Estimating species trees from unrooted gene trees.
Liang Liu,Lili Yu +1 more
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TLDR
Under the coalescent model, it is shown that if gene trees are known or estimated correctly, the NJ(st) method is statistically consistent in estimating unrooted species trees and is thus useful in phylogenomic studies in which data sets often contain missing loci for some individuals.Abstract:
In this study, we develop a distance method for inferring unrooted species trees from a collection of unrooted gene trees. The species tree is estimated by the neighbor joining (NJ) tree built from a distance matrix in which the distance between two species is defined as the average number of internodes between two species across gene trees, that is, average gene-tree internode distance. The distance method is named NJ(st) to distinguish it from the original NJ method. Under the coalescent model, we show that if gene trees are known or estimated correctly, the NJ(st) method is statistically consistent in estimating unrooted species trees. The simulation results suggest that NJ(st) and STAR (another coalescence-based method for inferring species trees) perform almost equally well in estimating topologies of species trees, whereas the Bayesian coalescence-based method, BEST, outperforms both NJ(st) and STAR. Unlike BEST and STAR, the NJ(st) method can take unrooted gene trees to infer species trees without using an outgroup. In addition, the NJ(st) method can handle missing data and is thus useful in phylogenomic studies in which data sets often contain missing loci for some individuals.read more
Citations
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OrthoFinder: phylogenetic orthology inference for comparative genomics
David M. Emms,Steven L. Kelly +1 more
TL;DR: This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative genomics statistics.
Posted ContentDOI
OrthoFinder: phylogenetic orthology inference for comparative genomics
David M. Emms,Steven L. Kelly +1 more
TL;DR: This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted genes trees, gene duplication events, the rooted species tree, and comparative genomic statistics.
Journal ArticleDOI
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees.
TL;DR: ASTRAL-III is a faster version of the ASTRAL method for phylogenetic reconstruction and can scale up to 10,000 species and removes low support branches from gene trees, resulting in improved accuracy.
Journal ArticleDOI
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
Richard O. Prum,Richard O. Prum,Jacob S. Berv,Alex Dornburg,Alex Dornburg,Alex Dornburg,Daniel J. Field,Daniel J. Field,Jeffrey P. Townsend,Emily Moriarty Lemmon,Alan R. Lemmon +10 more
TL;DR: The results of the divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous–Palaeogene (K–Pg) mass extinction.
Journal ArticleDOI
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes.
Siavash Mirarab,Tandy Warnow +1 more
TL;DR: A new version of ASTRAL is presented, which is statistically consistent under the multi-species coalescent model and which is more accurate than other coalescent-based methods on the datasets the authors examined, and has substantially better accuracy under some conditions.
References
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The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Book
Fuzzy sets
TL;DR: A separation theorem for convex fuzzy sets is proved without requiring that the fuzzy sets be disjoint.
Journal ArticleDOI
MrBayes 3: Bayesian phylogenetic inference under mixed models
TL;DR: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models to analyze heterogeneous data sets and explore a wide variety of structured models mixing partition-unique and shared parameters.
Journal ArticleDOI
MRBAYES: Bayesian inference of phylogenetic trees
TL;DR: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo, and an executable is available at http://brahms.rochester.edu/software.html.