Data from: Disentangling the genetic effects of refugial isolation and range expansion in a trans-continentally distributed species

In wide-ranging taxa with historically dynamic ranges, past allopatric
isolation and range expansion can both influence the current structure of
genetic diversity. Considering alternate historical scenarios involving
expansion from either a single refugium or from multiple refugia can be
useful in differentiating the effects of isolation and expansion. Here, we
examined patterns of genetic variability in the trans-continentally
distributed painted turtle (Chrysemys picta). We utilized an existing
phylogeographic dataset for the mitochondrial control region and generated
additional data from nine populations for the mitochondrial control region
(n = 302) and for eleven nuclear microsatellite loci (n = 247). We created
a present-day ecological niche model (ENM) for C. picta and hindcast this
model to three reconstructions of historical climate to define three
potential scenarios with one, two, or three refugia. Finally, we employed
spatially-explicit coalescent simulations and an approximate Bayesian
computation (ABC) framework to test which scenario best fit the observed
genetic data. Simulations indicated that phylogeographic and multilocus
population-level sampling both could differentiate among refugial
scenarios, although inferences made using mitochondrial data were less
accurate when a longer coalescence time was assumed. Furthermore, all
empirical genetic datasets were most consistent with expansion from a
single refugium based on ABC. Our results indicate a stronger role for
post-glacial range expansion, rather than isolation in allopatric refugia
followed by range expansion, in structuring diversity in this species. To
distinguish among complex historical scenarios, we recommend explicitly
modeling the effects of range expansion and evaluating alternate refugial
scenarios for wide-ranging taxa.

对于历史分布范围动态变化的广布分类群而言，过往的异域隔离（allopatric isolation）事件与分布范围扩张过程，均可对当前遗传多样性的结构特征产生影响。通过构建单一冰期避难所（refugium）扩张或多冰期避难所扩张这两类替代性历史情景，有助于区分异域隔离与分布扩张各自带来的影响。本研究针对跨大陆分布的锦龟（*Chrysemys picta*），分析了其遗传变异模式。我们使用了一套已公开的线粒体控制区（mitochondrial control region）系统地理（phylogeographic）数据集，并新增了9个种群的相关数据：其中线粒体控制区样本量为302个（n = 302），核微卫星位点（nuclear microsatellite loci）共11个，有效样本量为247个（n = 247）。我们构建了锦龟当前的生态位模型（ecological niche model, ENM），并将该模型回溯预测至三类历史气候重建结果，以此界定出拥有1个、2个或3个冰期避难所的三类潜在历史情景。最后，我们采用空间显式溯祖模拟（spatially-explicit coalescent simulations）与近似贝叶斯计算（approximate Bayesian computation, ABC）框架，检验哪一类情景最契合观测得到的遗传数据。模拟结果显示，系统地理与多位点种群水平的采样均可区分不同避难所情景，但当假设溯合时间较长时，基于线粒体数据的推断准确性会有所下降。此外，基于ABC分析的结果显示，所有实测遗传数据集均与单一避难所扩张的情景最为吻合。本研究结果表明，在锦龟的多样性结构塑造过程中，冰期后分布范围扩张的作用要强于“异域避难所隔离后再扩张”这一过程。针对广布类群的复杂历史情景区分问题，我们建议通过显式建模分布范围扩张的影响，并评估替代性避难所情景来开展相关研究。