Data from: Differentiation in neutral genes and a candidate gene in the pied flycatcher: using biological archives to track global climate change

Global climate change is one of the major driving forces for adaptive shifts in migration and breeding phenology and possibly impacts demographic changes if a species fails to adapt sufficiently. In Western Europe, pied flycatchers (Ficedula hypoleuca) have insufficiently adapted their breeding phenology to the ongoing advance of food peaks within their breeding area and consequently suffered local population declines. We address the question whether this population decline led to a loss of genetic variation, using two neutral marker sets (mitochondrial control region and microsatellites), and one potentially selectively non-neutral marker (avian Clock gene). We report temporal changes in genetic diversity in extant populations and biological archives over more than a century, using samples from sites differing in the extent of climate change. Comparing genetic differentiation over this period revealed that only the recent Dutch population, which underwent population declines, showed slightly lower genetic variation than the historic Dutch population. As that loss of variation was only moderate and not observed in all markers, current gene flow across Western and Central European populations might have compensated local loss of variation over the last decades. A comparison of genetic differentiation in neutral loci versus the Clock gene locus provided evidence for stabilizing selection. Furthermore, in all genetic markers, we found a greater genetic differentiation in space than in time. This pattern suggests that local adaptation or historic processes might have a stronger effect on the population structure and genetic variation in the pied flycatcher than recent global climate changes.

全球气候变化是驱动迁徙与繁殖物候适应性演化的核心驱动因素之一，若物种无法实现充分适应，则可能对其种群动态变化产生影响。在西欧地区，斑姬鹟（Ficedula hypoleuca）未能针对繁殖区域内食源高峰的持续提前调整其繁殖物候，因此出现了局域种群数量下降的情况。本研究采用两套中性分子标记——线粒体控制区（mitochondrial control region）与微卫星（microsatellites），以及一套潜在受选择影响的非中性分子标记——鸟类Clock基因（Clock gene），旨在探究此次种群下降是否引发了遗传变异的丢失。研究采集了不同气候变化程度区域的样本，对超过一个世纪以来现存种群与生物馆藏样本的遗传多样性时序变化进行了分析。通过比对该时段内的遗传分化情况，研究发现仅经历了种群下降的近期荷兰种群，其遗传变异水平较历史荷兰种群略低。由于此次遗传变异的丢失程度较为温和，且并非在所有分子标记中均有体现，近几十年来西欧与中欧种群间的当前基因流，或已弥补了局域种群的变异丢失。通过对比中性位点与Clock基因位点的遗传分化情况，本研究为稳定选择提供了相关证据。此外，在所有遗传标记中，研究均发现空间尺度上的遗传分化程度高于时间尺度。该格局表明，相较于近期的全球气候变化，局域适应或历史演化过程对斑姬鹟的种群结构与遗传变异的影响更为显著。