Parallelism in eco-morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish

Ecological factors and morphological traits are associated with repeated genomic differentiation between lake and stream stickleback

(2019) Diana J. Rennison et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Cryptic genetic variation accelerates evolution by opening access to diverse adaptive peaks

(2019) Jia Zheng et al.   SCIENCE

Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister species complex

(2019) Clément Rougeux et al.   MOLECULAR ECOLOGY

Ecological opportunity shapes a large Arctic charr species radiation

(2019) Carmela J. Doenz et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast

(2019) Hernán E. Morales et al.   Science Advances

Inferring phylogenetic structure, hybridization and divergence times within Salmoninae (Teleostei: Salmonidae) using RAD-sequencing

(2018) Laurène A. Lecaudey et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Natural selection and the predictability of evolution inTimemastick insects

(2018) Patrik Nosil et al.   SCIENCE

The Genetic Architecture Underlying the Evolution of a Rare Piscivorous Life History Form in Brown Trout after Secondary Contact and Strong Introgression

(2018) Arne Jacobs et al.   Genes

(Non)Parallel Evolution

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

The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly

(2018) Kris A. Christensen et al.   PLoS One

Contingency and determinism in evolution: Replaying life’s tape

(2018) Zachary D. Blount et al.   SCIENCE

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

Predictability and Parallelism of Multitrait Adaptation

(2017) Randall Brian Langerhans   JOURNAL OF HEREDITY

WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit

(2017) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

Ecosystem size predicts eco-morphological variability in a postglacial diversification

(2017) Hans Recknagel et al.   Ecology and Evolution

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

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

Parallel phenotypic evolution of skull-bone structures and head measurements of Arctic charr morphs in two subarctic lakes

(2016) E. Saltykova et al.   ENVIRONMENTAL BIOLOGY OF FISHES

Morphological, ecological and behavioural differentiation of sympatric profundal and pelagic Arctic charr (Salvelinus alpinus) in Loch Dughaill Scotland

(2016) O. E. Hooker et al.   HYDROBIOLOGIA

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of genomic islands by increased establishment probability of linked alleles

(2016) Sam Yeaman et al.   MOLECULAR ECOLOGY

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

Multispecies Outcomes of Sympatric Speciation after Admixture with the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids

(2016) Andreas F. Kautt et al.   PLoS Genetics

Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences

(2016) Gaik Tamazian et al.   GigaScience

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Sympatric ecological divergence associated with a color polymorphism

(2015) Henrik Kusche et al.   BMC BIOLOGY

Parallel evolutionary divergence in Arctic char Salvelinus alpinus complex from Transbaikalia: variation in differentiation degree and segregation of genetic diversity among sympatric forms

(2015) Natalia V. Gordeeva et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Double-digest RAD sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with nonmodel organisms

(2015) Hans Recknagel et al.   Molecular Ecology Resources

popart: full-feature software for haplotype network construction

(2015) Jessica W. Leigh et al.   Methods in Ecology and Evolution

Morphological divergence between three Arctic charr morphs - the significance of the deep-water environment

(2015) Sigrid Skoglund et al.   Ecology and Evolution

ALLMAPS: robust scaffold ordering based on multiple maps

(2015) Haibao Tang et al.   GENOME BIOLOGY

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

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

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Fine-scale phylogeographic contact zone in Austrian brown trout Salmo trutta reveals multiple waves of post-glacial colonization and a pre-dominance of natural versus anthropogenic admixture

(2014) T. Schenekar et al.   CONSERVATION GENETICS

The genomic signature of parallel adaptation from shared genetic variation

(2014) Marius Roesti et al.   MOLECULAR ECOLOGY

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

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

Parallel evolution of Nicaraguan crater lake cichlid fishes via non-parallel routes

(2014) Kathryn R. Elmer et al.   Nature Communications

THE GENETIC ARCHITECTURE OF REPRODUCTIVE ISOLATION DURING SPECIATION-WITH-GENE-FLOW IN LAKE WHITEFISH SPECIES PAIRS ASSESSED BY RAD SEQUENCING

(2013) Pierre-Alexandre Gagnaire et al.   EVOLUTION

Gene Coexpression Networks Reveal Key Drivers of Phenotypic Divergence in Lake Whitefish

(2013) Marie Filteau et al.   MOLECULAR BIOLOGY AND EVOLUTION

Convergence in feeding posture occurs through different genetic loci in independently evolved cave populations of Astyanax mexicanus

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

Exceptional Convergence on the Macroevolutionary Landscape in Island Lizard Radiations

(2013) D. L. Mahler et al.   SCIENCE

Parallel and non-parallel morphological divergence among foraging specialists in European whitefish (Coregonus lavaretus)

(2013) Anna Siwertsson et al.   Ecology and Evolution

Ecological speciation in postglacial European whitefish: rapid adaptive radiations into the littoral, pelagic, and profundal lake habitats

(2013) Kim Praebel et al.   Ecology and Evolution

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Convergent evolutionary processes driven by foraging opportunity in two sympatric morph pairs of Arctic charr with contrasting post-glacial origins

(2012) MONICA V. GARDUÑO-PAZ et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

The probability of genetic parallelism and convergence in natural populations

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

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

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

PARALLEL AND NONPARALLEL ASPECTS OF ECOLOGICAL, PHENOTYPIC, AND GENETIC DIVERGENCE ACROSS REPLICATE POPULATION PAIRS OF LAKE AND STREAM STICKLEBACK

(2011) Renaud Kaeuffer et al.   EVOLUTION

Adaptation in the age of ecological genomics: insights from parallelism and convergence

(2011) Kathryn R. Elmer et al.   TRENDS IN ECOLOGY & EVOLUTION

Rapid sympatric ecological differentiation of crater lake cichlid fishes within historic times

(2010) Kathryn R Elmer et al.   BMC BIOLOGY

On the origin of species: insights from the ecological genomics of lake whitefish

(2010) L. Bernatchez et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Fast model-based estimation of ancestry in unrelated individuals

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

Phylogeography and sympatric differentiation of the Arctic charrSalvelinus alpinus(L.) complex in Siberia as revealed by mtDNA sequence analysis

(2009) S. S. Alekseyev et al.   JOURNAL OF FISH BIOLOGY

On the Origin and Spread of an Adaptive Allele in Deer Mice

(2009) C. R. Linnen et al.   SCIENCE

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

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

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

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

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