Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers

Ancient introgression underlying the unusual mito‐nuclear discordance and coat phenotypic variation in the Moupin pika

(2022) Deyan Ge et al.   DIVERSITY AND DISTRIBUTIONS

Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malawi

(2022) Mark D Scherz et al.   SYSTEMATIC BIOLOGY

Rampant Nuclear‐Mitochondrial‐Plastid Phylogenomic Discordance in Globally Distributed Calcifying Microalgae

(2022) Tzu‐Tong Kao et al.   NEW PHYTOLOGIST

Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays

(2022) Devon A DeRaad et al.   SYSTEMATIC BIOLOGY

Phylogenomics reveals extensive introgression and a case of mito-nuclear discordance in the killifish genus Kryptolebias

(2022) Waldir M. Berbel-Filho et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomics Reveals that Mitochondrial Capture and Nuclear Introgression Characterizes Skua Species Proposed to be of Hybrid Origin

(2022) Else K Mikkelsen et al.   SYSTEMATIC BIOLOGY

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

Prevalence of Genetically Complex Leishmania Strains With Hybrid and Mito-Nuclear Discordance

(2021) Hirotomo Kato et al.   Frontiers in Cellular and Infection Microbiology

How Mitonuclear Discordance and Geographic Variation Have Confounded Species Boundaries in a Widely Studied Snake

(2021) Thomas L. Marshall et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Mitonuclear conflict in a macaque species exhibiting phylogenomic discordance

(2021) Nick P. Bailey et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Displaced clines in an avian hybrid zone (Thamnophilidae: Rhegmatorhina ) within an Amazonian interfluve

(2021) Glaucia Del‐Rio et al.   EVOLUTION

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

(2021) Rebecca T. Kimball et al.   GENE

Mito‐nuclear discordance at a mimicry color transition zone in bumble bee Bombus melanopygus

(2021) Briana E. Wham et al.   Ecology and Evolution

Phylogenomic approaches to detecting and characterizing introgression

(2021) Mark S Hibbins et al.   GENETICS

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cryptic and extensive hybridization between ancient lineages of American crows

(2020) David L. Slager et al.   MOLECULAR ECOLOGY

New methods to calculate concordance factors for phylogenomic datasets

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Finding complexity in complexes: Assessing the causes of mitonuclear discordance in a problematic species complex of Mesoamerican toads

(2020) Thomas J. Firneno et al.   MOLECULAR ECOLOGY

Genome-wide data reveal discordant mitonuclear introgression in the intermediate horseshoe bat (Rhinolophus affinis)

(2020) Xiuguang Mao et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

How far east can a Western Whistler go? Genomic data reveal large eastward range extension, taxonomic and nomenclatural change, and reassessment of conservation needs

(2020) Leo Joseph et al.   Emu-Austral Ornithology

Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere

(2020) Fernando Lopes et al.   SYSTEMATIC BIOLOGY

Large ancestral effective population size explains the difficult phylogenetic placement of owl monkeys

(2019) Carlos G. Schrago et al.   AMERICAN JOURNAL OF PRIMATOLOGY

Aberrantly plumaged orioles from the Trans-Fly savannas of New Guinea and their ecological and evolutionary significance

(2019) Leo Joseph et al.   EMU

A mirage of cryptic species: Genomics uncover striking mitonuclear discordance in the butterfly Thymelicus sylvestris

(2019) Joan C. Hinojosa et al.   MOLECULAR ECOLOGY

One, two or more species? Mitonuclear discordance and species delimitation

(2019) Laurence Després   MOLECULAR ECOLOGY

Stacks 2: analytical methods for paired‐end sequencing improve RADseq‐based population genomics

(2019) Nicolas C. Rochette et al.   MOLECULAR ECOLOGY

A Laurasian origin for a pantropical bird radiation is supported by genomic and fossil data (Aves: Coraciiformes)

(2019) Jenna M. McCullough et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Versatile genome assembly evaluation with QUAST-LG

(2018) Alla Mikheenko et al.   BIOINFORMATICS

Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression

(2018) Vladislav Ivanov et al.   MOLECULAR ECOLOGY

Multiple origins of downy mildews and mito-nuclear discordance within the paraphyletic genus Phytophthora

(2018) Tyler B. Bourret et al.   PLoS One

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

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

(2017) Timothée Bonnet et al.   EVOLUTION

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

A phylogeny of kingfishers reveals an Indomalayan origin and elevated rates of diversification on oceanic islands

(2017) Michael J. Andersen et al.   JOURNAL OF BIOGEOGRAPHY

UFBoot2: Improving the Ultrafast Bootstrap Approximation

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

Range instability leads to cytonuclear discordance in a morphologically cryptic ground squirrel species complex

(2017) Mark A. Phuong et al.   MOLECULAR ECOLOGY

Incomplete Lineage Sorting in Mammalian Phylogenomics

(2016) Celine Scornavacca et al.   SYSTEMATIC BIOLOGY

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

Gene Tree Discordance Causes Apparent Substitution Rate Variation

(2016) Fábio K. Mendes et al.   SYSTEMATIC BIOLOGY

Tectonic collision and uplift of Wallacea triggered the global songbird radiation

(2016) Robert G. Moyle et al.   Nature Communications

Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus

(2016) David Peris et al.   PLoS Genetics

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Isolation by environment in White-breasted Nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach

(2015) Joseph D. Manthey et al.   MOLECULAR ECOLOGY

Positive and purifying selection in mitochondrial genomes of a bird with mitonuclear discordance

(2015) Hernán E. Morales et al.   MOLECULAR ECOLOGY

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

(2015) Alexander Suh et al.   PLOS BIOLOGY

Rapid diversification and secondary sympatry in Australo-Pacific kingfishers (Aves: Alcedinidae: Todiramphus)

(2015) M. J. Andersen et al.   Royal Society Open Science

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

Evolutionary basis of mitonuclear discordance between sister species of mole salamanders (Ambystomasp.)

(2014) Robert D. Denton et al.   MOLECULAR ECOLOGY

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting

(2014) Siavash Mirarab et al.   SYSTEMATIC BIOLOGY

Australia’s arid-adapted butcherbirds experienced range expansions during Pleistocene glacial maxima

(2014) Anna M. Kearns et al.   Nature Communications

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Phylogeography of the Variable Dwarf-KingfisherCeyx Lepidus(Aves: Alcedinidae) inferred from mitochondrial and nuclear DNA sequences

(2013) Michael J. Andersen et al.   AUK

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

Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation

(2013) Philip W. Hedrick   MOLECULAR ECOLOGY

A molecular phylogeny of Pacific honeyeaters (Aves: Meliphagidae) reveals extensive paraphyly and an isolated Polynesian radiation

(2013) Michael J. Andersen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Molecular systematics of the world's most polytypic bird: thePachycephala pectoralis/melanura(Aves: Pachycephalidae) species complex

(2013) Michael J. Andersen et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

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

Concordance analysis in mitogenomic phylogenetics

(2012) David W. Weisrock   MOLECULAR PHYLOGENETICS AND EVOLUTION

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

Testing for Ancient Admixture between Closely Related Populations

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

Genome-wide synteny through highly sensitive sequence alignment: Satsuma

(2010) M. G. Grabherr et al.   BIOINFORMATICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

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

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

Fast model-based estimation of ancestry in unrelated individuals

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

The causes of mitochondrial DNA gene tree paraphyly in birds

(2009) Bailey D. McKay et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Explosive Pleistocene diversification and hemispheric expansion of a “great speciator”

(2009) Robert G. Moyle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Maximum Likelihood Estimates of Species Trees: How Accuracy of Phylogenetic Inference Depends upon the Divergence History and Sampling Design

(2009) John E. McCormack et al.   SYSTEMATIC BIOLOGY