The BPP program for species tree estimation and species delimitation

By Ziheng Yang. 2015

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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 time 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) : – , 2015 ].

Subfields: Ecological Modeling, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9daf9d57185eb8c2c789067fadd98d77b7f630ba

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Citations in the corpus

Integrative approaches for species delimitation in Ascomycota (2021, background): “As predicted, ABGD, TCS, BPP, PTP, GMYC, and STACEY resulted in different numbers of putative species (Figs.”
Species Delimitation in Herpetology (2019, background): “Hence, multispecies coalescent theory (MSC) often is applied to the species delimitation problem (Leaché and Fujita, 2010; Yang and Rannala, 2010; Zhang et al., 2011; Leaché et al., 2014; Yang, 2015).”
Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics (2021, methodology): “2013), and/or assess coalescence between markers, such as Bayesian species delimitation, the Bayesian Phylogenetics and Phylogeography (BPP) approach and the Accurate Species TRee ALgorithm or ASTRAL (Yang and Rannala 2010; Fujita et al. 2012; Mirarab et al. 2014; Yang 2015).”
Multispecies coalescent delimits structure, not species (2017, methodology): “Specifically, we simulate genetic data under a protracted speciation model (21), such that the degree of genetic structure accumulating among lineages differs (7), depending on the duration of speciation (21), and investigate the accuracy of inferences from the popular model-based species delimitati”
StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates (2016, methodology): “Given the current challenges of using large phylogenomic data sets with *BEAST there have been three broad alternatives available to researchers; concatenate sequences from multiple loci, use heuristic methods statistically consistent with the MSC, or choose a tractable subset of loci to use with a ”
More grist for the mill? Species delimitation in the genomic era and its implications for conservation (2019, background): “Developments in coalescent theory has allowed for the investigation of lineage diversification (Yang 2015).”