An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives

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

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

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

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

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

Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci

(2019) Marshal Hedin et al.   PeerJ

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

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

An In Silico Comparison of Protocols for Dated Phylogenomics

(2018) Rupert A Collins et al.   SYSTEMATIC BIOLOGY

A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements

(2018) Shahan Derkarabetian et al.   ZooKeys

On the universality of target-enrichment baits for phylogenomic research

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

Taxonomy based on science is necessary for global conservation

(2018) Scott A. Thomson et al.   PLOS BIOLOGY

An inverse latitudinal gradient in speciation rate for marine fishes

(2018) Daniel L. Rabosky et al.   NATURE

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

Exploring the genetic diversity of shallow-water Agariciidae (Cnidaria: Anthozoa) from the Saudi Arabian Red Sea

(2017) Tullia I. Terraneo et al.   Marine Biodiversity

Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status

(2016) João Filipe Riva Tonini et al.   BIOLOGICAL CONSERVATION

The evolution of fishes and corals on reefs: form, function and interdependence

(2016) David R. Bellwood et al.   BIOLOGICAL REVIEWS

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

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

High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

(2016) James Starrett et al.   Molecular Ecology Resources

Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus:Piranga)

(2016) Joseph D. Manthey et al.   SYSTEMATIC BIOLOGY

Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics

(2016) Michael G. Harvey et al.   SYSTEMATIC BIOLOGY

A Trait-Based Approach to Advance Coral Reef Science

(2016) Joshua S. Madin et al.   TRENDS IN ECOLOGY & EVOLUTION

Open Nomenclature in the biodiversity era

(2016) Marco Sigovini et al.   Methods in Ecology and Evolution

Are coral reefs victims of their own past success?

(2016) W. Renema et al.   Science Advances

PHYLUCE is a software package for the analysis of conserved genomic loci

(2015) Brant C. Faircloth   BIOINFORMATICS

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

(2015) Rebecca Fisher et al.   CURRENT BIOLOGY

Depth specialization in mesophotic corals (Leptoseris spp.) and associated algal symbionts in Hawai'i

(2015) X. Pochon et al.   Royal Society Open Science

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

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

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

(2013) R Pyron et al.   BMC EVOLUTIONARY BIOLOGY

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

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

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

Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales

(2013) Brian Tilston Smith et al.   SYSTEMATIC BIOLOGY

Pocillopora aliciae: a new species of scleractinian coral (Scleractinia, Pocilloporidae) from subtropical Eastern Australia

(2013) SEBASTIAN SCHMIDT-ROACH et al.   ZOOTAXA

PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences

(2013) Gavin H. Thomas et al.   Methods in Ecology and Evolution

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

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

The global diversity of birds in space and time

(2012) W. Jetz et al.   NATURE

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

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

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC 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

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Limitations of mitochondrial gene barcoding in Octocorallia

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

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