Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes

Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye

(2016) Richard C. Harrington et al.   BMC EVOLUTIONARY BIOLOGY

Resolving Cypriniformes relationships using an anchored enrichment approach

(2016) Carla C. Stout et al.   BMC EVOLUTIONARY BIOLOGY

South American Weakly Electric Fish (Gymnotiformes) Are Long-Wavelength-Sensitive Cone Monochromats

(2016) Da-Wei Liu et al.   BRAIN BEHAVIOR AND EVOLUTION

Evolution of the immune system influences speciation rates in teleost fishes

(2016) Martin Malmstrøm et al.   NATURE GENETICS

Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).

(2016) Charles W. Linkem et al.   SYSTEMATIC BIOLOGY

A Time-Calibrated Mitogenome Phylogeny of Catfish (Teleostei: Siluriformes)

(2016) Ilias Kappas et al.   PLoS One

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record

(2015) Allison Y Hsiang et al.   BMC EVOLUTIONARY BIOLOGY

Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment

(2015) Ron I. Eytan et al.   BMC EVOLUTIONARY BIOLOGY

A New Species ofRhamphichthys(Gymnotiformes: Rhamphichthyidae) from the Amazon Basin

(2015) Tiago P. Carvalho et al.   COPEIA

Origins, Innovations, and Diversification of Suction Feeding in Vertebrates

(2015) P. C. Wainwright et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Phylogenetic analysis of molecular and morphological data highlights uncertainty in the relationships of fossil and living species of Elopomorpha (Actinopterygii: Teleostei)

(2015) Alex Dornburg et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes

(2015) Princess S. Gilbert et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Molecular phylogeny of Percomorpha resolves Trichonotus as the sister lineage to Gobioidei (Teleostei: Gobiiformes) and confirms the polyphyly of Trachinoidei

(2015) Christine E. Thacker et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny

(2015) Meng-Yun Chen et al.   SYSTEMATIC BIOLOGY

Three new species of saddled loricariid catfishes, and a review of Hemiancistrus, Peckoltia, and allied genera (Siluriformes)

(2015) Jonathan W. Armbruster et al.   ZooKeys

Morphology should not be forgotten in the era of genomics–a phylogenetic perspective

(2015) Gonzalo Giribet   ZOOLOGISCHER ANZEIGER

Oligosarcus amome (Ostariophysi: Characidae), a new species from the río Uruguay basin, Misiones, Argentina

(2015) ADRIANA ALMIRÓN et al.   ZOOTAXA

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

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

The impact of shifts in marine biodiversity hotspots on patterns of range evolution: Evidence from the Holocentridae (squirrelfishes and soldierfishes)

(2014) Alex Dornburg et al.   EVOLUTION

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

The drivers of tropical speciation

(2014) Brian Tilston Smith et al.   NATURE

Family-group names of Recent fishes

(2014) RICHARD VAN DER LAAN et al.   ZOOTAXA

State-of the art methodologies dictate new standards for phylogenetic analysis

(2013) Maria Anisimova et al.   BMC EVOLUTIONARY BIOLOGY

EVOLUTIONARY ORIGIN AND EARLY BIOGEOGRAPHY OF OTOPHYSAN FISHES (OSTARIOPHYSI: TELEOSTEI)

(2013) Wei-Jen Chen et al.   EVOLUTION

Phylogenetic Models of Molecular Evolution: Next-Generation Data, Fit, and Performance

(2013) David Posada   JOURNAL OF MOLECULAR EVOLUTION

Discordance of Species Trees with Their Most Likely Gene Trees: A Unifying Principle

(2013) N. A. Rosenberg   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Are characiform Fishes Gondwanan in Origin? Insights from a Time-Scaled Molecular Phylogeny of the Citharinoidei (Ostariophysi: Characiformes)

(2013) Jairo Arroyave et al.   PLoS One

GenSeq: An updated nomenclature and ranking for genetic sequences from type and non-type sources

(2013) Prosanta Chakrabarty et al.   ZooKeys

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

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

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

(2012) N. Rohland et al.   GENOME RESEARCH

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

Five hundred million years of extinction and recovery: a phanerozoic survey of large-scale diversity patterns in fishes

(2012) MATT FRIEDMAN et al.   PALAEONTOLOGY

Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

(2012) Brant C. Faircloth et al.   PLoS One

Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny

(2012) Jeffrey P. Townsend et al.   SYSTEMATIC BIOLOGY

Treating Fossils as Terminal Taxa in Divergence Time Estimation Reveals Ancient Vicariance Patterns in the Palpimanoid Spiders

(2012) Hannah Marie Wood et al.   SYSTEMATIC BIOLOGY

The Evolution of Pharyngognathy: A Phylogenetic and Functional Appraisal of the Pharyngeal Jaw Key Innovation in Labroid Fishes and Beyond

(2012) P. C. Wainwright et al.   SYSTEMATIC BIOLOGY

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

(2011) Masanori Nakatani 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

Applications of next-generation sequencing to phylogeography and phylogenetics

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

The genome sequence of Atlantic cod reveals a unique immune system

(2011) Bastiaan Star et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Divergence Time Estimation Using Fossils as Terminal Taxa and the Origins of Lissamphibia

(2011) R. Alexander Pyron   SYSTEMATIC BIOLOGY

SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees

(2011) Kevin Liu et al.   SYSTEMATIC BIOLOGY

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

(2011) Sheila Fisher et al.   GENOME BIOLOGY

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Combining Phylogenomics and Fossils in Higher-Level Squamate Reptile Phylogeny: Molecular Data Change the Placement of Fossil Taxa

(2010) John J. Wiens et al.   SYSTEMATIC BIOLOGY

Higher and lower-level relationships of the deep-sea fish order Alepocephaliformes (Teleostei: Otocephala) inferred from whole mitogenome sequences

(2009) JAN Y. POULSEN et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees

(2009) K. Liu et al.   SCIENCE

Phylogenetic Analysis in the Anomaly Zone

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Optimal Data Partitioning and a Test Case for Ray-Finned Fishes (Actinopterygii) Based on Ten Nuclear Loci

(2008) Chenhong Li et al.   SYSTEMATIC BIOLOGY