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

Genome analysis of the rice coral Montipora capitata

(2019) Alexander Shumaker et al.   Scientific Reports

Physiological responses of hydroponically-grown Japanese mint under nutrient deficiency

(2019) Chananchida Janpen et al.   PeerJ

Coral color and depth drive symbiosis ecology of Montipora capitata in Kāne‘ohe Bay, O‘ahu, Hawai‘i

(2018) T. Innis et al.   CORAL REEFS

Trade-offs in disease and bleaching susceptibility among two color morphs of the Hawaiian reef coral, Montipora capitata

(2018) Amanda Shore-Maggio et al.   CORAL REEFS

The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte

(2018) Mark N. Puttick et al.   CURRENT BIOLOGY

Genomic and geographic footprints of differential introgression between two divergent fish species (Solea spp.)

(2018) Ahmed Souissi et al.   HEREDITY

Bayesian species identification under the multispecies coalescent provides significant improvements to DNA barcoding analyses

(2017) Ziheng Yang et al.   MOLECULAR ECOLOGY

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

Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata

(2017) Hollie M. Putnam et al.   PeerJ

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

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

Getting a grip at the edge: recolonization and introgression in eastern PacificPoritescorals

(2016) Michael E. Hellberg et al.   JOURNAL OF BIOGEOGRAPHY

Parapatric genetic introgression and phenotypic assimilation: testing conditions for introgression between Hercules beetles (Dynastes , Dynastinae)

(2016) Jen-Pan Huang   MOLECULAR ECOLOGY

RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa

(2016) Santiago Herrera et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Rarity and Incomplete Sampling in DNA-Based Species Delimitation

(2016) Dirk Ahrens et al.   SYSTEMATIC BIOLOGY

High-throughput biodiversity analysis: Rapid assessment of species richness and ecological interactions of Chrysomelidae (Coleoptera) in the tropics

(2016) Jesus Gomez-Zurita et al.   ZooKeys

Setting evolutionary-based conservation priorities for a phylogenetically data-poor taxonomic group (Scleractinia)

(2015) D. J. Curnick et al.   ANIMAL CONSERVATION

Differences in Bacterial Community Structure in Two Color Morphs of the Hawaiian Reef Coral Montipora capitata

(2015) Amanda Shore-Maggio et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis

(2015) S. Lin et al.   SCIENCE

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

(2015) James B. Pease et al.   SYSTEMATIC BIOLOGY

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

(2015) Alexander Nater et al.   SYSTEMATIC BIOLOGY

Extensive phenotypic plasticity of a Red Sea coral over a strong latitudinal temperature gradient suggests limited acclimatization potential to warming

(2015) Yvonne Sawall et al.   Scientific Reports

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

DNA-based species delimitation in algae

(2014) Frederik Leliaert et al.   EUROPEAN JOURNAL OF PHYCOLOGY

Demystifying the RAD fad

(2014) Jonathan B. Puritz et al.   MOLECULAR ECOLOGY

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

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

Species Delimitation using Genome-Wide SNP Data

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

Mitochondrial Phylogenomics of Early Land Plants: Mitigating the Effects of Saturation, Compositional Heterogeneity, and Codon-Usage Bias

(2014) Yang Liu et al.   SYSTEMATIC BIOLOGY

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

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

(2014) Jonathan B. Puritz et al.   PeerJ

Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure

(2013) Eiichi Shoguchi et al.   CURRENT BIOLOGY

Heterogeneous Models Place the Root of the Placental Mammal Phylogeny

(2013) Claire C. Morgan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

(2013) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

(2013) Marie Cariou et al.   Ecology and Evolution

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

(2013) Robert J. Toonen et al.   PeerJ

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

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

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond 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

Threatened Reef Corals of the World

(2012) Danwei Huang   PLoS One

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

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

EVOLUTIONARY DIVERSIFICATION OF REEF CORALS: A COMPARISON OF THE MOLECULAR AND FOSSIL RECORDS

(2011) Carl Simpson et al.   EVOLUTION

Polymorphism in a common Atlantic reef coral (Montastraea cavernosa) and its long-term evolutionary implications

(2011) Ann F. Budd et al.   EVOLUTIONARY ECOLOGY

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Parallelization of the MAFFT multiple sequence alignment program

(2010) Kazutaka Katoh et al.   BIOINFORMATICS

Preservation of corals in salt-saturated DMSO buffer is superior to ethanol for PCR experiments

(2010) M. R. Gaither et al.   CORAL REEFS

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

Ecomorph or Endangered Coral? DNA and Microstructure Reveal Hawaiian Species Complexes: Montipora dilatata/flabellata/turgescens & M. patula/verrilli

(2010) Zac H. Forsman et al.   PLoS One

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences

(2008) Yoichiro Azuma et al.   BMC EVOLUTIONARY BIOLOGY

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS

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

The archaebacterial origin of eukaryotes

(2008) C. J. Cox et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionarily distinctive species often capture more phylogenetic diversity than expected

(2007) David W. Redding et al.   JOURNAL OF THEORETICAL BIOLOGY