What can be learned by scanning the genome for molecular convergence in wild populations?

Minor allele frequency thresholds strongly affect population structure inference with genomic datasets

(2019) Ethan Linck et al.   Molecular Ecology Resources

DNA fragility in the parallel evolution of pelvic reduction in stickleback fish

(2019) Kathleen T. Xie et al.   SCIENCE

The genetics of convergent evolution: insights from plant photosynthesis

(2019) Karolina Heyduk et al.   NATURE REVIEWS GENETICS

The genomic pool of standing structural variation outnumbers single nucleotide polymorphism by three-fold in the marine teleost Chrysophrys auratus

(2019) Andrew Catanach et al.   MOLECULAR ECOLOGY

The Effects of Epistasis and Pleiotropy on Genome-Wide Scans for Adaptive Outlier Loci

(2019) Adam G Jones et al.   JOURNAL OF HEREDITY

Population genomics perspectives on convergent adaptation

(2019) Kristin M. Lee et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genetic constraints on adaptation: a theoretical primer for the genomics era

(2018) Tim Connallon et al.   Annals of the New York Academy of Sciences

Genomics of Parallel Ecological Speciation in Lake Victoria Cichlids

(2018) Joana Isabel Meier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptive population divergence and directional gene flow across steep elevational gradients in a climate-sensitive mammal

(2018) Matthew D. Waterhouse et al.   MOLECULAR ECOLOGY

Detecting the genomic signal of polygenic adaptation and the role of epistasis in evolution

(2018) Katalin Csilléry et al.   MOLECULAR ECOLOGY

The search for loci under selection: trends, biases and progress

(2018) Collin W. Ahrens et al.   MOLECULAR ECOLOGY

Founder-specific inbreeding depression affects racing performance in Thoroughbred horses

(2018) Evelyn T. Todd et al.   Scientific Reports

Human demographic history has amplified the effects of background selection across the genome

(2018) Raul Torres et al.   PLoS Genetics

Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation

(2018) Jacob L. Steenwyk et al.   Frontiers in Microbiology

Experimental evidence for rapid genomic adaptation to a new niche in an adaptive radiation

(2018) David A. Marques et al.   Nature Ecology & Evolution

(Non)Parallel Evolution

(2018) Daniel I. Bolnick et al.   Annual Review of Ecology Evolution and Systematics

Divergent Uses of “Parallel Evolution” during the History of The American Naturalist

(2018) Yoel E. Stuart   AMERICAN NATURALIST

Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes

(2018) Rui Faria et al.   MOLECULAR ECOLOGY

Contingency and determinism in evolution: Replaying life’s tape

(2018) Zachary D. Blount et al.   SCIENCE

Quantifying how constraints limit the diversity of viable routes to adaptation

(2018) Sam Yeaman et al.   PLoS Genetics

The Spread of an Inversion with Migration and Selection

(2017) Brian Charlesworth et al.   GENETICS

Genomic Scans across Three Eucalypts Suggest that Adaptation to Aridity is a Genome-Wide Phenomenon

(2017) Dorothy A. Steane et al.   Genome Biology and Evolution

Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

(2017) M. Ravinet et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans

(2017) J.T. Daub et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

All roads lead to weediness: Patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian Oryza

(2017) Zhongyun Huang et al.   MOLECULAR ECOLOGY

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

(2017) Kieran Samuk et al.   MOLECULAR ECOLOGY

RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al . (2016)

(2017) Garrett J. McKinney et al.   Molecular Ecology Resources

Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations

(2017) Julian M. Catchen et al.   Molecular Ecology Resources

Variation in recombination frequency and distribution across eukaryotes: patterns and processes

(2017) Jessica Stapley et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean

(2017) Sangeet Lamichhaney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

(2017) Ludovic Dutoit et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Population genomics of the eastern cottonwood (Populus deltoides )

(2017) Annette M. Fahrenkrog et al.   Ecology and Evolution

The Spread of an Inversion with Migration and Selection

(2017) Brian Charlesworth et al.   GENETICS

Range-wide parallel climate-associated genomic clines in Atlantic salmon

(2017) Nicholas W. Jeffery et al.   Royal Society Open Science

Contrasting effects of environment and genetics generate a continuum of parallel evolution

(2017) Yoel E. Stuart et al.   Nature Ecology & Evolution

Conserved Genetic Architecture Underlying Individual Recombination Rate Variation in a Wild Population of Soay Sheep ( Ovis aries )

(2016) Susan E. Johnston et al.   GENETICS

The Impact of Linked Selection in Chimpanzees: A Comparative Study

(2016) Susanne P. Pfeifer et al.   Genome Biology and Evolution

The probability of parallel genetic evolution from standing genetic variation

(2016) A. MacPherson et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Parallel Evolution of Copy-Number Variation across Continents inDrosophila melanogaster

(2016) Daniel R. Schrider et al.   MOLECULAR BIOLOGY AND EVOLUTION

Powerful methods for detecting introgressed regions from population genomic data

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

Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes

(2016) Quentin Rougemont 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

Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation

(2016) David B. Lowry et al.   Molecular Ecology Resources

pcadapt: anRpackage to perform genome scans for selection based on principal component analysis

(2016) Keurcien Luu et al.   Molecular Ecology Resources

Determinants of genetic diversity

(2016) Hans Ellegren et al.   NATURE REVIEWS GENETICS

Causes of molecular convergence and parallelism in protein evolution

(2016) Jay F. Storz   NATURE REVIEWS GENETICS

Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution

(2016) Tom Vogwill et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Convergent local adaptation to climate in distantly related conifers

(2016) S. Yeaman et al.   SCIENCE

Detecting Polygenic Evolution: Problems, Pitfalls, and Promises

(2016) Maren Wellenreuther et al.   TRENDS IN GENETICS

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

(2016) James B. Pease et al.   PLOS BIOLOGY

Conserved Genetic Architecture Underlying Individual Recombination Rate Variation in a Wild Population of Soay Sheep ( Ovis aries )

(2016) Susan E. Johnston et al.   GENETICS

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

Repeated evolution and the impact of evolutionary history on adaptation

(2015) Terry J. Ord et al.   BMC EVOLUTIONARY BIOLOGY

Adaptive introgression as a resource for management and genetic conservation in a changing climate

(2015) Jill A. Hamilton et al.   CONSERVATION BIOLOGY

Independent Molecular Basis of Convergent Highland Adaptation in Maize

(2015) Shohei Takuno et al.   GENETICS

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

The Effect of Selection Environment on the Probability of Parallel Evolution

(2015) Susan F. Bailey et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide-toxic habitats of a neotropical fish (Poecilia mexicana)

(2015) Markus Pfenninger et al.   MOLECULAR ECOLOGY

RAD sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels

(2015) M. Laporte et al.   MOLECULAR ECOLOGY

Integration of Random Forest with population-based outlier analyses provides insight on the genomic basis and evolution of run timing in Chinook salmon (Oncorhynchus tshawytscha)

(2015) Marine S. O. Brieuc et al.   MOLECULAR ECOLOGY

Population genomics of natural and experimental populations of guppies (Poecilia reticulata)

(2015) Bonnie A. Fraser et al.   MOLECULAR ECOLOGY

The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

(2015) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

Genome-wide patterns and properties of de novo mutations in humans

(2015) Laurent C Francioli et al.   NATURE GENETICS

Elucidating the molecular architecture of adaptation via evolve and resequence experiments

(2015) Anthony Long et al.   NATURE REVIEWS GENETICS

Genetic rescue to the rescue

(2015) Andrew R. Whiteley et al.   TRENDS IN ECOLOGY & EVOLUTION

LEA: AnRpackage for landscape and ecological association studies

(2015) Eric Frichot et al.   Methods in Ecology and Evolution

Independent Molecular Basis of Convergent Highland Adaptation in Maize

(2015) Shohei Takuno et al.   GENETICS

Detection of Convergent Genome-Wide Signals of Adaptation to Tropical Forests in Humans

(2015) Carlos Eduardo G. Amorim et al.   PLoS One

Widespread Signals of Convergent Adaptation to High Altitude in Asia and America

(2014) Matthieu Foll et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Molecular Basis of Phenotypic Convergence

(2014) Erica Bree Rosenblum et al.   Annual Review of Ecology Evolution and Systematics

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Parallel selection on gene copy number variations through evolution of three-spined stickleback genomes

(2014) Shotaro Hirase et al.   BMC GENOMICS

Convergent Genetic Architecture Underlies Social Organization in Ants

(2014) Jessica Purcell et al.   CURRENT BIOLOGY

Evidence of Convergent Evolution in Humans and Macaques Supports an Adaptive Role for Copy Number Variation of the β-Defensin-2 Gene

(2014) Barbara Ottolini et al.   Genome Biology and Evolution

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

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

The genomic signature of parallel adaptation from shared genetic variation

(2014) Marius Roesti et al.   MOLECULAR ECOLOGY

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

Comparative population genomics in animals uncovers the determinants of genetic diversity

(2014) J. Romiguier et al.   NATURE

Empirical fitness landscapes and the predictability of evolution

(2014) J. Arjan G.M. de Visser et al.   NATURE REVIEWS GENETICS

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

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

A Population Genetic Signal of Polygenic Adaptation

(2014) Jeremy J. Berg et al.   PLoS Genetics

Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination

(2013) Carina F Mugal et al.   BMC GENOMICS

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Background Selection 20 Years on

(2013) Brian Charlesworth   JOURNAL OF HEREDITY

Evidence for Polygenic Adaptation to Pathogens in the Human Genome

(2013) Josephine T. Daub et al.   MOLECULAR BIOLOGY AND EVOLUTION

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

The genetic causes of convergent evolution

(2013) David L. Stern   NATURE REVIEWS GENETICS

How Hot Are Drosophila Hotspots? Examining Recombination Rate Variation and Associations with Nucleotide Diversity, Divergence, and Maternal Age in Drosophila pseudoobscura

(2013) Brenda Manzano-Winkler et al.   PLoS One

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

A coalescent model of background selection with recombination, demography and variation in selection coefficients

(2012) K Zeng   HEREDITY

Genomic signatures of divergent selection and speciation patterns in a ‘natural experiment’, the young parallel radiations of Nicaraguan crater lake cichlid fishes

(2012) Andreas F. Kautt et al.   MOLECULAR ECOLOGY

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

(2012) Kanchon K. Dasmahapatra et al.   NATURE

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

The probability of genetic parallelism and convergence in natural populations

(2012) G. L. Conte et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks

(2011) Felicity C. Jones et al.   CURRENT BIOLOGY

THE QTN PROGRAM AND THE ALLELES THAT MATTER FOR EVOLUTION: ALL THAT'S GOLD DOES NOT GLITTER

(2011) Matthew V. Rockman   EVOLUTION

ESTABLISHMENT AND MAINTENANCE OF ADAPTIVE GENETIC DIVERGENCE UNDER MIGRATION, SELECTION, AND DRIFT

(2011) Sam Yeaman et al.   EVOLUTION

CONVERGENCE, ADAPTATION, AND CONSTRAINT

(2011) Jonathan B. Losos   EVOLUTION

Linkage Disequilibrium Under Recurrent Bottlenecks

(2011) E. Schaper et al.   GENETICS

Recombination rate variation in closely related species

(2011) C S Smukowski et al.   HEREDITY

Comparison ofFSToutlier tests for SNP loci under selection

(2011) SHAWN R. NARUM et al.   Molecular Ecology Resources

Variation in the mutation rate across mammalian genomes

(2011) Alan Hodgkinson et al.   NATURE REVIEWS GENETICS

The ecological causes of evolution

(2011) Andrew D.C. MacColl   TRENDS IN ECOLOGY & EVOLUTION

ABC as a flexible framework to estimate demography over space and time: some cons, many pros

(2010) G. BERTORELLE et al.   MOLECULAR ECOLOGY

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature

(2010) I. R. Bradbury et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

Copy Number Variation in Human Health, Disease, and Evolution

(2009) Feng Zhang et al.   Annual Review of Genomics and Human Genetics

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Statistical mechanics of convergent evolution in spatial patterning

(2009) B. S. Khatri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

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

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

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

(2008) Tiago Antao et al.   BMC BIOINFORMATICS

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

(2008) David L. Stern et al.   EVOLUTION

An Approximate Bayesian Computation Approach to Overcome Biases That Arise When Using Amplified Fragment Length Polymorphism Markers to Study Population Structure

(2008) Matthieu Foll et al.   GENETICS

Fine-scale mapping of recombination rate in Drosophila refines its correlation to diversity and divergence

(2008) R. J. Kulathinal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

(2008) Z. D. Blount et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human-macaque comparisons illuminate variation in neutral substitution rates

(2008) Svitlana Tyekucheva et al.   GENOME BIOLOGY

Are cattle, sheep, and goats endangered species?

(2007) P. TABERLET et al.   MOLECULAR ECOLOGY

Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation?

(2007) J ARENDT et al.   TRENDS IN ECOLOGY & EVOLUTION

Adaptation from standing genetic variation

(2007) R BARRETT et al.   TRENDS IN ECOLOGY & EVOLUTION