Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)?

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

Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods

(2016) Huw A. Ogilvie et al.   SYSTEMATIC BIOLOGY

Evolving from static to dynamic signals: evolutionary compensation between two communicative signals

(2015) Emília P. Martins et al.   ANIMAL BEHAVIOUR

Phylogenomics of Horned Lizards (Genus:Phrynosoma) Using Targeted Sequence Capture Data

(2015) Adam D. Leaché et al.   COPEIA

Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing

(2015) Adam D. Leaché et al.   Genome Biology and Evolution

Correlaciones Morfológicas entre la Forma de la Cabeza, Dieta y uso de Hábitat de Algunos Sceloporus de México: Un Análisis Cuantitativo

(2015) Sandra Galindo-Gil et al.   INTERNATIONAL JOURNAL OF MORPHOLOGY

Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genusSceloporus) in the southern Mexican highlands

(2015) Jared A. Grummer et al.   MOLECULAR ECOLOGY

Model Inadequacy and Mistaken Inferences of Trait-Dependent Speciation

(2015) Daniel L. Rabosky et al.   SYSTEMATIC BIOLOGY

The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews

(2015) Thomas C. Giarla et al.   SYSTEMATIC BIOLOGY

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

(2015) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

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

Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae

(2014) Shannon C.K. Straub et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A hybrid phylogenetic–phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification

(2014) Adam D. Leaché et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees

(2014) Daniel L. Rabosky   PLoS One

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

The Unsolved Challenge to Phylogenetic Correlation Tests for Categorical Characters

(2014) Wayne P. Maddison et al.   SYSTEMATIC BIOLOGY

Information content is more important than sensory system or physical distance in guiding the long-term evolutionary relationships between signaling modalities in Sceloporus lizards

(2013) Alison G. Ossip-Klein et al.   BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY

Exploring power and parameter estimation of the BiSSE method for analyzing species diversification

(2013) Matthew P Davis et al.   BMC EVOLUTIONARY BIOLOGY

DIVERSITY AND NICHE EVOLUTION ALONG ARIDITY GRADIENTS IN NORTH AMERICAN LIZARDS (PHRYNOSOMATIDAE)

(2013) John J. Wiens et al.   EVOLUTION

Comparative Species Divergence across Eight Triplets of Spiny Lizards (Sceloporus) Using Genomic Sequence Data

(2013) Adam D. Leaché et al.   Genome Biology and Evolution

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

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

Species Delimitation Using Bayes Factors: Simulations and Application to the Sceloporus scalaris Species Group (Squamata: Phrynosomatidae)

(2013) Jared A. Grummer et al.   SYSTEMATIC BIOLOGY

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

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

Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

(2012) J. J. Wiens et al.   Biology Letters

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ecological opportunity and sexual selection together predict adaptive radiation

(2012) Catherine E. Wagner et al.   NATURE

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

Diversitree: comparative phylogenetic analyses of diversification in R

(2012) Richard G. FitzJohn   Methods in Ecology and Evolution

Unraveling the rapid radiation of crested newts (Triturus cristatus superspecies) using complete mitogenomic sequences

(2011) Ben Wielstra 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

Quartet MaxCut: A fast algorithm for amalgamating quartet trees

(2011) Sagi Snir et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Multi-Locus Estimates of Population Structure and Migration in a Fence Lizard Hybrid Zone

(2011) Adam D. Leaché   PLoS One

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Chromosome Evolution and Diversification in North American Spiny Lizards (Genus Sceloporus)

(2010) A.D. Leaché et al.   CYTOGENETIC AND GENOME RESEARCH

Chromosome Variation, Genomics, Speciation and Evolution in Sceloporus Lizards

(2010) W.P. Hall   CYTOGENETIC AND GENOME RESEARCH

Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales

(2009) Ye Xiong et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic relationships of phrynosomatid lizards based on nuclear and mitochondrial data, and a revised phylogeny for Sceloporus

(2009) John J. Wiens et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Species trees for spiny lizards (Genus Sceloporus): Identifying points of concordance and conflict between nuclear and mitochondrial data

(2009) Adam D. Leaché   MOLECULAR PHYLOGENETICS AND EVOLUTION

Species Tree Discordance Traces to Phylogeographic Clade Boundaries in North American Fence Lizards (Sceloporus)

(2009) Adam D. Leaché   SYSTEMATIC BIOLOGY

The conditioned reconstructed process

(2008) Tanja Gernhard   JOURNAL OF THEORETICAL BIOLOGY

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

A Phylogenomic Study of Birds Reveals Their Evolutionary History

(2008) S. J. Hackett et al.   SCIENCE

Branch Lengths, Support, and Congruence: Testing the Phylogenomic Approach with 20 Nuclear Loci in Snakes

(2008) John J. Wiens et al.   SYSTEMATIC BIOLOGY