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

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

When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny

(2015) Shea M. Lambert et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A phylogenomic analysis of turtles

(2015) Nicholas G. Crawford et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa

(2015) Tod W. Reeder et al.   PLoS One

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab 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

Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs

(2014) Jeffrey W. Streicher et al.   MOLECULAR ECOLOGY

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

(2014) Brant C. Faircloth et al.   Molecular Ecology Resources

Should genes with missing data be excluded from phylogenetic analyses?

(2014) Wei Jiang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Divergent maximum-likelihood-branch-support values for polytomies

(2014) Mark P. Simmons 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

The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach

(2014) K. Sun et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies

(2014) Zhenxiang Xi et al.   SYSTEMATIC BIOLOGY

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting

(2014) Siavash Mirarab et al.   SYSTEMATIC BIOLOGY

Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences

(2014) Huateng Huang et al.   SYSTEMATIC BIOLOGY

High-Throughput Genomic Data in Systematics and Phylogenetics

(2013) Emily Moriarty Lemmon et al.   Annual Review of Ecology Evolution and Systematics

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

(2013) R Pyron et al.   BMC EVOLUTIONARY BIOLOGY

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Effects of missing data on species tree estimation under the coalescent

(2013) Rasmus Hovmöller et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

STRAW: Species TRee Analysis Web server

(2013) Timothy I. Shaw et al.   NUCLEIC ACIDS RESEARCH

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

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

Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

(2013) Marie Cariou et al.   Ecology and Evolution

Contrasting global-scale evolutionary radiations: phylogeny, diversification, and morphological evolution in the major clades of iguanian lizards

(2012) Thomas Blankers et al.   BIOLOGICAL 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

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

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

Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture

(2012) Lecong Zhou et al.   BMC GENOMICS

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

(2012) N. Rohland et al.   GENOME RESEARCH

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

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

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Next-generation phylogenetics takes root

(2012) John E. McCormack et al.   MOLECULAR ECOLOGY

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

Inferring Phylogenies from RAD Sequence Data

(2012) Benjamin E. R. Rubin et al.   PLoS One

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

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

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

Phylogenetic Insights on Evolutionary Novelties in Lizards and Snakes: Sex, Birth, Bodies, Niches, and Venom

(2011) Jack W. Sites et al.   Annual Review of Ecology Evolution and Systematics

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

Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation

(2011) Ted M. Townsend et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The genome of the green anole lizard and a comparative analysis with birds and mammals

(2011) Jessica Alföldi et al.   NATURE

Estimating Species Trees from Unrooted Gene Trees

(2011) Liang Liu et al.   SYSTEMATIC BIOLOGY

Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data

(2011) John J. Wiens et al.   SYSTEMATIC BIOLOGY

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods

(2010) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

(2008) T.-K. Seo   MOLECULAR BIOLOGY AND EVOLUTION