John D. Cooper Archaeological and Paleontological Center, Department of Geological Sciences, California State University, Fullerton, CA 92834, USA.
Mol Phylogenet Evol. 2013 Apr;67(1):176-87. doi: 10.1016/j.ympev.2013.01.004. Epub 2013 Jan 23.
Determining whether a conflict between gene trees and species trees represents incomplete lineage sorting (ILS) or hybridization involving native and/or invasive species has implications for reconstructing evolutionary relationships and guiding conservation decisions. Among vertebrates, turtles represent an exceptional case for exploring these issues because of the propensity for even distantly related lineages to hybridize. In this study we investigate a group of freshwater turtles (Trachemys) from a part of its range (the Greater Antilles) where it is purported to have undergone reticulation events from both natural and anthropogenic processes. We sequenced mtDNA for 83 samples, sequenced three nuDNA markers for 45 samples, and cloned 29 polymorphic sequences, to identify species boundaries, hybridization, and intergrade zones for Antillean Trachemys and nearby mainland populations. Initial coalescent analyses of phased nuclear alleles (using (*)BEAST) recovered a Bayesian species tree that strongly conflicted with the mtDNA phylogeny and traditional taxonomy, and appeared to be confounded by hybridization. Therefore, we undertook exploratory phylogenetic analyses of mismatched alleles from the "coestimated" gene trees (Heled and Drummond, 2010) in order to identify potential hybrid origins. The geography, morphology, and sampling context of most samples with potential introgressed alleles suggest hybridization over ILS. We identify contact zones between different species on Jamaica (T. decussata × T. terrapen), on Hispaniola (T. decorata × T. stejnegeri), and in Central America (T. emolli × T. venusta). We are unable to determine whether the distribution of T. decussata on Jamaica is natural or the result of prehistoric introduction by Native Americans. This uncertainty means that the conservation status of the Jamaican T. decussata populations and contact zone with T. terrapen are unresolved. Human-mediated dispersal events were more conclusively implicated for the prehistoric translocation of T. stejnegeri between Puerto Rico and Hispaniola, as well as the more recent genetic pollution of native species by an invasive pet turtle native to the USA (T. scripta elegans). Finally, we test the impact of introgressed alleles using the multispecies coalescent in a Bayesian framework and show that studies that do not phase heterozygote sequences of hybrid individuals may recover the correct species tree, but overall support for clades that include hybrid individuals may be reduced.
确定基因树与物种树之间的冲突是代表不完全谱系分选（ILS）还是涉及本地和/或入侵物种的杂交，这对重建进化关系和指导保护决策具有重要意义。在脊椎动物中，海龟是探索这些问题的一个特殊案例，因为即使是亲缘关系较远的谱系也有杂交的倾向。在这项研究中，我们调查了大安的列斯群岛（Greater Antilles）部分地区的一组淡水龟（Trachemys），据推测，这些地区发生了自然和人为过程引起的网状事件。我们对 83 个样本进行了 mtDNA 测序，对 45 个样本进行了 3 个核 DNA 标记测序，并克隆了 29 个多态性序列，以确定安的列斯群岛 Trachemys 及其附近大陆种群的物种边界、杂交和杂交带。利用（*）BEAST 对相分离核等位基因进行的初始合并分析，恢复了一个强烈与 mtDNA 系统发育和传统分类学相冲突的贝叶斯物种树，并且似乎受到了杂交的混淆。因此，我们对“共同估计”基因树中的不匹配等位基因进行了探索性的系统发育分析（Heled 和 Drummond，2010），以确定潜在的杂种起源。具有潜在渗入等位基因的大多数样本的地理位置、形态和采样背景表明杂交多于不完全谱系分选。我们在牙买加（T. decussata×T. terrapen）、伊斯帕尼奥拉岛（T. decorata×T. stejnegeri）和中美洲（T. emolli×T. venusta）之间的不同物种之间发现了接触区。我们无法确定牙买加 T. decussata 的分布是自然的还是美洲原住民史前引入的结果。这种不确定性意味着牙买加 T. decussata 种群的保护状况及其与 T. terrapen 的接触区仍未得到解决。人类介导的扩散事件更明确地暗示了史前时期波多黎各和伊斯帕尼奥拉岛之间的 T. stejnegeri 转移，以及最近美国原产的入侵宠物龟（T. scripta elegans）对本地物种的遗传污染。最后，我们在贝叶斯框架中使用多物种合并来测试渗入等位基因的影响，并表明未对杂交个体的异质序列进行相位处理的研究可能会恢复正确的物种树，但包括杂交个体的分支的总体支持可能会降低。
