A Versatile and Highly Efficient Toolkit Including 102 Nuclear Markers for Vertebrate Phylogenomics, Tested by Resolving the Higher Level Relationships of the Caudata

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

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

Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets

(2012) Béatrice Roure et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

EvolMarkers: a database for mining exon and intron markers for evolution, ecology and conservation studies

(2012) CHENHONG LI et al.   Molecular Ecology Resources

The Development of Three Long Universal Nuclear Protein-Coding Locus Markers and Their Application to Osteichthyan Phylogenetics with Nested PCR

(2012) Xing-Xing Shen et al.   PLoS One

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

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

A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia

(2012) Jonathan J. Fong et al.   PLoS One

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

(2012) S. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon 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

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

Multiple Genome Alignments Facilitate Development of NPCL Markers: A Case Study of Tetrapod Phylogeny Focusing on the Position of Turtles

(2011) X.-X. Shen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata

(2011) Jonathan J. Fong et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians

(2011) R. Alexander Pyron 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

Identification of 104 rapidly-evolving nuclear protein-coding markers for amplification across scaled reptiles using genomic resources

(2011) Daniel M. Portik et al.   Conservation Genetics Resources

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary Origin and Phylogeny of the Modern Holocephalans (Chondrichthyes: Chimaeriformes): A Mitogenomic Perspective

(2010) J. G. Inoue et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-enabled development of DNA markers for ecology, evolution and conservation

(2010) ROBERT C. THOMSON et al.   MOLECULAR ECOLOGY

Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species

(2010) AXEL KÜNSTNER et al.   MOLECULAR ECOLOGY

Developing a series of conservative anchor markers and their application to phylogenomics of Laurasiatherian mammals

(2010) XUMING ZHOU et al.   Molecular Ecology Resources

A multilocus timescale for the origin of extant amphibians

(2010) Diego San Mauro   MOLECULAR PHYLOGENETICS AND EVOLUTION

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Testing avian, squamate, and mammalian nuclear markers for cross amplification in turtles

(2010) Phillip Q. Spinks et al.   Conservation Genetics Resources

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles

(2009) Phillip Q Spinks et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenomics Revives Traditional Views on Deep Animal Relationships

(2009) Hervé Philippe et al.   CURRENT BIOLOGY

Higher-level salamander relationships and divergence dates inferred from complete mitochondrial genomes

(2009) Peng Zhang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Microdroplet-based PCR enrichment for large-scale targeted sequencing

(2009) Ryan Tewhey et al.   NATURE BIOTECHNOLOGY

The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

(2009) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

A Multilocus Molecular Phylogeny of the Parrots (Psittaciformes): Support for a Gondwanan Origin during the Cretaceous

(2008) Timothy F. Wright et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: An example from squamate reptiles

(2008) Ted M. Townsend et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles

(2008) Robert C. Thomson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Parallel tagged sequencing on the 454 platform

(2008) Matthias Meyer et al.   Nature Protocols