The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages

Historical introgression among the American live oaks and the comparative nature of tests for introgression

(2015) Deren A. R. Eaton et al.   EVOLUTION

Genome-wide SNPs reveal fine-scale differentiation among wingless alpine stonefly populations and introgression between winged and wingless forms

(2015) Nicolas Dussex et al.   EVOLUTION

Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach

(2015) K. R. Veeramah et al.   GENETICS

An Exon-Capture System for the Entire Class Ophiuroidea

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

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

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genotyping by sequencing for genomic prediction in a soybean breeding population

(2014) Diego Jarquín et al.   BMC GENOMICS

Use of RAD sequencing for delimiting species

(2014) E Pante et al.   HEREDITY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Stick Insect Genomes Reveal Natural Selection's Role in Parallel Speciation

(2014) V. Soria-Carrasco et al.   SCIENCE

Species Delimitation using Genome-Wide SNP Data

(2014) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Rafting dispersal constrained by an oceanographic boundary

(2013) CJ Garden et al.   MARINE ECOLOGY PROGRESS SERIES

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol

(2013) Fei Lu et al.   PLoS Genetics

RAD tag sequencing as a source of SNP markers in Cynara cardunculus L

(2012) Davide Scaglione et al.   BMC GENOMICS

The Influence of Rate Heterogeneity among Sites on the Time Dependence of Molecular Rates

(2012) Julien Soubrier 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

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey et al.   MOLECULAR ECOLOGY

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

Founder takes all: density-dependent processes structure biodiversity

(2012) Jonathan M. Waters et al.   TRENDS IN ECOLOGY & EVOLUTION

Next-generation hybridization and introgression

(2011) A D Twyford et al.   HEREDITY

Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape

(2011) GEOFFREY P. MORRIS et al.   MOLECULAR ECOLOGY

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Exploring Phylogeographic Congruence in a Continental Island System

(2011) Julia Goldberg et al.   Insects

Multigene phylogeny of the southern bull-kelp genus Durvillaea (Phaeophyceae: Fucales)

(2010) Ceridwen I. Fraser et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Late-Cenozoic origin and diversification of Chatham Islands endemic plant species revealed by analyses of DNA sequence data

(2010) PB Heenan et al.   NEW ZEALAND JOURNAL OF BOTANY

Oceanic rafting by a coastal community

(2010) C. I. Fraser et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics

(2010) HOJUN SONG et al.   SYSTEMATIC ENTOMOLOGY

Kelp genes reveal effects of subantarctic sea ice during the Last Glacial Maximum

(2009) C. I. Fraser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Maximum-Likelihood Estimation of Site-Specific Mutation Rates in Human Mitochondrial DNA From Partial Phylogenetic Classification

(2008) Saharon Rosset et al.   GENETICS

Evolution of New Zealand's terrestrial fauna: a review of molecular evidence

(2008) J. Goldberg et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One