Shallow genetic divergence and distinct phenotypic differences between two Andean hummingbirds: Speciation with gene flow?

A review of Gloger's rule, an ecogeographical rule of colour: definitions, interpretations and evidence

(2019) Kaspar Delhey   BIOLOGICAL REVIEWS

A flicker of hope: Genomic data distinguish Northern Flicker taxa despite low levels of divergence

(2018) Stepfanie M. Aguillon et al.   AUK

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene Flow

(2018) Susanne P Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Multi-allele species reconstruction using ASTRAL

(2018) Maryam Rabiee et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Consequences of divergence and introgression for speciation in Andean cloud forest birds

(2017) Benjamin M. Winger   EVOLUTION

Genomic evidence for convergent evolution of a key trait underlying divergence in island birds

(2017) Elizabeth A. Cooper et al.   MOLECULAR ECOLOGY

Repeated divergent selection on pigmentation genes in a rapid finch radiation

(2017) Leonardo Campagna et al.   Science Advances

Mosaic genome evolution in a recent and rapid avian radiation

(2017) Katherine Faust Stryjewski et al.   Nature Ecology & Evolution

The evolutionary history of bears is characterized by gene flow across species

(2017) Vikas Kumar et al.   Scientific Reports

Plumage Genes and Little Else Distinguish the Genomes of Hybridizing Warblers

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

Candidate Gene Analysis Suggests Untapped Genetic Complexity in Melanin-Based Pigmentation in Birds

(2016) Yann X. C. Bourgeois et al.   JOURNAL OF HEREDITY

The Evolution of Genome Structure by Natural and Sexual Selection

(2016) Mark Kirkpatrick   JOURNAL OF HEREDITY

Rapid divergence and gene flow at high latitudes shape the history of Holarctic ground squirrels ( Urocitellus )

(2016) Bryan S. McLean et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Recurrent hybridization and recent origin obscure phylogenetic relationships within the ‘white-headed’ gull ( Larus sp.) complex

(2016) Sarah A. Sonsthagen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

(2016) Polina Yu Novikova et al.   NATURE GENETICS

Remotely Sensed High-Resolution Global Cloud Dynamics for Predicting Ecosystem and Biodiversity Distributions

(2016) Adam M. Wilson et al.   PLOS BIOLOGY

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

(2015) Brant C. Faircloth   BIOINFORMATICS

Divergence with gene flow across a speciation continuum of Heliconius butterflies

(2015) Megan A. Supple et al.   BMC EVOLUTIONARY BIOLOGY

Sex-linked genomic variation and its relationship to avian plumage dichromatism and sexual selection

(2015) Huateng Huang et al.   BMC EVOLUTIONARY BIOLOGY

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

(2015) Benjamin M. Winger et al.   EVOLUTION

Geography, assortative mating, and the effects of sexual selection on speciation with gene flow

(2015) Maria R. Servedio   Evolutionary Applications

Sexual selection drives evolution and rapid turnover of male gene expression

(2015) Peter W. Harrison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

(2015) Alexander Suh et al.   PLOS BIOLOGY

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

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

How populations differentiate despite gene flow: sexual and natural selection drive phenotypic divergence within a land fish, the Pacific leaping blenny

(2014) Courtney L Morgans et al.   BMC EVOLUTIONARY BIOLOGY

Molecular Phylogenetics and the Diversification of Hummingbirds

(2014) Jimmy A. McGuire et al.   CURRENT BIOLOGY

Locally adapted traits maintained in the face of high gene flow

(2014) S. W. Fitzpatrick et al.   ECOLOGY LETTERS

Clinal variation in the morph ratio of Black SparrowhawksAccipiter melanoleucusin South Africa and its correlation with environmental variables

(2014) Arjun Amar et al.   IBIS

Melanin-Based Color of Plumage: Role of Condition and of Feathers' Microstructure

(2014) L. D'Alba et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Bears in a Forest of Gene Trees: Phylogenetic Inference Is Complicated by Incomplete Lineage Sorting and Gene Flow

(2014) Verena E. Kutschera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Into turbulent air: size-dependent effects of von Karman vortex streets on hummingbird flight kinematics and energetics

(2014) V. M. Ortega-Jimenez et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

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

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

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

(2013) Simon H. Martin et al.   GENOME RESEARCH

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

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

Incomplete Lineage Sorting Is Common in Extant Gibbon Genera

(2013) Jeffrey D. Wall et al.   PLoS One

Key ornamental innovations facilitate diversification in an avian radiation

(2013) R. Maia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetics of colouration in birds

(2013) Alexandre Roulin et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

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

(2013) Frank E. Rheindt et al.   SYSTEMATIC BIOLOGY

The role of glacial cycles in promoting genetic diversity in the Neotropics: the case of cloud forests during the Last Glacial Maximum

(2013) Santiago Ramírez-Barahona et al.   Ecology and Evolution

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Accelerated speciation in colour-polymorphic birds

(2012) Andrew F. Hugall et al.   NATURE

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

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

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

Measuring ecological niche overlap from occurrence and spatial environmental data

(2011) Olivier Broennimann et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

MC1R-dependent, melanin-based colour polymorphism is associated with cell-mediated response in the Eleonora’s falcon

(2011) L. GANGOSO et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Testing for Ancient Admixture between Closely Related Populations

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

Rapid phenotypic evolution during incipient speciation in a continental avian radiation

(2011) L. Campagna et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Magic traits in speciation: ‘magic’ but not rare?

(2011) Maria R. Servedio et al.   TRENDS IN ECOLOGY & EVOLUTION

CliMond: global high-resolution historical and future scenario climate surfaces for bioclimatic modelling

(2011) Darren J. Kriticos et al.   Methods in Ecology and Evolution

Divergence with Gene Flow: Models and Data

(2010) Catarina Pinho et al.   Annual Review of Ecology Evolution and Systematics

Testing the molecular and evolutionary causes of a ‘leapfrog’ pattern of geographical variation in coloration

(2010) C. D. CADENA et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Mate choice and mate competition by a tropical hummingbird at a floral resource

(2010) E. J. Temeles et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

Dark Color of the Coastal Plain Swamp Sparrow (Melospiza georgiana nigrescens) May Be an Evolutionary Response to Occurrence and Abundance of Salt-tolerant Feather-degrading Bacilli in Its Plumage

(2009) Ashley M. Peele et al.   AUK

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

COLOR EVOLUTION IN THE HUMMINGBIRD GENUSCOELIGENA

(2009) Juan Luis Parra   EVOLUTION

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Pattern, process and geographic modes of speciation

(2009) B. M. FITZPATRICK et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Molecular phylogenetics of the hummingbird genus Coeligena

(2009) Juan Luis Parra et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Evidence for Ecological Speciation and Its Alternative

(2009) D. Schluter   SCIENCE

Ecological explanations for (incomplete) speciation

(2009) Patrik Nosil et al.   TRENDS IN ECOLOGY & EVOLUTION

ENVIRONMENTAL NICHE EQUIVALENCY VERSUS CONSERVATISM: QUANTITATIVE APPROACHES TO NICHE EVOLUTION

(2008) Dan L. Warren et al.   EVOLUTION

Speciation with gene flow could be common

(2008) PATRIK NOSIL   MOLECULAR ECOLOGY

An analysis of population genetic differentiation and genotype-phenotype association across the hybrid zone of carrion and hooded crows using microsatellites andMC1R

(2008) FREDRIK HAAS et al.   MOLECULAR ECOLOGY