Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods

Systematic Biology
Huw A OgilvieAlexei J Drummond

Abstract

Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common genealogical history, thereby equating gene coalescence with species divergence. The multispecies coalescent is supported by previous studies which found that its predicted distributions fit empirical data, and that concatenation is not a consistent estimator of the species tree. *BEAST, a fully Bayesian implementation of the multispecies coalescent, is popular but computationally intensive, so the increasing size of phylogenetic data sets is both a computational challenge and an opportunity for better systematics. Using simulation studies, we characterize the scaling behavior of *BEAST, and enable quantitative prediction of the impact increasing the number of loci has on both computational performance and statistical accuracy. Follow-up simulations over a wide range of parameters show that the statistical performance of *BEAST relative to concatenation improves both as branch length is reduced and as the number of loci is increased. Finally, using simulations based on estimated parameters fro...Continue Reading

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Citations

May 1, 2016·Systematic Biology·David Posada
Nov 20, 2016·Molecular Ecology Resources·Jason G BraggCraig Moritz
Apr 22, 2017·Molecular Biology and Evolution·Huw A OgilvieAlexei J Drummond
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Apr 9, 2019·PLoS Computational Biology·Remco BouckaertAlexei J Drummond
Jun 5, 2019·Proceedings. Biological Sciences·Mozes P K BlomCraig Moritz
Feb 23, 2020·Molecular Biology and Evolution·Yaxuan WangLuay Nakhleh
Feb 9, 2017·BMC Evolutionary Biology·Remco R Bouckaert, Alexei J Drummond
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May 5, 2017·Systematic Biology·Étienne Léveillé-BourretAlan R Lemmon
Oct 27, 2017·Evolution; International Journal of Organic Evolution·Craig C MoritzPaul M Oliver
Sep 12, 2020·Systematic Biology·Chris Simon
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Jul 7, 2021·Systematic Biology·Huw A OgilvieAlexei J Drummond
Jul 30, 2021·Systematic Biology·Anton SuvorovSeth M Bybee

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