Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia

Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome

(2017) Daniel R. Schrider et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic basis of octanoic acid resistance inDrosophila sechellia: functional analysis of a fine-mapped region

(2017) J. M. Andrade López et al.   MOLECULAR ECOLOGY

Multilocus phylogeny of alligator lizards ( Elgaria , Anguidae): Testing mtDNA introgression as the source of discordant molecular phylogenetic hypotheses

(2017) Dean H. Leavitt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evidence for Adaptive Introgression of Disease Resistance Genes Among Closely Related Arabidopsis Species

(2017) Jesper Bechsgaard et al.   G3-Genes Genomes Genetics

Hybrid Incompatibilities, Local Adaptation, and the Genomic Distribution of Natural Introgression between Species

(2016) Christina A. Muirhead et al.   AMERICAN NATURALIST

Para-allopatry in hybridizing fire-bellied toads (Bombina bombinaandB. variegata): Inference from transcriptome-wide coalescence analyses

(2016) Beate Nürnberger et al.   EVOLUTION

The Genetic Cost of Neanderthal Introgression

(2016) Kelley Harris et al.   GENETICS

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

(2016) D. R. Schrider et al.   GENETICS

Powerful methods for detecting introgressed regions from population genomic data

(2016) Benjamin K. Rosenzweig et al.   MOLECULAR ECOLOGY

FlyBase at 25: looking to the future

(2016) L. Sian Gramates et al.   NUCLEIC ACIDS RESEARCH

Hybridization in Plants: Old Ideas, New Techniques

(2016) Benjamin E. Goulet et al.   PLANT PHYSIOLOGY

Deep Learning for Population Genetic Inference

(2016) Sara Sheehan et al.   PLoS Computational Biology

The Strength of Selection against Neanderthal Introgression

(2016) Ivan Juric et al.   PLoS Genetics

S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning

(2016) Daniel R. Schrider et al.   PLoS Genetics

The Genetic Cost of Neanderthal Introgression

(2016) Kelley Harris et al.   GENETICS

Natural Hybridization between Genera That Diverged from Each Other Approximately 60 Million Years Ago

(2015) Carl J. Rothfels et al.   AMERICAN NATURALIST

Reliable ABC model choice via random forests

(2015) Pierre Pudlo et al.   BIOINFORMATICS

Expression Divergence of Chemosensory Genes betweenDrosophila sechelliaand Its Sibling Species and Its Implications for Host Shift

(2015) Meng-Shin Shiao et al.   Genome Biology and Evolution

The consequences of not accounting for background selection in demographic inference

(2015) Gregory B. Ewing et al.   MOLECULAR ECOLOGY

Deep learning

(2015) Yann LeCun et al.   NATURE

Adaptive introgression in an African malaria mosquito coincident with the increased usage of insecticide-treated bed nets

(2015) Laura C. Norris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genetics of Resistance to Morinda Fruit Toxin During the Postembryonic Stages in Drosophila sechellia

(2015) Yan Huang et al.   G3-Genes Genomes Genetics

A New Method to Scan Genomes for Introgression in a Secondary Contact Model

(2015) Anthony J. Geneva et al.   PLoS One

Distinguishing migration from isolation using genes with intragenic recombination: detecting introgression in the Drosophila simulans species complex

(2014) Miguel Navascués et al.   BMC EVOLUTIONARY BIOLOGY

Genome-Wide Patterns of Differentiation Among House Mouse Subspecies

(2014) Megan Phifer-Rixey et al.   GENETICS

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

Detecting Structure of Haplotypes and Local Ancestry

(2014) Y. Guan   GENETICS

Population genomics of parallel hybrid zones in the mimetic butterflies,H. melpomeneandH. erato

(2014) Nicola J. Nadeau et al.   GENOME RESEARCH

Hybridization occurs betweenDrosophila simulansandD. sechelliain the Seychelles archipelago

(2014) D. R. Matute et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Landscape of Standing Variation for Tandem Duplications in Drosophila yakuba and Drosophila simulans

(2014) Rebekah L. Rogers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

(2014) Emilia Huerta-Sánchez et al.   NATURE

The genomic landscape of Neanderthal ancestry in present-day humans

(2014) Sriram Sankararaman et al.   NATURE

Extensive introgression in a malaria vector species complex revealed by phylogenomics

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

Multiple recent horizontal transfers of a large genomic region in cheese making fungi

(2014) Kevin Cheeseman et al.   Nature Communications

Speciation and Introgression between Mimulus nasutus and Mimulus guttatus

(2014) Yaniv Brandvain et al.   PLoS Genetics

The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit

(2014) Miguel Carneiro et al.   PLoS Genetics

Rates and Genomic Consequences of Spontaneous Mutational Events in Drosophila melanogaster

(2013) Daniel R. Schrider et al.   GENETICS

A Locus in Drosophila sechellia Affecting Tolerance of a Host Plant Toxin

(2013) Eric A. Hungate et al.   GENETICS

Learning Natural Selection from the Site Frequency Spectrum

(2013) R. Ronen et al.   GENETICS

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

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

A Selective Sweep across Species Boundaries in Drosophila

(2013) Cara L. Brand et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) Philip W. Hedrick   MOLECULAR ECOLOGY

Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes

(2013) Pierre Gladieux et al.   MOLECULAR ECOLOGY

Neutral genomic regions refine models of recent rapid human population growth

(2013) E. Gazave et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Robust Estimation of Local Genetic Ancestry in Admixed Populations Using a Nonparametric Bayesian Approach

(2012) K.-A. Sohn et al.   GENETICS

Genomic Variation in Natural Populations of Drosophila melanogaster

(2012) C. H. Langley et al.   GENETICS

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence

(2012) T. T. Hu et al.   GENOME RESEARCH

Genome sequencing reveals complex speciation in the Drosophila simulans clade

(2012) D. Garrigan et al.   GENOME RESEARCH

Estimating Divergence Dates and Substitution Rates in the Drosophila Phylogeny

(2012) Darren J. Obbard et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improved whole-chromosome phasing for disease and population genetic studies

(2012) Olivier Delaneau et al.   NATURE METHODS

Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster

(2012) Andrew H. Chan et al.   PLoS Genetics

Adaptive Introgression across Species Boundaries in Heliconius Butterflies

(2012) Carolina Pardo-Diaz et al.   PLoS Genetics

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

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

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

Constrained structural design optimization via a parallel augmented Lagrangian particle swarm optimization approach

(2011) P.W. Jansen et al.   COMPUTERS & STRUCTURES

Adaptive Introgression of Anticoagulant Rodent Poison Resistance by Hybridization between Old World Mice

(2011) Ying Song et al.   CURRENT BIOLOGY

Microsatellite variation suggests a recent fine-scale population structure of Drosophila sechellia, a species endemic of the Seychelles archipelago

(2011) Delphine Legrand et al.   GENETICA

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

(2011) Mark A DePristo et al.   NATURE GENETICS

pyOpt: a Python-based object-oriented framework for nonlinear constrained optimization

(2011) Ruben E. Perez et al.   STRUCTURAL AND MULTIDISCIPLINARY OPTIMIZATION

Distinguishing Positive Selection From Neutral Evolution: Boosting the Performance of Summary Statistics

(2010) K. Lin et al.   GENETICS

Searching for Footprints of Positive Selection in Whole-Genome SNP Data From Nonequilibrium Populations

(2010) P. Pavlidis et al.   GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Patterns of hybridization in plants

(2010) Kenneth D. Whitney et al.   PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Genetic Evidence for Hybrid Trait Speciation in Heliconius Butterflies

(2010) Camilo Salazar et al.   PLoS Genetics

A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting

(2009) Simon Joly et al.   AMERICAN NATURALIST

Variant Ionotropic Glutamate Receptors as Chemosensory Receptors in Drosophila

(2009) Richard Benton et al.   CELL

ASSORTATIVE MATING PREFERENCES AMONG HYBRIDS OFFERS A ROUTE TO HYBRID SPECIATION

(2009) Maria C. Melo et al.   EVOLUTION

Species-Wide Genetic Variation and Demographic History of Drosophila sechellia , a Species Lacking Population Structure

(2009) Delphine Legrand et al.   GENETICS

Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines

(2009) P. D. Keightley et al.   GENOME RESEARCH

Fast model-based estimation of ancestry in unrelated individuals

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

Non-linear regression models for Approximate Bayesian Computation

(2009) Michael G. B. Blum et al.   STATISTICS AND COMPUTING

The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing

(2009) Rob J. Kulathinal et al.   PLoS Genetics

Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations

(2009) Alkes L. Price et al.   PLoS Genetics

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

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

The role of hybridization in evolution

(2003) N. H. Barton   MOLECULAR ECOLOGY