A hybrid-capture approach to reconstruct the phylogeny of Scleractinia (Cnidaria: Hexacorallia)

Phylogenetics and taxonomy of the scleractinian coral family Euphylliidae

(2023) Roberto Arrigoni et al.   CONTRIBUTIONS TO ZOOLOGY

Re-Examination of the Phylogenetic Relationship among Merulinidae Subclades in Non-Reefal Coral Communities of Northeastern Taiwan

(2022) Chieh-Jhen Chen et al.   Diversity-Basel

Phylogeography of recent Plesiastrea (Scleractinia: Plesiastreidae) based on an integrated taxonomic approach

(2022) David J. Juszkiewicz et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Caryophylliids (Anthozoa, Scleractinia) and mitochondrial gene order: Insights from mitochondrial and nuclear phylogenomics

(2022) I.G.L. Seiblitz et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evidence for adaptive morphological plasticity in the Caribbean coral, Acropora cervicornis

(2022) Wyatt C. Million et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Application of phylogenomic tools to unravel anthozoan evolution

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

Integrative systematics of the scleractinian coral genera Caulastraea , Erythrastrea and Oulophyllia

(2021) Roberto Arrigoni et al.   ZOOLOGICA SCRIPTA

Morphological stasis masks ecologically divergent coral species on tropical reefs

(2021) Pim Bongaerts et al.   CURRENT BIOLOGY

Distinct lineages and population genomic structure of the coral Pachyseris speciosa in the small equatorial reef system of Singapore

(2021) Bar Feldman et al.   CORAL REEFS

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

Phylogenomics of Porites from the Arabian Peninsula

(2021) Tullia I. Terraneo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Solving the Coral Species Delimitation Conundrum

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

Lineage-specific variation in the evolutionary stability of coral photosymbiosis

(2021) Jordan A. Gault et al.   Science Advances

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

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

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

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

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

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

Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods

(2020) Stéphane Guindon   Frontiers in Genetics

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

The Origin and Correlated Evolution of Symbiosis and Coloniality in Scleractinian Corals

(2020) Ana Navarro Campoy et al.   Frontiers in Marine Science

Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae)

(2020) Z. H. Forsman et al.   Scientific Reports

Coral-Associated Viral Assemblages From the Central Red Sea Align With Host Species and Contribute to Holobiont Genetic Diversity

(2020) Anny Cárdenas et al.   Frontiers in Microbiology

Palaeoclimate ocean conditions shaped the evolution of corals and their skeletons through deep time

(2020) Andrea M. Quattrini et al.   Nature Ecology & 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 modern scleractinian coral with a two-component calcite–aragonite skeleton

(2020) Jarosław Stolarski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The earliest diverging extant scleractinian corals recovered by mitochondrial genomes

(2020) Isabela G. L. Seiblitz et al.   Scientific Reports

Phylogenomics, Origin, and Diversification of Anthozoans (Phylum Cnidaria)

(2020) Catherine S McFadden et al.   SYSTEMATIC BIOLOGY

Effects of missing data and data type on phylotranscriptomic analysis of stony corals (Cnidaria: Anthozoa: Scleractinia)

(2019) Zheng Bin Randolph Quek et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Environmental latitudinal gradients and host‐specificity shape Symbiodiniaceae distribution in Red Sea Porites corals

(2019) Tullia I. Terraneo et al.   JOURNAL OF BIOGEOGRAPHY

Phylotranscriptomics confirms Alveopora is sister to Montipora within the family Acroporidae

(2019) Zoe T. Richards et al.   Marine Genomics

Morphology and molecules reveal two new species of Porites (Scleractinia, Poritidae) from the Red Sea and the Gulf of Aden

(2019) Tullia I. Terraneo et al.   SYSTEMATICS AND BIODIVERSITY

The effect of alignment uncertainty, substitution models and priors in building and dating the mammal tree of life

(2019) Yan Du et al.   BMC EVOLUTIONARY BIOLOGY

Fungia fungites (Linnaeus, 1758) (Scleractinia, Fungiidae) is a species complex that conceals large phenotypic variation and a previously unrecognized genus

(2019) Yutaro Oku et al.   CONTRIBUTIONS TO ZOOLOGY

Genomic insights into hybridization of reef corals

(2019) Yafei Mao   CORAL REEFS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits

(2018) Ehsan Kayal et al.   BMC EVOLUTIONARY BIOLOGY

Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

(2018) Mario Dos Reis et al.   SYSTEMATIC BIOLOGY

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

The Roles of Introgression and Climate Change in the Rise to Dominance of Acropora Corals

(2018) Yafei Mao et al.   CURRENT BIOLOGY

Combining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae

(2018) Silas Bossert et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2017) Danwei Huang et al.   EVOLUTION

Genome-Based Analyses of Six Hexacorallian Species Reject the “Naked Coral” Hypothesis

(2017) Xin Wang et al.   Genome Biology and Evolution

A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications

(2017) Roberto Arrigoni et al.   Molecular Ecology Resources

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

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

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

Transcriptome and target DNA enrichment sequence data provide new insights into the phylogeny of vespid wasps (Hymenoptera: Aculeata: Vespidae)

(2017) Sarah Bank et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics

(2017) Jesse W. Breinholt et al.   SYSTEMATIC BIOLOGY

Resurrecting a subgenus to genus: molecular phylogeny of Euphyllia and Fimbriaphyllia (order Scleractinia; family Euphyllidae; clade V)

(2017) Katrina S. Luzon et al.   PeerJ

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

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

Environmental tolerance governs the presence of reef corals at latitudes beyond reef growth

(2016) Toni L. Mizerek et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Monophyly of Anthozoa (Cnidaria): why do nuclear and mitochondrial phylogenies disagree?

(2016) Marine Pratlong et al.   ZOOLOGICA SCRIPTA

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

(2016) Danwei Huang et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Restructuring the Traditional Suborders in the Order Scleractinia Based on Embryogenetic Morphological Characteristics

(2016) Nami Okubo   ZOOLOGICAL SCIENCE

HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

(2016) Matthew G. Johnson et al.   Applications in Plant Sciences

Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses

(2016) Mei Fang Lin et al.   PeerJ

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data

(2015) Konstantin Okonechnikov et al.   BIOINFORMATICS

Microstructural disparity between basal micrabaciids and other Scleractinia: new evidence from NeogeneStephanophyllia

(2015) Katarzyna Janiszewska et al.   LETHAIA

An Exon-Capture System for the Entire Class Ophiuroidea

(2015) Andrew F. Hugall et al.   MOLECULAR BIOLOGY AND EVOLUTION

The future of evolutionary diversity in reef corals

(2015) D. Huang et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Scleractinian corals (Fungiidae, Agariciidae and Euphylliidae) of Pulau Layang-Layang, Spratly Islands, with a note on Pavona maldivensis (Gardiner, 1905)

(2015) Zarinah Waheed et al.   ZooKeys

Phylogenomic Analyses Support Traditional Relationships within Cnidaria

(2015) Felipe Zapata et al.   PLoS One

Clock model makes a large difference to age estimates of long-stemmed clades with no internal calibration: a test using Australian grasstrees

(2014) Michael D Crisp et al.   BMC EVOLUTIONARY BIOLOGY

Mitochondrial Genome Rearrangements in the Scleractinia/Corallimorpharia Complex: Implications for Coral Phylogeny

(2014) Mei-Fang Lin et al.   Genome Biology and Evolution

ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

(2014) Andre J. Aberer et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

The “Naked Coral” Hypothesis Revisited – Evidence for and Against Scleractinian Monophyly

(2014) Marcelo V. Kitahara et al.   PLoS One

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

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

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

A phylogeny reconstruction of the Dendrophylliidae (Cnidaria, Scleractinia) based on molecular and micromorphological criteria, and its ecological implications

(2014) Roberto Arrigoni et al.   ZOOLOGICA SCRIPTA

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

(2014) Danwei Huang et al.   ZOOLOGICA SCRIPTA

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

Cnidarian phylogenetic relationships as revealed by mitogenomics

(2013) Ehsan Kayal et al.   BMC EVOLUTIONARY BIOLOGY

A practical guide to molecular dating

(2013) Hervé Sauquet   COMPTES RENDUS PALEVOL

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

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

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

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

A Simple Method for Estimating Informative Node Age Priors for the Fossil Calibration of Molecular Divergence Time Analyses

(2013) Michael D. Nowak et al.   PLoS One

Comparative Embryology of Eleven Species of Stony Corals (Scleractinia)

(2013) Nami Okubo et al.   PLoS One

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

(2013) Daniel G. Luck et al.   PeerJ

The first modern solitary Agariciidae (Anthozoa, Scleractinia) revealed by molecular and microstructural analysis

(2012) Marcelo V. Kitahara et al.   INVERTEBRATE SYSTEMATICS

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

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

Skeletal ontogeny in basal scleractinian micrabaciid corals

(2012) Katarzyna Janiszewska et al.   JOURNAL OF MORPHOLOGY

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

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

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Threatened Reef Corals of the World

(2012) Danwei Huang   PLoS One

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

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

Deltocyathiidae, an early-diverging family of Robust corals (Anthozoa, Scleractinia)

(2012) Marcelo V. Kitahara et al.   ZOOLOGICA SCRIPTA

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

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

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

The ancient evolutionary origins of Scleractinia revealed by azooxanthellate corals

(2011) Jarosław Stolarski et al.   BMC EVOLUTIONARY BIOLOGY

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

(2011) Danwei Huang et al.   BMC EVOLUTIONARY BIOLOGY

Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record

(2011) Eunji Park et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Best Practices for Justifying Fossil Calibrations

(2011) James F. Parham et al.   SYSTEMATIC BIOLOGY

Monophyletic origin ofCaryophyllia(Scleractinia, Caryophylliidae), with descriptions of six new species

(2011) Marcelo V. Kitahara et al.   SYSTEMATICS AND BIODIVERSITY

Archetypal ‘elkhorn’ coral discovered in the Pacific Ocean

(2011) Zoe T. Richards et al.   SYSTEMATICS AND BIODIVERSITY

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

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

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

A unique skeletal microstructure of the deep-sea micrabaciid scleractinian corals

(2010) Katarzyna Janiszewska et al.   JOURNAL OF MORPHOLOGY

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

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

Effects of Substitution Models on Divergence Time Estimates: Simulations and an Empirical Study of Model Uncertainty Using Cornales

(2010) John J. Schenk et al.   SYSTEMATIC BOTANY

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

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

Calibrating the Tree of Life: fossils, molecules and evolutionary timescales

(2009) Félix Forest   ANNALS OF BOTANY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

An examination of phylogenetic models of substitution rate variation among lineages

(2009) S. Y.W. Ho   Biology Letters

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

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

Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times

(2009) Simon Y. W. Ho et al.   SYSTEMATIC BIOLOGY

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

FIRST RECORD OF THE INDO-PACIFIC REEF CORAL GENUSISOPORAIN THE CARIBBEAN REGION: TWO NEW SPECIES FROM THE NEOGENE OF CURAÇAO, NETHERLANDS ANTILLES

(2008) ANN F. BUDD et al.   PALAEONTOLOGY

Some Rare Indo-Pacific Coral Species Are Probable Hybrids

(2008) Zoe T. Richards et al.   PLoS One

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