Species Tree Inference by Minimizing Deep Coalescences
نویسندگان
چکیده
منابع مشابه
Species Tree Inference by Minimizing Deep Coalescences
In a 1997 seminal paper, W. Maddison proposed minimizing deep coalescences, or MDC, as an optimization criterion for inferring the species tree from a set of incongruent gene trees, assuming the incongruence is exclusively due to lineage sorting. In a subsequent paper, Maddison and Knowles provided and implemented a search heuristic for optimizing the MDC criterion, given a set of gene trees. H...
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Methods for inferring species trees from sets of gene trees need to account for the possibility of discordance among the gene trees. Assuming that discordance is caused by incomplete lineage sorting, species tree estimates can be obtained by finding those species trees that minimize the number of "deep" coalescence events required for a given collection of gene trees. Efficient algorithms now e...
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One approach for inferring a species tree from a given multi-locus data set entails computing a tree that optimizes a certain criterion. In 1997, W. Maddison proposed “minimizing deep coalescences”, or MDC, as one such criterion. This is a parsimonious criterion that, roughly speaking, seeks the tree that minimizes a quantity called extra lineages when all gene trees are reconciled within its b...
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When gene copies are sampled from various species, the resulting gene tree might disagree with the containing species tree. The primary causes of gene tree and species tree discord include lineage sorting, horizontal gene transfer, and gene duplication and loss. Each of these events yields a different parsimony criterion for inferring the (containing) species tree from gene trees. With lineage ...
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The multispecies coalescent model describes the generation of gene trees from a rooted metric species tree and thus provides a framework for the inference of species trees from sampled gene trees. We prove that the STAR method of Liu et al. (2009) and generalizations of it, are statistically consistent methods of topological species tree inference under this model. We discuss the impact of gene...
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ژورنال
عنوان ژورنال: PLoS Computational Biology
سال: 2009
ISSN: 1553-7358
DOI: 10.1371/journal.pcbi.1000501