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

Cryptic speciation and gene flow in a migratory songbird Species Complex: Insights from the Red-Eyed Vireo ( Vireo olivaceus )

(2017) C.J. Battey et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

An analytical review of Halffter's Mexican transition zone, and its relevance for evolutionary biogeography, ecology and biogeographical regionalization

(2017) GONZALO HALFFTER et al.   ZOOTAXA

Repeated divergent selection on pigmentation genes in a rapid finch radiation

(2017) Leonardo Campagna et al.   Science Advances

Genomic approaches to understanding population divergence and speciation in birds

(2016) David P. L. Toews et al.   AUK

Comparative Phylogeography of Two Bird Species,Tachyphonus phoenicius(Thraupidae) andPolytmus theresiae(Trochilidae), Specialized in Amazonian White-sand Vegetation

(2016) Maysa V. Matos et al.   BIOTROPICA

Plumage Genes and Little Else Distinguish the Genomes of Hybridizing Warblers

(2016) David P.L. Toews et al.   CURRENT BIOLOGY

Bird conservation and biodiversity research in Mexico: status and priorities

(2016) A. Townsend Peterson et al.   JOURNAL OF FIELD ORNITHOLOGY

Geographic isolation drives divergence of uncorrelated genetic and song variation in the Ruddy-capped Nightingale-Thrush ( Catharus frantzii ; Aves: Turdidae)

(2016) Marco F. Ortiz-Ramírez et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phenotypes in phylogeography: Species’ traits, environmental variation, and vertebrate diversification

(2016) Kelly R. Zamudio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reticulation, divergence, and the phylogeography–phylogenetics continuum

(2016) Scott V. Edwards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics

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

A genus-level classification of the family Thraupidae (Class Aves: Order Passeriformes)

(2016) KEVIN J. BURNS et al.   ZOOTAXA

Wild Vertebrates Kept as Pets in the Semiarid Region of Brazil

(2016) Mauricélia Macário Alves et al.   Tropical Conservation Science

AMAS: a fast tool for alignment manipulation and computing of summary statistics

(2016) Marek L. Borowiec   PeerJ

New insights into New World biogeography: An integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies

(2015) F. Keith Barker et al.   AUK

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

(2015) Brant C. Faircloth   BIOINFORMATICS

The tempo of trait divergence in geographic isolation: Avian speciation across the Marañon Valley of Peru

(2015) Benjamin M. Winger et al.   EVOLUTION

Hybridization in headwater regions, and the role of rivers as drivers of speciation in Amazonian birds

(2015) Jason T. Weir et al.   EVOLUTION

Differentially expressed genes match bill morphology and plumage despite largely undifferentiated genomes in a Holarctic songbird

(2015) Nicholas A. Mason et al.   MOLECULAR ECOLOGY

Inferring speciation history in the Andes with reduced-representation sequence data: an example in the bay-backed antpittas (Aves; Grallariidae; Grallaria hypoleuca s. l.)

(2015) Benjamin M. Winger et al.   MOLECULAR ECOLOGY

Continental-scale analysis reveals deep diversification within the polytypic Red-crowned Ant Tanager (Habia rubica, Cardinalidae)

(2015) Pablo D. Lavinia 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

Deceptive Desmas: Molecular Phylogenetics Suggests a New Classification and Uncovers Convergent Evolution of Lithistid Demosponges

(2015) Astrid Schuster et al.   PLoS One

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

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

Trends in Illegal Trade of Wild Birds in Amazonas State, Brazil

(2015) Carlos Augusto Rodrigues do Nascimento et al.   Tropical Conservation Science

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae)

(2014) Gustavo A. Bravo et al.   EVOLUTION

Multilocus phylogeography and morphology give insights into the recent evolution of a Mexican endemic songbird:Vireo hypochryseus

(2014) Enrique Arbeláez-Cortés et al.   JOURNAL OF AVIAN BIOLOGY

The influence of the complex topography and dynamic history of the montane Neotropics on the evolutionary differentiation of a cloud forest bird (Premnoplex brunnescens, Furnariidae)

(2014) Eugenio Valderrama et al.   JOURNAL OF BIOGEOGRAPHY

Biogeography of the Andean metaltail hummingbirds: contrasting evolutionary histories of tree line and habitat-generalist clades

(2014) Phred M. Benham et al.   JOURNAL OF BIOGEOGRAPHY

Phylogenetics and diversification of tanagers (Passeriformes: Thraupidae), the largest radiation of Neotropical songbirds

(2014) Kevin J. Burns et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The drivers of tropical speciation

(2014) Brian Tilston Smith et al.   NATURE

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

(2014) J. W. Poelstra et al.   SCIENCE

Species Delimitation using Genome-Wide SNP Data

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

Model Selection in Historical Biogeography Reveals that Founder-Event Speciation Is a Crucial Process in Island Clades

(2014) Nicholas J. Matzke   SYSTEMATIC BIOLOGY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

A new species of gray seedeater (Emberizidae:Sporophila) from upland grasslands of southern Brazil

(2013) Márcio Repenning et al.   AUK

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

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

Broad polyphyly and historical biogeography of the neotropical wasp genus Notiospathius (Braconidae: Doryctinae)

(2013) Fadia Sara Ceccarelli et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Convergent evolution of ecomorphological adaptations in geographically isolated Bay gobies (Teleostei: Gobionellidae) of the temperate North Pacific

(2013) Ryan A. Ellingson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Multilocus analysis of intraspecific differentiation in three endemic bird species from the northern Neotropical dry forest

(2013) Enrique Arbeláez-Cortés et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn 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

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

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

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

Molecular evidence of the taxonomic status of western Mexican populations of Phaethornis longirostris (Aves: Trochilidae)

(2013) ENRIQUE ARBELÁEZ-CORTÉS et al.   ZOOTAXA

Coalescent analyses show isolation without migration in two closely related tropical orioles: the case ofIcterus graduacaudaandIcterus chrysater

(2013) Nandadevi Cortés-Rodríguez et al.   Ecology and Evolution

The Role of Physical Barriers in the Location of Avian Suture Zones in the Guiana Shield, Northern Amazonia

(2012) Luciano Nicolas Naka et al.   AMERICAN NATURALIST

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

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

An Integrative Approach to Species-Level Systematics Reveals the Depth of Diversification in an Andean Thamnophilid, the Long-tailed Antbird

(2012)   CONDOR

Phylogeography of the chestnut-tailed antbird (Myrmeciza hemimelaena) clarifies the role of rivers in Amazonian biogeography

(2012) Alexandre M. Fernandes et al.   JOURNAL OF BIOGEOGRAPHY

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

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeographical patterns shed light on evolutionary process in South America

(2012) A. C. Turchetto-Zolet et al.   MOLECULAR ECOLOGY

Non-monophyly and deep genetic differentiation across low-elevation barriers in a Neotropical montane bird (Basileuterus tristriatus; Aves: Parulidae)

(2012) Natalia Gutiérrez-Pinto et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

(2012) Brant C. Faircloth et al.   PLoS One

Evaluating the role of contracting and expanding rainforest in initiating cycles of speciation across the Isthmus of Panama

(2012) B. T. Smith et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

Coalescent-based species delimitation in an integrative taxonomy

(2012) Matthew K. Fujita et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Selection and geographic isolation influence hummingbird speciation: genetic, acoustic and morphological divergence in the wedge-tailed sabrewing (Campylopterus curvipennis)

(2011) Clementina González 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

Phylogeography of Middle American gophersnakes: mixed responses to biogeographical barriers across the Mexican Transition Zone

(2011) Robert W. Bryson et al.   JOURNAL OF BIOGEOGRAPHY

Diversification in Adelomyia hummingbirds follows Andean uplift

(2011) JAIME A. CHAVES et al.   MOLECULAR ECOLOGY

A molecular phylogeny of the Sierra-Finches (Phrygilus, Passeriformes): Extreme polyphyly in a group of Andean specialists

(2011) Leonardo Campagna et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolutionary patterns of diversification in the Andean hummingbird genus Adelomyia

(2011) Jaime A. Chaves et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Applications of next-generation sequencing to phylogeography and phylogenetics

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

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

Progress and Promise of Genome-Wide Association Studies for Human Complex Trait Genetics

(2010) B. E. Stranger et al.   GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna

(2010) B. R. Barber et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Hypothesis testing in biogeography

(2010) Michael D. Crisp et al.   TRENDS IN ECOLOGY & EVOLUTION

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

Areas of endemism of Mexican mammals: reanalysis applying the optimality criterion

(2009) TANIA ESCALANTE et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Are the Northern Andes a species pump for Neotropical birds? Phylogenetics and biogeography of a clade of Neotropical tanagers (Aves: Thraupini)

(2009) Raul E. Sedano et al.   JOURNAL OF BIOGEOGRAPHY

The genetics of quantitative traits: challenges and prospects

(2009) Trudy F. C. Mackay et al.   NATURE REVIEWS GENETICS

The Great American Biotic Interchange in birds

(2009) J. T. Weir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Wild-bird trade and exotic invasions: a new link of conservation concern?

(2008) Martina Carrete et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Multilocus phylogeography and phylogenetics using sequence-based markers

(2008) Patrícia H. Brito et al.   GENETICA

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

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

Comparative phylogeography of pitvipers suggests a consensus of ancient Middle American highland biogeography

(2008) Todd A. Castoe et al.   JOURNAL OF BIOGEOGRAPHY

The Great American Interchange in birds: a phylogenetic perspective with the genus Trogon

(2008) JEFFREY M. DACOSTA et al.   MOLECULAR ECOLOGY

Calibrating the avian molecular clock

(2008) J. T. WEIR et al.   MOLECULAR ECOLOGY

Maximum Likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction, and Cladogenesis

(2008) Richard H. Ree et al.   SYSTEMATIC BIOLOGY