Towards a rigorous species delimitation framework for scleractinian corals based on RAD sequencing: the case study of Leptastrea from the Indo-Pacific

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

Molecular operational taxonomic units reveal restricted geographic ranges and regional endemism in the Indo‐Pacific octocoral family Xeniidae

(2019) Catherine S. McFadden et al.   JOURNAL OF BIOGEOGRAPHY

Global warming impairs stock–recruitment dynamics of corals

(2019) Terry P. Hughes et al.   NATURE

A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

(2019) Andrea M. Quattrini et al.   BMC EVOLUTIONARY BIOLOGY

Uncovering hidden coral diversity: a new cryptic lobophylliid scleractinian from the Indian Ocean

(2018) Roberto Arrigoni et al.   CLADISTICS

Spatial and temporal patterns of mass bleaching of corals in the Anthropocene

(2018) Terry P. Hughes et al.   SCIENCE

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

The complete mitochondrial genome of Porites harrisoni (Cnidaria: Scleractinia) obtained using next-generation sequencing

(2018) Tullia Isotta Terraneo et al.   Mitochondrial DNA Part B-Resources

Using ezRAD to reconstruct the complete mitochondrial genome of Porites fontanesii (Cnidaria: Scleractinia)

(2018) Tullia I. Terraneo et al.   Mitochondrial DNA Part B-Resources

An integrated morpho-molecular approach to delineate species boundaries of Millepora from the Red Sea

(2018) Roberto Arrigoni et al.   CORAL REEFS

Finding stories in noise: Mitochondrial portraits from RAD data

(2018) C. S. Stobie et al.   Molecular Ecology Resources

The origin and evolution of coral species richness in a marine biodiversity hotspot*

(2017) Danwei Huang et al.   EVOLUTION

Genetic and epigenetic insight into morphospecies in a reef coral

(2017) James L. Dimond et al.   MOLECULAR ECOLOGY

Haplotyping RAD loci: an efficient method to filter paralogs and account for physical linkage

(2017) Stuart C. Willis et al.   Molecular Ecology Resources

Species boundaries in the absence of morphological, ecological or geographical differentiation in the Red Sea octocoral genus Ovabunda (Alcyonacea: Xeniidae)

(2017) Catherine S. McFadden et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Coral hybridization or phenotypic variation? Genomic data reveal gene flow between Porites lobata and P. Compressa

(2017) Z.H. Forsman et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study

(2017) Tomasz Suchan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Reevaluating species number, distribution and endemism of the coral genus Pocillopora Lamarck, 1816 using species delimitation methods and microsatellites

(2017) P. Gélin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Coral reefs in the Anthropocene

(2017) Terry P. Hughes et al.   NATURE

Biodiversity losses and conservation responses in the Anthropocene

(2017) Christopher N. Johnson et al.   SCIENCE

From population connectivity to the art of striping Russian dolls: the lessons from Pocillopora corals

(2017) Pauline Gélin et al.   Ecology and Evolution

A genomic glance through the fog of plasticity and diversification in Pocillopora

(2017) Erika C. Johnston et al.   Scientific Reports

Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: A case study in Carex sect. Racemosae

(2016) R. Massatti et al.   AMERICAN JOURNAL OF BOTANY

Cryptic genetic divergence within threatened species of Acropora coral from the Indian and Pacific Oceans

(2016) Zoe T. Richards et al.   CONSERVATION GENETICS

Clustering Genes of Common Evolutionary History

(2016) Kevin Gori et al.   MOLECULAR BIOLOGY AND EVOLUTION

Species delimitation in the coral genus Goniopora (Scleractinia, Poritidae) from the Saudi Arabian Red Sea

(2016) Tullia I. Terraneo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Species delimitation in the reef coral genera Echinophyllia and Oxypora (Scleractinia, Lobophylliidae) with a description of two new species

(2016) Roberto Arrigoni et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa

(2016) Santiago Herrera 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

Recent origin and semi-permeable species boundaries in the scleractinian coral genus Stylophora from the Red Sea

(2016) Roberto Arrigoni et al.   Scientific Reports

Switch between Morphospecies of Pocillopora Corals

(2015) David A. Paz-García et al.   AMERICAN NATURALIST

An Indian Ocean centre of origin revisited: Palaeogene and Neogene influences defining a biogeographic realm

(2015) David O. Obura   JOURNAL OF BIOGEOGRAPHY

Unexpected cryptic species diversity in the widespread coralSeriatopora hystrixmasks spatial-genetic patterns of connectivity

(2015) Patricia A. Warner et al.   MOLECULAR ECOLOGY

Marine defaunation: Animal loss in the global ocean

(2015) D. J. McCauley et al.   SCIENCE

Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae)

(2015) Yan Hou et al.   PLoS One

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

Genetic species delineation among branching Caribbean Porites corals

(2014) C. Prada et al.   CORAL REEFS

Can we derive macroecological patterns from primary Global Biodiversity Information Facility data?

(2014) Emilio García-Roselló et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Use of RAD sequencing for delimiting species

(2014) E Pante et al.   HEREDITY

A Phylogeny of the Family Poritidae (Cnidaria, Scleractinia) Based on Molecular and Morphological Analyses

(2014) Yuko F. Kitano et al.   PLoS One

Species Delimitation using Genome-Wide SNP Data

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

Forgotten in the taxonomic literature: resurrection of the scleractinian coral genusSclerophyllia(Scleractinia, Lobophylliidae) from the Arabian Peninsula and its phylogenetic relationships

(2014) Roberto Arrigoni et al.   SYSTEMATICS AND BIODIVERSITY

Pachyseris inattesa sp. n. (Cnidaria, Anthozoa, Scleractinia): a new reef coral species from the Red Sea and its phylogenetic relationships

(2014) Tullia Isotta Terraneo et al.   ZooKeys

Towards a phylogenetic classification of reef corals: the Indo-Pacific generaMerulina,GoniastreaandScapophyllia(Scleractinia, Merulinidae)

(2014) Danwei Huang et al.   ZOOLOGICA SCRIPTA

With eyes wide open: a revision of species within and closely related to thePocillopora damicornisspecies complex (Scleractinia; Pocilloporidae) using morphology and genetics

(2014) Sebastian Schmidt-Roach et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Taxonomic classification of the reef coral families Merulinidae, Montastraeidae, and Diploastraeidae (Cnidaria: Anthozoa: Scleractinia)

(2014) Danwei Huang et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

(2014) Jonathan B. Puritz et al.   PeerJ

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Blind to morphology: genetics identifies several widespread ecologically common species and few endemics among Indo-Pacific cauliflower corals (Pocillopora, Scleractinia)

(2013) Jorge H. Pinzón et al.   JOURNAL OF BIOGEOGRAPHY

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

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

Faunal breaks and species composition of Indo-Pacific corals: the role of plate tectonics, environment and habitat distribution

(2013) S. A. Keith et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

(2013) Marie Cariou et al.   Ecology and Evolution

ezRAD: a simplified method for genomic genotyping in non-model organisms

(2013) Robert J. Toonen et al.   PeerJ

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 effect of RAD allele dropout on the estimation of genetic variation within and between populations

(2012) Mathieu Gautier 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

Molecular phylogeny of the Robust clade (Faviidae, Mussidae, Merulinidae, and Pectiniidae): An Indian Ocean perspective

(2012) Roberto Arrigoni et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Inferring Phylogenies from RAD Sequence Data

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

The Diversity and Biogeography of Western Indian Ocean Reef-Building Corals

(2012) David Obura   PLoS One

Systematics of the coral genusCraterastrea(Cnidaria, Anthozoa, Scleractinia) and description of a new family through combined morphological and molecular analyses

(2012) Francesca Benzoni et al.   SYSTEMATICS AND BIODIVERSITY

Taxonomic classification of the reef coral family Mussidae (Cnidaria: Anthozoa: Scleractinia)

(2012) ANN F. BUDD et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

(2011) H. E. L. Lischer et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

RADSeq: next-generation population genetics

(2011) J. W. Davey et al.   Briefings in Functional Genomics

Comparison of morphological and genetic analyses reveals cryptic divergence and morphological plasticity in Stylophora (Cnidaria, Scleractinia)

(2011) Fabrizio Stefani et al.   CORAL REEFS

THE QUANTITATIVE GENETICS OF INCIPIENT SPECIATION: HERITABILITY AND GENETIC CORRELATIONS OF SKELETAL TRAITS IN POPULATIONS OF DIVERGING FAVIA FRAGUM ECOMORPHS

(2011) David B. Carlon et al.   EVOLUTION

Incongruence between morphotypes and genetically delimited species in the coral genus Stylophora: phenotypic plasticity, morphological convergence, morphological stasis or interspecific hybridization?

(2011) Jean-François Flot et al.   BMC ECOLOGY

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Tectonic history of the western Tethys since the Late Triassic

(2010) A. Schettino et al.   GEOLOGICAL SOCIETY OF AMERICA BULLETIN

Semi-permeable species boundaries in the coral genus Madracis: Introgression in a brooding coral system

(2010) P.R. Frade et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Ecomorph or Endangered Coral? DNA and Microstructure Reveal Hawaiian Species Complexes: Montipora dilatata/flabellata/turgescens & M. patula/verrilli

(2010) Zac H. Forsman et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Shape-shifting corals: Molecular markers show morphology is evolutionarily plastic in Porites

(2009) Zac H Forsman et al.   BMC EVOLUTIONARY BIOLOGY

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Morphological plasticity in scleractinian corals

(2008) Peter A. Todd   BIOLOGICAL REVIEWS

Mitochondrial and Nuclear Genes Suggest that Stony Corals Are Monophyletic but Most Families of Stony Corals Are Not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria)

(2008) Hironobu Fukami et al.   PLoS One

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

Hemiplasy: A New Term in the Lexicon of Phylogenetics

(2008) John C. Avise et al.   SYSTEMATIC BIOLOGY