Application of phylogenomic tools to unravel anthozoan evolution

Phylogenetic Relationships Within Chrysogorgia (Alcyonacea: Octocorallia), a Morphologically Diverse Genus of Octocoral, Revealed Using a Target Enrichment Approach

(2021) Candice Bobby Untiedt et al.   Frontiers in Marine Science

Tentacle Transcriptomes of the Speckled Anemone (Actiniaria: Actiniidae: Oulactis sp.): Venom-Related Components and Their Domain Structure

(2020) Michela L. Mitchell et al.   MARINE BIOTECHNOLOGY

The genome of the sea anemone Actinia equina (L.): Meiotic toolkit genes and the question of sexual reproduction

(2020) Craig S. Wilding et al.   Marine Genomics

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

TREEasy: an automated workflow to infer gene trees, species trees, and phylogenetic networks from multilocus data

(2020) Yafei Mao et al.   Molecular Ecology Resources

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

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

Large scale genome skimming from herbarium material for accurate plant identification and phylogenomics

(2020) Paul G. Nevill et al.   Plant Methods

Evolutionary Traits that Enable Scleractinian Corals to Survive Mass Extinction Events

(2020) Gal Dishon et al.   Scientific Reports

Characterization of the complete mitochondrial genome sequences of three Merulinidae corals and novel insights into the phylogenetics

(2020) Wentao Niu et al.   PeerJ

A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

(2020) Tobias Andermann et al.   Frontiers in Genetics

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

Evolutionary implications of analyses of complete mitochondrial genomes across order Zoantharia (Cnidaria: Hexacorallia)

(2020) Angelo Poliseno et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics

(2020) Rémi Allio et al.   Molecular Ecology Resources

Phylogenetic tree building in the genomic age

(2020) Paschalia Kapli et al.   NATURE REVIEWS GENETICS

The complete mitochondrial genome of Plesiastrea versipora (Scleractinia, Plesiastreidae) sheds light on its phylogeny and taxonomy of the family Plesiastreidae

(2020) Wentao Niu et al.   SAUDI JOURNAL OF BIOLOGICAL SCIENCES

Atlantia, a new genus of Dendrophylliidae (Cnidaria, Anthozoa, Scleractinia) from the eastern Atlantic

(2020) Kátia C.C. Capel et al.   PeerJ

Revisiting ceriantharian (Anthozoa) mitochondrial genomes: casting doubts about their structure and size

(2020) David Roy Smith   Genome Biology and Evolution

Biochemical characterization of diverse deep-sea anthozoan bioluminescence systems

(2020) Manabu Bessho-Uehara et al.   MARINE BIOLOGY

Transcriptomic Analysis of Four Cerianthid (Cnidaria, Ceriantharia) Venoms

(2020) Anna M. L. Klompen et al.   Marine Drugs

Is phylotranscriptomics as reliable as phylogenomics?

(2020) Seongmin Cheon et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Morphological and molecular description of a new genus and species of black coral (Cnidaria: Anthozoa: Hexacorallia: Antipatharia: Antipathidae: Blastopathes) from Papua New Guinea 

(2020) JEREMY HOROWITZ et al.   ZOOTAXA

The Genome Sequence of the Octocoral Paramuricea clavata - A Key Resource To Study the Impact of Climate Change in the Mediterranean

(2020) Jean-Baptiste Ledoux et al.   G3-Genes Genomes Genetics

Phylogenetics and Mitogenome Organisation in Black Corals (Anthozoa: Hexacorallia: Antipatharia): An Order-Wide Survey Inferred From Complete Mitochondrial Genomes

(2020) Nick J. Barrett et al.   Frontiers in Marine Science

The genome of the cauliflower coral Pocillopora verrucosa

(2020) Carol Buitrago-López et al.   Genome Biology and Evolution

ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy

(2020) Chao Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Population genetic structure of the great star coral, Montastraea cavernosa, across the Cuban archipelago with comparisons between microsatellite and SNP markers

(2020) Alexis B. Sturm et al.   Scientific Reports

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

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

Initial data release and announcement of the 10,000 Fish Genomes Project (Fish10K)

(2020) Guangyi Fan et al.   GigaScience

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

Deep-water sea anemone with a two-chromosome mitochondrial genome

(2019) Arseny Dubin et al.   GENE

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

Phylogenomics from Low-coverage Whole-genome Sequencing

(2019) Feng Zhang et al.   Methods in Ecology and Evolution

Complete mitochondrial genome of Callogorgia cf. gracilis (Octocorallia: Calcaxonia: Primnoidae)

(2019) Erin E. Easton et al.   Mitochondrial DNA Part B-Resources

The current application of ecological connectivity in the design of marine protected areas

(2019) Arieanna C. Balbar et al.   Global Ecology and Conservation

Towards population genomics in non-model species with large genomes: a case study of the marine zooplankton Calanus finmarchicus

(2019) Marvin Choquet et al.   Royal Society Open Science

Genomic Variants Among Threatened Acropora Corals

(2019) Sheila A. Kitchen et al.   G3-Genes Genomes Genetics

Genome analysis of the rice coral Montipora capitata

(2019) Alexander Shumaker et al.   Scientific Reports

Model selection may not be a mandatory step for phylogeny reconstruction

(2019) Shiran Abadi et al.   Nature Communications

The draft genome of an octocoral, Dendronephthya gigantea

(2019) Yeonsu Jeon et al.   Genome Biology and Evolution

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

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

Development of a transcriptomic database for 14 species of scleractinian corals

(2019) Yanjie Zhang et al.   BMC GENOMICS

First transcriptome assembly of the temperate azooxanthellate octocoral Eleutherobia rubra

(2019) Taewoo Ryu et al.   Marine Genomics

Model Choice, Missing Data and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships

(2019) Arun N Prasanna et al.   SYSTEMATIC BIOLOGY

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome

(2019) Justin B Jiang et al.   GigaScience

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

Rare coral under the genomic microscope: timing and relationships among Hawaiian Montipora

(2019) Regina L. Cunha et al.   BMC EVOLUTIONARY BIOLOGY

Revisiting metazoan phylogeny with genomic sampling of all phyla

(2019) Christopher E. Laumer et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Linear Mitochondrial Genome in Anthozoa (Cnidaria): A Case Study in Ceriantharia

(2019) Sérgio N. Stampar et al.   Scientific Reports

Novel diversity in mitochondrial genomes of deep-sea Pennatulacea (Cnidaria: Anthozoa: Octocorallia)

(2019) Raissa I. Hogan et al.   Mitochondrial DNA Part A

New non-bilaterian transcriptomes provide novel insights into the evolution of coral skeletomes.

(2019) Nicola Conci et al.   Genome Biology and Evolution

The many faced symbiotic snakelocks anemone (Anemonia viridis, Anthozoa): host and symbiont genetic differentiation among colour morphs

(2019) Barbara Porro et al.   HEREDITY

Phylotranscriptomics confirms Alveopora is sister to Montipora within the family Acroporidae

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

Extensive coral mortality and critical habitat loss following dredging and their association with remotely-sensed sediment plumes

(2019) Ross Cunning et al.   MARINE POLLUTION BULLETIN

ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models

(2019) Diego Darriba et al.   MOLECULAR BIOLOGY AND EVOLUTION

Stacks 2: analytical methods for paired‐end sequencing improve RADseq‐based population genomics

(2019) Nicolas C. Rochette et al.   MOLECULAR ECOLOGY

Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan (Hexacorallia: Actiniaria)

(2019) Benjamin M. Titus et al.   MOLECULAR ECOLOGY

The draft genome of Actinia tenebrosa reveals insights into toxin evolution

(2019) Joachim M. Surm et al.   Ecology and Evolution

A genomic view of the reef-building coral Porites lutea and its microbial symbionts

(2019) Steven J. Robbins et al.   Nature Microbiology

RADseq population genomics confirms divergence across closely related species in blue coral (Heliopora coerulea)

(2019) Akira Iguchi et al.   BMC EVOLUTIONARY BIOLOGY

Genomic insights into hybridization of reef corals

(2019) Yafei Mao   CORAL REEFS

Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

(2019) Benjamin R Karin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic relationships among the clownfish-hosting sea anemones

(2019) Benjamin M. Titus et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

One thousand plant transcriptomes and the phylogenomics of green plants

(2019)   NATURE

Combined cultivation and single-cell approaches to the phylogenomics of nucleariid amoebae, close relatives of fungi

(2019) Luis Javier Galindo et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mitogenomic phylogenetic analyses of Leptogorgia virgulata and Leptogorgia hebes (Anthozoa: Octocorallia) from the Gulf of Mexico provides insight on Gorgoniidae divergence between Pacific and Atlantic lineages

(2019) Samantha Silvestri et al.   Ecology and Evolution

Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype

(2019) Kenji Takata et al.   PeerJ

Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

(2019) Andrew D. Young et al.   SYSTEMATIC ENTOMOLOGY

Molecular phylogeny of Ceriantharia (Cnidaria: Anthozoa) reveals non-monophyly of traditionally accepted families

(2019) Anny C Forero Mejia et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Mitogenomics suggests a sister relationship of Relicanthus daphneae (Cnidaria: Anthozoa: Hexacorallia: incerti ordinis) with Actiniaria

(2019) Madelyne Xiao et al.   Scientific Reports

Global Neuropeptide Annotations From the Genomes and Transcriptomes of Cubozoa, Scyphozoa, Staurozoa (Cnidaria: Medusozoa), and Octocorallia (Cnidaria: Anthozoa)

(2019) Thomas L. Koch et al.   Frontiers in Endocrinology

Phylogenomics provides robust support for a two-domains tree of life

(2019) Tom A. Williams et al.   Nature Ecology & Evolution

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

Long reads: their purpose and place

(2018) Martin O Pollard et al.   HUMAN MOLECULAR GENETICS

The Holo-Transcriptome of the Zoantharian Protopalythoa variabilis (Cnidaria: Anthozoa): A Plentiful Source of Enzymes for Potential Application in Green Chemistry, Industrial and Pharmaceutical Biotechnology

(2018) Jean-Étienne R. L. Morlighem et al.   Marine Drugs

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

The search for loci under selection: trends, biases and progress

(2018) Collin W. Ahrens et al.   MOLECULAR ECOLOGY

Hierarchical biogeographical processes largely explain the genomic divergence pattern in a species complex of sea anemones (Metridioidea: Sagartiidae: Anthothoe )

(2018) Carlos A. Spano et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genomics: Next regeneration sequencing for reference genomes

(2018) Darren J. Burgess   NATURE REVIEWS GENETICS

Hox and Wnt pattern the primary body axis of an anthozoan cnidarian before gastrulation

(2018) Timothy Q. DuBuc et al.   Nature Communications

On the universality of target-enrichment baits for phylogenomic research

(2018) Silas Bossert et al.   Methods in Ecology and Evolution

Transcriptome analysis of the reef-building octocoral, Heliopora coerulea

(2018) Christine Guzman et al.   Scientific Reports

Practical considerations for plant phylogenomics

(2018) Michael R. McKain et al.   Applications in Plant Sciences

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

The complete mitochondrial genome of the Montipora peltiformi (Scleractinia: Acroporidae)

(2018) Xin Wang et al.   Mitochondrial DNA Part B-Resources

Holobiont transcriptome of colonial scleractinian coral Alveopora japonica

(2018) Taewoo Ryu et al.   Marine Genomics

Ecosystem restructuring along the Great Barrier Reef following mass coral bleaching

(2018) Rick D. Stuart-Smith et al.   NATURE

Global warming transforms coral reef assemblages

(2018) Terry P. Hughes et al.   NATURE

Integrated evidence reveals a new species in the ancient blue coral genus Heliopora (Octocorallia)

(2018) Zoe T. Richards et al.   Scientific Reports

Comparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution

(2018) R. Cunning et al.   Scientific Reports

ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes

(2018) Benoit Morel et al.   BIOINFORMATICS

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

Complete mitochondrial genome of Echinophyllia aspera (Scleractinia, Lobophylliidae): Mitogenome characterization and phylogenetic positioning

(2018) Wentao Niu et al.   ZooKeys

Hybrid Capture-Based Next Generation Sequencing and Its Application to Human Infectious Diseases

(2018) Maxime Gaudin et al.   Frontiers in Microbiology

Complete mitochondrial genome of Acropora valida (Scleractinia, Acroporidae): mitogenome characterization and phylogenetic positioning

(2018) Shuangen Yu et al.   Mitochondrial DNA Part B-Resources

Molecular phylogeny and diversity of sea pens (Cnidaria: Octocorallia: Pennatulacea) with a focus on shallow water species of the northwestern Pacific Ocean

(2018) Yuka Kushida et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Zoantharian mitochondrial genomes contain unique complex group I introns and highly conserved intergenic regions

(2017) Sylvia Ighem Chi et al.   GENE

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

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

Analyses of Corallimorpharian Transcriptomes Provide New Perspectives on the Evolution of Calcification in the Scleractinia (Corals)

(2017) Mei-Fang Lin et al.   Genome Biology and Evolution

PhyloNetworks: A Package for Phylogenetic Networks

(2017) Claudia Solís-Lemus 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

Draft genomes of the corallimorpharians Amplexidiscus fenestrafer and Discosoma sp.

(2017) Xin Wang 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

Intragenic DNA methylation prevents spurious transcription initiation

(2017) Francesco Neri et al.   NATURE

Coral reefs in the Anthropocene

(2017) Terry P. Hughes et al.   NATURE

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

Biodiversity losses and conservation responses in the Anthropocene

(2017) Christopher N. Johnson et al.   SCIENCE

Phylogeny of the manta and devilrays (Chondrichthyes: mobulidae), with an updated taxonomic arrangement for the family

(2017) William T White et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Identification of long non-coding RNAs in two anthozoan species and their possible implications for coral bleaching

(2017) Chen Huang et al.   Scientific Reports

Three decades of coral reef community dynamics in St. John, USVI: a contrast of scleractinians and octocorals

(2017) Georgios Tsounis et al.   Ecosphere

Evidence for a genetic sex determination in Cnidaria, the Mediterranean red coral (Corallium rubrum)

(2017) M. Pratlong et al.   Royal Society Open Science

Deep reefs are not universal refuges: Reseeding potential varies among coral species

(2017) Pim Bongaerts et al.   Science Advances

Next-generation sequencing yields the complete mitogenome of stony coral (Favites abdita)

(2017) Wentao Niu et al.   Mitochondrial DNA Part B-Resources

The complete mitochondrial genome of the Cyphastrea serailia

(2017) Wentao Niu et al.   Mitochondrial DNA Part B-Resources

Transcriptome profiling of Galaxea fascicularis and its endosymbiont Symbiodinium reveals chronic eutrophication tolerance pathways and metabolic mutualism between partners

(2017) Zhenyue Lin et al.   Scientific Reports

The molecular basis of differential morphology and bleaching thresholds in two morphs of the coral Pocillopora acuta

(2017) Hillary Smith et al.   Scientific Reports

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

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

Conservation of reef corals in the South China Sea based on species and evolutionary diversity

(2016) Danwei Huang et al.   BIODIVERSITY AND CONSERVATION

RADIS:analysis ofRAD-seq data for interspecific phylogeny

(2016) Astrid Cruaud et al.   BIOINFORMATICS

A comparative view of early development in the corals Favia lizardensis, Ctenactis echinata, and Acropora millepora - morphology, transcriptome, and developmental gene expression

(2016) Nami Okubo et al.   BMC EVOLUTIONARY BIOLOGY

Genome-wide polymorphism and signatures of selection in the symbiotic sea anemone Aiptasia

(2016) Emily S. Bellis et al.   BMC GENOMICS

Genomics and development of Nematostella vectensis and other anthozoans

(2016) Fabian Rentzsch et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Impacts of climate change and ocean acidification on coral reef fisheries: An integrated ecological–economic model

(2016) Ann E. Speers et al.   ECOLOGICAL ECONOMICS

The Transcriptome of the ZoanthidProtopalythoa variabilis(Cnidaria, Anthozoa) Predicts a Basal Repertoire of Toxin-like and Venom-Auxiliary Polypeptides

(2016) Chen Huang et al.   Genome Biology and Evolution

Homoplasious colony morphology and mito-nuclear phylogenetic discordance among Eastern Pacific octocorals

(2016) Sandra L. Ament-Velásquez 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

Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms

(2016) Cyrielle Gasc et al.   NUCLEIC ACIDS RESEARCH

Stepwise Evolution of Coral Biomineralization Revealed with Genome-Wide Proteomics and Transcriptomics

(2016) Takeshi Takeuchi et al.   PLoS One

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

(2016) Marine Pratlong et al.   ZOOLOGICA SCRIPTA

Global marine protected areas do not secure the evolutionary history of tropical corals and fishes

(2016) D. Mouillot et al.   Nature Communications

Reefgenomics.Org - a repository for marine genomics data

(2016) Yi Jin Liew et al.   Database-The Journal of Biological Databases and Curation

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

(2016) Claudia Solís-Lemus et al.   PLoS Genetics

Comparative genomics explains the evolutionary success of reef-forming corals

(2016) Debashish Bhattacharya et al.   eLife

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

(2016) Mei Fang Lin et al.   PeerJ

Next-generation sequencing yields the complete mitogenome of massive coral, Porites lutea (Cnidaria: Poritidae)

(2016) Wentao Niu et al.   Mitochondrial DNA Part B-Resources

The complete mitogenome of the Galaxy Coral, Galaxea fascicularis (Cnidaria: Oculinidae)

(2016) Wentao Niu et al.   Mitochondrial DNA Part B-Resources

The complete mitochondrial genome of the lobe coral Porites lobata (Anthozoa: Scleractinia) sequenced using ezRAD

(2016) Kaho H. Tisthammer et al.   Mitochondrial DNA Part B-Resources

ExaML version 3: a tool for phylogenomic analyses on supercomputers

(2015) Alexey M. Kozlov et al.   BIOINFORMATICS

Gene duplications are extensive and contribute significantly to the toxic proteome of nematocysts isolated from Acropora digitifera (Cnidaria: Anthozoa: Scleractinia)

(2015) Ranko Gacesa et al.   BMC GENOMICS

Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa

(2015) Marek L. Borowiec et al.   BMC GENOMICS

An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data

(2015) Huan Fan et al.   BMC GENOMICS

Massively parallel sequencing (MPS) assays for sequencing mitochondrial genomes: the phylogenomic implications for Acropora staghorn corals (Scleractinia; Acroporidae)

(2015) Shang-Yin Vanson Liu et al.   MARINE BIOLOGY

Multiplexed pyrosequencing of nine sea anemone (Cnidaria: Anthozoa: Hexacorallia: Actiniaria) mitochondrial genomes

(2015) Jonathan Foox et al.   Mitochondrial DNA

The Impact of Missing Data on Species Tree Estimation

(2015) Zhenxiang Xi et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Exon-Capture System for the Entire Class Ophiuroidea

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

When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny

(2015) Shea M. Lambert et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogeny and systematics of deep-sea precious corals (Anthozoa: Octocorallia: Coralliidae)

(2015) Tzu-Hsuan Tu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals

(2015) David J. Combosch et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Bird sequencing project takes off

(2015) Guojie Zhang   NATURE

The future of evolutionary diversity in reef corals

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

Fossils, phylogenies, and the challenge of preserving evolutionary history in the face of anthropogenic extinctions

(2015) Danwei Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Error, signal, and the placement of Ctenophora sister to all other animals

(2015) Nathan V. Whelan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome ofAiptasia, a sea anemone model for coral symbiosis

(2015) Sebastian Baumgarten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fifteen forms of biodiversity trend in the Anthropocene

(2015) Brian J. McGill et al.   TRENDS IN ECOLOGY & EVOLUTION

MIG-seq: an effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform

(2015) Yoshihisa Suyama et al.   Scientific Reports

De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes

(2015) Sheila A. Kitchen et al.   G3-Genes Genomes Genetics

Microbes in the coral holobiont: partners through evolution, development, and ecological interactions

(2015) Janelle R. Thompson et al.   Frontiers in Cellular and Infection Microbiology

Overview of the order Zoantharia (Cnidaria: Anthozoa) in Brazil

(2015) Maria Eduarda Alves Santos et al.   Marine Biodiversity

From promise to practice: pairing non-invasive sampling with genomics in conservation

(2015) Michael A. Russello et al.   PeerJ

Accelerated modern human-induced species losses: Entering the sixth mass extinction

(2015) G. Ceballos et al.   Science Advances

Phylogenomic Analyses Support Traditional Relationships within Cnidaria

(2015) Felipe Zapata et al.   PLoS One

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

TIR-domain-containing protein repertoire of nine anthozoan species reveals coral–specific expansions and uncharacterized proteins

(2014) Angela Z. Poole et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

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

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

Octocoral Mitochondrial Genomes Provide Insights into the Phylogenetic History of Gene Order Rearrangements, Order Reversals, and Cnidarian Phylogenetics

(2014) D. F. Figueroa et al.   Genome Biology and Evolution

Use of RAD sequencing for delimiting species

(2014) E Pante et al.   HEREDITY

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

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

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

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

Long Term Storage of Dry versus Frozen RNA for Next Generation Molecular Studies

(2014) Eric Seelenfreund et al.   PLoS One

Maximum likelihood inference of reticulate evolutionary histories

(2014) Yun Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Distance for a General Non-Stationary Markov Substitution Process

(2014) Benjamin D. Kaehler et al.   SYSTEMATIC BIOLOGY

Geneious! Simplified Genome Skimming Methods for Phylogenetic Systematic Studies: A Case Study inOreocarya(Boraginaceae)

(2014) Lee A. Ripma et al.   Applications in Plant Sciences

The evolution and future of carbonate precipitation in marine invertebrates: Witnessing extinction or documenting resilience in the Anthropocene?

(2014) Jeana L. Drake et al.   Elementa-Science of the Anthropocene

Genome Sequence Analysis Indicates that the Model Eukaryote Nematostella vectensis Harbors Bacterial Consorts

(2013) Irena I. Artamonova et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Cnidarian phylogenetic relationships as revealed by mitogenomics

(2013) Ehsan Kayal et al.   BMC EVOLUTIONARY BIOLOGY

Complete mitochondrial genomes elucidate phylogenetic relationships of the deep-sea octocoral families Coralliidae and Paragorgiidae

(2013) Diego F. Figueroa et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

(2013)   JOURNAL OF HEREDITY

Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics

(2013) A. M. Reitzel et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Relative Importance of Coral Cover, Habitat Complexity and Diversity in Determining the Structure of Reef Fish Communities

(2013) Valeriya Komyakova et al.   PLoS One

Genomic basis for coral resilience to climate change

(2013) Daniel J. Barshis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatial community shift from hard to soft corals in acidified water

(2013) Shihori Inoue et al.   Nature Climate Change

Anthropogenic extinction threats and future loss of evolutionary history in reef corals

(2013) Danwei Huang et al.   Ecology and Evolution

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

(2013) Robert J. Toonen et al.   PeerJ

Targeted enrichment strategies for next-generation plant biology

(2012) Richard Cronn et al.   AMERICAN JOURNAL OF BOTANY

Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython

(2012) Eric Talevich et al.   BMC BIOINFORMATICS

Coral reef ecosystems protect shore from high-energy waves under climate change scenarios

(2012) Cesar Villanoy et al.   CLIMATIC CHANGE

Steroids from the Soft Coral Sinularia crassa

(2012) Chih-Hua Chao et al.   Marine Drugs

Digital Marine Bioprospecting: Mining New Neurotoxin Drug Candidates from the Transcriptomes of Cold-Water Sea Anemones

(2012) Ilona Urbarova et al.   Marine Drugs

Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets

(2012) Béatrice Roure et al.   MOLECULAR BIOLOGY AND EVOLUTION

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 transcriptomic response to thermal stress is immediate, transient and potentiated by ultraviolet radiation in the sea anemoneAnemonia viridis

(2012) A. MOYA et al.   MOLECULAR ECOLOGY

Inferring Phylogenies from RAD Sequence Data

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

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

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

Phylogenetic diversity and nature conservation: where are we?

(2012) Marten Winter et al.   TRENDS IN ECOLOGY & EVOLUTION

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

A unique horizontal gene transfer event has provided the octocoral mitochondrial genome with an active mismatch repair gene that has potential for an unusual self-contained function

(2011) Jaret P Bilewitch et al.   BMC EVOLUTIONARY BIOLOGY

Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation

(2011) Ted M. Townsend et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Using the Acropora digitifera genome to understand coral responses to environmental change

(2011) Chuya Shinzato et al.   NATURE

Has the Earth’s sixth mass extinction already arrived?

(2011) Anthony D. Barnosky et al.   NATURE

Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads

(2011) Paul D. Etter et al.   PLoS One

The Diversity of Coral Reefs: What Are We Missing?

(2011) Laetitia Plaisance et al.   PLoS One

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Deep-water scleractinian corals promote higher biodiversity in deep-sea meiofaunal assemblages along continental margins

(2010) L. Bongiorni et al.   BIOLOGICAL CONSERVATION

A response to recent proposals for integrative taxonomy

(2010) JOSÉ M. PADIAL et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

The integrative future of taxonomy

(2010) Jose M. Padial et al.   Frontiers in Zoology

Molecular Phylogenetic Insights into the Evolution of Octocorallia: A Review

(2010) C. S. McFadden et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

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

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

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions

(2009) Gregory E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating Species Trees: Methods of Phylogenetic Analysis When There Is Incongruence across Genes

(2009) L. Lacey Knowles   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

Comparative Analyses of Coding and Noncoding DNA Regions Indicate that Acropora (Anthozoa: Scleractina) Possesses a Similar Evolutionary Tempo of Nuclear vs. Mitochondrial Genomes as in Plants

(2008) I.-Ping Chen et al.   MARINE BIOTECHNOLOGY

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird 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