A tenuis relationship: traditional taxonomy obscures systematics and biogeography of the ‘Acropora tenuis’ (Scleractinia: Acroporidae) species complex

Large-scale biogeographic patterns are reflected in the genetic structure of a broadcast spawning stony coral

(2022) R. M. van der Ven et al.   CORAL REEFS

Cryptic diversity and spatial genetic variation in the coral Acropora tenuis and its endosymbionts across the Great Barrier Reef

(2022) Ambrocio Melvin A. Matias et al.   Evolutionary Applications

Cophylogeny and specificity between cryptic coral species ( Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae)

(2022) Erika C. Johnston et al.   MOLECULAR ECOLOGY

Quantitative three-dimensional morphological analysis supports species discrimination in complex-shaped and taxonomically challenging corals

(2022) Catalina Ramírez-Portilla et al.   Frontiers in Marine Science

Application of phylogenomic tools to unravel anthozoan evolution

(2021) Z. B. Randolph Quek et al.   CORAL REEFS

Morphological stasis masks ecologically divergent coral species on tropical reefs

(2021) Pim Bongaerts et al.   CURRENT BIOLOGY

Genome‐wide SNP genotyping reveals hidden population structure of an acroporid species at a subtropical coral island: Implications for coral restoration

(2021) Yuna Zayasu et al.   AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS

Types, topotypes and vouchers are the key to progress in coral taxonomy: Comment on Wepfer et al. (2020)

(2021) Victor E. Bonito et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Solving the Coral Species Delimitation Conundrum

(2021) Catalina Ramírez-Portilla et al.   SYSTEMATIC BIOLOGY

Consensus Guidelines for Advancing Coral Holobiont Genome and Specimen Voucher Deposition

(2021) Christian R. Voolstra et al.   Frontiers in Marine Science

Hybridisation and the evolution of coral reef biodiversity

(2021) Jean-Paul A. Hobbs et al.   CORAL REEFS

Biogeography, reproductive biology and phylogenetic divergence within the Fungiidae (mushroom corals)

(2021) Mila Grinblat et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genomic analysis of distinct bleaching tolerances among cryptic coral species

(2021) Noah H. Rose et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Global warming decreases connectivity among coral populations

(2021) Joana Figueiredo et al.   Nature Climate Change

Complete mitochondrial genomes of three reef forming Acropora corals (Acroporidae, Scleractinia) from Chagos Archipelago, Indian Ocean

(2021) Luigi Colin et al.   Biodiversity Data Journal

Incongruence between life-history traits and conservation status in reef corals

(2020) Tom C. L. Bridge et al.   CORAL REEFS

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcriptome‐based target‐enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)

(2020) Randolph Z.B. Quek et al.   Molecular Ecology Resources

Geography and spawning season drive genetic divergence among populations of the hard coral Acropora tenuis from Indonesia and Western Australia

(2020) N. L. Rosser et al.   CORAL REEFS

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

(2020) Roberto Arrigoni et al.   CORAL REEFS

New methods to calculate concordance factors for phylogenomic datasets

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Extreme seascape drives local recruitment and genetic divergence in brooding and spawning corals in remote north‐west Australia

(2020) Jim N. Underwood et al.   Evolutionary Applications

New approaches to species delimitation and population structure of anthozoans: two case studies of octocorals using ultraconserved elements and exons

(2020) Katie L. Erickson et al.   Molecular Ecology Resources

Eighteen Coral Genomes Reveal the Evolutionary Origin of Acropora Strategies to Accommodate Environmental Changes

(2020) Chuya Shinzato et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary biogeography of the reef-building coral genus Galaxea across the Indo-Pacific ocean

(2020) Patricia H. Wepfer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives

(2020) Peter F. Cowman et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Reproductive strategies in the intercrossing corals Acropora donei and A. tenuis to prevent hybridization

(2019) Masaya Morita et al.   CORAL REEFS

A demonstration of unsupervised machine learning in species delimitation

(2019) Shahan Derkarabetian et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees

(2018) Uyen Mai et al.   BMC GENOMICS

Accurate population genetic measurements require cryptic species identification in corals

(2018) Elizabeth A. Sheets et al.   CORAL REEFS

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

(2018) Cene Fišer et al.   MOLECULAR ECOLOGY

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

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

(2018) Eugenia Zarza et al.   PeerJ

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems

(2017) Andrea M. Quattrini et al.   Molecular Ecology Resources

Global warming and recurrent mass bleaching of corals

(2017) Terry P. Hughes et al.   NATURE

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Multispecies coalescent delimits structure, not species

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

Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genusAcropora

(2017) Natalie L. Rosser et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Genetic evidence of peripheral isolation and low diversity in marginal populations of the Acropora hyacinthus complex

(2016) Go Suzuki et al.   CORAL REEFS

Fecundity and the demographic strategies of coral morphologies

(2016) Mariana Álvarez-Noriega et al.   ECOLOGY

pophelper: an R package and web app to analyse and visualize population structure

(2016) R. M. Francis   Molecular Ecology Resources

Demographic history and asynchronous spawning shape genetic differentiation among populations of the hard coral Acropora tenuis in Western Australia

(2016) Natalie L. Rosser   MOLECULAR PHYLOGENETICS AND EVOLUTION

Switch between Morphospecies of Pocillopora Corals

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

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

(2015) Brant C. Faircloth   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Acropora(Scleractinia) from the Oligocene and Miocene of Europe: species longevity, origination and turnover following the Eocene–Oligocene transition

(2014) Carden C. Wallace et al.   JOURNAL OF SYSTEMATIC PALAEONTOLOGY

Lobophylliidae (Cnidaria, Scleractinia) reshuffled: Pervasive non-monophyly at genus level

(2014) Roberto Arrigoni et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Species Delimitation using Genome-Wide SNP Data

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

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

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

(2013) Simon H. Martin et al.   GENOME RESEARCH

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

(2013) Sergey Nurk et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Ultrafast Approximation for Phylogenetic Bootstrap

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

Gene flow and the maintenance of species boundaries

(2013) Erica L. Larson et al.   MOLECULAR ECOLOGY

Molecular phylogenetics of geographically restricted Acropora species: Implications for threatened species conservation

(2013) Z.T. Richards et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Long prereproductive selection and divergence by depth in a Caribbean candelabrum coral

(2013) C. Prada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unrecognized coral species diversity masks differences in functional ecology

(2013) J. N. Boulay et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

DNA barcoding reveals the coral “laboratory-rat”, Stylophora pistillata encompasses multiple identities

(2013) Shashank Keshavmurthy et al.   Scientific Reports

Polyphyly and hidden species among Hawaiʻi’s dominant mesophotic coral genera,LeptoserisandPavona(Scleractinia: Agariciidae)

(2013) Daniel G. Luck et al.   PeerJ

Synthesizing larval competence dynamics and reef-scale retention reveals a high potential for self-recruitment in corals

(2012) Joana Figueiredo et al.   ECOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Extensive sympatry, cryptic diversity and introgression throughout the geographic distribution of two coral species complexes

(2012) JASON T. LADNER et al.   MOLECULAR ECOLOGY

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

Mass digitization of scientific collections: New opportunities to transform the use of biological specimens and underwrite biodiversity science

(2012) Nico Cellinese et al.   ZooKeys

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

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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Cleaning up the 'Bigmessidae': Molecular phylogeny of scleractinian corals from Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae

(2011) Danwei Huang et al.   BMC EVOLUTIONARY BIOLOGY

Speciation with gene flow on Lord Howe Island

(2011) Alexander S. T. Papadopulos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Thibaut Jombart et al.   BMC GENETICS

Estimating dispersal potential for marine larvae: dynamic models applied to scleractinian corals

(2010) Sean R. Connolly et al.   ECOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Rethinking the Phylogeny of Scleractinian Corals: A Review of Morphological and Molecular Data

(2010) A. F. Budd et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

A Comprehensive Phylogenetic Analysis of the Scleractinia (Cnidaria, Anthozoa) Based on Mitochondrial CO1 Sequence Data

(2010) Marcelo V. Kitahara et al.   PLoS One

The name game: morpho-molecular species boundaries in the genus Psammocora (Cnidaria, Scleractinia)

(2010) FRANCESCA BENZONI et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

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

(2008) Thibaut Jombart   BIOINFORMATICS

Morphological plasticity in scleractinian corals

(2008) Peter A. Todd   BIOLOGICAL REVIEWS

Slow Mitochondrial COI Sequence Evolution at the Base of the Metazoan Tree and Its Implications for DNA Barcoding

(2008) Danwei Huang et al.   JOURNAL OF MOLECULAR EVOLUTION

More evidence for pervasive paraphyly in scleractinian corals: Systematic study of Southeast Asian Faviidae (Cnidaria; Scleractinia) based on molecular and morphological data

(2008) Danwei Huang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

One-Third of Reef-Building Corals Face Elevated Extinction Risk from Climate Change and Local Impacts

(2008) K. E. Carpenter et al.   SCIENCE