Title: Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model

Journal Article · · Bioinformatics
ORCiD logo; ;

Abstract Motivation The classic multispecies coalescent (MSC) model provides the means for theoretical justification of incomplete lineage sorting-aware species tree inference methods. This has motivated an extensive body of work on phylogenetic methods that are statistically consistent under MSC. One such particularly popular method is ASTRAL, a quartet-based species tree inference method. Novel studies suggest that ASTRAL also performs well when given multi-locus gene trees in simulation studies. Further, Legried et al. recently demonstrated that ASTRAL is statistically consistent under the gene duplication and loss model (GDL). GDL is prevalent in evolutionary histories and is the first core process in the powerful duplication-loss-coalescence evolutionary model (DLCoal) by Rasmussen and Kellis. Results In this work, we prove that ASTRAL is statistically consistent under the general DLCoal model. Therefore, our result supports the empirical evidence from the simulation-based studies. More broadly, we prove that the quartet-based inference approach is statistically consistent under DLCoal. Supplementary information Supplementary data are available at Bioinformatics online.

Research Organization:
Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN (United States)
Sponsoring Organization:
Defense Advanced Research Projects Agency (DARPA); National Science Foundation (NSF); USDA; USDOE
Grant/Contract Number:
AC05-06OR23100
OSTI ID:
1868110
Journal Information:
Bioinformatics, Journal Name: Bioinformatics Journal Issue: 22 Vol. 37; ISSN 1367-4803
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United Kingdom
Language:
English

References (19)

Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent journal July 2010
Split Probabilities and Species Tree Inference Under the Multispecies Coalescent Model journal November 2017
Inferring Metric Trees from Weighted Quartets via an Intertaxon Distance journal July 2020
Line-of-descent and genealogical processes, and their applications in population genetics models journal October 1984
Bayesian gene/species tree reconciliation and orthology analysis using MCMC journal July 2003
STEM: species tree estimation using maximum likelihood for gene trees under coalescence journal February 2009
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis journal September 2010
Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci journal August 2003
Properties of Consensus Methods for Inferring Species Trees from Gene Trees journal February 2009
Estimating Species Phylogenies Using Coalescence Times among Sequences journal July 2009
Estimating Species Trees from Unrooted Gene Trees journal March 2011
Unified modeling of gene duplication, loss, and coalescence using a locus tree journal January 2012
Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci journal January 2010
Species Tree Inference from Gene Splits by Unrooted STAR Methods journal January 2018
Topological Metrizations of Trees, and New Quartet Methods of Tree Inference journal November 2020
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model journal January 2010
Rooted triple consensus and anomalous gene trees journal January 2008
ASTRID: Accurate Species TRees from Internode Distances journal October 2015
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees journal May 2018

Similar Records

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
biochemistry & molecular biology
biotechnology & applied microbiology
computer science
mathematical & computational biology
mathematics