Genome-informed integrative taxonomic description of three cryptic species in the earthworm genus Carpetania (Oligochaeta, Hormogastridae)

Local adaptation fuels cryptic speciation in terrestrial annelids

(2020) Daniel Fernández Marchán et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogeny and species delimitation of Near Eastern Neurergus newts (Salamandridae) based on genome-wide RADseq data analysis

(2019) Loïs Rancilhac et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Multilevel fine-scale diversity challenges the ‘cryptic species’ concept

(2019) Tatiana Korshunova et al.   Scientific Reports

A reference library of DNA barcodes for the earthworms from Upper Normandy: Biodiversity assessment, new records, potential cases of cryptic diversity and ongoing speciation

(2018) David Porco et al.   APPLIED SOIL ECOLOGY

Molecular differentiation of epigeic and anceic forms of Drawida ghilarovi Gates, 1969 (Moniligastridae, Clitellata) in the Russian Far East: Sequence data of two mitochondrial genes

(2018) Gennady N. Ganin et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Integrative systematic revision of a Mediterranean earthworm family: Hormogastridae (Annelida, Oligochaeta)

(2018) Daniel Fernández Marchán et al.   INVERTEBRATE SYSTEMATICS

Cryptic species as a window into the paradigm shift of the species concept

(2018) Cene Fišer et al.   MOLECULAR ECOLOGY

Complex taxonomy of the ‘brush tail’ peregrine earthworm Pontoscolex corethrurus

(2018) S. Taheri et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Cryptic Species – Conceptual or Terminological Chaos? A Response to Struck et al .

(2018) Michael Heethoff   TRENDS IN ECOLOGY & EVOLUTION

Cryptic Species – More Than Terminological Chaos: A Reply to Heethoff

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

Constraints on the FST–Heterozygosity Outlier Approach

(2017) Sarah P Flanagan et al.   JOURNAL OF HEREDITY

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pinpointing cryptic borders: Fine-scale phylogeography and genetic landscape analysis of the Hormogaster elisae complex (Oligochaeta, Hormogastridae)

(2017) Daniel F. Marchán et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Hybridization relics complicate barcode-based identification of species in earthworms

(2016) L. Dupont et al.   Molecular Ecology Resources

Genome-wide data help identify an avian species-level lineage that is morphologically and vocally cryptic

(2016) Kritika M. Garg et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Two's company, three's a crowd: new insights on spruce budworm species boundaries using genotyping-by-sequencing in an integrative species assessment (Lepidoptera: Tortricidae)

(2016) BRYAN M. T. BRUNET et al.   SYSTEMATIC ENTOMOLOGY

Evaluating evolutionary pressures and phylogenetic signal in earthworms: a case study - the number of typhlosole lamellae in Hormogastridae (Annelida, Oligochaeta)

(2016) Daniel F. Marchán et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Cryptic characters for cryptic taxa: On the taxonomic utility of the genital chaetae in earthworms (Oligochaeta, Hormogastridae)

(2016) Daniel F. Marchán et al.   ZOOLOGISCHER ANZEIGER

Formal nomenclature and description of cryptic species of the Encyrtus sasakii complex (Hymenoptera: Encyrtidae)

(2016) Ying Wang et al.   Scientific Reports

Deeply divergent sympatric mitochondrial lineages of the earthworm Lumbricus rubellus are not reproductively isolated

(2015) Iwona Giska et al.   BMC EVOLUTIONARY BIOLOGY

Genomics and introgression: Discovery and mapping of thousands of species-diagnostic SNPs using RAD sequencing

(2015) Brian K. Hand et al.   Current Zoology

The BPP program for species tree estimation and species delimitation

(2015) Ziheng Yang   Current Zoology

Cryptic or pseudocryptic: can morphological methods inform copepod taxonomy? An analysis of publications and a case study of theEurytemora affinisspecies complex

(2015) Dmitry Lajus et al.   Ecology and Evolution

Genomics and introgression: Discovery and mapping of thousands of species-diagnostic SNPs using RAD sequencing

(2015) Brian K. Hand et al.   Current Zoology

The BPP program for species tree estimation and species delimitation

(2015) Ziheng Yang   Current Zoology

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Genome Scans for Detecting Footprints of Local Adaptation Using a Bayesian Factor Model

(2014) Nicolas Duforet-Frebourg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Potential of DNA barcoding for earthworm research in taxonomy and ecology

(2013) Thibaud Decaëns et al.   APPLIED SOIL ECOLOGY

A general species delimitation method with applications to phylogenetic placements

(2013) Jiajie Zhang et al.   BIOINFORMATICS

Cryptic diversity within the Nordenskiold's earthworm, Eisenia nordenskioldi subsp. nordenskioldi (Lumbricidae, Annelida)

(2013) S.V. Shekhovtsov et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

How to describe a cryptic species? Practical challenges of molecular taxonomy

(2013) Katharina M Jörger et al.   Frontiers in Zoology

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

A species-diagnostic SNP panel for discriminating lodgepole pine, jack pine, and their interspecific hybrids

(2013) C. I. Cullingham et al.   Tree Genetics & Genomes

Cryptic polychaete diversity: a review

(2013) Arne Nygren   ZOOLOGICA SCRIPTA

Appearances can be deceptive: different diversification patterns within a group of Mediterranean earthworms (Oligochaeta, Hormogastridae)

(2012) MARTA NOVO et al.   MOLECULAR ECOLOGY

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

Adding complexity to the complex: New insights into the phylogeny, diversification and origin of parthenogenesis in the Aporrectodea caliginosa species complex (Oligochaeta, Lumbricidae)

(2012) Rosa Fernández et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2011) Thibaut Jombart et al.   BIOINFORMATICS

ABGD, Automatic Barcode Gap Discovery for primary species delimitation

(2011) N. PUILLANDRE et al.   MOLECULAR ECOLOGY

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

What We Don't Recognize Can Hurt Us: A Plea for Awareness About Cryptic Species

(2010) Gerardo Pérez-Ponce de León et al.   JOURNAL OF PARASITOLOGY

Cryptic speciation of hormogastrid earthworms revealed by mitochondrial and nuclear data

(2010) Marta Novo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic analysis of New Zealand earthworms (Oligochaeta: Megascolecidae) reveals ancient clades and cryptic taxonomic diversity

(2010) Thomas R. Buckley et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Mate choice of an endogeic earthworm revealed by microsatellite markers

(2010) Marta Novo et al.   PEDOBIOLOGIA

DNA Barcoding Reveals Cryptic Diversity in Lumbricus terrestris L., 1758 (Clitellata): Resurrection of L. herculeus (Savigny, 1826)

(2010) Samuel W. James et al.   PLoS One

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

DNA barcodes for soil animal taxonomy

(2009) Rodolphe Rougerie et al.   PESQUISA AGROPECUARIA BRASILEIRA

High genetic divergence of hormogastrid earthworms (Annelida, Oligochaeta) in the central Iberian Peninsula: evolutionary and demographic implications

(2009) Marta Novo et al.   ZOOLOGICA SCRIPTA

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

(2008) Thibaut Jombart   BIOINFORMATICS

Opening a can of worms: unprecedented sympatric cryptic diversity within British lumbricid earthworms

(2008) R. ANDREW KING et al.   MOLECULAR ECOLOGY

Molecular systematics and phylogeography of the gigantic earthworms of the Metaphire formosae species group (Clitellata, Megascolecidae)

(2008) C CHANG et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Perspectives: Cryptic species diversity should not be trivialised

(2008) Peter Trontelj et al.   SYSTEMATICS AND BIODIVERSITY