Data from: Isolation by environment in white-breasted nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach

Understanding landscape processes driving patterns of population genetic differentiation and diversity has been a long-standing focus of ecology and evolutionary biology. Gene flow may be reduced by historical, ecological or geographic factors, resulting in patterns of isolation by distance (IBD) or isolation by environment (IBE). Although IBE has been found in many natural systems, most studies investigating patterns of IBD and IBE in nature have used anonymous neutral genetic markers, precluding inference of selection mechanisms or identification of genes potentially under selection. Using landscape genomics, the simultaneous study of genomic and ecological landscapes, we investigated the processes driving population genetic patterns of White-breasted Nuthatches (Sitta carolinensis) in sky islands (montane forest habitat islands) of the Madrean Archipelago. Using more than 4000 single nucleotide polymorphisms and multiple tests to investigate the relationship between genetic differentiation and geographic or ecological distance, we identified IBE, and a lack of IBD, among sky island populations of S. carolinensis. Using three tests to identify selection, we found 79 loci putatively under selection; of these, seven matched CDS regions in the Zebra Finch. The loci under selection were highly associated with climate extremes (maximum temperature of warmest month and minimum precipitation of driest month). These results provide evidence for IBE – disentangled from IBD – in sky island vertebrates and identify potential adaptive genetic variation.

解析驱动种群遗传分化与多样性格局的景观过程，一直是生态学与进化生物学领域长期以来的核心研究议题。历史、生态或地理因素可能降低基因流，进而形成距离隔离（isolation by distance, IBD）或环境隔离（isolation by environment, IBE）格局。尽管诸多自然系统中均已发现环境隔离现象，但目前绝大多数探究自然种群IBD与IBE格局的研究，均采用匿名中性遗传标记，这使得研究者无法推断选择作用机制，亦无法鉴定潜在受选择基因。本研究采用景观基因组学，即同步解析基因组与生态景观的研究手段，针对马德雷群岛天空岛（山地森林生境岛）生境中的白胸鳾（Sitta carolinensis）种群遗传格局的驱动过程展开研究。本研究依托超过4000个单核苷酸多态性（single nucleotide polymorphisms, SNPs）位点，通过多种检验方法探究遗传分化与地理距离或生态距离之间的关联，结果发现白胸鳾天空岛种群存在环境隔离现象，且不存在距离隔离格局。通过三种选择检验方法，本研究共鉴定出79个潜在受选择的基因座；其中7个基因座与斑胸草雀的编码序列（Coding Sequence, CDS）区域相匹配。这些受选择基因座与极端气候因子（最热月最高温、最干月最低降水量）显著相关。本研究结果为天空岛脊椎动物中与距离隔离相区分的环境隔离现象提供了实证支持，并鉴定出潜在的适应性遗传变异。