A Rapid and Scalable Method for Multilocus Species Delimitation Using Bayesian Model Comparison and Rooted Triplets

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci

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

Species detection and individual assignment in species delimitation: can integrative data increase efficacy?

(2014) D. L. Edwards et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Bayesian Species Delimitation Can Be Robust to Guide-Tree Inference Errors

(2014) Chi Zhang et al.   SYSTEMATIC BIOLOGY

Disentangling Methodological and Biological Sources of Gene Tree Discordance on Oryza (Poaceae) Chromosome 3

(2014) Derrick J. Zwickl et al.   SYSTEMATIC BIOLOGY

A general species delimitation method with applications to phylogenetic placements

(2013) Jiajie Zhang et al.   BIOINFORMATICS

Bayesian species delimitation reveals generalist and specialist parasitic wasps on Galerucella beetles (Chrysomelidae): sorting by herbivore or plant host

(2013) Peter A Hambäck et al.   BMC EVOLUTIONARY BIOLOGY

How to fail at species delimitation

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

Multilocus Species Delimitation in a Complex of Morphologically Conserved Trapdoor Spiders (Mygalomorphae, Antrodiaetidae, Aliatypus)

(2013) Jordan D. Satler et al.   SYSTEMATIC BIOLOGY

Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets

(2013) Tomochika Fujisawa et al.   SYSTEMATIC BIOLOGY

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

Evolving Concepts of Bacterial Species

(2012) Timothy G. Barraclough et al.   Evolutionary Biology

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic species recognition reveals host-specific lineages among poplar rust fungi

(2012) Agathe Vialle et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Coalescent-based species delimitation in an integrative taxonomy

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

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

ABGD, Automatic Barcode Gap Discovery for primary species delimitation

(2011) N. PUILLANDRE et al.   MOLECULAR ECOLOGY

Inferring Species-Level Phylogenies and Taxonomic Distinctiveness Using Multilocus Data in Sistrurus Rattlesnakes

(2011) Laura S. Kubatko et al.   SYSTEMATIC BIOLOGY

Recombination and Population Structure in Salmonella enterica

(2011) Xavier Didelot et al.   PLoS Genetics

pegas: an R package for population genetics with an integrated-modular approach

(2010) E. Paradis   BIOINFORMATICS

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Inference of Homologous Recombination in Bacteria Using Whole-Genome Sequences

(2010) X. Didelot et al.   GENETICS

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

Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus)

(2010) A. D. Leache et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Fast and Consistent Estimation of Species Trees Using Supermatrix Rooted Triples

(2009) Michael DeGiorgio et al.   MOLECULAR BIOLOGY AND EVOLUTION

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

New Heuristic Methods for Joint Species Delimitation and Species Tree Inference

(2009) Brian C. O'Meara   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

Rooted triple consensus and anomalous gene trees

(2008) Gregory B Ewing et al.   BMC EVOLUTIONARY BIOLOGY

Correlation-Based Inference for Linkage Disequilibrium With Multiple Alleles

(2008) D. V. Zaykin et al.   GENETICS

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

Optimal Data Partitioning and a Test Case for Ray-Finned Fishes (Actinopterygii) Based on Ten Nuclear Loci

(2008) Chenhong Li et al.   SYSTEMATIC BIOLOGY