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

A Combinatorial View on Speciation and Adaptive Radiation

(2019) David A. Marques et al.   TRENDS IN ECOLOGY & EVOLUTION

Model‐based demographic inference of introgression history in European whitefish species pairs'

(2019) Clément Rougeux et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Do differences in the activities of carbohydrate metabolism enzymes between Lake Whitefish ecotypes match predictions from transcriptomic studies?

(2018) Anne C. Dalziel et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

Genomics of Parallel Ecological Speciation in Lake Victoria Cichlids

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

Comparing methods for detecting multilocus adaptation with multivariate genotype-environment associations

(2018) Brenna R. Forester et al.   MOLECULAR ECOLOGY

Evaluation of redundancy analysis to identify signatures of local adaptation

(2018) Thibaut Capblancq et al.   Molecular Ecology Resources

GOATOOLS: A Python library for Gene Ontology analyses

(2018) D. V. Klopfenstein et al.   Scientific Reports

Diversifying selection drives parallel evolution of gill raker number and body size along the speciation continuum of European whitefish

(2018) Katja Häkli et al.   Ecology and Evolution

Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations

(2017) Mi Wang et al.   Genome Biology and Evolution

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, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches

(2017) Fan Han et al.   GENOME RESEARCH

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

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

Speciation as a sieve for ancestral polymorphism

(2017) Rafael F. Guerrero et al.   MOLECULAR ECOLOGY

Detecting gene subnetworks under selection in biological pathways

(2017) Alexandre Gouy et al.   NUCLEIC ACIDS RESEARCH

Gene co-expression network connectivity is an important determinant of selective constraint

(2017) Niklas Mähler et al.   PLoS Genetics

Adaptation and acclimation of traits associated with swimming capacity in Lake Whitefish (coregonus clupeaformis) ecotypes

(2016) Martin Laporte et al.   BMC EVOLUTIONARY BIOLOGY

Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database

(2016) Jeremy Pasquier et al.   BMC GENOMICS

Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches

(2016) Pierre-Alexandre Gagnaire et al.   Current Zoology

Convergence in organ size but not energy metabolism enzyme activities among wild Lake Whitefish (Coregonus clupeaformis) species pairs

(2016) Anne C. Dalziel et al.   MOLECULAR ECOLOGY

Demographic modelling with whole-genome data reveals parallel origin of similarPundamiliacichlid species after hybridization

(2016) Joana I. Meier et al.   MOLECULAR ECOLOGY

Divergence in gene expression within and between two closely related flycatcher species

(2016) Severin Uebbing et al.   MOLECULAR ECOLOGY

Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact

(2016) A. Le Moan et al.   MOLECULAR ECOLOGY

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

(2016) Keurcien Luu et al.   Molecular Ecology Resources

Dissection of expression-quantitative trait locus and allele specificity using a haploid/diploid plant system - insights into compensatory evolution of transcriptional regulation within populations

(2016) Jukka-Pekka Verta et al.   NEW PHYTOLOGIST

Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches

(2016) Pierre-Alexandre Gagnaire et al.   Current Zoology

Local Adaptation by Alleles of Small Effect

(2015) Sam Yeaman   AMERICAN NATURALIST

Adaptation and acclimation of aerobic exercise physiology in Lake Whitefish ecotypes (Coregonus clupeaformis)

(2015) Anne C. Dalziel et al.   EVOLUTION

Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation

(2015) Christopher H. Martin et al.   EVOLUTION

Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data

(2015) Nicolas Duforet-Frebourg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Shared and nonshared genomic divergence in parallel ecotypes ofLittorina saxatilisat a local scale

(2015) Mark Ravinet et al.   MOLECULAR ECOLOGY

RAD-QTL Mapping Reveals Both Genome-Level Parallelism and Different Genetic Architecture Underlying the Evolution of Body Shape in Lake Whitefish ( Coregonus clupeaformis ) Species Pairs

(2015) Martin Laporte et al.   G3-Genes Genomes Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Standing and flowing: the complex origins of adaptive variation

(2014) John J. Welch et al.   MOLECULAR ECOLOGY

The genomic signature of parallel adaptation from shared genetic variation

(2014) Marius Roesti et al.   MOLECULAR ECOLOGY

Do the same genes underlie parallel phenotypic divergence in differentLittorina saxatilispopulations?

(2014) A. M. Westram 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 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

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish(Coregonus clupeaformis)

(2012) Pierre-Alexandre Gagnaire et al.   MOLECULAR ECOLOGY

Mitogenome sequencing reveals shallow evolutionary histories and recent divergence time between morphologically and ecologically distinct European whitefish (Coregonusspp.)

(2012) MAGNUS W. JACOBSEN et al.   MOLECULAR ECOLOGY

The genetic differentiation at quantitative trait loci under local adaptation

(2012) VALÉRIE LE CORRE et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead 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

Regulatory Variation Within and Between Species

(2011) Wei Zheng et al.   Annual Review of Genomics and Human Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

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

(2011) Matthew V. Rockman   EVOLUTION

CONVERGENCE, ADAPTATION, AND CONSTRAINT

(2011) Jonathan B. Losos   EVOLUTION

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence

(2011) Patricia J. Wittkopp et al.   NATURE REVIEWS GENETICS

Genome-wide patterns of divergence during speciation: the lake whitefish case study

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

Population genomics of parallel phenotypic evolution in stickleback across stream-lake ecological transitions

(2011) B. E. Deagle et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Developmental Role of Agouti in Color Pattern Evolution

(2011) M. Manceau et al.   SCIENCE

The evolution of gene expression and the transcriptome–phenotype relationship

(2011) Peter W. Harrison et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Regulatory versus coding signatures of natural selection in a candidate gene involved in the adaptive divergence of whitefish species pairs (Coregonusspp.)

(2011) Julie Jeukens et al.   Ecology and Evolution

The role of gene expression in ecological speciation

(2010) Scott A. Pavey et al.   Annals of the New York Academy of Sciences

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

Convergence in pigmentation at multiple levels: mutations, genes and function

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

3′ UTRs Are the Primary Regulators of Gene Expression in the C. elegans Germline

(2008) Christopher Merritt et al.   CURRENT BIOLOGY

Candidate Genes and Adaptive Radiation: Insights from Transcriptional Adaptation to the Limnetic Niche among Coregonine Fishes (Coregonus spp., Salmonidae)

(2008) J. Jeukens et al.   MOLECULAR BIOLOGY AND EVOLUTION

The transcriptomics of life-history trade-offs in whitefish species pairs (Coregonussp.)

(2008) J. ST-CYR et al.   MOLECULAR ECOLOGY

Adaptation from standing genetic variation

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