Habitat loss and fragmentation），加之过往过度捕猎以及可能与同域分布石貂（Martes foina）之间的种间竞争，极有可能是我们观测到的空间遗传结构的主要成因。本研究结果强调，在景观遗传学研究中，亟需更全面地评估调控基因流的离散与渐变式假说，以及不同限制因子在不同空间尺度下对遗传结构的潜在影响。