Data from: Geography and past climate changes have shaped the evolution of a widespread lizard from the Chilean hotspot

The complex orogenic history and structure of Southern South America, coupled with Pleistocene glacial cycles, have generated paleoclimatic and environmental changes that influenced the spatial distribution and genetic composition of natural populations. Despite the increased number of phylogeographic studies in this region and given the frequent idiosyncratic phylogeographic patterns, there is still the need to focus research especially on species that are currently distributed within a wide range of bioclimatic regimes, and that historically have been subject to contrasting scenarios. Liolaemus tenuis is a widely distributed lizard species inhabiting latitudinally in almost 1,000 km through central and southern Chile. Here we describe the geographical patterns of genetic variation and lineage diversification within L. tenuis, and their association with geography and Pleistocene glaciations, using sequences from one mitochondrial and two nuclear genes, and five microsatellite loci, and covering most of the species distributional range. Our results revealed a high diversity both within and among populations, as well as two phylogeographic breaks, which are consistent with two of the larger rivers of central Chile, the Maipo and Biobío Rivers. Liolaemus tenuis is characterized by several allopatric lineages, especially in its north and central range, which suggest a history of multiple vicariance processes. Conversely, populations found in the southern range, south of the Biobío River, show signatures of recent decreases in effective population sizes, coupled with recent range expansions and secondary contact. Niche “envelope” data are consistent with patterns of genetic variation; both suggest a history of discontinuous areas of relatively stable populations throughout all of the distribution of L. tenuis. These data are also consistent with higher probabilities of habitat suitability north of the Maipo River (ca. 33°S), in both coastal areas and the “Intermediate Depression” between 34° - 37°S, as well as in the southern Coastal Cordillera between the Biobío and Araucanía regions. Interestingly, both molecular and niche envelope modelling data suggest that some populations may have persisted in fragmented refugia in Andean valleys, within the limits of the ice sheet. Finally, our results suggest that several populations of L. tenuis colonized glaciated regions from refugial areas in lowlands and coastal regions, and in the southern distribution, historic migration events would have occurred from refugial areas within the limits of the ice sheet.

南美南部复杂的造山历史与构造格局，加之更新世冰期旋回，引发了古气候与环境变化，进而影响了自然种群的空间分布与遗传组成。尽管该区域的系统地理学（phylogeographic）研究数量有所增加，且频繁出现独特的系统地理格局，但目前仍有必要聚焦研究那些当前分布于多样生物气候区、历史上经历过迥异环境场景的物种。细身龙蜥（Liolaemus tenuis）是一种分布广泛的蜥蜴物种，其纬度分布跨度近1000公里，涵盖智利中部与南部区域。本研究依托覆盖该物种大部分分布范围的样本，利用1个线粒体基因、2个核基因序列以及5个微卫星位点（microsatellite loci），解析了细身龙蜥的遗传变异地理格局与谱系分化模式，并探讨其与地理因素及更新世冰期的关联。研究结果显示，种群内部及种群间均存在较高的遗传多样性，同时存在两处系统地理断裂带，与智利中部两条大型河流——迈波河（Maipo）与比奥比奥河（Biobío）——的分布相吻合。细身龙蜥存在多个异域分布谱系，尤其在其北部与中部分布区，这暗示其经历过多次隔离分化过程。相反，分布于比奥比奥河以南的南部种群则表现出有效种群大小近期缩减、种群范围近期扩张以及次生接触的遗传信号。生态位包络（niche envelope）数据与遗传变异格局相符：两者均表明，细身龙蜥的整个分布范围内曾存在多个相对稳定的间断种群区域。这些数据还支持迈波河以北（约南纬33°）、沿海区域以及南纬34°-37°之间的“中间洼地”，以及比奥比奥与阿劳卡尼亚地区之间的南部海岸山脉的生境适宜性概率更高。有趣的是，分子数据与生态位包络模型结果均表明，部分种群可能在冰盖范围内的安第斯山谷碎片化避难所中存续。最后，本研究结果显示，细身龙蜥的多个种群从低地与沿海的避难所扩散至曾被冰川覆盖的区域；而在其南部分布区，历史迁移事件则可能源自冰盖范围内的避难所。