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Coalescent methods for estimating species trees from phylogenomic data
Author(s) -
Liu Liang,
Wu Shaoyuan,
Yu Lili
Publication year - 2015
Publication title -
journal of systematics and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.249
H-Index - 46
eISSN - 1759-6831
pISSN - 1674-4918
DOI - 10.1111/jse.12160
Subject(s) - coalescent theory , phylogenetic tree , biology , evolutionary biology , phylogenetics , tree (set theory) , coalescence (physics) , genome , phylogenomics , maximum likelihood , gene , genetics , mathematics , statistics , clade , mathematical analysis , astrobiology
Genome‐scale sequence data have become increasingly available in the phylogenetic studies for understanding the evolutionary histories of species. However, it is challenging to develop probabilistic models to account for heterogeneity of phylogenomic data. The multispecies coalescent model describes gene trees as independent random variables generated from a coalescence process occurring along the lineages of the species tree. Since the multispecies coalescent model allows gene trees to vary across genes, coalescent‐based methods have been popularly used to account for heterogeneous gene trees in phylogenomic data analysis. In this paper, we summarize and evaluate the performance of coalescent‐based methods for estimating species trees from genome‐scale sequence data. We investigate the effects of deep coalescence and mutation on the performance of species tree estimation methods. We found that the coalescent‐based methods perform well in estimating species trees for a large number of genes, regardless of the degree of deep coalescence and mutation. The performance of the coalescent methods is negatively correlated with the lengths of internal branches of the species tree.