Genotyping‐by‐sequencing illuminates high levels of divergence among sympatric forms of coregonines in the Laurentian Great Lakes

The evolution of hybrid fitness during speciation

(2019) Andrius J. Dagilis et al.   PLoS Genetics

Stacks 2: analytical methods for paired‐end sequencing improve RADseq‐based population genomics

(2019) Nicolas C. Rochette et al.   MOLECULAR ECOLOGY

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

(2019) Clément Rougeux et al.   MOLECULAR ECOLOGY

Evolution and diversity of two cisco forms in an outlet of glacial Lake Algonquin

(2019) Gabriel Piette‐Lauzière et al.   Ecology and Evolution

Genomic signatures of environmental selection despite near-panmixia in summer flounder

(2018) Jennifer A. Hoey et al.   Evolutionary Applications

Genomics and conservation units: The genetic basis of adult migration timing in Pacific salmonids

(2018) Robin S. Waples et al.   Evolutionary Applications

Population structure and genomic variation of ecological life history diversity in wild-caught Lake Superior brook trout, Salvelinus fontinalis

(2018) Ashley Elias et al.   JOURNAL OF GREAT LAKES RESEARCH

Genomic insights into the vulnerability of sympatric whitefish species flocks

(2018) Philine G.D. Feulner et al.   MOLECULAR ECOLOGY

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

Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior

(2017) Alysse Perreault-Payette et al.   MOLECULAR ECOLOGY

RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity

(2017) David L. J. Vendrami et al.   Royal Society Open Science

Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: comparing microsatellites and RAD-Seq and investigating loci filtering

(2017) Richard G. J. Hodel et al.   Scientific Reports

Managing cryptic biodiversity: Fine-scale intralacustrine speciation along a benthic gradient in Alpine whitefish (Coregonusspp.)

(2016) Alan G. Hudson et al.   Evolutionary Applications

Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci

(2016) R K Waples et al.   HEREDITY

Loss of genetic diversity and reduction of genetic distance among lake trout Salvelinus namaycush ecomorphs, Lake Superior 1959 to 2013

(2016) Shauna M. Baillie et al.   JOURNAL OF GREAT LAKES RESEARCH

Genomic islands of divergence linked to ecotypic variation in sockeye salmon

(2016) Wesley A. Larson et al.   MOLECULAR ECOLOGY

Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping-by-sequencing data from natural populations

(2016) Garrett J. McKinney 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

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

Local Adaptation by Alleles of Small Effect

(2015) Sam Yeaman   AMERICAN NATURALIST

Morphological and genetic variation in Cisco (Coregonus artedi) and Shortjaw Cisco (C. zenithicus): multiple origins of Shortjaw Cisco in inland lakes require a lake-specific conservation approach

(2015) Julie Turgeon et al.   CONSERVATION GENETICS

Identifying designatable units for intraspecific conservation prioritization: a hierarchical approach applied to the lake whitefish species complex (Coregonusspp.)

(2015) Jonathan A. Mee et al.   Evolutionary Applications

RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping

(2015) O. A. Ali et al.   GENETICS

Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range

(2015) Benjamin C. Hecht 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

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

Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)

(2014) Wesley A. Larson et al.   Evolutionary Applications

Depth gradients in food-web processes linking habitats in large lakes: Lake Superior as an exemplar ecosystem

(2014) Michael E. Sierszen et al.   FRESHWATER BIOLOGY

Effects of Overlapping Generations on Linkage Disequilibrium Estimates of Effective Population Size

(2014) Robin S. Waples et al.   GENETICS

Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci

(2014) Jean-Sébastien Moore 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

Ontogenetic shifts in morphology and resource use of ciscoCoregonus artedi

(2013) A. M. Muir et al.   JOURNAL OF FISH BIOLOGY

Evidence of Hybridization between Common Gartersnakes (Thamnophis sirtalis) and Butler's Gartersnakes (Thamnophis butleri) in Wisconsin, USA

(2013) Joshua M. Kapfer et al.   JOURNAL OF HERPETOLOGY

Integrating genetic data and population viability analyses for the identification of harbour seal (Phoca vitulina) populations and management units

(2013) Morten T. Olsen et al.   MOLECULAR ECOLOGY

NeEstimatorv2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data

(2013) C. Do et al.   Molecular Ecology Resources

diveRsity: AnRpackage for the estimation and exploration of population genetics parameters and their associated errors

(2013) Kevin Keenan et al.   Methods in 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

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

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

Eutrophication causes speciation reversal in whitefish adaptive radiations

(2012) P. Vonlanthen et al.   NATURE

Harnessing genomics for delineating conservation units

(2012) W. Chris Funk et al.   TRENDS IN ECOLOGY & EVOLUTION

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

(2011) H. E. L. Lischer et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Empirical assessment of software efficiency and accuracy to detect introgression under variable stocking scenarios in brook charr (Salvelinus fontinalis)

(2011) A. D. Marie et al.   CONSERVATION GENETICS

THE GENETIC ARCHITECTURE OF ADAPTATION UNDER MIGRATION-SELECTION BALANCE

(2011) Sam Yeaman et al.   EVOLUTION

Species introduction promotes hybridization and introgression in Coregonus: is there sign of selection against hybrids?

(2011) KIMMO K. KAHILAINEN et al.   MOLECULAR ECOLOGY

All roads lead to home: panmixia of European eel in the Sargasso Sea

(2011) THOMAS D. ALS et al.   MOLECULAR ECOLOGY

Variation in genome-wide mutation rates within and between human families

(2011) Donald F Conrad et al.   NATURE GENETICS

Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow

(2011) S. Via   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Historical and contemporary trophic niche partitioning among Laurentian Great Lakes coregonines

(2010) Stephanie N. Schmidt et al.   ECOLOGICAL APPLICATIONS

Detecting populations in the ‘ambiguous’ zone: kinship-based estimation of population structure at low genetic divergence

(2010) PER J. PALSBØLL et al.   Molecular Ecology Resources

Assessing population structure: FST and related measures

(2010) PATRICK G. MEIRMANS et al.   Molecular Ecology Resources

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

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

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

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

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

Long-term food web change in Lake Superior

(2009) Stephanie N. Schmidt et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Reduced sperm performance in backcross hybrids between species pairs of whitefish (Coregonus clupeaformis)

(2009) A. R. Whiteley et al.   CANADIAN JOURNAL OF ZOOLOGY

Linkage disequilibrium estimates of contemporaryNeusing highly variable genetic markers: a largely untapped resource for applied conservation and evolution

(2009) Robin S. Waples et al.   Evolutionary Applications

Fast model-based estimation of ancestry in unrelated individuals

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

Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species

(2009) M A F Noor et al.   HEREDITY

Panmixia in European eel revisited: no genetic difference between maturing adults from southern and northern Europe

(2009) S Palm et al.   HEREDITY

Gene Expression Divergence and Hybrid Misexpression between Lake Whitefish Species Pairs (Coregonus spp. Salmonidae)

(2009) S. Renaut et al.   MOLECULAR BIOLOGY AND EVOLUTION

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

INTERPOPULATION HYBRID BREAKDOWN MAPS TO THE MITOCHONDRIAL GENOME

(2008) Christopher K. Ellison et al.   EVOLUTION

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

(2008) M. Foll et al.   GENETICS

The genetic mosaic suggests a new role for hitchhiking in ecological speciation

(2008) SARA VIA et al.   MOLECULAR ECOLOGY

Conservation Genetics of Lake Superior Brook Trout: Issues, Questions, and Directions

(2008) Chris C. Wilson et al.   NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT

genepop’007: a complete re-implementation of the genepop software for Windows and Linux

(2007) FRANÇOIS ROUSSET   Molecular Ecology Resources