Flouris, T;
Jiao, X;
Rannala, B;
Yang, Z;
(2018)
Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent.
Molecular Biology and Evolution
, 35
(10)
pp. 2585-2593.
10.1093/molbev/msy147.
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Abstract
The multispecies coalescent provides a natural framework for accommodating ancestral genetic polymorphism and coalescent processes that can cause different genomic regions to have different genealogical histories. The Bayesian program BPP includes a full-likelihood implementation of the multispecies coalescent, using transmodel Markov chain Monte Carlo to calculate the posterior probabilities of different species trees. BPP is suitable for analyzing multilocus sequence data sets and it accommodates the heterogeneity of gene trees (both the topology and branch lengths) among loci and gene tree uncertainties due to limited phylogenetic information at each locus. Here, we provide a practical guide to the use of BPP in species tree estimation. BPP is a command-line program that runs on LINUX, MACOSX, and WINDOWS. This protocol shows how to use both BPP 3.4 (http://abacus.gene.ucl.ac.uk/software/) and BPP 4.0 (https://github.com/bpp/).
| Type: | Article |
|---|---|
| Title: | Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1093/molbev/msy147 |
| Publisher version: | https://doi.org/10.1093/molbev/msy147 |
| Language: | English |
| Additional information: | © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). |
| Keywords: | BPP, MCMC, multispecies coalescent, species tree inference |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/10052941 |
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