Introgression and Phenotypic Assimilation in Zimmerius Flycatchers (Tyrannidae): Population Genetic and Phylogenetic Inferences from Genome-Wide SNPs

A distinctive genetic footprint of ancient hybridization

(2013) John E. McCormack et al.   AUK

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

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

A multi-locus phylogeny suggests an ancient hybridization event between Campephilus and melanerpine woodpeckers (Aves: Picidae)

(2013) Jérôme Fuchs et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

(2013) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

Cis-regulatory sequence variation and association withMycoplasmaload in natural populations of the house finch (Carpodacus mexicanus)

(2013) Niclas Backström et al.   Ecology and Evolution

Characterization of whole genome amplified (WGA) DNA for use in genotyping assay development

(2012) Tao Han et al.   BMC GENOMICS

GENOMIC REGIONS WITH A HISTORY OF DIVERGENT SELECTION AFFECT FITNESS OF HYBRIDS BETWEEN TWO BUTTERFLY SPECIES

(2012) Zachariah Gompert et al.   EVOLUTION

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

The molecular basis of the plumage colour polymorphism in the Tahiti reed-warbler Acrocephalus caffer

(2012) Alice Cibois et al.   JOURNAL OF AVIAN BIOLOGY

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

Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex

(2012) Eric M. O'Neill et al.   MOLECULAR ECOLOGY

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Estimates of Genetic Differentiation Measured by FST Do Not Necessarily Require Large Sample Sizes When Using Many SNP Markers

(2012) Eva-Maria Willing et al.   PLoS One

The genomics of speciation-with-gene-flow

(2012) Jeffrey L. Feder et al.   TRENDS IN GENETICS

Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus)

(2012) Fabian Staubach et al.   PLoS Genetics

Genetic Introgression: An Integral but neglected component of speciation in birds

(2011) Frank E. Rheindt et al.   AUK

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

Candidate genes for carotenoid coloration in vertebrates and their expression profiles in the carotenoid-containing plumage and bill of a wild bird

(2011) N. Walsh et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies

(2010) E. R. Martin et al.   BIOINFORMATICS

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

HISTORICAL DIVERGENCE AND GENE FLOW: COALESCENT ANALYSES OF MITOCHONDRIAL, AUTOSOMAL AND SEX-LINKED LOCI IN PASSERINA BUNTINGS

(2010) Matthew D. Carling et al.   EVOLUTION

Analysis from avian visual perspective reveals plumage colour differences among females of capuchino seedeaters (Sporophila)

(2010) Pilar Benites et al.   JOURNAL OF AVIAN BIOLOGY

Genome-wide SNP detection in the great titParus majorusing high throughput sequencing

(2010) NIKKIE E. M. VAN BERS et al.   MOLECULAR ECOLOGY

Genetic history of an archaic hominin group from Denisova Cave in Siberia

(2010) David Reich et al.   NATURE

Conspecific versus heterospecific gene exchange between populations of Darwin's finches

(2010) P. R. Grant et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Evolutionary stasis: the stable chromosomes of birds

(2010) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Understanding the onset of hybrid speciation

(2010) Arne W. Nolte et al.   TRENDS IN GENETICS

Difference in Plumage Color Used in Species Recognition between Incipient Species Is Linked to a Single Amino Acid Substitution in the Melanocortin‐1 Receptor

(2009) J. Albert C. Uy et al.   AMERICAN NATURALIST

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Variable patterns of introgression in two sculpin hybrid zones suggest that genomic isolation differs among populations

(2009) A. W. NOLTE et al.   MOLECULAR ECOLOGY

The timing of Neotropical speciation dynamics: A reconstruction of Myiopagis flycatcher diversification using phylogenetic and paleogeographic data

(2009) Frank E. Rheindt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

Molecular and Evolutionary History of Melanism in North American Gray Wolves

(2009) T. M. Anderson et al.   SCIENCE

Genetic introgression, incomplete lineage sorting and faulty taxonomy create multiple cases of polyphyly in a montane clade of tyrant-flycatchers (Elaenia, Tyrannidae)

(2009) Frank E. Rheindt et al.   ZOOLOGICA SCRIPTA

The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing

(2009) Rob J. Kulathinal et al.   PLoS Genetics

Evolution of Avian Plumage Color in a Tetrahedral Color Space: A Phylogenetic Analysis of New World Buntings

(2008) Mary Caswell Stoddard et al.   AMERICAN NATURALIST

Habitat shifts in the evolutionary history of a Neotropical flycatcher lineage from forest and open landscapes

(2008) Frank E Rheindt et al.   BMC EVOLUTIONARY BIOLOGY

DIVERGENCE ACROSS AUSTRALIA'S CARPENTARIAN BARRIER: STATISTICAL PHYLOGEOGRAPHY OF THE RED-BACKED FAIRY WREN (MALURUS MELANOCEPHALUS)

(2008) June Y. Lee et al.   EVOLUTION

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

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

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

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

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

Subdivision in an Ancestral Species Creates Asymmetry in Gene Trees

(2008) M. Slatkin et al.   MOLECULAR BIOLOGY AND EVOLUTION

DNA evidence shows vocalizations to be a better indicator of taxonomic limits than plumage patterns in Zimmerius tyrant-flycatchers

(2008) Frank E. Rheindt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic relationships of tyrant-flycatchers (Aves: Tyrannidae), with an emphasis on the elaeniine assemblage

(2007) Frank E. Rheindt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION