Identifying targets of selection in mosaic genomes with machine learning: applications inAnopheles gambiaefor detecting sites within locally adapted chromosomal inversions

Adaptive divergence in the monkey flower Mimulus guttatus is maintained by a chromosomal inversion

(2015) Alex D. Twyford et al.   EVOLUTION

Genome-wide tests for introgression between cactophilicDrosophilaimplicate a role of inversions during speciation

(2015) Konrad Lohse et al.   EVOLUTION

The Effect of Linkage on Establishment and Survival of Locally Beneficial Mutations

(2014) Simon Aeschbacher et al.   GENETICS

Evaluation of demographic history and neutral parameterization on the performance ofFSToutlier tests

(2014) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

Stick Insect Genomes Reveal Natural Selection's Role in Parallel Speciation

(2014) V. Soria-Carrasco et al.   SCIENCE

Extensive introgression in a malaria vector species complex revealed by phylogenomics

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

Demography-adjusted tests of neutrality based on genome-wide SNP data

(2014) M. Rafajlović et al.   THEORETICAL POPULATION BIOLOGY

Learning Natural Selection from the Site Frequency Spectrum

(2013) R. Ronen et al.   GENETICS

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Genomic rearrangements and the evolution of clusters of locally adaptive loci

(2013) S. Yeaman   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Mutations in the neverland Gene Turned Drosophila pachea into an Obligate Specialist Species

(2012) M. Lang et al.   SCIENCE

A New Chromosomal Phylogeny Supports the Repeated Origin of Vectorial Capacity in Malaria Mosquitoes of the Anopheles gambiae Complex

(2012) Maryam Kamali et al.   PLoS Pathogens

THE GENETIC ARCHITECTURE OF ADAPTATION UNDER MIGRATION-SELECTION BALANCE

(2011) Sam Yeaman et al.   EVOLUTION

Ecological Genomics of Anopheles gambiae Along a Latitudinal Cline: A Population-Resequencing Approach

(2011) C. Cheng et al.   GENETICS

Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry

(2011) Mathieu Joron et al.   NATURE

Genomic divergence during speciation: causes and consequences

(2011) P. Nosil et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Coalescent patterns for chromosomal inversions in divergent populations

(2011) R. F. Guerrero et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic islands of divergence in hybridizingHeliconiusbutterflies identified by large-scale targeted sequencing

(2011) Nicola J. Nadeau et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus

(2010) Gregory Ewing et al.   BIOINFORMATICS

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

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

(2010) P. Pavlidis et al.   GENETICS

Detecting Selection in Population Trees: The Lewontin and Krakauer Test Extended

(2010) Maxime Bonhomme et al.   GENETICS

Population Genetic Structure of Anopheles gambiae and Anopheles arabiensis in Niger

(2010) Cyrille Czeher et al.   JOURNAL OF MEDICAL ENTOMOLOGY

Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion

(2010) Neil F Lobo et al.   MALARIA JOURNAL

A New Test for Detecting Recent Positive Selection that is Free from the Confounding Impacts of Demography

(2010) H. Li   MOLECULAR BIOLOGY AND EVOLUTION

SNP Genotyping Defines Complex Gene-Flow Boundaries Among African Malaria Vector Mosquitoes

(2010) D. E. Neafsey et al.   SCIENCE

A Widespread Chromosomal Inversion Polymorphism Contributes to a Major Life-History Transition, Local Adaptation, and Reproductive Isolation

(2010) David B. Lowry et al.   PLOS BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The Population Genomics of Trans-Specific Inversion Polymorphisms in Anopheles gambiae

(2009) B. J. White et al.   GENETICS

Efficient Approximate Bayesian Computation Coupled With Markov Chain Monte Carlo Without Likelihood

(2009) Daniel Wegmann et al.   GENETICS

Inversion 2La is associated with enhanced desiccation resistance in Anopheles gambiae

(2009) Emilie M Gray et al.   MALARIA JOURNAL

Ecological explanations for (incomplete) speciation

(2009) Patrik Nosil et al.   TRENDS IN ECOLOGY & EVOLUTION

Ecological niche partitioning between Anopheles gambiae molecular forms in Cameroon: the ecological side of speciation

(2009) Frédéric Simard et al.   BMC ECOLOGY

LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method

(2008) Tiago Antao et al.   BMC BIOINFORMATICS

Annotation and analysis of a large cuticular protein family with the R&R Consensus in Anopheles gambiae

(2008) R Scott Cornman et al.   BMC GENOMICS

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS