Plotting for change: an analytical framework to aid decisions on which lineages are candidate species in phylogenomic species discovery

Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex

(2020) Kin O. Chan et al.   MOLECULAR ECOLOGY

The Multispecies Coalescent Over-Splits Species in the Case of Geographically Widespread Taxa

(2019) E Anne Chambers et al.   SYSTEMATIC BIOLOGY

What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species

(2018) C Ryan Campbell et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Collection of Scientific Specimens: Benefits for Biodiversity Sciences and Limited Impacts on Communities of Small Mammals

(2018) Andrew G Hope et al.   BIOSCIENCE

Population genomic data reveal extreme geographic subdivision and novel conservation actions for the declining foothill yellow-legged frog

(2018) Evan McCartney-Melstad et al.   HEREDITY

dartr : An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing

(2018) Bernd Gruber et al.   Molecular Ecology Resources

Cryptic biodiversity in the freshwater fishes of the Kimberley endemism hotspot, northwestern Australia

(2018) James J. Shelley et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Earth BioGenome Project: Sequencing life for the future of life

(2018) Harris A. Lewin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted Sampling and Target Capture: Assessing Phylogeographic Concordance with Genome-wide Data

(2018) Lisa N. Barrow et al.   SYSTEMATIC BIOLOGY

A Framework for Resolving Cryptic Species: A Case Study from the Lizards of the Australian Wet Tropics

(2018) Sonal Singhal et al.   SYSTEMATIC BIOLOGY

Comparison of Methods for Molecular Species Delimitation Across a Range of Speciation Scenarios

(2018) Arong Luo et al.   SYSTEMATIC BIOLOGY

The Spectre of Too Many Species

(2018) Adam D Leaché et al.   SYSTEMATIC BIOLOGY

Finding Evolutionary Processes Hidden in Cryptic Species

(2018) Torsten H. Struck et al.   TRENDS IN ECOLOGY & EVOLUTION

Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex

(2018) Md Rakeb-Ul Islam et al.   PeerJ

Multivariate species boundaries and conservation of harlequin poison frogs

(2018) Andrés Posso-Terranova et al.   MOLECULAR ECOLOGY

Genomewide SNP markers breathe new life into phylogeography and species delimitation for the problematic short‐necked turtles (Chelidae: Emydura ) of eastern Australia

(2018) Arthur Georges et al.   MOLECULAR ECOLOGY

Cryptic lineage diversity, body size divergence, and sympatry in a species complex of Australian lizards (Gehyra )

(2017) Craig C. Moritz et al.   EVOLUTION

PhyloNetworks: A Package for Phylogenetic Networks

(2017) Claudia Solís-Lemus et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods

(2017) Erin K Molloy et al.   SYSTEMATIC BIOLOGY

Genomics clarifies taxonomic boundaries in a difficult species complex

(2017) Jason Baumsteiger et al.   PLoS One

The importance of naming cryptic species and the conservation of endemic subterranean amphipods

(2017) Teo Delić et al.   Scientific Reports

Dating early animal evolution using phylogenomic data

(2017) Martin Dohrmann et al.   Scientific Reports

An algorithm for reconstructing ultrametric tree-child networks from inter-taxa distances

(2016) M. Bordewich et al.   DISCRETE APPLIED MATHEMATICS

Genealogies: Pedigrees and Phylogenies are Reticulating Networks Not Just Divergent Trees

(2016) David A. Morrison   Evolutionary Biology

Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

(2016) Bo Xu et al.   GENETICS

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

(2016) Dingqiao Wen et al.   MOLECULAR ECOLOGY

The influence of locus number and information content on species delimitation: an empirical test case in an endangered Mexican salamander

(2016) Paul M. Hime et al.   MOLECULAR ECOLOGY

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

(2016) Scott V. Edwards et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

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

Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

(2016) Bo Xu et al.   GENETICS

How reticulated are species?

(2015) James Mallet et al.   BIOESSAYS

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

(2015) Claudia Solís-Lemus et al.   EVOLUTION

Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites

(2015) Julia Chifman et al.   JOURNAL OF THEORETICAL BIOLOGY

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

Exploring Tree-Like and Non-Tree-Like Patterns Using Genome Sequences: An Example Using the Inbreeding Plant SpeciesArabidopsis thaliana(L.) Heynh

(2015) Noah W. M. Stenz et al.   SYSTEMATIC BIOLOGY

Species delimitation and relationships: The dance of the seven veils

(2015) Yamama Naciri et al.   TAXON

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

Global Biodiversity Assessment and Hyper-Cryptic Species Complexes: More Than One Species of Elephant in the Room?

(2014) Mark Adams et al.   SYSTEMATIC BIOLOGY

Declining Rates of Species Described per Taxonomist: Slowdown of Progress or a Side-effect of Improved Quality in Taxonomy?

(2014) George Sangster et al.   SYSTEMATIC BIOLOGY

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

High-Throughput Genomic Data in Systematics and Phylogenetics

(2013) Emily Moriarty Lemmon et al.   Annual Review of Ecology Evolution and Systematics

PERSISTENCE OF WITHIN-SPECIES LINEAGES: A NEGLECTED CONTROL OF SPECIATION RATES

(2013) Mats Dynesius et al.   EVOLUTION

A molecular assessment of species boundaries and phylogenetic affinities in Mogurnda (Eleotridae): a case study of cryptic biodiversity in the Australian freshwater fishes

(2013) Mark Adams et al.   MARINE AND FRESHWATER RESEARCH

A road map for molecular ecology

(2013) Rose L. Andrew et al.   MOLECULAR ECOLOGY

How to fail at species delimitation

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

Effects of missing data on species tree estimation under the coalescent

(2013) Rasmus Hovmöller et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

New Metrics for Comparison of Taxonomies Reveal Striking Discrepancies among Species Delimitation Methods in Madascincus Lizards

(2013) Aurélien Miralles et al.   PLoS One

21 years of shelf life between discovery and description of new species

(2012) Benoît Fontaine et al.   CURRENT BIOLOGY

Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding

(2012) SAMUEL D. J. BROWN et al.   Molecular Ecology Resources

Is Recombination a Problem for Species-Tree Analyses?

(2012) Hayley C. Lanier et al.   SYSTEMATIC BIOLOGY

Coalescent-based species delimitation in an integrative taxonomy

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

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

Recovery Plan for the Endangered Taxonomy Profession

(2011) David L. Pearson et al.   BIOSCIENCE

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

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

A Survey of Combinatorial Methods for Phylogenetic Networks

(2010) Daniel H. Huson et al.   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

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

Harnessing genomics for evolutionary insights

(2009) Antonis Rokas et al.   TRENDS IN ECOLOGY & EVOLUTION

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

(2008) Cuong Than et al.   BMC BIOINFORMATICS