School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, United States of America.
PLoS One. 2013;8(2):e55161. doi: 10.1371/journal.pone.0055161. Epub 2013 Feb 15.
Estimates of speciation times are subject to a number of potential errors. One source of bias is that effective population size (Ne) has been shown to influence substitution rates. This issue is of particular interest for phylogeographic studies because population sizes can vary dramatically among genetically structured populations across species' ranges. In this study, we used multilocus data to examine temporal phylogeographic patterns in a widespread North American songbird, the Northern Cardinal (Cardinalis cardinalis). Species tree estimation indicated that the phylogeographic structure of C. cardinalis was comprised of four well-supported mainland lineages with large population sizes (large Ne) and two island lineages comprised of much smaller populations (small Ne). We inferred speciation times from mtDNA and multilocus data and found there was discordance between events that represented island-mainland divergences, whereas both estimates were similar for divergences among mainland lineages. We performed coalescent simulations and found that the difference in speciation times could be attributed to stochasticity for a recently diverged island lineage. However, the magnitude of the change between speciation times estimated from mtDNA and multilocus data of an older island lineage was substantially greater than predicted by coalescent simulations. For this divergence, we found the discordance in time estimates was due to a substantial increase in the mtDNA substitution rate in the small island population. These findings indicate that in phylogeographic studies the relative tempo of evolution between mtDNA and nuclear DNA can become highly discordant in small populations.
物种形成时间的估计受到许多潜在误差的影响。一个有偏差的来源是，有效种群大小（Ne）已被证明会影响替代率。这个问题对于系统地理学研究特别感兴趣，因为种群大小在物种分布范围内的遗传结构种群中可能会有很大的差异。在这项研究中，我们使用多基因数据来研究广泛分布的北美鸣禽——红雀（Cardinalis cardinalis）的时间系统地理学格局。物种树估计表明，C. cardinalis 的系统地理学结构由四个具有较大种群大小（大 Ne）的大陆支系和两个由较小种群组成的岛屿支系组成（小 Ne）。我们从 mtDNA 和多基因数据推断了物种形成时间，发现代表岛屿-大陆分化的事件之间存在不一致，而在大陆支系之间的分化中，这两个估计值是相似的。我们进行了合并模拟，发现新分化的岛屿支系的随机性可以解释物种形成时间的差异。然而，从 mtDNA 和多基因数据估计的物种形成时间之间的变化幅度远大于合并模拟预测的幅度。对于这个分歧，我们发现时间估计的不一致是由于小岛种群中 mtDNA 替代率的大幅增加所致。这些发现表明，在系统地理学研究中，mtDNA 和核 DNA 之间的相对进化速度在小种群中可能会高度不一致。
