Literature DB >> 28113601

Species Tree Inference from Gene Splits by Unrooted STAR Methods.

Elizabeth S Allman, James H Degnan, John A Rhodes.   

Abstract

The method was proposed by Liu and Yu to infer a species tree topology from unrooted topological gene trees. While its statistical consistency under the multispecies coalescent model was established only for a four-taxon tree, simulations demonstrated its good performance on gene trees inferred from sequences for many taxa. Here, we prove the statistical consistency of the method for an arbitrarily large species tree. Our approach connects to a generalization of the STAR method of Liu, Pearl, and Edwards, and a previous theoretical analysis of it. We further show utilizes only the distribution of splits in the gene trees, and not their individual topologies. Finally, we discuss how multiple samples per taxon per gene should be handled for statistical consistency.

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Year:  2016        PMID: 28113601      PMCID: PMC5388605          DOI: 10.1109/TCBB.2016.2604812

Source DB:  PubMed          Journal:  IEEE/ACM Trans Comput Biol Bioinform        ISSN: 1545-5963            Impact factor:   3.710


  15 in total

1.  Properties of consensus methods for inferring species trees from gene trees.

Authors:  James H Degnan; Michael DeGiorgio; David Bryant; Noah A Rosenberg
Journal:  Syst Biol       Date:  2009-06-04       Impact factor: 15.683

2.  Estimating species phylogenies using coalescence times among sequences.

Authors:  Liang Liu; Lili Yu; Dennis K Pearl; Scott V Edwards
Journal:  Syst Biol       Date:  2009-07-16       Impact factor: 15.683

3.  Robustness to divergence time underestimation when inferring species trees from estimated gene trees.

Authors:  Michael DeGiorgio; James H Degnan
Journal:  Syst Biol       Date:  2013-08-29       Impact factor: 15.683

4.  Incomplete lineage sorting: consistent phylogeny estimation from multiple loci.

Authors:  Elchanan Mossel; Sebastien Roch
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2010 Jan-Mar       Impact factor: 3.710

5.  Estimating species trees from unrooted gene trees.

Authors:  Liang Liu; Lili Yu
Journal:  Syst Biol       Date:  2011-03-28       Impact factor: 15.683

6.  BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.

Authors:  O Gascuel
Journal:  Mol Biol Evol       Date:  1997-07       Impact factor: 16.240

7.  On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods.

Authors:  Sebastien Roch; Tandy Warnow
Journal:  Syst Biol       Date:  2015-03-25       Impact factor: 15.683

8.  Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent.

Authors:  Sebastien Roch; Mike Steel
Journal:  Theor Popul Biol       Date:  2014-12-26       Impact factor: 1.570

9.  Species tree inference by the STAR method and its generalizations.

Authors:  Elizabeth S Allman; James H Degnan; John A Rhodes
Journal:  J Comput Biol       Date:  2013-01       Impact factor: 1.479

10.  ASTRID: Accurate Species TRees from Internode Distances.

Authors:  Pranjal Vachaspati; Tandy Warnow
Journal:  BMC Genomics       Date:  2015-10-02       Impact factor: 3.969

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  11 in total

1.  Inferring rooted species trees from unrooted gene trees using approximate Bayesian computation.

Authors:  Ayed R A Alanzi; James H Degnan
Journal:  Mol Phylogenet Evol       Date:  2017-08-02       Impact factor: 4.286

2.  DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition.

Authors:  James Willson; Mrinmoy Saha Roddur; Baqiao Liu; Paul Zaharias; Tandy Warnow
Journal:  Syst Biol       Date:  2022-04-19       Impact factor: 9.160

3.  A stochastic Farris transform for genetic data under the multispecies coalescent with applications to data requirements.

Authors:  Gautam Dasarathy; Elchanan Mossel; Robert Nowak; Sebastien Roch
Journal:  J Math Biol       Date:  2022-04-08       Impact factor: 2.164

4.  BCD Beam Search: considering suboptimal partial solutions in Bad Clade Deletion supertrees.

Authors:  Markus Fleischauer; Sebastian Böcker
Journal:  PeerJ       Date:  2018-06-08       Impact factor: 2.984

5.  Inferring Metric Trees from Weighted Quartets via an Intertaxon Distance.

Authors:  Samaneh Yourdkhani; John A Rhodes
Journal:  Bull Math Biol       Date:  2020-07-16       Impact factor: 1.758

6.  Topological Metrizations of Trees, and New Quartet Methods of Tree Inference.

Authors:  John A Rhodes
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2020-12-08       Impact factor: 3.710

7.  Statistical inconsistency of the unrooted minimize deep coalescence criterion.

Authors:  Ayed A R Alanzi; James H Degnan
Journal:  PLoS One       Date:  2021-05-10       Impact factor: 3.240

8.  Bad Clade Deletion Supertrees: A Fast and Accurate Supertree Algorithm.

Authors:  Markus Fleischauer; Sebastian Böcker
Journal:  Mol Biol Evol       Date:  2017-09-01       Impact factor: 16.240

9.  TreeMerge: a new method for improving the scalability of species tree estimation methods.

Authors:  Erin K Molloy; Tandy Warnow
Journal:  Bioinformatics       Date:  2019-07-15       Impact factor: 6.937

10.  Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge.

Authors:  Erin K Molloy; Tandy Warnow
Journal:  Algorithms Mol Biol       Date:  2019-07-19       Impact factor: 1.405

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