The role of subjectivity in reconstructing ancestral character states: A Bayesian approach to unknown rates, states, and transformation asymmetries
The role of subjectivity in reconstructing ancestral character states: A Bayesian approach to unknown rates, states, and transformation asymmetries
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DOI：
10.1080/106351599260229
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发表时间：
1999-09-01
影响因子：
6.5
通讯作者：
Churchill, GA
中科院分区：
文献类型：
--
作者：
Schultz, TR;Churchill, GA
来自生态学和分类学的数据的综合使之成为可能，至少是印刷出来的？Cple，重建已灭绝祖先的特征。然而，这种重建的可靠性是一个相当令人担忧的问题。例如，常用的简约特征状态优化方法(Farris，1970；Hartigan，1973；Swofford and Maddison，1987)经常(但不总是)赋值Un？完全解析树的内部(祖先)节点的模棱两可的字符状态，但很明显，一些这样的赋值比其他更可靠？ERS(图1)。各种可能的冰毒？ODS(包括最大似然AP？用于确定相对Re？祖先国家转让的责任已经被提出，这一切都取决于关于角色Evo的各种模型假设？(例如，Frumhoff和Reve，1994；Maddison，1995；Schluter，1995；Schultz等人，1996；Schluter等人，1997；Cunningham等人，1998)。这些通用模型需要描述角色状态之间变化概率的参数的似是而非的值，这些值可以从数据估计，也可以从独立的来源得出。例如，最大似然重构？核苷酸进化的结果(它们不一定明确地与差异有关？三种状态)通常从考虑的所有序列的相对基频得出四个核苷酸之间的变化概率(Felsen？Stein，1981；在Swofford等人的评论中，
The synthesis of data from ecology and systematics makes possible, at least in prin? ciple, the reconstruction of features of extinct ancestors. The reliability of such reconstructions, however, is a matter of considerable concern. For example, the commonly used method of parsimony character-state optimization (Farris, 1970; Hartigan, 1973; Swofford and Maddison, 1987) often (but not always) assigns un? ambiguous character states to internal (ancestral) nodes of fully resolved trees, but it is intuitively clear that some such assignments are more reliable than oth? ers (Fig. 1). Various probabilistic meth? ods (including maximum-likelihood ap? proaches) for determining the relative re? liability of ancestral state assignments have been proposed, all depending on various model assumptions about character evo? lution (eg, Frumhoff and Reeve, 1994; Maddison, 1995; Schluter, 1995; Schultz et al, 1996; Schluter et al, 1997; reviewed in Cunningham et al, 1998). These general models require plausible values for the parameters describing the probability of change between character states, and these values can either be estimated from the data or derived from independent sources. For example, maximum-likelihood reconstruc? tions of nucleotide evolution (which are not necessarily explicitly concerned with ances? tral states) usually derive the probabilities of change between the four nucleotides from the relative base frequencies across all of thesequences under consideration (Felsen? stein, 1981; reviewed in Swofford et al.,