从基因树推断物种树的一致性方法的性质
Properties of Consensus Methods for Inferring Species Trees from Gene Trees
摘要：
共识方法提供了一个有用的策略，从基因树的集合的信息相结合。一致性方法的一个重要应用是结合基因树来估计物种树。为了研究根据基本进化模型从大量基因座进化中获得的共识树的理论性质，我们从独立基因树构建共识树，这些独立基因树与来自溯祖理论的基因树概率成比例。我们认为多数规则，根三元组（R*），和贪婪的共识树构建从已知的基因树，无论是在渐近的情况下，基因树的数量接近无穷大和有限数量的基因。我们的研究结果表明，对于某些组合的物种树分支长度，增加独立位点的数量可以使多数规则的共识树更有可能是至少部分未解决的和贪婪的共识树不太可能匹配的物种树。然而，当基因树的数量接近无穷大时，R* 共有树具有物种树拓扑的概率接近1。虽然当增加基因树的数量时，贪婪共识算法可以最快地收敛到正确的物种树上，但它也可能是积极的误导。多数规则一致树不是物种树拓扑的误导性估计，R* 一致树是物种树拓扑的统计一致估计。因此，我们的研究结果提出了一种使用多个位点来推断物种树拓扑结构的方法，即使它与最有可能的基因树不一致。
英文摘要：
Consensus methods provide a useful strategy for combining information from a collection of gene trees. An important application of consensus methods is to combine gene trees to estimate a species tree. To investigate the theoretical properties of consensus trees that would be obtained from large numbers of loci evolving according to a basic evolutionary model, we construct consensus trees from independent gene trees that occur in proportion to gene tree probabilities derived from coalescent theory. We consider majority-rule, rooted triple (R*), and greedy consensus trees constructed from known gene trees, both in the asymptotic case as numbers of gene trees approach infinity and for finite numbers of genes. Our results show that for some combinations of species tree branch lengths, increasing the number of independent loci can make the majority-rule consensus tree more likely to be at least partially unresolved and the greedy consensus tree less likely to match the species tree. However, the probability that the R* consensus tree has the species tree topology approaches 1 as the number of gene trees approaches infinity. Although the greedy consensus algorithm can be the quickest to converge on the correct species tree when increasing the number of gene trees, it can also be positively misleading. The majority-rule consensus tree is not a misleading estimator of the species tree topology, and the R* consensus tree is a statistically consistent estimator of the species tree topology. Our results therefore suggest a method for using multiple loci to infer the species tree topology, even when it is discordant with the most likely gene tree.
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