2007
DOI: 10.1073/pnas.0607004104
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High-resolution species trees without concatenation

Abstract: The vast majority of phylogenetic models focus on resolution of gene trees, despite the fact that phylogenies of species in which gene trees are embedded are of primary interest. We analyze a Bayesian model for estimating species trees that accounts for the stochastic variation expected for gene trees from multiple unlinked loci sampled from a single species history after a coalescent process. Application of the model to a 106-gene data set from yeast shows that the set of gene trees recovered by statistically… Show more

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Cited by 553 publications
(447 citation statements)
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References 46 publications
(38 reference statements)
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“…deep coalescence). In such instances, concatenation of data from several genes has been shown to be a poor method for estimating the species tree (Edwards et al 2007;Kubatko & Degnan 2007). Unlike in the case of Degelia plumbea, pointing out a single culprit offending congruence is not possible.…”
Section: Gene Tree Conflictsmentioning
confidence: 99%
“…deep coalescence). In such instances, concatenation of data from several genes has been shown to be a poor method for estimating the species tree (Edwards et al 2007;Kubatko & Degnan 2007). Unlike in the case of Degelia plumbea, pointing out a single culprit offending congruence is not possible.…”
Section: Gene Tree Conflictsmentioning
confidence: 99%
“…4). Testing this ''deep coalescence'' hypothesis for the mtDNA genealogy requires the collection of additional multilocus nuclear data that are variable at this temporal level in conjunction with species tree inference methods that account for the process of lineage sorting (35,36).…”
Section: Figmentioning
confidence: 99%
“…These properties, exhibited and highlighted by cladists decades ago are valid, whether or not lineage sorting was incomplete in some recently diverged groups of species. Recent approaches explicitly modelling the process of gene coalescence have been developed to reconstruct a species tree based on multiple, incongruent gene phylogenies (Edwards et al 2007;.…”
Section: Should We Try To Recover the Species Tree?mentioning
confidence: 99%