Phylogenomic Assessment of Biodiversity Using a Reference-Based Taxonomy: An Example With Horned Lizards (Phrynosoma)

Incorporating the speciation process into species delimitation

(2021) Jeet Sukumaran et al.   PLoS Computational Biology

Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance

(2020) Nicholas A. Mason et al.   SYSTEMATICS AND BIODIVERSITY

Stable species boundaries despite ten million years of hybridization in tropical eels

(2020) Julia M. I. Barth et al.   Nature Communications

Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent

(2020) Jelmer Poelstra et al.   SYSTEMATIC BIOLOGY

Defining Species When There is Gene Flow

(2020) Xiyun Jiao et al.   SYSTEMATIC BIOLOGY

Resolving spatial complexities of hybridization in the context of the gray zone of speciation in North American ratsnakes ( Pantherophis obsoletus complex)

(2020) Frank T. Burbrink et al.   EVOLUTION

To split or not to split? Multilocus phylogeny and molecular species delimitation of southeast Asian toads (family: Bufonidae)

(2019) Kin Onn Chan et al.   BMC EVOLUTIONARY BIOLOGY

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Phylogenetic Trees and Networks Can Serve as Powerful and Complementary Approaches for Analysis of Genomic Data

(2019) Christopher Blair et al.   SYSTEMATIC BIOLOGY

Process‐based species delimitation leads to identification of more biologically relevant species

(2019) Megan L. Smith et al.   EVOLUTION

Model-based species delimitation: are coalescent species reproductively isolated?

(2019) Luke C Campillo et al.   SYSTEMATIC BIOLOGY

ipyrad: Interactive assembly and analysis of RADseq datasets

(2019) Deren A R Eaton et al.   BIOINFORMATICS

The Spectre of Too Many Species

(2018) Adam D Leaché et al.   SYSTEMATIC BIOLOGY

Bayesian Divergence-Time Estimation with Genome-Wide Single-Nucleotide Polymorphism Data of Sea Catfishes (Ariidae) Supports Miocene Closure of the Panamanian Isthmus

(2018) Madlen Stange et al.   SYSTEMATIC BIOLOGY

Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome

(2018) Blair W Perry et al.   Genome Biology and Evolution

Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent

(2018) Tomáš Flouri et al.   MOLECULAR BIOLOGY AND EVOLUTION

Delineating species in the speciation continuum: a proposal

(2018) Nicolas Galtier   Evolutionary Applications

Bayesian species identification under the multispecies coalescent provides significant improvements to DNA barcoding analyses

(2017) Ziheng Yang et al.   MOLECULAR ECOLOGY

Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma )

(2017) Christopher Blair et al.   Molecular Ecology Resources

Multispecies coalescent delimits structure, not species

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

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

(2017) Anthony J Barley et al.   SYSTEMATIC BIOLOGY

Reticulation, divergence, and the phylogeography–phylogenetics continuum

(2016) Scott V. Edwards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomics of Horned Lizards (Genus:Phrynosoma) Using Targeted Sequence Capture Data

(2015) Adam D. Leaché et al.   COPEIA

The art and science of species delimitation

(2015) Bruce Rannala   Current Zoology

The BPP program for species tree estimation and species delimitation

(2015) Ziheng Yang   Current Zoology

Bayesian species delimitation combining multiple genes and traits in a unified framework

(2015) Claudia Solís-Lemus et al.   EVOLUTION

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

(2015) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

A taxonomic revision of the Phrynosoma douglasii species complex (Squamata: Phrynosomatidae)

(2015) RICHARD R. MONTANUCCI   ZOOTAXA

The art and science of species delimitation

(2015) Bruce Rannala   Current Zoology

The BPP program for species tree estimation and species delimitation

(2015) Ziheng Yang   Current Zoology

DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent

(2014) Graham Jones et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Genetic structure of the endangered Greater Short-horned Lizard (Phrynosoma hernandesi) in Canada: evidence from mitochondrial and nuclear genes

(2014) M.N.-Y. Leung et al.   CANADIAN JOURNAL OF ZOOLOGY

Hybridization, Introgression, and the Nature of Species Boundaries

(2014) Richard G. Harrison et al.   JOURNAL OF HEREDITY

How to fail at species delimitation

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

Macroevolutionary speciation rates are decoupled from the evolution of intrinsic reproductive isolation in Drosophila and birds

(2013) D. L. Rabosky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coalescent Species Delimitation in Milksnakes (Genus Lampropeltis) and Impacts on Phylogenetic Comparative Analyses

(2013) S. Ruane et al.   SYSTEMATIC BIOLOGY

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

The biogeography of mitochondrial and nuclear discordance in animals

(2012) DAVID P. L. TOEWS et al.   MOLECULAR ECOLOGY

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Coalescent-based species delimitation in an integrative taxonomy

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

POPULATION GENETICS AND OBJECTIVITY IN SPECIES DIAGNOSIS

(2011) Jody Hey et al.   EVOLUTION

The integrative future of taxonomy

(2010) Jose M. Padial et al.   Frontiers in Zoology

Quantitative criteria for species delimitation

(2010) JOSEPH A. TOBIAS et al.   IBIS

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

A coalescent perspective on delimiting and naming species: a reply to Bauer et al.

(2010) M. K. Fujita et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS