Data from: Quantifying the similarity between genes and geography across Alaska's alpine small mammals

Aim: Quantitatively evaluate the similarity of genomic variation and geography in five different alpine small mammals in Alaska, and use this quantitative assessment of concordance as a framework for refining hypotheses about the processes structuring population genetic variation in either a species-specific or shared manner. Location: Alaska and adjacent north-western Canada. Methods: For each taxon we generated 3500–7500 single-nucleotide polymorphisms and applied a Procrustes analysis to find an optimal transformation that maximizes the similarity between principal components analysis maps of genetic variation and geographical maps of sample locations. We generate stability maps using projected distributions from ecological niche models of the Last Glacial Maximum and the present. Results: Significant similarity between genes and geography exists across taxa. However, the extent to which geography is predictive of patterns of genetic variation not only differs among taxa, but the correspondence between genes and geography varies over space. Geographical areas where genetic structure aligns poorly with the geographical coordinates are of particular interest because they indicate regions where processes other than isolation by distance (IBD) have influenced genetic variation. The clustering of individuals according to their sample location does not support suppositions of admixture, despite the presumed high vagility of some species (e.g. arctic ground squirrels). Main conclusions: Genomic data indicate a more nuanced biogeographical history for the taxa than suggested by previous studies based on mtDNA alone. These include departures from IBD that are shared among taxa, which suggest some shared processes structuring genetic variation, including new potential ancestral source populations. In addition, some regions fit expectations of IBD where incremental migration and gene flow play a strong role in population structure, despite any ecological difference among taxa. Differences in dispersal capabilities do not result in different species-specific local patterns of population structure, at least at the sampling scale examined here. We highlight how the general fit to, as well as departures from, expectations for patterns of genetic variation based on the Procrustes analyses can be used to generate hypotheses about the underlying processes.

研究目的：对阿拉斯加境内5种不同高山小型哺乳动物的基因组变异与地理分布的相似性进行定量评估，并将该一致性定量评估作为框架，以细化关于以物种特异性或共享方式构建种群遗传变异的过程的假说。
研究区域：阿拉斯加及毗邻的加拿大西北部地区。
研究方法：针对每个类群，我们生成了3500~7500个单核苷酸多态性（single-nucleotide polymorphisms, SNP）位点，并运用普氏分析（Procrustes analysis）寻找最优变换，以最大化遗传变异主成分分析（principal components analysis）图谱与样本地理位置图谱之间的相似性。我们利用末次冰盛期及当前的生态位模型（ecological niche models）预测分布生成稳定性图谱。
研究结果：所有类群的基因组变异与地理分布均存在显著相似性。然而，地理因素对遗传变异格局的预测能力不仅在不同类群间存在差异，且基因组与地理的对应关系也随空间尺度发生变化。遗传结构与地理坐标匹配度较低的区域尤为值得关注，因为这表明除距离隔离（isolation by distance, IBD）过程外，其他过程同样对遗传变异产生了影响。尽管部分物种（如北极地松鼠）被认为具有较强的扩散能力，但基于样本来源地的个体聚类结果并不支持种群混合的推测。
主要结论：基因组数据表明，这些类群的生物地理历史比此前仅基于线粒体DNA（mtDNA）的研究更为复杂细致。研究结果包括类群间共有的距离隔离偏离现象，这提示存在一些共享的遗传变异构建过程，包括新发现的潜在祖先源种群。此外，尽管不同类群存在生态差异，但部分区域符合距离隔离的预期格局，即渐进式迁移与基因流在种群结构形成中发挥了重要作用。至少在本研究的采样尺度下，扩散能力的差异并未导致类群间种群结构的物种特异性局部格局差异。我们阐明了如何通过普氏分析得到的遗传变异格局与预期的匹配程度及偏离情况，来推导背后的潜在过程。