Using natural history to guide supervised machine learning for cryptic species delimitation with genetic data

Incorporating the speciation process into species delimitation

(2021) Jeet Sukumaran et al.   PLoS Computational Biology

Predictors of phylogeographic structure among codistributed taxa across the complex Australian monsoonal tropics

(2021) Jessica Fenker et al.   MOLECULAR ECOLOGY

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

(2021) Adam D. Leaché et al.   Frontiers in Ecology and Evolution

Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex

(2020) Lacie G. Newton et al.   MOLECULAR ECOLOGY

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

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

Life history and ecology might explain incongruent population structure in two co-distributed montane bird species of the Atlantic Forest

(2020) Tiago da Silva Ribeiro et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Ecology of Nonecological Speciation and Nonadaptive Radiations

(2019) Jesse E. Czekanski-Moir et al.   TRENDS IN ECOLOGY & EVOLUTION

Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci

(2019) Marshal Hedin et al.   PeerJ

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

(2019) E Anne Chambers et al.   SYSTEMATIC BIOLOGY

Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault

(2019) Shahan Derkarabetian et al.   Molecular Ecology Resources

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

(2019) Megan L. Smith et al.   EVOLUTION

A demonstration of unsupervised machine learning in species delimitation

(2019) Shahan Derkarabetian et al.   MOLECULAR PHYLOGENETICS AND 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

Incongruence in molecular species delimitation schemes: What to do when adding more data is difficult

(2018) Sarah J. Jacobs et al.   MOLECULAR ECOLOGY

CLADES: A classification-based machine learning method for species delimitation from population genetic data

(2018) Jingwen Pei et al.   Molecular Ecology Resources

Bayesian selection of misspecified models is overconfident and may cause spurious posterior probabilities for phylogenetic trees

(2018) Ziheng Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Spectre of Too Many Species

(2018) Adam D Leaché et al.   SYSTEMATIC BIOLOGY

Sequence capture phylogenomics of eyeless Cicurina spiders from Texas caves, with emphasis on US federally-endangered species from Bexar County (Araneae, Hahniidae)

(2018) Marshal Hedin et al.   ZooKeys

A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements

(2018) Shahan Derkarabetian et al.   ZooKeys

Cryptic diversity in the southern Appalachian Mountains: genetic data reveal that the red centipede, Scolopocryptops sexspinosus, is a species complex

(2018) R. C. Garrick et al.   JOURNAL OF INSECT CONSERVATION

Combining ultraconserved elements and mtDNA data to uncover lineage diversity in a Mexican highland frog (Sarcohyla; Hylidae)

(2018) Eugenia Zarza et al.   PeerJ

Different species or genetically divergent populations? Integrative species delimitation of the Primulina hochiensis complex from isolated karst habitats

(2018) Lihua Yang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Biogeographical evidence for common vicariance and rare dispersal in a southern Appalachian harvestman (Sabaconidae, Sabacon cavicolens )

(2017) Marshal Hedin et al.   JOURNAL OF BIOGEOGRAPHY

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

A short-range endemic species from south-eastern Atlantic Rain Forest shows deep signature of historical events: phylogeography of harvestmen Acutisoma longipes (Arachnida: Opiliones)

(2017) Elen Arroyo Peres et al.   SYSTEMATICS AND BIODIVERSITY

Biological traits yield divergent phylogeographical patterns between two aphids living on the same host plants

(2016) Fang Fang et al.   JOURNAL OF BIOGEOGRAPHY

Population genomic evidence for multiple Pliocene refugia in a montane-restricted harvestman (Arachnida, Opiliones,Sclerobunus robustus) from the southwestern United States

(2016) Shahan Derkarabetian et al.   MOLECULAR ECOLOGY

Contrasting support for alternative models of genomic variation based on microhabitat preference: species-specific effects of climate change in alpine sedges

(2016) Rob Massatti et al.   MOLECULAR ECOLOGY

Genomic data reveal ancient microendemism in forest scorpions across the California Floristic Province

(2016) Robert W. Bryson et al.   MOLECULAR ECOLOGY

High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

(2016) James Starrett et al.   Molecular Ecology Resources

Comparative performance of double-digest RAD sequencing across divergent arachnid lineages

(2016) Mercedes Burns et al.   Molecular Ecology Resources

Phylogenomics, biogeography and diversification of obligate mealybug-tending ants in the genus Acropyga

(2016) Bonnie B. Blaimer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Identifying cryptic diversity with predictive phylogeography

(2016) Anahí Espíndola et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

New species in the Sitalcina sura species group (Opiliones, Laniatores, Phalangodidae), with evidence for a biogeographic link between California desert canyons and Arizona sky islands

(2016) Marshal Hedin et al.   ZooKeys

A new monster from southwest Oregon forests: Cryptomaster behemoth sp. n. (Opiliones, Laniatores, Travunioidea)

(2016) James Starrett et al.   ZooKeys

AMAS: a fast tool for alignment manipulation and computing of summary statistics

(2016) Marek L. Borowiec   PeerJ

PHYLUCE is a software package for the analysis of conserved genomic loci

(2015) Brant C. Faircloth   BIOINFORMATICS

Sky island diversification meets the multispecies coalescent - divergence in the spruce-fir moss spider (Microhexura montivaga,Araneae, Mygalomorphae) on the highest peaks of southern Appalachia

(2015) Marshal Hedin et al.   MOLECULAR ECOLOGY

Clumpak : a program for identifying clustering modes and packaging population structure inferences across K

(2015) Naama M. Kopelman et al.   Molecular Ecology Resources

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

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

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

MICROHABITAT DIFFERENCES IMPACT PHYLOGEOGRAPHIC CONCORDANCE OF CODISTRIBUTED SPECIES: GENOMIC EVIDENCE IN MONTANE SEDGES (CAREXL.) FROM THE ROCKY MOUNTAINS

(2014) Rob Massatti et al.   EVOLUTION

Integrative Taxonomy and Species Delimitation in Harvestmen: A Revision of the Western North American Genus Sclerobunus (Opiliones: Laniatores: Travunioidea)

(2014) Shahan Derkarabetian et al.   PLoS One

Prediction of phylogeographic endemism in an environmentally complex biome

(2014) A. C. Carnaval et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Species Delimitation using Genome-Wide SNP Data

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

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

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

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Species Delimitation Using Bayes Factors: Simulations and Application to the Sceloporus scalaris Species Group (Squamata: Phrynosomatidae)

(2013) Jared A. Grummer et al.   SYSTEMATIC BIOLOGY

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

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

Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales

(2013) Brian Tilston Smith et al.   SYSTEMATIC BIOLOGY

Extreme mitochondrial population subdivision in southern Appalachian paleoendemic spiders (Araneae: Hypochilidae: Hypochilus), with implications for species delimitation

(2012) Robin Keith et al.   JOURNAL OF ARACHNOLOGY

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

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

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

LIBSVM

(2012) Chih-Chung Chang et al.   ACM Transactions on Intelligent Systems and Technology

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

DELIMITING SPECIES USING MULTILOCUS DATA: DIAGNOSING CRYPTIC DIVERSITY IN THE SOUTHERN CAVEFISH, TYPHLICHTHYS SUBTERRANEUS (TELEOSTEI: AMBLYOPSIDAE)

(2011) Matthew L. Niemiller et al.   EVOLUTION

Genetic diversification without obvious genitalic morphological divergence in harvestmen (Opiliones, Laniatores, Sclerobunus robustus) from montane sky islands of western North America

(2011) Shahan Derkarabetian et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Niche Conservatism Drives Elevational Diversity Patterns in Appalachian Salamanders

(2010) Kenneth H. Kozak et al.   AMERICAN NATURALIST

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

(2010) Thibaut Jombart et al.   BMC GENETICS

Repeated and Time-Correlated Morphological Convergence in Cave-Dwelling Harvestmen (Opiliones, Laniatores) from Montane Western North America

(2010) Shahan Derkarabetian et al.   PLoS One

A revision of the Appalachian millipede genus Brachoria Chamberlin, 1939 (Polydesmida: Xystodesmidae: Apheloriini)

(2010) PAUL E. MAREK   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Integrative Taxonomy: A Multisource Approach to Exploring Biodiversity

(2009) Birgit C. Schlick-Steiner et al.   Annual Review of Entomology

Molecular systematics of eastern North American Phalangodidae (Arachnida: Opiliones: Laniatores), demonstrating convergent morphological evolution in caves

(2009) Marshal Hedin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Adaptive radiation, nonadaptive radiation, ecological speciation and nonecological speciation

(2009) Rebecca J. Rundell et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2008) Thibaut Jombart   BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Multigenic phylogeographic divergence in the paleoendemic southern Appalachian opilionid Fumontana deprehendor Shear (Opiliones, Laniatores, Triaenonychidae)

(2007) Steven M. Thomas et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION