Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome

A comprehensive non-redundant reference transcriptome for the Atlantic silverside Menidia menidia

(2020) Nina Overgaard Therkildsen et al.   Marine Genomics

Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish

(2020) Tony Kess et al.   Ecology and Evolution

ngsLD: evaluating linkage disequilibrium using genotype likelihoods

(2019) Emma A Fox et al.   BIOINFORMATICS

Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing

(2019) Nina O. Therkildsen et al.   SCIENCE

A chromosome-level assembly of the Atlantic herring genome—detection of a supergene and other signals of selection

(2019) Mats E. Pettersson et al.   GENOME RESEARCH

Exploring rain forest diversification using demographic model testing in the African foam‐nest treefrog Chiromantis rufescens

(2019) Adam D. Leaché et al.   JOURNAL OF BIOGEOGRAPHY

Full mitochondrial genome sequences reveal new insights about post-glacial expansion and regional phylogeographic structure in the Atlantic silverside (Menidia menidia)

(2018) Runyang Nicolas Lou et al.   MARINE BIOLOGY

Batch effects in a multiyear sequencing study: False biological trends due to changes in read lengths

(2018) D. M. Leigh et al.   Molecular Ecology Resources

Eco-Evolutionary Genomics of Chromosomal Inversions

(2018) Maren Wellenreuther et al.   TRENDS IN ECOLOGY & EVOLUTION

Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes

(2018) Rui Faria et al.   MOLECULAR ECOLOGY

Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation

(2017) Julien Jouganous et al.   GENETICS

Modeling the Multiple Facets of Speciation-with-Gene-Flow toward Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus clupeaformis)

(2017) Clément Rougeux et al.   Genome Biology and Evolution

Gene flow and selection interact to promote adaptive divergence in regions of low recombination

(2017) Kieran Samuk et al.   MOLECULAR ECOLOGY

Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees

(2017) Andreas Wallberg et al.   PLoS Genetics

Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation

(2017) Julien Jouganous et al.   GENETICS

Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection

(2016) Erik Kjærner-Semb et al.   BMC GENOMICS

Genomic Evidence for Adaptive Inversion Clines inDrosophila melanogaster

(2016) Martin Kapun et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomics of local adaptation with gene flow

(2016) Anna Tigano et al.   MOLECULAR ECOLOGY

Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species

(2016) Darren E. Irwin et al.   MOLECULAR ECOLOGY

Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species

(2016) Nina Overgaard Therkildsen et al.   Molecular Ecology Resources

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

(2016) Alvaro Martinez Barrio et al.   eLife

Characterizing Transcriptional Networks in Male Rainbow Darter (Etheostoma caeruleum) that Regulate Testis Development over a Complete Reproductive Cycle

(2016) Paulina A. Bahamonde et al.   PLoS One

Modern Approaches to Local Adaptation

(2015) Michael C. Whitlock   AMERICAN NATURALIST

Local Adaptation by Alleles of Small Effect

(2015) Sam Yeaman   AMERICAN NATURALIST

Reliable Detection of Loci Responsible for Local Adaptation: Inference of a Null Model through Trimming the Distribution of FST

(2015) Michael C. Whitlock et al.   AMERICAN NATURALIST

ngsTools: methods for population genetics analyses from next-generation sequencing data

(2014) Matteo Fumagalli et al.   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

The location, strength, and mechanisms behind marine biogeographic boundaries of the east coast of North America

(2014) Paula Pappalardo et al.   ECOGRAPHY

A RAD-Tag Genetic Map for the Platyfish ( Xiphophorus maculatus ) Reveals Mechanisms of Karyotype Evolution Among Teleost Fish

(2014) Angel Amores et al.   GENETICS

Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants

(2014) Zachariah Gompert 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

The Genome and Linkage Map of the Northern Pike (Esox lucius): Conserved Synteny Revealed between the Salmonid Sister Group and the Neoteleostei

(2014) Eric B. Rondeau et al.   PLoS One

Atlantic salmon show capability for cardiac acclimation to warm temperatures

(2014) Katja Anttila et al.   Nature Communications

A genomic island linked to ecotype divergence in Atlantic cod

(2013) Jakob Hemmer-Hansen et al.   MOLECULAR ECOLOGY

Decadal Changes in the World's Coastal Latitudinal Temperature Gradients

(2013) Hannes Baumann et al.   PLoS One

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

Spatial scale and divergent patterns of variation in adapted traits in the ocean

(2012) Lyndie A. Hice et al.   ECOLOGY LETTERS

The response of correlated traits following cessation of fishery-induced selection

(2012) Santiago Salinas et al.   Evolutionary Applications

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Megabase-Scale Inversion Polymorphism in the Wild Ancestor of Maize

(2012) Zhou Fang et al.   GENETICS

Genome-wide patterns of latitudinal differentiation among populations ofDrosophila melanogasterfrom North America

(2012) Daniel K. Fabian et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Can Diversifying Selection Be Distinguished from History in Geographic Clines? A Population Genomic Study of Killifish (Fundulus heteroclitus)

(2012) Allan E. Strand et al.   PLoS One

Resolution of ray-finned fish phylogeny and timing of diversification

(2012) T. J. Near et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

THE GENETIC ARCHITECTURE OF ADAPTATION UNDER MIGRATION-SELECTION BALANCE

(2011) Sam Yeaman et al.   EVOLUTION

A realignment of marine biogeographic provinces with particular reference to fish distributions

(2011) John C. Briggs et al.   JOURNAL OF BIOGEOGRAPHY

Climate change and evolutionary adaptation

(2011) Ary A. Hoffmann et al.   NATURE

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

High connectivity among locally adapted populations of a marine fish (Menidia menidia)

(2010) Lora M. Clarke et al.   ECOLOGY

Regional differentiation and post-glacial expansion of the Atlantic silverside, Menidia menidia, an annual fish with high dispersal potential

(2010) Megan E. Mach et al.   MARINE BIOLOGY

Gene function analysis in complex data sets using ErmineJ

(2010) Jesse Gillis et al.   Nature Protocols

How and Why Chromosome Inversions Evolve

(2010) Mark Kirkpatrick   PLOS BIOLOGY

The Covariance between Genetic and Environmental Influences across Ecological Gradients

(2009) David O. Conover et al.   Annals of the New York Academy of Sciences

Expression profiling of rainbow trout testis development identifies evolutionary conserved genes involved in spermatogenesis

(2009) Antoine D Rolland et al.   BMC GENOMICS

PERSPECTIVE: The role of experiments in understanding fishery-induced evolution

(2009) David O. Conover et al.   Evolutionary Applications

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

The effect of acute temperature increases on the cardiorespiratory performance of resting and swimming sockeye salmon (Oncorhynchus nerka)

(2008) M. F. Steinhausen et al.   JOURNAL OF EXPERIMENTAL BIOLOGY