The BPP program for species tree estimation and species delimitation
The BPP program for species tree estimation and species delimitation
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DOI：
10.1093/czoolo/61.5.854
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发表时间：
2015-10-01
期刊：
影响因子：
2.2
通讯作者：
Yang, Ziheng
中科院分区：
文献类型：
--
作者：
Yang, Ziheng
BPP程序是一种贝叶斯MCMC程序，用于在多物种聚结模型下分析多位点基因组序列数据。本文以东亚褐蛙5个核基因座为例，分析了在固定物种系统发育条件下，多物种凝聚模型下物种分化时间和种群大小参数的估计（A00）、在固定分配和物种划分条件下的物种树估计（A01）、在固定引导树下的物种划分（A10）和在固定引导树下的物种划分（A10）。联合物种划分和种树估算或无指导物种划分（A11）。对于联合分析（A11），引入了两个新的先验，它们为不同数量的被划分物种分配了统一的概率，这对于在一次联合分析中推断分配、物种划分和物种系统发育都是有用的。本文最后讨论了BPP分析的假设、优势和劣势[Current Zoology 61(5): 854-865, 2015]。
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].