Assigning sequences to species in the absence of large interspecific differences
Assigning sequences to species in the absence of large interspecific differences
复制标题
DOI：
10.1016/j.ympev.2010.01.002
复制
发表时间：
2010-07-01
影响因子：
4.1
通讯作者：
Golding, G. Brian
中科院分区：
文献类型：
--
作者：
Lou, Melanie;Golding, G. Brian
条形码是一项定义标准 DNA 片段的举措，用于将未知序列分配给外部（由分类学家）预先识别的现有已知物种组。已经描述了几种尝试将此分配放入贝叶斯统计框架的方法。在这里，我们描述了一种利用分离位点的算法，并检查了这些方法在不存在种间“条形码间隙”的情况下的表现如何。当存在条形码间隙时，即当数据被明确界定时，大多数方法都表现良好。在这里，我们使用了来自果蝇属的数据，因为该属包括兄弟物种，并且该物种内的物种关系虽然复杂，但可以说比任何其他群体更好地理解。结果表明，即使没有条形码间隙，贝叶斯方法也能表现良好。来自果蝇的序列被正确识别，并且只有当模拟中或果蝇物种内部的不完整谱系排序程度极端时，它们才会失败，即使这样，“正确”物种也具有很高的后验概率。 (C) 2010 Elsevier Inc. 保留所有权利。
Barcoding is an initiative to define a standard fragment of DNA to be used to assign unknown sequences to existing known species groups that have been pre-identified externally (by a taxonomist). Several methods have been described that attempt to place this assignment into a Bayesian statistical framework. Here we describe an algorithm that makes use of segregating sites and we examine how well these methods perform in the absence of an interspecific 'barcoding gap'. When a barcoding gap exists, that is when the data are clearly delimited, most methods perform well. Here we have used data from the Drosophila genus because this genus includes sibling species and the species relationships within this species while complex are, arguably, better understood than in any other group. The results show that the Bayesian methods perform well even in the absence of a barcoding gap. The sequences from Drosophila are correctly identified and only when the degree of incomplete lineage sorting is extreme in simulations or within the Drosophila species, do they fail in their identifications and even then, the "correct" species has a high posterior probability. (C) 2010 Elsevier Inc. All rights reserved.