Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)

The origin and spread of locally adaptive seasonal camouflage in snowshoe hares

(2020) Matthew R. Jones et al.   AMERICAN NATURALIST

Robbery in progress: Historical museum collections bring to light a mitochondrial capture within a bird species widespread across southern Australia, the Copperback Quail‐thrush Cinclosoma clarum

(2020) Kerensa McElroy et al.   Ecology and Evolution

Insights from genomes into the evolutionary importance and prevalence of hybridization in nature

(2019) Scott A. Taylor et al.   Nature Ecology & Evolution

Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome

(2019) Fei He et al.   NATURE GENETICS

A phylogenomic rodent tree reveals the repeated evolution of masseter architectures

(2019) Mark T. Swanson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

An invariants-based method for efficient identification of hybrid species from large-scale genomic data

(2019) Laura S. Kubatko et al.   BMC EVOLUTIONARY BIOLOGY

Genomic architecture and introgression shape a butterfly radiation

(2019) Nathaniel B. Edelman et al.   SCIENCE

Eukaryote hybrid genomes

(2019) Anna Runemark et al.   PLoS Genetics

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

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

(2018) Diego F. Morales-Briones et al.   NEW PHYTOLOGIST

Natural selection interacts with recombination to shape the evolution of hybrid genomes

(2018) Molly Schumer et al.   SCIENCE

Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares

(2018) Matthew R. Jones et al.   SCIENCE

HyDe: A Python Package for Genome-Scale Hybridization Detection

(2018) Paul D Blischak et al.   SYSTEMATIC BIOLOGY

Genomic evidence of speciation reversal in ravens

(2018) Anna M. Kearns et al.   Nature Communications

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

(2018) Milan Malinsky et al.   Nature Ecology & Evolution

A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes

(2017) Timothée Bonnet et al.   EVOLUTION

The on-again, off-again relationship between mitochondrial genomes and species boundaries

(2017) Daniel B. Sloan et al.   MOLECULAR ECOLOGY

Range expansion underlies historical introgressive hybridization in the Iberian hare

(2017) João P. Marques et al.   Scientific Reports

The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans

(2016) Sriram Sankararaman et al.   CURRENT BIOLOGY

Hybridization and extinction

(2016) Marco Todesco et al.   Evolutionary Applications

The Genetic Cost of Neanderthal Introgression

(2016) Kelley Harris et al.   GENETICS

The Baculum was Gained and Lost Multiple Times during Mammalian Evolution

(2016) Nicholas G. Schultz et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Towards a uniform nomenclature for ground squirrels: the status of the Holarctic chipmunks

(2016) Bruce D. Patterson et al.   MAMMALIA

A genomic perspective on hybridization and speciation

(2016) Bret A. Payseur et al.   MOLECULAR ECOLOGY

Ancient gene flow from early modern humans into Eastern Neanderthals

(2016) Martin Kuhlwilm et al.   NATURE

Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap

(2016) Geoffrey E. Hill   Ecology and Evolution

The Genetic Cost of Neanderthal Introgression

(2016) Kelley Harris et al.   GENETICS

Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks

(2015) Jeffrey M. Good et al.   EVOLUTION

Targeted capture in evolutionary and ecological genomics

(2015) Matthew R. Jones et al.   MOLECULAR ECOLOGY

On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods

(2015) Sebastien Roch et al.   SYSTEMATIC BIOLOGY

Similar Efficacies of Selection Shape Mitochondrial and Nuclear Genes in Both Drosophila melanogaster and Homo sapiens

(2015) Brandon S. Cooper et al.   G3-Genes Genomes Genetics

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

The Elusive Nature of Adaptive Mitochondrial DNA Evolution of an Arctic Lineage Prone to Frequent Introgression

(2014) José Melo-Ferreira et al.   Genome Biology and Evolution

Divergence with gene flow within the recent chipmunk radiation (Tamias)

(2014) J Sullivan et al.   HEREDITY

Hybridization, Introgression, and the Nature of Species Boundaries

(2014) Richard G. Harrison et al.   JOURNAL OF HEREDITY

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

Naive binning improves phylogenomic analyses

(2013) Md Shamsuzzoha Bayzid et al.   BIOINFORMATICS

Baculum morphology predicts reproductive success of male house mice under sexual selection

(2013) Paula Stockley et al.   BMC BIOLOGY

EXPERIMENTAL EVIDENCE FOR THE EVOLUTION OF THE MAMMALIAN BACULUM BY SEXUAL SELECTION

(2013) Leigh W. Simmons et al.   EVOLUTION

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

Unlocking the vault: next-generation museum population genomics

(2013) Ke Bi et al.   MOLECULAR ECOLOGY

No evidence for nuclear introgression despite complete mtDNA replacement in the Carpathian newt (Lissotriton montandoni)

(2013) P. Zieliński et al.   MOLECULAR ECOLOGY

Factors affecting male and female reproductive success in a chipmunk (Tamias sibiricus) with a scramble competition mating system

(2012) Julie Marmet et al.   BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY

treePL: divergence time estimation using penalized likelihood for large phylogenies

(2012) Stephen A. Smith et al.   BIOINFORMATICS

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

(2012) Ke Bi et al.   BMC GENOMICS

The biogeography of mitochondrial and nuclear discordance in animals

(2012) DAVID P. L. TOEWS et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Testing for Ancient Admixture between Closely Related Populations

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

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Phylogeny Estimation of the Radiation of Western North American Chipmunks (Tamias) in the Face of Introgression Using Reproductive Protein Genes

(2011) Noah Reid et al.   SYSTEMATIC BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Introgression at differentially aged hybrid zones in red-tailed chipmunks

(2010) Sarah Hird et al.   GENETICA

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

(2010) A. McKenna et al.   GENOME RESEARCH

Examination of nuclear loci across a zone of mitochondrial introgression between Tamias ruficaudus and T. amoenus

(2010) Noah Reid et al.   JOURNAL OF MAMMALOGY

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Simultaneous Genotype Calling and Haplotype Phasing Improves Genotype Accuracy and Reduces False-Positive Associations for Genome-wide Association Studies

(2009) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals

(2009) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2009) P. Librado et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

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

Mitochondrial DNA as a marker of molecular diversity: a reappraisal

(2009) N. GALTIER et al.   MOLECULAR ECOLOGY

Assessment of gene flow across a hybrid zone in red-tailed chipmunks (Tamias ruficaudus)

(2009) SARAH HIRD et al.   MOLECULAR ECOLOGY

The causes of mutation accumulation in mitochondrial genomes

(2009) M. Neiman et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes

(2009) A. W. Briggs et al.   SCIENCE

Phyutility: a phyloinformatics tool for trees, alignments and molecular data

(2008) S. A. Smith et al.   BIOINFORMATICS

Ecological niche modelling of montane mammals in the Great Basin, North America: examining past and present connectivity of species across basins and ranges

(2008) Eric Waltari et al.   JOURNAL OF BIOGEOGRAPHY

Ancient hybridization and mitochondrial capture between two species of chipmunks

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