Saving the spandrels? Adaptive genomic variation in conservation and fisheries management

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

(2016) Sean Hoban et al.   AMERICAN NATURALIST

Is there a future for genome-editing technologies in conservation?

(2016) J. A. Johnson et al.   ANIMAL CONSERVATION

The paradox of “premature migration” by adult anadromous salmonid fishes: patterns and hypotheses

(2016) Thomas P. Quinn et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Role of genomics and transcriptomics in selection of reintroduction source populations

(2016) Xiaoping He et al.   CONSERVATION BIOLOGY

Population genetic structure and ancestry of steelhead/rainbow trout (Oncorhynchus mykiss) at the extreme southern edge of their range in North America

(2016) Alicia Abadía-Cardoso et al.   CONSERVATION GENETICS

Ancestry and adaptive evolution of anadromous, resident, and adfluvial rainbow trout (Oncorhynchus mykiss) in the San Francisco bay area: application of adaptive genomic variation to conservation in a highly impacted landscape

(2016) Maeva Leitwein et al.   Evolutionary Applications

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

(2016) Kathryn R. Elmer   HYDROBIOLOGIA

Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer

(2016) Jiajun Shi et al.   INTERNATIONAL JOURNAL OF CANCER

On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes

(2016) L. Bernatchez   JOURNAL OF FISH BIOLOGY

Two adjacent inversions maintain genomic differentiation between migratory and stationary ecotypes of Atlantic cod

(2016) Tina Graceline Kirubakaran et al.   MOLECULAR ECOLOGY

Conservation genomics of natural and managed populations: building a conceptual and practical framework

(2016) Laura Marilyn Benestan et al.   MOLECULAR ECOLOGY

Genomic analyses identify molecular subtypes of pancreatic cancer

(2016) Peter Bailey et al.   NATURE

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

Local adaptation in transgenerational responses to predators

(2016) Matthew R. Walsh et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing

(2016) Jon E. Hess et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Adaptive tolerance to a pathogenic fungus drives major histocompatibility complex evolution in natural amphibian populations

(2016) Anna E. Savage et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A beak size locus in Darwins finches facilitated character displacement during a drought

(2016) S. Lamichhaney et al.   SCIENCE

Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application

(2016) Brittany A. Garner et al.   TRENDS IN ECOLOGY & EVOLUTION

Reply to Garner et al.

(2016) Aaron B.A. Shafer et al.   TRENDS IN ECOLOGY & EVOLUTION

A single generation of domestication heritably alters the expression of hundreds of genes

(2016) Mark R. Christie et al.   Nature Communications

Molecular signatures of transgenerational response to ocean acidification in a species of reef fish

(2016) Celia Schunter et al.   Nature Climate Change

Discriminating Selection on Lateral Plate Phenotype and Its Underlying Gene, Ectodysplasin, in Threespine Stickleback

(2015) Diana J. Rennison et al.   AMERICAN NATURALIST

Anadromy and residency in steelhead and rainbow trout (Oncorhynchus mykiss): a review of the processes and patterns

(2015) Neala W. Kendall et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

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

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

Parallel evolution of the summer steelhead ecotype in multiple populations from Oregon and Northern California

(2015) Martha Arciniega et al.   CONSERVATION GENETICS

The application of genomics to inform conservation of a functionally important reef fish (Scarus niger) in the Philippines

(2015) Brian L. Stockwell et al.   CONSERVATION GENETICS

Beyond dichotomous life histories in partially migrating populations: cessation of anadromy in a long-lived fish

(2015) Morgan H. Bond et al.   ECOLOGY

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

(2015) M Kardos et al.   HEREDITY

Shifting Thresholds: Rapid Evolution of Migratory Life Histories in Steelhead/Rainbow Trout,Oncorhynchus mykiss

(2015) Corey C. Phillis et al.   JOURNAL OF HEREDITY

Key Questions on the Role of Phenotypic Plasticity in Eco-Evolutionary Dynamics

(2015) Andrew P. Hendry   JOURNAL OF HEREDITY

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

Whole-genome resequencing uncovers molecular signatures of natural and sexual selection in wild bighorn sheep

(2015) Marty Kardos et al.   MOLECULAR ECOLOGY

Migration-related phenotypic divergence is associated with epigenetic modifications in rainbow trout

(2015) Melinda R. Baerwald et al.   MOLECULAR ECOLOGY

Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon

(2015) Nicola J. Barson et al.   NATURE

A supergene determines highly divergent male reproductive morphs in the ruff

(2015) Clemens Küpper et al.   NATURE GENETICS

Fish Hatchery Genetic Management Techniques: Integrating Theory with Implementation

(2015) Kathleen M. Fisch et al.   NORTH AMERICAN JOURNAL OF AQUACULTURE

Genomics and the challenging translation into conservation practice

(2015) Aaron B.A. Shafer et al.   TRENDS IN ECOLOGY & EVOLUTION

Genetic rescue to the rescue

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

The vgll3 Locus Controls Age at Maturity in Wild and Domesticated Atlantic Salmon (Salmo salar L.) Males

(2015) Fernando Ayllon et al.   PLoS Genetics

Genome-Wide Association Study (GWAS) for Growth Rate and Age at Sexual Maturation in Atlantic Salmon (Salmo salar)

(2015) Alejandro P. Gutierrez et al.   PLoS One

Prescriptive Evolution to Conserve and Manage Biodiversity

(2014) Thomas B. Smith et al.   Annual Review of Ecology Evolution and Systematics

Selection for complex traits leaves little or no classic signatures of selection

(2014) Kathryn E Kemper et al.   BMC GENOMICS

How and why should we implement genomics into conservation?

(2014) Barry J. McMahon et al.   Evolutionary Applications

Genome-wide SNP analysis reveals a genetic basis for sea-age variation in a wild population of Atlantic salmon (Salmo salar)

(2014) Susan E. Johnston et al.   MOLECULAR ECOLOGY

A role for migration-linked genes and genomic islands in divergence of a songbird

(2014) Kristen Ruegg et al.   MOLECULAR ECOLOGY

The genomic signature of parallel adaptation from shared genetic variation

(2014) Marius Roesti et al.   MOLECULAR ECOLOGY

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

Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche

(2014) John R. B. Perry et al.   NATURE

doublesex is a mimicry supergene

(2014) K. Kunte et al.   NATURE

Planning Pacific Salmon and Steelhead Reintroductions Aimed at Long-Term Viability and Recovery

(2014) Joseph H. Anderson et al.   NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT

Transgenic American chestnuts show enhanced blight resistance and transmit the trait to T1 progeny

(2014) Andrew E. Newhouse et al.   PLANT SCIENCE

On the Prospect of Identifying Adaptive Loci in Recently Bottlenecked Populations

(2014) Yu-Ping Poh et al.   PLoS One

Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

(2014) D. E. Pearse et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Advances and limits of using population genetics to understand local adaptation

(2014) Peter Tiffin et al.   TRENDS IN ECOLOGY & EVOLUTION

Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

(2014) Wanneng Yang et al.   Nature Communications

Genetic and phenotypic effects on reproductive outcomes for captively-reared coho salmon, Oncorhynchus kisutch

(2013) J. Louise Conrad et al.   AQUACULTURE

The evolutionary ecology of alternative migratory tactics in salmonid fishes

(2013) Julian J. Dodson et al.   BIOLOGICAL REVIEWS

LANDSCAPE GENOMICS IN ATLANTIC SALMON (SALMO SALAR): SEARCHING FOR GENE-ENVIRONMENT INTERACTIONS DRIVING LOCAL ADAPTATION

(2013) Bourret Vincent et al.   EVOLUTION

Recent advances of genome mapping and marker-assisted selection in aquaculture

(2013) Gen Hua Yue   FISH AND FISHERIES

Implementing genomic medicine in the clinic: the future is here

(2013) Teri A. Manolio et al.   GENETICS IN MEDICINE

Key questions in the genetics and genomics of eco-evolutionary dynamics

(2013) A P Hendry   HEREDITY

A genomic island linked to ecotype divergence in Atlantic cod

(2013) Jakob Hemmer-Hansen 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

Next-generation sequencing for molecular ecology: a caveat regarding pooled samples

(2013) Eric C. Anderson et al.   MOLECULAR ECOLOGY

Ecology: Gene tweaking for conservation

(2013) Michael A. Thomas et al.   NATURE

Genetic engineering in conservation

(2013) Philip W. Hedrick et al.   NATURE

A Y-like social chromosome causes alternative colony organization in fire ants

(2013) John Wang et al.   NATURE

Life history trade-offs at a single locus maintain sexually selected genetic variation

(2013) Susan E. Johnston et al.   NATURE

Does genomic selection have a future in plant breeding?

(2013) Elisabeth Jonas et al.   TRENDS IN BIOTECHNOLOGY

A Critical Assessment of Storytelling: Gene Ontology Categories and the Importance of Validating Genomic Scans

(2012) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide association reveals genetic basis for the propensity to migrate in wild populations of rainbow and steelhead trout

(2012) Benjamin C. Hecht et al.   MOLECULAR ECOLOGY

Should I Stay or Should I Go? The Influence of Genetic Origin on Emigration Behavior and Physiology of Resident and Anadromous JuvenileOncorhynchus mykiss

(2012) Sean A. Hayes et al.   NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT

Harnessing genomics for delineating conservation units

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

Gene-associated markers provide tools for tackling illegal fishing and false eco-certification

(2012) Einar E. Nielsen et al.   Nature Communications

Evolutionary principles and their practical application

(2011) Andrew P. Hendry et al.   Evolutionary Applications

A conserved haplotype controls parallel adaptation in geographically distant salmonid populations

(2011) MICHAEL R. MILLER et al.   MOLECULAR ECOLOGY

Detecting signatures of positive selection in partial sequences generated on a large scale: pitfalls, procedures and resources

(2011) MARINE S. O. BRIEUC et al.   Molecular Ecology Resources

Comparison ofFSToutlier tests for SNP loci under selection

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

Molecular spandrels: tests of adaptation at the genetic level

(2011) Rowan D. H. Barrett et al.   NATURE REVIEWS GENETICS

A Microsatellite Genome Screen Identifies Chromosomal Regions under Differential Selection in Steelhead and Rainbow Trout

(2011) Andrés Martínez et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

Genomics and the future of conservation genetics

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

Adaptation genomics: the next generation

(2010) Jessica Stapley et al.   TRENDS IN ECOLOGY & EVOLUTION

Conservation genetics in transition to conservation genomics

(2010) N. Joop Ouborg et al.   TRENDS IN GENETICS

From Conservation Genetics to Conservation Genomics

(2009) Craig R. Primmer   Annals of the New York Academy of Sciences

ADAPTIONISM-30 YEARS AFTER GOULD AND LEWONTIN

(2009) Rasmus Nielsen   EVOLUTION

Over the Falls? Rapid Evolution of Ecotypic Differentiation in Steelhead/Rainbow Trout (Oncorhynchus mykiss)

(2009) Devon E. Pearse et al.   JOURNAL OF HEREDITY

Mapping genes for complex traits in domestic animals and their use in breeding programmes

(2009) Michael E. Goddard et al.   NATURE REVIEWS GENETICS

Population genetic structure and ancestry of Oncorhynchus mykiss populations above and below dams in south-central California

(2008) Anthony J. Clemento et al.   CONSERVATION GENETICS

Bridging the gap between the genotype and the phenotype: linking genetic variation, selection and adaptation in fishes

(2008) Kerry A Naish et al.   FISH AND FISHERIES

The Genetic Basis of Smoltification-Related Traits in Oncorhynchus mykiss

(2008) K. M. Nichols et al.   GENETICS

Highly effective SNP-based association mapping and management of recessive defects in livestock

(2008) Carole Charlier et al.   NATURE GENETICS

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS