The BPP program for species tree estimation and species delimitation
This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five nuclear loci from the East Asian brown frogs is used to illustrate four different an...
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Published in | Current zoology Vol. 61; no. 5; pp. 854 - 865 |
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Main Author | |
Format | Journal Article |
Language | English |
Published |
01.10.2015
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Subjects | |
Online Access | Get full text |
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Summary: | This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five nuclear loci from the East Asian brown frogs is used to illustrate four different analyses, including estimation of species divergence times and population size parameters under the multispecies coalescent model on a fixed species phylogeny (A00), species tree estimation when the assignment and species delimitation are fixed (A01), species delimitation using a fixed guide tree (A10), and joint species delimitation and species-tree estimation or unguided species delimitation (A11). For the joint analysis (A11), two new priors are introduced, which assign uniform probabilities for the different numbers of delimited species, which may be useful when assignment, species delimitation, and species phylogeny are all inferred in one joint analysis. The paper ends with a discussion of the assumptions, the strengths and weaknesses of the BPP analysis [Current Zoology 61 (5): 854-865, 2015]. |
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Bibliography: | This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five nuclear loci from the East Asian brown frogs is used to illustrate four different analyses, including estimation of species divergence times and population size parameters under the multispecies coalescent model on a fixed species phylogeny (A00), species tree estimation when the assignment and species delimitation are fixed (A01), species delimitation using a fixed guide tree (A10), and joint species delimitation and species-tree estimation or unguided species delimitation (A11). For the joint analysis (A11), two new priors are introduced, which assign uniform probabilities for the different numbers of delimited species, which may be useful when assignment, species delimitation, and species phylogeny are all inferred in one joint analysis. The paper ends with a discussion of the assumptions, the strengths and weaknesses of the BPP analysis [Current Zoology 61 (5): 854-865, 2015]. 11-5794/Q BPP, MCMC, Multispecies coalescent, Species delimitation, Species tree |
ISSN: | 1674-5507 2396-9814 |
DOI: | 10.1093/czoolo/61.5.854 |