Species delimitation with gene flow: A methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs

Multispecies coalescent delimits structure, not species

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

Hidden histories of gene flow in highland birds revealed with genomic markers

(2016) Eugenia Zarza et al.   MOLECULAR ECOLOGY

Navigating the pitfalls and promise of landscape genetics

(2016) Jonathan L. Richardson et al.   MOLECULAR ECOLOGY

Species Delimitation with Gene Flow

(2016) Nathan D. Jackson et al.   SYSTEMATIC BIOLOGY

Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)

(2016) R. Alexander Pyron et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Polyphyly of Asian Tree Toads, Genus Pedostibes Günther, 1876 (Anura: Bufonidae), and the Description of a New Genus from Southeast Asia

(2016) Kin Onn Chan et al.   PLoS One

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

Historical introgression among the American live oaks and the comparative nature of tests for introgression

(2015) Deren A. R. Eaton et al.   EVOLUTION

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

(2015) Claudia Solís-Lemus et al.   EVOLUTION

RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus)

(2015) Laura Benestan et al.   MOLECULAR ECOLOGY

Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt

(2015) John R. Candy et al.   Molecular Ecology Resources

The fine-scale genetic structure of the British population

(2015) Stephen Leslie et al.   NATURE

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

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

LEA: AnRpackage for landscape and ecological association studies

(2015) Eric Frichot et al.   Methods in Ecology and Evolution

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

Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species

(2015) Michael G. Harvey et al.   PeerJ

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

DNA-based species delimitation in algae

(2014) Frederik Leliaert et al.   EUROPEAN JOURNAL OF PHYCOLOGY

Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)

(2014) Wesley A. Larson et al.   Evolutionary Applications

Fast and Efficient Estimation of Individual Ancestry Coefficients

(2014) Eric Frichot et al.   GENETICS

A New Species of Frog (Amphibia: Anura: Ranidae) of theHylarana signataComplex from Peninsular Malaysia

(2014) Kin Onn Chan et al.   HERPETOLOGICA

Population Genetics Methods Applied to a Species Delimitation Problem: Endemic Trumpet Daffodils (Narcissus Section Pseudonarcissi) from the Southern Iberian Peninsula

(2014) Mónica Medrano et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs

(2014) Jeffrey W. Streicher et al.   MOLECULAR ECOLOGY

Species Delimitation using Genome-Wide SNP Data

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

Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences

(2014) Huateng Huang et al.   SYSTEMATIC BIOLOGY

Genetic divergences of South and Southeast Asian frogs: a case study of several taxa based on 16S ribosomal RNA gene data with notes on the generic name Fejervarya

(2014) Mahmudul HASAN et al.   TURKISH JOURNAL OF ZOOLOGY

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

Reappraisal of the Javanese Bullfrog complex, Kaloula baleata (Müller, 1836) (Amphibia: Anura: Microhylidae), reveals a new species from Peninsular Malaysia

(2014) KIN ONN CHAN et al.   ZOOTAXA

Systematics and natural history of Southeast Asian Rock Geckos (genus Cnemaspis Strauch, 1887) with descriptions of eight new species from Malaysia, Thailand, and Indonesia

(2014) L. LEE GRISMER et al.   ZOOTAXA

Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

(2014) Cuong Q. Tang et al.   Methods in Ecology and Evolution

A general species delimitation method with applications to phylogenetic placements

(2013) Jiajie Zhang et al.   BIOINFORMATICS

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

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

How to fail at species delimitation

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

Understanding the origin of species with genome-scale data: modelling gene flow

(2013) Vitor Sousa et al.   NATURE REVIEWS GENETICS

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

(2013) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

Navjot's nightmare revisited: logging, agriculture, and biodiversity in Southeast Asia

(2013) David S. Wilcove et al.   TRENDS IN ECOLOGY & EVOLUTION

Integrative taxonomy uncovers high levels of cryptic species diversity inHemiphyllodactylus Bleeker, 1860 (Squamata: Gekkonidae) and the description of a new species from Peninsular Malaysia

(2013) L. Lee Grismer et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

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

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

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 trouble with isolation by distance

(2012) PATRICK G. MEIRMANS   MOLECULAR ECOLOGY

Population genomics based on low coverage sequencing: how low should we go?

(2012) C. Alex Buerkle et al.   MOLECULAR ECOLOGY

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

Inferring Phylogenies from RAD Sequence Data

(2012) Benjamin E. R. Rubin et al.   PLoS One

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Coalescent-based species delimitation in an integrative taxonomy

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

Genetic structure of the snakehead murrel, Channa striata (channidae) based on the cytochrome c oxidase subunit I gene: influence of historical and geomorphological factors

(2011) Jamsari Amirul Firdaus Jamaluddin et al.   GENETICS AND MOLECULAR BIOLOGY

Multiplexed shotgun genotyping for rapid and efficient genetic mapping

(2011) P. Andolfatto et al.   GENOME RESEARCH

Deforestation rates in insular Southeast Asia between 2000 and 2010

(2011) JUKKA MIETTINEN et al.   GLOBAL CHANGE BIOLOGY

Testing for Ancient Admixture between Closely Related Populations

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

and D do not replace FST

(2011) MICHAEL C. WHITLOCK   MOLECULAR ECOLOGY

Reservoirs of richness: least disturbed tropical forests are centres of undescribed species diversity

(2011) X. Giam et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evaluation of a Bayesian Coalescent Method of Species Delimitation

(2011) Chi Zhang et al.   SYSTEMATIC BIOLOGY

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

Quantitative criteria for species delimitation

(2010) JOSEPH A. TOBIAS et al.   IBIS

Assessing population structure: FST and related measures

(2010) PATRICK G. MEIRMANS et al.   Molecular Ecology Resources

SpedeSTEM: a rapid and accurate method for species delimitation

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

Of Least Concern? Systematics of a cryptic species complex: Limnonectes kuhlii (Amphibia: Anura: Dicroglossidae)

(2010) David S. McLeod   MOLECULAR PHYLOGENETICS AND EVOLUTION

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 under the General Lineage Concept: An Empirical Example Using Wild North American Hops (Cannabaceae: Humulus lupulus)

(2010) Patrick A. Reeves et al.   SYSTEMATIC BIOLOGY

Along the speciation continuum in sticklebacks

(2009) A. P. Hendry et al.   JOURNAL OF FISH BIOLOGY

Evidence for Ecological Speciation and Its Alternative

(2009) D. Schluter   SCIENCE

Gene flow and species delimitation

(2009) Rémy J. Petit et al.   TRENDS IN ECOLOGY & EVOLUTION

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

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

(2008) Thibaut Jombart   BIOINFORMATICS

Recent divergence with gene flow in Tennessee cave salamanders (Plethodontidae:Gyrinophilus) inferred from gene genealogies

(2008) MATTHEW L. NIEMILLER et al.   MOLECULAR ECOLOGY

Speciation with gene flow could be common

(2008) PATRIK NOSIL   MOLECULAR ECOLOGY

GSTand its relatives do not measure differentiation

(2008) LOU JOST   MOLECULAR ECOLOGY

genepop’007: a complete re-implementation of the genepop software for Windows and Linux

(2007) FRANÇOIS ROUSSET   Molecular Ecology Resources

The phylogenetic problem of Huia (Amphibia: Ranidae)

(2007) Bryan L. Stuart   MOLECULAR PHYLOGENETICS AND EVOLUTION