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

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

(2021) Roberto Arrigoni et al.   ZOOLOGICA SCRIPTA

An Indo-Pacific coral spawning database

(2021) Andrew H. Baird et al.   Scientific Data

Environmental factors explain spawning day deviation from full moon in the scleractinian coral Acropora

(2020) Yusuke Sakai et al.   Biology Letters

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

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

Multispecific coral spawning events and extended breeding periods on an equatorial reef

(2020) Marine Gouezo et al.   CORAL REEFS

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

A unique reproductive strategy in the mushroom coral Fungia fungites

(2020) Lee Eyal-Shaham et al.   CORAL REEFS

Differences in spawning time drive cryptic speciation in the coral Acropora divaricata

(2020) Mao Furukawa et al.   MARINE BIOLOGY

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

(2020) Andrea M. Quattrini et al.   Nature Ecology & Evolution

Simulated climate change scenarios impact the reproduction and early life stages of a soft coral

(2020) Ronen Liberman et al.   MARINE ENVIRONMENTAL RESEARCH

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

Repetitive sex change in the stony coral Herpolitha limax across a wide geographic range

(2019) Lee Eyal-Shaham et al.   Scientific Reports

MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization

(2019) Guanliang Meng et al.   NUCLEIC ACIDS RESEARCH

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

The Prevalence and Impact of Model Violations in Phylogenetic Analysis

(2019) Suha Naser-Khdour et al.   Genome Biology and Evolution

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

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

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

(2018) Roberto Arrigoni et al.   CLADISTICS

Accurate population genetic measurements require cryptic species identification in corals

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

Finding Evolutionary Processes Hidden in Cryptic Species

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

Split spawning realigns coral reproduction with optimal environmental windows

(2018) Taryn Foster et al.   Nature Communications

A simple molecular technique for distinguishing species reveals frequent misidentification of Hawaiian corals in the genus Pocillopora

(2018) Erika C. Johnston et al.   PeerJ

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

(2018) Roberto Arrigoni et al.   CORAL REEFS

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

(2018) Eugenia Zarza et al.   PeerJ

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

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

Morpho-Molecular Evidence for Polymorphism in the Mushroom Coral Cycloseris hexagonalis (Scleractinia: Fungiidae), with a New Phylogenetic Position and the Establishment of a New Genus for the Species

(2017) Yutaro Oku et al.   ZOOLOGICAL 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

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

(2016) Robert Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) R. M. Francis   Molecular Ecology Resources

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

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

Annual Variation in the Timing of Coral Spawning in a High-Latitude Environment: Influence of Temperature

(2016) Yoko Nozawa   BIOLOGICAL BULLETIN

Switch between Morphospecies of Pocillopora Corals

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

Species Richness on Coral Reefs and the Pursuit of Convergent Global Estimates

(2015) Rebecca Fisher et al.   CURRENT BIOLOGY

Asynchronous spawning in sympatric populations of a hard coral reveals cryptic species and ancient genetic lineages

(2015) Natalie L. Rosser   MOLECULAR ECOLOGY

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

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

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

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Geographic differences in vertical connectivity in the Caribbean coralMontastraea cavernosadespite high levels of horizontal connectivity at shallow depths

(2014) X. Serrano et al.   MOLECULAR ECOLOGY

Elevated Temperature Alters the Lunar Timing of Planulation in the Brooding Coral Pocillopora damicornis

(2014) Camerron M. Crowder et al.   PLoS One

The “Fungia patella group” (Scleractinia, Fungiidae) revisited with a description of the mini mushroom coral Cycloseris boschmai sp. n.

(2014) Bert Hoeksema   ZooKeys

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

Insect Mitochondrial Genomics: Implications for Evolution and Phylogeny

(2013) Stephen L. Cameron   Annual Review of Entomology

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

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

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

A molecular and morphological exploration of the generic boundaries in the family Melithaeidae (Coelenterata: Octocorallia) and its taxonomic consequences

(2013) Bastian T. Reijnen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Counting the spots: a molecular and morphological phylogeny of the spotted darnerBoyeria(Odonata: Anisoptera: Aeshnidae) with an emphasis on European taxa

(2013) MANPREET KAUR KOHLI et al.   SYSTEMATIC ENTOMOLOGY

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

(2013) Shashank Keshavmurthy et al.   Scientific Reports

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Assessing hidden species diversity in the coral Pocillopora damicornis from Eastern Australia

(2012) S. Schmidt-Roach et al.   CORAL REEFS

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

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

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

Broadcast Spawning by Pocillopora Species on the Great Barrier Reef

(2012) Sebastian Schmidt-Roach et al.   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

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

GENETIC, SPATIAL, AND TEMPORAL COMPONENTS OF PRECISE SPAWNING SYNCHRONY IN REEF BUILDING CORALS OF THE MONTASTRAEA ANNULARIS SPECIES COMPLEX

(2011) Don R. Levitan et al.   EVOLUTION

Complete sequences of mitochondria genomes of Aedes aegypti and Culex quinquefasciatus and comparative analysis of mitochondrial DNA fragments inserted in the nuclear genomes

(2011) Susanta K. Behura et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Twilight spectral dynamics and the coral reef invertebrate spawning response

(2011) A. M. Sweeney et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

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

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

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

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

(2010) Thibaut Jombart et al.   BMC GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Limitations of mitochondrial gene barcoding in Octocorallia

(2010) CATHERINE S. McFADDEN et al.   Molecular Ecology Resources

Correlated evolution of sex and reproductive mode in corals (Anthozoa: Scleractinia)

(2010) A. M. Kerr et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Biannual spawning, rapid larval development and evidence of self-seeding for scleractinian corals at an isolated system of reefs

(2009) James P. Gilmour et al.   MARINE BIOLOGY

Calm before the spawn: global coral spawning patterns are explained by regional wind fields

(2009) R. van Woesik   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Larval Dispersal and Marine Population Connectivity

(2008) Robert K. Cowen et al.   Annual Review of Marine Science

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

Genetic structure of Heliofungia actiniformis (Scleractinia: Fungiidae) populations in the Indo-Malay Archipelago: implications for live coral trade management efforts

(2008) Leyla Knittweis et al.   CONSERVATION GENETICS

Interspecific cross of Brassica oleracea var. alboglabra and B. napus: effects of growth condition and silique age on the efficiency of hybrid production, and inheritance of erucic acid in the self-pollinated backcross generation

(2008) Rick A. Bennett et al.   EUPHYTICA

Population structure is not a simple function of reproductive mode and larval type: insights from tropical corals

(2008) Karen J. Miller et al.   JOURNAL OF ANIMAL ECOLOGY

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

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

Bidirectional sex change in mushroom stony corals

(2008) Y. Loya et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

DNA BARCODING: Barcoding corals: limited by interspecific divergence, not intraspecific variation

(2007) T. L. SHEARER et al.   Molecular Ecology Resources