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

Phylogenomics using formalin-fixed and 100+ year-old intractable natural history specimens

(2017) Sara Ruane 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

Anthopleura and the phylogeny of Actinioidea (Cnidaria: Anthozoa: Actiniaria)

(2017) M. Daly et al.   ORGANISMS DIVERSITY & EVOLUTION

Ultraconserved elements show utility in phylogenetic inference of Adephaga (Coleoptera) and suggest paraphyly of ‘Hydradephaga’

(2017) STEPHEN M. BACA et al.   SYSTEMATIC ENTOMOLOGY

Contentious relationships in phylogenomic studies can be driven by a handful of genes

(2017) Xing-Xing Shen et al.   Nature Ecology & Evolution

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

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

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

(2016) James Starrett et al.   Molecular Ecology Resources

Elucidating the evolutionary relationships of the Aiptasiidae, a widespread cnidarian–dinoflagellate model system (Cnidaria: Anthozoa: Actiniaria: Metridioidea)

(2016) Alejandro Grajales 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

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

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

(2016) Marine Pratlong et al.   ZOOLOGICA SCRIPTA

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

(2016) Mei Fang Lin et al.   PeerJ

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

(2015) Brant C. Faircloth   BIOINFORMATICS

An Exon-Capture System for the Entire Class Ophiuroidea

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

Sequence capture of ultraconserved elements from bird museum specimens

(2015) John E. McCormack et al.   Molecular Ecology Resources

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

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

How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards

(2015) Jeffrey W. Streicher et al.   SYSTEMATIC BIOLOGY

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference

(2015) Ge Tan et al.   SYSTEMATIC BIOLOGY

Phylogenomic Analyses Support Traditional Relationships within Cnidaria

(2015) Felipe Zapata et al.   PLoS One

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Genetic species delineation among branching Caribbean Porites corals

(2014) C. Prada et al.   CORAL REEFS

Use of RAD sequencing for delimiting species

(2014) E Pante et al.   HEREDITY

Morphological and molecular variability of the sea anemone Phymanthus crucifer (Cnidaria, Anthozoa, Actiniaria, Actinoidea)

(2014) Ricardo González-Muñoz et al.   JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM

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

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

A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics

(2014) Katriina L. Ilves et al.   Molecular Ecology Resources

Molecular systematics of the deep-sea bamboo corals (Octocorallia: Isididae: Keratoisidinae) from New Zealand with descriptions of two new species of Keratoisis

(2014) Luisa F. Dueñas et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast-Evolving Mitochondrial DNA in Ceriantharia: A Reflection of Hexacorallia Paraphyly?

(2014) Sérgio N. Stampar et al.   PLoS One

Hidden among Sea Anemones: The First Comprehensive Phylogenetic Reconstruction of the Order Actiniaria (Cnidaria, Anthozoa, Hexacorallia) Reveals a Novel Group of Hexacorals

(2014) Estefanía Rodríguez et al.   PLoS One

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

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

Cnidarian phylogenetic relationships as revealed by mitogenomics

(2013) Ehsan Kayal et al.   BMC EVOLUTIONARY BIOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing

(2013) John E. McCormack et al.   PLoS One

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)

(2013) Brant C. Faircloth et al.   PLoS One

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

The evolutionary history of the order Antipatharia (Cnidaria: Anthozoa: Hexacorallia) as inferred from mitochondrial and nuclear DNA: implications for black coral taxonomy and systematics

(2013) Mercer R. Brugler et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

(2012) N. G. Crawford et al.   Biology Letters

The evolution of ultraconserved elements with different phylogenetic origins

(2012) Taewoo Ryu et al.   BMC EVOLUTIONARY BIOLOGY

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

(2012) Ke Bi et al.   BMC GENOMICS

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

Stoloniferous octocorals (Anthozoa, Octocorallia) from South Africa, with descriptions of a new family of Alcyonacea, a new genus of Clavulariidae, and a new species of Cornularia (Cornulariidae)

(2012) Catherine S. McFadden et al.   INVERTEBRATE SYSTEMATICS

Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling

(2012) John J. Wiens et al.   PLoS One

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

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

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

(2011) J. E. McCormack et al.   GENOME RESEARCH

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

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomics reveals deep molluscan relationships

(2011) Kevin M. Kocot et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) G. Lunter et al.   GENOME RESEARCH

Phylogenetic Signal in Mitochondrial and Nuclear Markers in Sea Anemones (Cnidaria, Actiniaria)

(2010) M. Daly et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Molecular Phylogenetic Insights into the Evolution of Octocorallia: A Review

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

Species delimitation of common reef corals in the genus Pocillopora using nucleotide sequence phylogenies, population genetics and symbiosis ecology

(2010) JORGE H. PINZÓN et al.   MOLECULAR ECOLOGY

Limitations of mitochondrial gene barcoding in Octocorallia

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

The Sequence Alignment/Map format and SAMtools

(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

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Molecular systematics of the speciose Indo-Pacific soft coral genus,Sinularia(Anthozoa: Octocorallia)

(2009) Catherine S. McFadden et al.   INVERTEBRATE BIOLOGY

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

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

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

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

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