RAPTURE (RAD capture) panel facilitates analyses characterizing sea lamprey reproductive ecology and movement dynamics

The future is now: amplicon sequencing and sequence capture usher in the conservation genomics era

(2019) Mariah H. Meek et al.   Molecular Ecology Resources

Dispersal of a nearshore marine fish connects marine reserves and adjacent fished areas along an open coast

(2019) Diana S. Baetscher et al.   MOLECULAR ECOLOGY

Rapid evolution meets invasive species control: the potential for pesticide resistance in sea lamprey

(2018) Erin S. Dunlop et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution

(2018) Jeramiah J. Smith et al.   NATURE GENETICS

Evaluation of Effective Number of Breeders and Coancestry among Progeny Produced Using Common Hatchery Mating Strategies

(2018) Meredith L. Bartron et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

Large-effect loci affect survival in Tasmanian devils (Sarcophilus harrisii ) infected with a transmissible cancer

(2018) Mark J. Margres et al.   MOLECULAR ECOLOGY

RADseq and mate choice assays reveal unidirectional gene flow among three lamprey ecotypes despite weak assortative mating: insights into the formation and stability of multiple ecotypes in sympatry

(2018) John B. Hume et al.   MOLECULAR ECOLOGY

A Versatile Rapture (RAD-Capture) Platform for Genotyping Marine Turtles

(2018) Lisa Komoroske et al.   Molecular Ecology Resources

Accurate aging of juvenile salmonids using fork lengths

(2017) Suresh Andrew Sethi et al.   FISHERIES RESEARCH

Genome architecture enables local adaptation of Atlantic cod despite high connectivity

(2017) Julia M. I. Barth et al.   MOLECULAR ECOLOGY

Genotype Calling from Population-Genomic Sequencing Data

(2017) Takahiro Maruki et al.   G3-Genes Genomes Genetics

The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation

(2017) Daniel J. Prince et al.   Science Advances

Genetic monitoring guides adaptive management of a migratory fish reintroduction program

(2016) N. M. Sard et al.   ANIMAL CONSERVATION

Genomics advances the study of inbreeding depression in the wild

(2016) Marty Kardos 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

Detection and identification of lampreys in Great Lakes streams using environmental DNA

(2016) Timothy D. Gingera et al.   JOURNAL OF GREAT LAKES RESEARCH

Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics

(2016) Brian K. Hand 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

RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data

(2016) Sandra L. Hoffberg et al.   Molecular Ecology Resources

Population ecology of the sea lamprey (Petromyzon marinus) as an invasive species in the Laurentian Great Lakes and an imperiled species in Europe

(2016) Michael J. Hansen et al.   REVIEWS IN FISH BIOLOGY AND FISHERIES

Absolute abundance of southern bluefin tuna estimated by close-kin mark-recapture

(2016) Mark V. Bravington et al.   Nature Communications

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

Lampreys as Diverse Model Organisms in the Genomics Era

(2015) David W. McCauley et al.   BIOSCIENCE

Genomics and introgression: Discovery and mapping of thousands of species-diagnostic SNPs using RAD sequencing

(2015) Brian K. Hand et al.   Current Zoology

Chemical cues and pheromones in the sea lamprey (Petromyzon marinus)

(2015) Tyler J. Buchinger et al.   Frontiers in Zoology

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

(2015) O. A. Ali et al.   GENETICS

Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees

(2015) M Kardos et al.   HEREDITY

How many markers are enough? Factors influencing parentage testing in different livestock populations

(2015) E.M. Strucken et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

Low reproductive isolation and highly variable levels of gene flow reveal limited progress towards speciation between European river and brook lampreys

(2015) Q. Rougemont et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Excess of rare, inherited truncating mutations in autism

(2015) Niklas Krumm et al.   NATURE GENETICS

Genomics and introgression: Discovery and mapping of thousands of species-diagnostic SNPs using RAD sequencing

(2015) Brian K. Hand et al.   Current Zoology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genes predict long distance migration and large body size in a migratory fish, Pacific lamprey

(2014) Jon E. Hess et al.   Evolutionary Applications

Survival and metamorphosis of low-density populations of larval sea lampreys (Petromyzon marinus) in streams following lampricide treatment

(2014) Nicholas S. Johnson et al.   JOURNAL OF GREAT LAKES RESEARCH

Use of genotyping by sequencing data to develop a high-throughput and multifunctional SNP panel for conservation applications in Pacific lamprey

(2014) Jon E. Hess et al.   Molecular Ecology Resources

Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing

(2014) Nathan R. Campbell et al.   Molecular Ecology Resources

SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it

(2013) Joseph Lachance et al.   BIOESSAYS

A validation of parentage-based tagging using hatchery steelhead in the Snake River basin

(2013) Craig A. Steele et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing

(2013) Paul A. Hohenlohe et al.   MOLECULAR ECOLOGY

Interannual variation in effective number of breeders and estimation of effective population size in long-lived iteroparous lake sturgeon (Acipenser fulvescens)

(2013) Thuy Yen Duong et al.   MOLECULAR ECOLOGY

Large-scale parentage analysis reveals reproductive patterns and heritability of spawn timing in a hatchery population of steelhead (Oncorhynchus mykiss)

(2013) Alicia Abadía-Cardoso et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

A simulation module in the computer programcolonyfor sibship and parentage analysis

(2013) Jinliang Wang   Molecular Ecology Resources

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

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species

(2012) Jon E. Hess et al.   MOLECULAR ECOLOGY

mmod: an R library for the calculation of population differentiation statistics

(2012) David J. Winter   Molecular Ecology Resources

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Exome-wide DNA capture and next generation sequencing in domestic and wild species

(2011) Ted Cosart et al.   BMC GENOMICS

Single nucleotide polymorphisms across a species’ range: implications for conservation studies of Pacific salmon

(2011) L. W. SEEB et al.   Molecular Ecology Resources

Evaluating SNP ascertainment bias and its impact on population assignment in Atlantic cod,Gadus morhua

(2011) IAN R. BRADBURY et al.   Molecular Ecology Resources

Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms

(2011) J. E. SEEB et al.   Molecular Ecology Resources

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

Lampreys of the Iberian Peninsula: distribution, population status and conservation

(2011) CS Mateus et al.   Endangered Species Research

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellites

(2010) R J Haasl et al.   HEREDITY

Ascertainment Biases in SNP Chips Affect Measures of Population Divergence

(2010) A. Albrechtsen et al.   MOLECULAR BIOLOGY AND EVOLUTION

On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs

(2010) ANNA W. SANTURE et al.   MOLECULAR ECOLOGY

The power of genetic monitoring for studying demography, ecology and genetics of a reintroduced brown bear population

(2010) M. DE BARBA et al.   MOLECULAR ECOLOGY

Spatial-temporal stratifications in natural populations and how they affect understanding and estimation of effective population size

(2010) ROBIN S. WAPLES   Molecular Ecology Resources

Genomics and the future of conservation genetics

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

Genetic Consequences of Range Expansions

(2009) Laurent Excoffier et al.   Annual Review of Ecology Evolution and Systematics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A new method for estimating effective population sizes from a single sample of multilocus genotypes

(2009) JINLIANG WANG   MOLECULAR ECOLOGY

COLONY: a program for parentage and sibship inference from multilocus genotype data

(2009) OWEN R. JONES et al.   Molecular Ecology Resources

An Assessment of Age Determination Methods for Great Lakes Larval Sea Lampreys

(2009) Heather A. Dawson et al.   NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT

Genome-wide scans for footprints of natural selection

(2009) T. K. Oleksyk et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2008) Thibaut Jombart   BIOINFORMATICS

Genetic compatibility and hatching success in the sea lamprey (Petromyzon marinus)

(2008) R. Rodriguez-Munoz et al.   Biology Letters

ldne: a program for estimating effective population size from data on linkage disequilibrium

(2008) ROBIN S. WAPLES et al.   Molecular Ecology Resources