Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow

Assortative mating in hybrid zones is remarkably ineffective in promoting speciation

(2020) Darren Irwin   AMERICAN NATURALIST

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

(2020) Milan Malinsky et al.   Molecular Ecology Resources

Phylotranscriptomic evidence for pervasive ancient hybridization among Old World salamanders

(2020) Loïs Rancilhac et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Recombination rate variation shapes barriers to introgression across butterfly genomes

(2019) Simon H. Martin et al.   PLOS BIOLOGY

‘Ghost introgression’ as a cause of deep mitochondrial divergence in a bird species complex

(2019) Dezhi Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recombination-aware phylogenomics reveals the structured genomic landscape of hybridizing cat species

(2019) Gang Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic architecture and introgression shape a butterfly radiation

(2019) Nathaniel B. Edelman et al.   SCIENCE

Genomic data reveal a protracted window of introgression during the diversification of a neotropical woodcreeper radiation

(2019) Paola Pulido‐Santacruz et al.   EVOLUTION

A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis

(2019) Tomáš Flouri et al.   MOLECULAR BIOLOGY AND EVOLUTION

Parallelization of MAFFT for large-scale multiple sequence alignments

(2018) Tsukasa Nakamura et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation

(2018) Per Alström et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Discordance between genomic divergence and phenotypic variation in a rapidly evolving avian genus ( Motacilla )

(2018) Rebecca B. Harris et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Biogeography of Deep Time Phylogenetic Reticulation

(2018) Frank T Burbrink et al.   SYSTEMATIC BIOLOGY

Phenotypic and Genetic Structure Support Gene Flow Generating Gene Tree Discordances in an Amazonian Floodplain Endemic Species

(2018) Gregory Thom et al.   SYSTEMATIC BIOLOGY

Inferring Phylogenetic Networks Using PhyloNet

(2018) Dingqiao Wen et al.   SYSTEMATIC BIOLOGY

Bayesian Divergence-Time Estimation with Genome-Wide Single-Nucleotide Polymorphism Data of Sea Catfishes (Ariidae) Supports Miocene Closure of the Panamanian Isthmus

(2018) Madlen Stange et al.   SYSTEMATIC BIOLOGY

Coalescent Analysis of Phylogenomic Data Confidently Resolves the Species Relationships in the Anopheles gambiae Species Complex

(2018) Yuttapong Thawornwattana et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenomic Signatures of Ancient Introgression in a Rogue Lineage of Darters (Teleostei: Percidae)

(2018) Daniel J MacGuigan et al.   SYSTEMATIC BIOLOGY

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Genomic differentiation and patterns of gene flow between two long-tailed tit species (Aegithalos )

(2017) Dezhi Zhang et al.   MOLECULAR ECOLOGY

Correlated patterns of genetic diversity and differentiation across an avian family

(2017) Benjamin M. Van Doren et al.   MOLECULAR ECOLOGY

Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa

(2017) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

Ancient hybridization fuels rapid cichlid fish adaptive radiations

(2017) Joana I. Meier et al.   Nature Communications

Avian introgression in the genomic era

(2017) Jente Ottenburghs et al.   Avian Research

Mosaic genome evolution in a recent and rapid avian radiation

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

Hidden histories of gene flow in highland birds revealed with genomic markers

(2016) Eugenia Zarza et al.   MOLECULAR ECOLOGY

Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

(2016) Dingqiao Wen et al.   MOLECULAR ECOLOGY

A genomic perspective on hybridization and speciation

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

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

(2016) Scott V. Edwards et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Redundans: an assembly pipeline for highly heterozygous genomes

(2016) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

Evolutionary signals of selection on cognition from the great tit genome and methylome

(2016) Veronika N. Laine et al.   Nature Communications

How reticulated are species?

(2015) James Mallet et al.   BIOESSAYS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

(2015) Gang Li et al.   GENOME RESEARCH

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum ofFicedulaflycatchers

(2015) Reto Burri et al.   GENOME RESEARCH

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

(2015) Alexander Nater et al.   SYSTEMATIC BIOLOGY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Estimation of linkage disequilibrium and interspecific gene flow inFicedulaflycatchers by a newly developed 50k single-nucleotide polymorphism array

(2014) Takeshi Kawakami et al.   Molecular Ecology Resources

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Extensive introgression in a malaria vector species complex revealed by phylogenomics

(2014) M. C. Fontaine et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

MORE ACCURATE PHYLOGENIES INFERRED FROM LOW-RECOMBINATION REGIONS IN THE PRESENCE OF INCOMPLETE LINEAGE SORTING

(2013) James B. Pease et al.   EVOLUTION

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

The Effects of Deleterious Mutations on Evolution at Linked Sites

(2012) Brian Charlesworth   GENETICS

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

The genomics of speciation-with-gene-flow

(2012) Jeffrey L. Feder et al.   TRENDS IN GENETICS

Genetic Introgression: An Integral but neglected component of speciation in birds

(2011) Frank E. Rheindt et al.   AUK

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Horizontal and elevational phylogeographic patterns of Himalayan and Southeast Asian forest passerines (Aves: Passeriformes)

(2011) Martin Päckert et al.   JOURNAL OF BIOGEOGRAPHY

Testing for Ancient Admixture between Closely Related Populations

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

Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice

(2011) M. W. Nachman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

The roles of time and ecology in the continental radiation of the Old World leaf warblers (Phylloscopus and Seicercus)

(2010) T. D. Price   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

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

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

The Golden-spectacled Warbler: a complex of sibling species, including a previously undescribed species

(2008) Per Alström et al.   IBIS

Hemiplasy: A New Term in the Lexicon of Phylogenetics

(2008) John C. Avise et al.   SYSTEMATIC BIOLOGY