Impact of Model Violations on the Inference of Species Boundaries Under the Multispecies Coalescent

Multispecies coalescent delimits structure, not species

(2017) Jeet Sukumaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multi-locus Analyses Reveal Four Giraffe Species Instead of One

(2016) Julian Fennessy et al.   CURRENT BIOLOGY

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

(2016) D. R. Schrider et al.   GENETICS

Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent

(2016) Graham Jones   JOURNAL OF MATHEMATICAL BIOLOGY

Assessing the performance of DNA barcoding using posterior predictive simulations

(2016) Anthony J. Barley et al.   MOLECULAR ECOLOGY

Genomics of local adaptation with gene flow

(2016) Anna Tigano et al.   MOLECULAR ECOLOGY

Species discovery and validation in a cryptic radiation of endangered primates: coalescent-based species delimitation in Madagascar's mouse lemurs

(2016) Scott Hotaling et al.   MOLECULAR ECOLOGY

A genomic perspective on hybridization and speciation

(2016) Bret A. Payseur et al.   MOLECULAR ECOLOGY

CoMuS: simulating coalescent histories and polymorphic data from multiple species

(2016) S. Papadantonakis et al.   Molecular Ecology Resources

A genomic history of Aboriginal Australia

(2016) Anna-Sapfo Malaspinas et al.   NATURE

Ancient gene flow from early modern humans into Eastern Neanderthals

(2016) Martin Kuhlwilm et al.   NATURE

Explosive ice age diversification of kiwi

(2016) Jason T. Weir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The BPP program for species tree estimation and species delimitation

(2015) Ziheng Yang   Current Zoology

Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations

(2015) David A. Duchêne et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sky island diversification meets the multispecies coalescent - divergence in the spruce-fir moss spider (Microhexura montivaga,Araneae, Mygalomorphae) on the highest peaks of southern Appalachia

(2015) Marshal Hedin et al.   MOLECULAR ECOLOGY

Posterior predictive checks of coalescent models: P2C2M, an R package

(2015) Michael Gruenstaeudl et al.   Molecular Ecology Resources

Testing Classical Species Properties with Contemporary Data: How “Bad Species” in the Brassy Ringlets (Erebia tyndaruscomplex, Lepidoptera) Turned Good

(2015) Paolo Gratton et al.   SYSTEMATIC BIOLOGY

Can We Identify Genes with Increased Phylogenetic Reliability?

(2015) Vinson P. Doyle et al.   SYSTEMATIC BIOLOGY

The BPP program for species tree estimation and species delimitation

(2015) Ziheng Yang   Current Zoology

Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci

(2014) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Isolation by environment

(2014) Ian J. Wang et al.   MOLECULAR ECOLOGY

Predictive Approaches to Assessing the Fit of Evolutionary Models

(2014) Jeremy M. Brown   SYSTEMATIC BIOLOGY

Detection of Implausible Phylogenetic Inferences Using Posterior Predictive Assessment of Model Fit

(2014) Jeremy M. Brown   SYSTEMATIC BIOLOGY

Species Delimitation using Genome-Wide SNP Data

(2014) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Considering gene flow when using coalescent methods to delimit lineages of North American pitvipers of the genusAgkistrodon

(2014) Frank T. Burbrink et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

THE CHALLENGE OF SPECIES DELIMITATION AT THE EXTREMES: DIVERSIFICATION WITHOUT MORPHOLOGICAL CHANGE IN PHILIPPINE SUN SKINKS

(2013) Anthony J. Barley et al.   EVOLUTION

GENETIC ISOLATION BY ENVIRONMENT OR DISTANCE: WHICH PATTERN OF GENE FLOW IS MOST COMMON?

(2013) Jason P. Sexton et al.   EVOLUTION

How to fail at species delimitation

(2013) Bryan C. Carstens et al.   MOLECULAR ECOLOGY

Posterior Predictive Bayesian Phylogenetic Model Selection

(2013) Paul O. Lewis et al.   SYSTEMATIC BIOLOGY

Poor Fit to the Multispecies Coalescent is Widely Detectable in Empirical Data

(2013) Noah M. Reid et al.   SYSTEMATIC BIOLOGY

Species Delimitation Using Bayes Factors: Simulations and Application to the Sceloporus scalaris Species Group (Squamata: Phrynosomatidae)

(2013) Jared A. Grummer et al.   SYSTEMATIC BIOLOGY

The Influence of Gene Flow on Species Tree Estimation: A Simulation Study

(2013) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Inferring Demographic History from a Spectrum of Shared Haplotype Lengths

(2013) Kelley Harris et al.   PLoS Genetics

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

SPECIES DELIMITATION WITH ABC AND OTHER COALESCENT-BASED METHODS: A TEST OF ACCURACY WITH SIMULATIONS AND AN EMPIRICAL EXAMPLE WITH LIZARDS OF THE LIOLAEMUS DARWINII COMPLEX (SQUAMATA: LIOLAEMIDAE)

(2012) Arley Camargo et al.   EVOLUTION

Unified modeling of gene duplication, loss, and coalescence using a locus tree

(2012) M. D. Rasmussen et al.   GENOME RESEARCH

Genome-scale coestimation of species and gene trees

(2012) B. Boussau et al.   GENOME RESEARCH

Ecological opportunity and sexual selection together predict adaptive radiation

(2012) Catherine E. Wagner et al.   NATURE

Coalescent-based species delimitation in an integrative taxonomy

(2012) Matthew K. Fujita et al.   TRENDS IN ECOLOGY & EVOLUTION

Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling

(2011) David Gerard et al.   BMC EVOLUTIONARY BIOLOGY

Statistics and Truth in Phylogenomics

(2011) S. Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evaluation of a Bayesian Coalescent Method of Species Delimitation

(2011) Chi Zhang et al.   SYSTEMATIC BIOLOGY

What role does natural selection play in speciation?

(2010) N. H. Barton   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Bayesian species delimitation using multilocus sequence data

(2010) Z. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species Delimitation Using a Combined Coalescent and Information-Theoretic Approach: An Example from North American Myotis Bats

(2010) Bryan C. Carstens et al.   SYSTEMATIC BIOLOGY

How Robust Are "Isolation with Migration" Analyses to Violations of the IM Model? A Simulation Study

(2009) J. L. Strasburg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Divergence of Chimpanzee Species and Subspecies as Revealed in Multipopulation Isolation-with-Migration Analyses

(2009) J. Hey   MOLECULAR BIOLOGY AND EVOLUTION

Fine-scale population structure in a desert amphibian: landscape genetics of the black toad (Bufo exsul)

(2009) IAN J. WANG   MOLECULAR ECOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Speciation with gene flow could be common

(2008) PATRIK NOSIL   MOLECULAR ECOLOGY

IBDSim: a computer program to simulate genotypic data under isolation by distance

(2008) RAPHAËL LEBLOIS et al.   Molecular Ecology Resources