Morphological stasis masks ecologically divergent coral species on tropical reefs

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

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

Intergenerational epigenetic inheritance in reef-building corals

(2020) Yi Jin Liew et al.   Nature Climate Change

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

Performing highly efficient genome scans for local adaptation with R package pcadapt version 4

(2020) Florian Privé et al.   MOLECULAR BIOLOGY AND EVOLUTION

Upwelling as the major source of nitrogen for shallow and deep reef‐building corals across an oceanic atoll system

(2019) Veronica Z. Radice et al.   FUNCTIONAL ECOLOGY

ipyrad: Interactive assembly and analysis of RADseq datasets

(2019) Deren A R Eaton et al.   BIOINFORMATICS

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Molecular characterization of larval development from fertilization to metamorphosis in a reef-building coral

(2018) Marie E. Strader 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

Adaptation to reef habitats through selection on the coral animal and its associated microbiome

(2018) Madeleine J. H. van Oppen et al.   MOLECULAR ECOLOGY

The proteomic response of the reef coral Pocillopora acuta to experimentally elevated temperatures

(2018) Anderson B. Mayfield et al.   PLoS One

CRISPR/Cas9-mediated genome editing in a reef-building coral

(2018) Phillip A. Cleves et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A fast likelihood solution to the genetic clustering problem

(2018) Marie-Pauline Beugin et al.   Methods in Ecology and Evolution

Deep reefs of the Great Barrier Reef offer limited thermal refuge during mass coral bleaching

(2018) Pedro R. Frade et al.   Nature Communications

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

(2018) Yafei Mao et al.   CURRENT BIOLOGY

Polygenic evolution drives species divergence and climate adaptation in corals

(2017) Noah H. Rose et al.   EVOLUTION

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Canonical and cellular pathways timing gamete release in Acropora digitifera, Okinawa, Japan

(2017) Y. Rosenberg et al.   MOLECULAR ECOLOGY

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

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

(2017) Pauline Gélin et al.   Ecology and Evolution

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

(2017) Pim Bongaerts et al.   Science Advances

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

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

Empty Niches after Extinctions Increase Population Sizes of Modern Corals

(2016) Carlos Prada et al.   CURRENT BIOLOGY

Developmental Progression in the CoralAcropora digitiferaIs Controlled by Differential Expression of Distinct Regulatory Gene Networks

(2016) Alejandro Reyes-Bermudez et al.   Genome Biology and Evolution

Congruent patterns of connectivity can inform management for broadcast spawning corals on the Great Barrier Reef

(2016) Vimoksalehi Lukoschek et al.   MOLECULAR ECOLOGY

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Biannual Spawning and Temporal Reproductive Isolation in Acropora Corals

(2016) James P. Gilmour et al.   PLoS One

The Microbial Signature Provides Insight into the Mechanistic Basis of Coral Success across Reef Habitats

(2016) Alejandra Hernandez-Agreda et al.   mBio

The Coral Trait Database, a curated database of trait information for coral species from the global oceans

(2016) Joshua S. Madin et al.   Scientific Data

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

(2015) Rebecca Fisher et al.   CURRENT BIOLOGY

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

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

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

(2015) Natalie L. Rosser   MOLECULAR ECOLOGY

popart: full-feature software for haplotype network construction

(2015) Jessica W. Leigh et al.   Methods in Ecology and Evolution

Signaling cascades and the importance of moonlight in coral broadcast mass spawning

(2015) Paulina Kaniewska et al.   eLife

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

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

Exploring genome characteristics and sequence quality without a reference

(2014) Jared T. Simpson   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

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

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

A coral reef refuge in the Red Sea

(2013) Maoz Fine et al.   GLOBAL CHANGE BIOLOGY

The Skeletal Proteome of the Coral Acropora millepora: The Evolution of Calcification by Co-Option and Domain Shuffling

(2013) Paula Ramos-Silva et al.   MOLECULAR BIOLOGY AND EVOLUTION

Revisiting the connectivity puzzle of the common coralPocillopora damicornis

(2013) G. Torda et al.   MOLECULAR ECOLOGY

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

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

The Dlx genes as clues to vertebrate genomics and craniofacial evolution

(2013) Masaki Takechi et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Overview of the taxonomy of zooxanthellate Scleractinia

(2013) John Veron   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies

(2012) R. Kofler et al.   BIOINFORMATICS

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

(2012) M. Kearse et al.   BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

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

(2012) Eric Talevich et al.   BMC BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

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

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

MITOS: Improved de novo metazoan mitochondrial genome annotation

(2012) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

A Lipidomic Approach to Understanding Free Fatty Acid Lipogenesis Derived from Dissolved Inorganic Carbon within Cnidarian-Dinoflagellate Symbiosis

(2012) Simon R. Dunn et al.   PLoS One

Overcoming Deep Roots, Fast Rates, and Short Internodes to Resolve the Ancient Rapid Radiation of Eupolypod II Ferns

(2012) Carl J. Rothfels et al.   SYSTEMATIC BIOLOGY

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

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Adaptive divergence in a scleractinian coral: physiological adaptation of Seriatopora hystrix to shallow and deep reef habitats

(2011) Pim Bongaerts 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

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

(2011) Fabrizio Stefani et al.   CORAL REEFS

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

Symbiodinium diversity in mesophotic coral communities on the Great Barrier Reef: a first assessment

(2011) P Bongaerts et al.   MARINE ECOLOGY PROGRESS SERIES

Historical and contemporary factors shape the population genetic structure of the broadcast spawning coral, Acropora millepora, on the Great Barrier Reef

(2011) MADELEINE J. H. Van OPPEN et al.   MOLECULAR ECOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

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

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

(2010) Thibaut Jombart et al.   BMC GENETICS

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

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Threatened Corals Provide Underexplored Microbial Habitats

(2010) Shinichi Sunagawa et al.   PLoS One

Genetic Divergence across Habitats in the Widespread Coral Seriatopora hystrix and Its Associated Symbiodinium

(2010) Pim Bongaerts et al.   PLoS One

Systematic and Biogeographical Patterns in the Reproductive Biology of Scleractinian Corals

(2009) Andrew H. Baird et al.   Annual Review of Ecology Evolution and Systematics

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

Effects of temperature on gene expression in embryos of the coral Montastraea faveolata

(2009) Christian R Voolstra et al.   BMC GENOMICS

Morphological plasticity in scleractinian corals

(2008) Peter A. Todd   BIOLOGICAL REVIEWS

FGF signalling controls formation of the apical sensory organ in the cnidarian Nematostella vectensis

(2008) F. Rentzsch et al.   DEVELOPMENT

Host pigments: potential facilitators of photosynthesis in coral symbioses

(2008) SOPHIE G. DOVE et al.   PLANT CELL AND ENVIRONMENT

Genetic Traces of Recent Long-Distance Dispersal in a Predominantly Self-Recruiting Coral

(2008) Madeleine J. H. van Oppen et al.   PLoS One