Accounting for coalescent stochasticity in testing phylogeographical hypotheses:: modelling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus
Accounting for coalescent stochasticity in testing phylogeographical hypotheses:: modelling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus
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DOI：
10.1111/j.1365-294x.2004.02404.x
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发表时间：
2005-01-01
影响因子：
4.9
通讯作者：
Sullivan, J
中科院分区：
文献类型：
--
作者：
Carstens, BC;Degenhardt, JD;Sullivan, J
一些理论研究已经证明了在地理学研究中考虑合并随机性的重要性，然而，在明确的假设检验的背景下这样做的实证例子很少。在这里，我们提供了一个例子，从爱达荷州大鲵（Dicamptodon atriermus）使用118 mtDNA序列，近2 kb的长度。本种为北方和爱达荷州中部的中温带森林特有种，根据古气候和共同分布的两栖动物的地理学研究，已经建立了几个先验假设。系统发育分析表明，D. aterrimus的数据表明，从一个单一的避难所鲑鱼河以南的扩张，而从嵌套的分支分析的推论是从一个单一的避难所在清水流域扩张之一。这些假设的明确测试，使用地理结构的聚结模拟竖立零分布，表明我们可以拒绝从清水排水（p（CLW）= 0.089）的扩张，但不能从鲑鱼排水（p（SAL）= 0.329）的南叉扩张。此外，从共同分布的两栖动物的数据表明，可能有两个避难所，和AMOVA显示，大部分的分子变异分配之间的清水和鲑鱼排水（54.40%; P < 0.001）和排水（43.61%; P < 0.001）。因此，我们还测试了三个先验假设，这些假设预测清水河和鲑鱼河流域在晚更新世都起到了避难所的作用;我们可以拒绝（P-CORD = 0.019）科迪勒拉冰川最大期的分歧日期[c. 20000年前（ybp）]，在Sangamon间冰期（c。35 000 ybp; p（SANG）= 0.032），以及前更新世分歧（c. 1.7 Ma; p（pP）< 0.001）。不匹配的分布和田岛的D内的个人排水提供了进一步的支持，最近的人口扩张。这项工作表明，合并的随机性是一个重要的现象，考虑在测试的地理假设，并建议，分析方法，未能充分量化这种不确定性可能会导致错误的信心，从这些方法得出的结论。
Several theoretical studies have demonstrated the importance of accounting for coalescent stochasticity in phylogeographical studies, however, there are few empirical examples that do so in the context of explicit hypothesis testing. Here, we provide an example from the Idaho giant salamander (Dicamptodon aterrimus) using 118 mtDNA sequences, nearly 2 kb in length. This species is endemic to mesic forests in northern and central Idaho, and several a priori hypotheses have been erected based both on palaeoclimatic grounds and from phylogeographical studies of codistributed amphibians. Phylogenetic analysis of the D. aterrimus data suggests an expansion from a single refugium south of the Salmon River, whereas the inference from nested clade analysis is one of expansion from a single refugium in the Clearwater drainage. Explicit testing of these hypotheses, using geographically structured coalescent simulations to erect null distributions, indicates we can reject expansion from the Clearwater drainage (p(CLW) = 0.089), but not expansion from the South Fork of the Salmon drainage (p(SAL) = 0.329). Furthermore, data from codistributed amphibians suggest that there may have been two refugia, and an AMOVA shows that most of the molecular variance partitioned between the Clearwater and the Salmon drainages (54.40%; P < 0.001) and within drainages (43.61%; P < 0.001). As a result, we also tested three a priori hypotheses which predicted that both the Clearwater and Salmon drainages functioned as refugia during the late Pleistocene; we could reject (P-CORD = 0.019) divergence dates during the Cordilleran glacial maxima [c. 20 000 years before present (ybp)], during the Sangamon interglacial (c. 35 000 ybp; p(SANG) = 0.032), as well as pre-Pleistocene divergence (c. 1.7 Ma; p(pP) < 0.001). Mismatch distributions and Tajima's D within the individual drainages provide further support to recent population expansion. This work demonstrates coalescent stochasticity is an important phenomenon to consider in testing phylogeographical hypotheses, and suggests that analytical methods which fail to sufficiently quantify this uncertainty can lead to false confidence in the conclusions drawn from these methods.