Patterns of cytonuclear discordance and divergence between subspecies of the scarlet macaw (Ara macao) in Central America

Evolutionary and ecological drivers of local adaptation and speciation in a North American avian species complex

(2022) Joshua I. Brown et al.   MOLECULAR ECOLOGY

Complex histories of gene flow and a mitochondrial capture event in a non‐sister pair of birds

(2021) Michael J. Andersen et al.   MOLECULAR ECOLOGY

When good mitochondria go bad: Cyto-nuclear discordance in landfowl (Aves: Galliformes)

(2021) Rebecca T. Kimball et al.   GENE

Dsuite ‐ Fast D ‐statistics and related admixture evidence from VCF files

(2020) Milan Malinsky et al.   Molecular Ecology Resources

Identifying hybrids & the genomics of hybridization: Mallards & American black ducks of Eastern North America

(2019) Philip Lavretsky et al.   Ecology and Evolution

Genetic analysis reveals strong phylogeographical divergences within the Scarlet Macaw Ara macao

(2019) Kari L. Schmidt et al.   IBIS

Occurrence and extent of hybridisation between the invasive Mallard Duck and native Yellow-billed Duck in South Africa

(2019) Kirstin Stephens et al.   BIOLOGICAL INVASIONS

Migratory divides coincide with reproductive barriers across replicated avian hybrid zones above the Tibetan Plateau

(2019) Elizabeth S. C. Scordato et al.   ECOLOGY LETTERS

Incomplete lineage sorting and introgression in the diversification of Chinese spot-billed ducks and mallards

(2018) Wenjuan Wang et al.   Current Zoology

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic approaches to understanding population divergence and speciation in birds

(2016) David P. L. Toews et al.   AUK

Ultrastructural Characterization of the Lower Motor System in a Mouse Model of Krabbe Disease

(2016) Valentina Cappello et al.   Scientific Reports

Clumpak : a program for identifying clustering modes and packaging population structure inferences across K

(2015) Naama M. Kopelman et al.   Molecular Ecology Resources

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

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

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

Testing hypotheses of mitochondrial gene-tree paraphyly: unravelling mitochondrial capture of the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (Pomatorhinus musicus)

(2014) Feng Dong et al.   MOLECULAR ECOLOGY

Extensive mitochondrial introgression in North American Great Black-backed Gulls (Larus marinus) from the American Herring Gull (Larus smithsonianus) with little nuclear DNA impact

(2013) J-M Pons et al.   HEREDITY

A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Macaw (Ara macao)

(2013) Christopher M. Seabury et al.   PLoS One

Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data

(2013) Krystyna Nadachowska-Brzyska et al.   PLoS Genetics

Understanding phylogenetic incongruence: lessons from phyllostomid bats

(2012) Liliana M. Dávalos et al.   BIOLOGICAL REVIEWS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Enhancements to the ADMIXTURE algorithm for individual ancestry estimation

(2011) David H Alexander et al.   BMC BIOINFORMATICS

Species tree inference in a recent radiation of orioles (Genus Icterus): Multiple markers and methods reveal cytonuclear discordance in the northern oriole group

(2011) Frode Jacobsen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2011) Mark A DePristo et al.   NATURE GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

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

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

The Impact of Natural Selection on the Genome: Emerging Patterns in Drosophila and Arabidopsis

(2008) Stephen I. Wright et al.   Annual Review of Ecology Evolution and Systematics

Genes mirror geography within Europe

(2008) John Novembre et al.   NATURE