Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event

Hidden endemism, deep polyphyly, and repeated dispersal across the Isthmus of Tehuantepec: Diversification of the White-collared Seedeater complex (Thraupidae: Sporophila torqueola )

(2018) Nicholas A. Mason et al.   Ecology and Evolution

Multispecies coalescent delimits structure, not species

(2017) Jeet Sukumaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Willet be one species or two? A genomic view of the evolutionary history ofTringa semipalmata

(2016) Jessica A. Oswald et al.   AUK

Direct estimate of the rate of germline mutation in a bird

(2016) Linnéa Smeds et al.   GENOME RESEARCH

Population genetics from 1966 to 2016

(2016) B Charlesworth et al.   HEREDITY

“Reverse Genomics” Predicts Function of Human Conserved Noncoding Elements

(2016) Amir Marcovitz et al.   MOLECULAR BIOLOGY AND EVOLUTION

Becoming pure: identifying generational classes of admixed individuals within lesser and greater scaup populations

(2016) Philip Lavretsky et al.   MOLECULAR ECOLOGY

Hidden histories of gene flow in highland birds revealed with genomic markers

(2016) Eugenia Zarza et al.   MOLECULAR ECOLOGY

High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

(2016) James Starrett et al.   Molecular Ecology Resources

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus:Piranga)

(2016) Joseph D. Manthey et al.   SYSTEMATIC BIOLOGY

Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics

(2016) Michael G. Harvey et al.   SYSTEMATIC BIOLOGY

PHYLUCE is a software package for the analysis of conserved genomic loci

(2015) Brant C. Faircloth   BIOINFORMATICS

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

IMa2p - parallel MCMC and inference of ancient demography under the Isolation with migration (IM) model

(2015) Arun Sethuraman et al.   Molecular Ecology Resources

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

Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow

(2015) Michael G. Harvey et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A new time tree reveals Earth historys imprint on the evolution of modern birds

(2015) S. Claramunt et al.   Science Advances

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Sampling strategies for frequency spectrum-based population genomic inference

(2014) John D Robinson et al.   BMC EVOLUTIONARY BIOLOGY

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

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

The Evolutionary Genomics of Birds

(2013) Hans Ellegren   Annual Review of Ecology Evolution and Systematics

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Using Tablet for visual exploration of second-generation sequencing data

(2012) I. Milne et al.   BRIEFINGS IN BIOINFORMATICS

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

(2012) N. Rohland et al.   GENOME RESEARCH

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

(2011) H. E. L. Lischer et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences

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

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Contrasting population genetic patterns within the white-throated sparrow genome (Zonotrichia albicollis)

(2010) Lynn Y Huynh et al.   BMC GENETICS

Reptiles and Mammals Have Differentially Retained Long Conserved Noncoding Sequences from the Amniote Ancestor

(2010) D.E. Janes et al.   Genome Biology and Evolution

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

(2010) A. McKenna et al.   GENOME RESEARCH

Diversification at high latitudes: speciation of buntings in the genusPlectrophenaxinferred from mitochondrial and nuclear markers

(2010) JAMES M. MALEY et al.   MOLECULAR ECOLOGY

Chapter 1: Subspecies Represent Geographically Partitioned Variation, A Gold Mine of Evolutionary Biology, and a Challenge for Conservation

(2010) Kevin Winker   ORNITHOLOGICAL MONOGRAPHS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

Nucleotide Variation, Linkage Disequilibrium and Founder-Facilitated Speciation in Wild Populations of the Zebra Finch (Taeniopygia guttata)

(2008) C. N. Balakrishnan et al.   GENETICS

Large-Scale Appearance of Ultraconserved Elements in Tetrapod Genomes and Slowdown of the Molecular Clock

(2007) S. Stephen et al.   MOLECULAR BIOLOGY AND EVOLUTION