# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz These observations would suggest the possibility of using analyses of branch lengths on a DNA tree for explicit tests of species boundaries, based on the difference in branching rates at the level of species and populations. Branch lengths between species are determined by speciation and extinction rates (macroevolution) (Nee et al., 1994), whereas branch lengths within a species reflect coalescence processes at the level of populations (microevolution) (Hudson, 1991; Rosenberg and Nordborg, 2002; Wakeley, 2006). Well-developed approaches exist for analyzing branching rates in either framework. Combining equations that describe processes of lineage birth at the species level with coalescence models within species, it is possible to develop a statistical framework for estimating the predicted shift in dynamics of branching associated with the species boundary. Here we develop a method that determines the locations of ancestral nodes that define putative species and applies a likelihood ratio test to assess the fit of the branch lengths to a mixed lineage birth-population coalescence model. 这些观察结果表明，根据物种和种群水平上的分支速率差异，可以利用 DNA 树上的分支长度分析来明确探测物种边界。物种间的分支长度由物种形成和灭绝率（宏观进化）决定（ Nee et al., 1994 ），而物种内的分支长度反映了种群水平上的溯祖过程（微观进化）（ Hudson, 1991; Rosenberg and Nordborg, 2002; Wakeley, 2006 ）。在这两个框架中，都存在分析分支率的成熟方法。将描述物种层次上谱系产生过程的方程与物种内部的溯祖模型相结合，可以建立一个统计框架来估计与物种边界相关的分支动态变化。在这里，我们开发了一种方法，确定祖先节点的位置以定义推定物种，并应用似然率测试来评估分支长度匹配混合的谱系发生 - 种群溯祖模型的程度。 Pons J, Barraclough T G, Gomez-Zurita J, et al. Sequence-based species delimitation for the DNA taxonomy of undescribed insects . Systematic biology, 2006, 55(4): 595-609.
# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz Current procedures for delimiting species from sequence data aggregate populations lacking discrete differences into a single species (Cracraft, 1983; Davis and Nixon, 1992; Sites and Marshall, 2003; Wiens and Penkrot, 2002). These “smallest detected sample of self-perpetuating organisms that have unique sets of characters” ( Nelson and Platnick, 1981 ) can be recognized based on fixed nucleotide differences unique to such (sets of) populations (the criterion of “diagnosability”; Cracraft, 1983 ), implemented in population aggregation analysis ( PAA; Davis and Nixon, 1992 ). A tree-based variant of this procedure ( cladistic haplotype analysis; CHA ) also considers homoplastic character states as diagnostic if they are shown to be uniquely derived for a particular group (Brower, 1999). The Wiens-Penkrot (WP) method (Sites and Marshall, 2003; Wiens and Penkrot, 2002) is also a tree-based method for delimiting phylogenetic species but uses the topology (rather than character polarity, as in CHA) to assess whether or not clades are restricted to a (set of) populations to the exclusion of clades elsewhere (criterion of “exclusivity”). 当前从序列数据界定物种的程序将缺乏离散差异的种群聚合为单个物种（ Cracraft, 1983; Davis and Nixon, 1992; Sites and Marshall, 2003; Wiens and Penkrot, 2002 ）。这些具有独特特征集的自我延续生物体的“最小检测样本”（ Nelson and Platnick, 1981 ）可根据这些（组）种群特有的固定核苷酸差异（鉴别性标准； Nelson and Platnick, 1981 ）加以识别，该标准包含在种群聚集分析中（ Paa ； Davis 和 Nixon ， 1992 ）。该程序中一个基于树的变异（支序单倍型分析； CHA ）也将同形性特征状态视为鉴别特征，如果它们被证明是在特定类群唯一衍生出来的（ Brower, 1999 ）。 Wiens-Penkrot (WP) 方法（ Sites and Marshall, 2003; Wiens and Penkrot, 2002 ）也是一种基于树的方法，用于划分系统发生物种，但使用拓扑结构（而不是特征极性，如 CHA ）来评估支系是否限制在具有排他性的种群水平。 Pons J, Barraclough T G, Gomez-Zurita J, et al. Sequence-based species delimitation for the DNA taxonomy of undescribed insects . Systematic biology, 2006, 55(4): 595-609.
标签: 系统发生种
