Martínez-Solano Iñigo, Jockusch Elizabeth L, Wake David B
Museum of Vertebrate Zoology, University of California, Berkeley, 3101 VLSB, Berkeley, California 94720, USA.
Mol Ecol. 2007 Oct;16(20):4335-55. doi: 10.1111/j.1365-294X.2007.03527.x. Epub 2007 Sep 14.
Low-vagility species with deep evolutionary histories are key to our understanding of the biogeographical history of geologically complex areas, such as the west coast of North America. We present a detailed study of the phylogeography of the salamander Batrachoseps attenuatus (Caudata: Plethodontidae) using sequences of the mitochondrial gene cob from 178 individuals sampled from throughout the species' range. Sequences of three other mitochondrial genes (16S, cox1, nad4) and a nuclear gene (RAG-1) were used to investigate the deeper evolutionary history of the species. We found high levels of genetic diversity and deep divergences within a mostly continuous distribution, with five genetically well-differentiated and geographically structured mitochondrial DNA clades. Significant association between geographical and genetic distances within these clades suggests demographic stability, whereas Fu's FS tests suggest demographic expansions in three of them. Mantel tests identify two biogeographical barriers, the San Andreas Fault and the Sacramento-San Joaquin Delta, as important in the diversification of lineages. The timing of the main splitting events between intraspecific lineages was estimated by applying relaxed molecular clock methods combining several mutation rates and a fossil calibration. The earliest splitting events are old (Pliocene/Miocene), with more recent (Pleistocene) subdivisions in some clades. Disjunct populations distributed along the western foothills of the Sierra Nevada colonized this area relatively recently from a single refugium east of San Francisco Bay. The combination of fine-scale, comprehensive sampling with phylogenetic, historical demographic and hypothesis-based tests allowed delineation of a complex biogeographical scenario with general implications for the study of codistributed taxa.
具有深厚进化历史的低扩散性物种对于我们理解地质复杂地区（如北美西海岸）的生物地理历史至关重要。我们利用从整个物种分布范围内采集的178个个体的线粒体基因cob序列，对蝾螈Batrachoseps attenuatus（有尾目：无肺螈科）的系统地理学进行了详细研究。另外三个线粒体基因（16S、cox1、nad4）和一个核基因（RAG - 1）的序列被用于研究该物种更深层次的进化历史。我们发现，在一个基本连续的分布范围内存在高水平的遗传多样性和深度分化，有五个遗传上高度分化且地理结构分明的线粒体DNA分支。这些分支内地理距离与遗传距离之间的显著关联表明种群数量稳定，而Fu氏F S检验表明其中三个分支存在种群扩张。Mantel检验确定了两个生物地理屏障，即圣安德烈亚斯断层和萨克拉门托 - 圣华金河三角洲，它们在谱系多样化中起着重要作用。通过应用结合多种突变率和化石校准的宽松分子钟方法，估计了种内谱系之间主要分裂事件的时间。最早的分裂事件发生在很久以前（上新世/中新世），一些分支在较近时期（更新世）出现了细分。沿内华达山西麓分布的间断种群是相对较近时期从旧金山湾以东的一个避难所殖民到该地区的。精细尺度的全面采样与系统发育、历史种群统计学和基于假设的检验相结合，描绘出了一个复杂的生物地理场景，对共分布类群的研究具有普遍意义。
