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

Simulating gene trees under the multispecies coalescent and time-dependent migration

(2013) Joseph Heled et al.   BMC EVOLUTIONARY BIOLOGY

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

(2012) Yun Yu et al.   PLoS Genetics

Genetic Introgression: An Integral but neglected component of speciation in birds

(2011) Frank E. Rheindt et al.   AUK

Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling

(2011) David Gerard et al.   BMC EVOLUTIONARY BIOLOGY

Joint Inference of Population Assignment and Demographic History

(2011) Sang Chul Choi et al.   GENETICS

A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids

(2011) Bridgett M. vonHoldt et al.   GENOME RESEARCH

JML: testing hybridization from species trees

(2011) SIMON JOLY   Molecular Ecology Resources

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Comparing Two Bayesian Methods for Gene Tree/Species Tree Reconstruction: Simulations with Incomplete Lineage Sorting and Horizontal Gene Transfer

(2011) Yujin Chung et al.   SYSTEMATIC BIOLOGY

Accuracy and Precision of Species Trees: Effects of Locus, Individual, and Base Pair Sampling on Inference of Species Trees in Lizards of the Liolaemus darwinii Group (Squamata, Liolaemidae)

(2011) Arley Camargo et al.   SYSTEMATIC BIOLOGY

Recent and Rapid Speciation with Limited Morphological Disparity in the Genus Rattus

(2011) Kevin C. Rowe et al.   SYSTEMATIC BIOLOGY

Evaluation of a Bayesian Coalescent Method of Species Delimitation

(2011) Chi Zhang et al.   SYSTEMATIC BIOLOGY

A Species Tree for the Australo-Papuan Fairy-wrens and Allies (Aves: Maluridae)

(2011) June Y. Lee et al.   SYSTEMATIC BIOLOGY

Divergence with Gene Flow: Models and Data

(2010) Catarina Pinho et al.   Annual Review of Ecology Evolution and Systematics

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

A Likelihood Ratio Test of Speciation with Gene Flow Using Genomic Sequence Data

(2010) Ziheng Yang   Genome Biology and Evolution

SpedeSTEM: a rapid and accurate method for species delimitation

(2010) DANIEL D. ENCE et al.   Molecular Ecology Resources

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

The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods

(2010) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting

(2009) Simon Joly et al.   AMERICAN NATURALIST

Isolation with Migration Models for More Than Two Populations

(2009) Jody Hey   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Inference of Species Trees from Multilocus Data

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

Coalescent methods for estimating phylogenetic trees

(2009) Liang Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Species Tree Discordance Traces to Phylogeographic Clade Boundaries in North American Fence Lizards (Sceloporus)

(2009) Adam D. Leaché   SYSTEMATIC BIOLOGY

Identifying Hybridization Events in the Presence of Coalescence via Model Selection

(2009) Laura Salter Kubatko   SYSTEMATIC BIOLOGY

Maximum Likelihood Estimates of Species Trees: How Accuracy of Phylogenetic Inference Depends upon the Divergence History and Sampling Design

(2009) John E. McCormack et al.   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

Phylogenetic Inference Using Whole Genomes

(2008) Bruce Rannala et al.   Annual Review of Genomics and Human Genetics

BEST: Bayesian estimation of species trees under the coalescent model

(2008) L. Liu   BIOINFORMATICS

ESTIMATING SPECIES TREES USING MULTIPLE-ALLELE DNA SEQUENCE DATA

(2008) Liang Liu et al.   EVOLUTION

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Multilocus phylogeography and phylogenetics using sequence-based markers

(2008) Patrícia H. Brito et al.   GENETICA

Integrating Phylogenetic and Population Genetic Analyses of Multiple Loci to Test Species Divergence Hypotheses in Passerina Buntings

(2008) Matt D. Carling et al.   GENETICS

Subdivision in an Ancestral Species Creates Asymmetry in Gene Trees

(2008) M. Slatkin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow

(2008) A ECKERT et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model

(2008) Chen Meng et al.   THEORETICAL POPULATION BIOLOGY

Coalescent genealogy samplers: windows into population history

(2008) Mary K. Kuhner   TRENDS IN ECOLOGY & EVOLUTION