Burbrink Frank T
Department of Biological Sciences, 206 Life Science Building, Louisiana State University, Baton Rouge 70803, USA.
Mol Phylogenet Evol. 2002 Dec;25(3):465-76. doi: 10.1016/s1055-7903(02)00306-8.
Most phylogeographic studies have used maximum likelihood or maximum parsimony to infer phylogeny and bootstrap analysis to evaluate support for trees. Recently, Bayesian methods using Marlov chain Monte Carlo to search tree space and simultaneously estimate tree support have become popular due to its fast search speed and ability to create a posterior distribution of parameters of interest. Here, I present a study that utilizes Bayesian methods to infer phylogenetic relationships of the cornsnake (Elaphe guttata) complex using cytochrome b sequences. Examination of the posterior probability distributions confirms the existence of three geographic lineages. Additionally, there is no support for the monophyly of the subspecies of E. guttata. Results suggest the three geographic lineages partially conform to the ranges of previously defined subspecies, although Shimodaira-Hasegawa tests suggest that subspecies-constrained trees produce significantly poorer likelihood estimates than the most likely trees reflecting the evolution of three geographic assemblages. Based on molecular support, these three geographic assemblages are recognized as species using evolutionary species criteria: E. guttata, Elaphe slowinskii, and Elaphe emoryi [phylogeographic, maximum likelihood, maximum parsimony, bootstrap, Bayesian, Markov chain Monte Carlo, cornsnake, Cytochrome b, geographic lineages, E. guttta, E. slowinskii, and E. emoryi].
大多数系统地理学研究都使用最大似然法或最大简约法来推断系统发育，并通过自展分析来评估对树状图的支持度。最近，利用马尔可夫链蒙特卡罗方法搜索树空间并同时估计树支持度的贝叶斯方法因其搜索速度快以及能够创建感兴趣参数的后验分布而变得流行起来。在此，我展示了一项利用贝叶斯方法，基于细胞色素b序列推断玉米锦蛇（Elaphe guttata）复合体系统发育关系的研究。对后验概率分布的检验证实了三个地理谱系的存在。此外，没有证据支持E. guttata亚种的单系性。结果表明，这三个地理谱系部分符合先前定义的亚种范围，尽管Shimodaira-Hasegawa检验表明，受亚种限制的树状图产生的似然估计值明显比反映三个地理组合进化的最可能树状图差。基于分子证据，根据进化物种标准，这三个地理组合被认定为物种：E. guttata、Elaphe slowinskii和Elaphe emoryi [系统地理学、最大似然法、最大简约法、自展法、贝叶斯方法、马尔可夫链蒙特卡罗方法、玉米锦蛇、细胞色素b、地理谱系、E. guttta、E. slowinskii和E. emoryi]
