Basto Mafalda P, Santos-Reis Margarida, Simões Luciana, Grilo Clara, Cardoso Luís, Cortes Helder, Bruford Michael W, Fernandes Carlos
Ce3C - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom.
PLoS One. 2016 Jan 4;11(1):e0145165. doi: 10.1371/journal.pone.0145165. eCollection 2016.
The identification of populations and spatial genetic patterns is important for ecological and conservation research, and spatially explicit individual-based methods have been recognised as powerful tools in this context. Mammalian carnivores are intrinsically vulnerable to habitat fragmentation but not much is known about the genetic consequences of fragmentation in common species. Stone martens (Martes foina) and red foxes (Vulpes vulpes) share a widespread Palearctic distribution and are considered habitat generalists, but in the Iberian Peninsula stone martens tend to occur in higher quality habitats. We compared their genetic structure in Portugal to see if they are consistent with their differences in ecological plasticity, and also to illustrate an approach to explicitly delineate the spatial boundaries of consistently identified genetic units. We analysed microsatellite data using spatial Bayesian clustering methods (implemented in the software BAPS, GENELAND and TESS), a progressive partitioning approach and a multivariate technique (Spatial Principal Components Analysis-sPCA). Three consensus Bayesian clusters were identified for the stone marten. No consensus was achieved for the red fox, but one cluster was the most probable clustering solution. Progressive partitioning and sPCA suggested additional clusters in the stone marten but they were not consistent among methods and were geographically incoherent. The contrasting results between the two species are consistent with the literature reporting stricter ecological requirements of the stone marten in the Iberian Peninsula. The observed genetic structure in the stone marten may have been influenced by landscape features, particularly rivers, and fragmentation. We suggest that an approach based on a consensus clustering solution of multiple different algorithms may provide an objective and effective means to delineate potential boundaries of inferred subpopulations. sPCA and progressive partitioning offer further verification of possible population structure and may be useful for revealing cryptic spatial genetic patterns worth further investigation.
识别种群和空间遗传模式对于生态和保护研究至关重要，在这种情况下，基于个体的空间明确方法已被视为强大的工具。哺乳动物食肉动物本质上易受栖息地破碎化的影响，但对于常见物种破碎化的遗传后果知之甚少。石貂（Martes foina）和赤狐（Vulpes vulpes）在古北区广泛分布，被认为是栖息地通才，但在伊比利亚半岛，石貂往往出现在质量较高的栖息地。我们比较了它们在葡萄牙的遗传结构，以了解它们是否与生态可塑性差异一致，同时也说明了一种明确划定一致识别的遗传单位空间边界的方法。我们使用空间贝叶斯聚类方法（在软件BAPS、GENELAND和TESS中实现）、逐步划分方法和多变量技术（空间主成分分析-sPCA）分析了微卫星数据。为石貂确定了三个一致的贝叶斯聚类。赤狐没有达成一致，但一个聚类是最可能的聚类解决方案。逐步划分和sPCA表明石貂中还有其他聚类，但这些聚类在方法之间不一致且在地理上不连贯。这两个物种的对比结果与文献报道的伊比利亚半岛石貂更严格的生态要求一致。在石貂中观察到的遗传结构可能受到景观特征的影响，特别是河流和破碎化。我们建议，基于多种不同算法的一致聚类解决方案的方法可能提供一种客观有效的手段来划定推断亚种群的潜在边界。sPCA和逐步划分进一步验证了可能的种群结构，可能有助于揭示值得进一步研究的隐秘空间遗传模式。
