Genomic consequences of a recent three-way admixture in supplemented wild brown trout populations revealed by local ancestry tracts

Signatures of hybridization and speciation in genomic patterns of ancestry

(2018) John A. Hvala et al.   EVOLUTION

The breakdown of genomic ancestry blocks in hybrid lineages given a finite number of recombination sites

(2018) Thijs Janzen et al.   EVOLUTION

Inference of multiple-wave admixtures by length distribution of ancestral tracks

(2018) Xumin Ni et al.   HEREDITY

Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans

(2018) Matthias Steinrücken et al.   MOLECULAR ECOLOGY

Breaking Barriers: Causes, Consequences, and Experimental Utility of Human-Mediated Hybridization

(2018) Kathryn C. Grabenstein et al.   TRENDS IN ECOLOGY & EVOLUTION

The origin and remolding of genomic islands of differentiation in the European sea bass

(2018) Maud Duranton et al.   Nature Communications

Variation and constraints in hybrid genome formation

(2018) Anna Runemark et al.   Nature Ecology & Evolution

Half a century of genetic interaction between farmed and wild Atlantic salmon: Status of knowledge and unanswered questions

(2017) Kevin A Glover et al.   FISH AND FISHERIES

Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice

(2017) Hongru Wang et al.   GENOME RESEARCH

Disentangling Timing of Admixture, Patterns of Introgression, and Phenotypic Indicators in a Hybridizing Wolf Population

(2017) Marco Galaverni et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetics and the conservation of natural populations: allozymes to genomes

(2017) Fred W. Allendorf   MOLECULAR ECOLOGY

Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks

(2017) Ivica Medugorac et al.   NATURE GENETICS

A signature of dynamic biogeography: enclaves indicate past species replacement

(2017) B. Wielstra et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Rapid hybrid speciation in Darwin’s finches

(2017) Sangeet Lamichhaney et al.   SCIENCE

A Dense Brown Trout ( Salmo trutta ) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity

(2017) Maeva Leitwein et al.   G3-Genes Genomes Genetics

A Hidden Markov Model Approach for Simultaneously Estimating Local Ancestry and Admixture Time Using Next Generation Sequence Data in Samples of Arbitrary Ploidy

(2017) Russell Corbett-Detig et al.   PLoS Genetics

Modeling Continuous Admixture Using Admixture-Induced Linkage Disequilibrium

(2017) Ying Zhou et al.   Scientific Reports

Genetic diversity and population structure of domestic brown trout (Salmo trutta) in France

(2016) Justin Bohling et al.   AQUACULTURE

Strategies to address the conservation threats posed by hybridization and genetic introgression

(2016) Justin H. Bohling   BIOLOGICAL CONSERVATION

What, if anything, are hybrids: enduring truths and challenges associated with population structure and gene flow

(2016) Zachariah Gompert et al.   Evolutionary Applications

Hybridization and extinction

(2016) Marco Todesco et al.   Evolutionary Applications

Genome-wide nucleotide diversity of hatchery-reared Atlantic and Mediterranean strains of brown troutSalmo truttacompared to wild Mediterranean populations

(2016) M. Leitwein et al.   JOURNAL OF FISH BIOLOGY

Genomewide introgressive hybridization patterns in wild Atlantic salmon influenced by inadvertent gene flow from hatchery releases

(2016) M. Y. Ozerov 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

Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes

(2016) Quentin Rougemont et al.   MOLECULAR ECOLOGY

Admixture mapping identifies introgressed genomic regions in North American canids

(2016) Bridgett M. vonHoldt et al.   MOLECULAR ECOLOGY

Hybridization and endangered species protection in the molecular era

(2016) Robert K. Wayne et al.   MOLECULAR ECOLOGY

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

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

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

Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon ( Salmo salar ) Genome

(2016) Hsin Y. Tsai et al.   G3-Genes Genomes Genetics

The role of Pleistocene glaciations in shaping the evolution of polar and brown bears. Evidence from a critical review of mitochondrial and nuclear genome analyses

(2015) Alexandre Hassanin   COMPTES RENDUS BIOLOGIES

Farmed Atlantic salmonSalmo salarL. parr may reduce early survival of wild fish

(2015) L. Sundt-Hansen et al.   JOURNAL OF FISH BIOLOGY

Transatlantic secondary contact in Atlantic Salmon, comparing microsatellites, a single nucleotide polymorphism array and restriction-site associated DNA sequencing for the resolution of complex spatial structure

(2015) Ian R. Bradbury et al.   MOLECULAR ECOLOGY

Quantitative trait locus mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower

(2015) Kenneth D. Whitney et al.   MOLECULAR ECOLOGY

An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)

(2015) G. J. McKinney et al.   Molecular Ecology Resources

Evidence for archaic adaptive introgression in humans

(2015) Fernando Racimo et al.   NATURE REVIEWS GENETICS

Genetic and phenotypic changes in an Atlantic salmon population supplemented with non-local individuals: a longitudinal study over 21 years

(2015) S. Le Cam et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic Insights into the Ancestry and Demographic History of South America

(2015) Julian R. Homburger et al.   PLoS Genetics

Hybridization in Parasites: Consequences for Adaptive Evolution, Pathogenesis, and Public Health in a Changing World

(2015) Kayla C. King et al.   PLoS Pathogens

The role of homoploid hybridization in evolution: A century of studies synthesizing genetics and ecology

(2014) S. B. Yakimowski et al.   AMERICAN JOURNAL OF BOTANY

Linkage maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing

(2014) Serap Gonen et al.   BMC GENOMICS

Genetic risks of supplementing trout populations with native stocks: a simulation case study from current Pyrenean populations

(2014) Raquel Fernández-Cebrián et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

HOW COMMON IS HOMOPLOID HYBRID SPECIATION?

(2014) Molly Schumer et al.   EVOLUTION

Does human-induced hybridization have long-term genetic effects? Empirical testing with domesticated, wild and hybridized fish populations

(2014) Andrew Harbicht et al.   Evolutionary Applications

Loss of genetic integrity in wild lake trout populations following stocking: insights from an exhaustive study of 72 lakes from Québec, Canada

(2014) Eliane Valiquette et al.   Evolutionary Applications

Detecting Structure of Haplotypes and Local Ancestry

(2014) Y. Guan   GENETICS

The Lengths of Admixture Tracts

(2014) M. Liang et al.   GENETICS

Adaptive admixture in the West African bovine hybrid zone: insight from the Borgou population

(2014) Laurence Flori et al.   MOLECULAR ECOLOGY

The genomic landscape of Neanderthal ancestry in present-day humans

(2014) Sriram Sankararaman et al.   NATURE

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

(2014) Camille Berthelot et al.   Nature Communications

A Dense Linkage Map for Chinook salmon ( Oncorhynchus tshawytscha ) Reveals Variable Chromosomal Divergence After an Ancestral Whole Genome Duplication Event

(2014) Marine S. O. Brieuc et al.   G3-Genes Genomes Genetics

Perspectives on the conservation of wild hybrids

(2013) Astrid V. Stronen et al.   BIOLOGICAL CONSERVATION

DIFFERENTIAL INTROGRESSION IN A MOSAIC HYBRID ZONE REVEALS CANDIDATE BARRIER GENES

(2013) Erica L. Larson et al.   EVOLUTION

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

Higher Levels of Neanderthal Ancestry in East Asians than in Europeans

(2013) Jeffrey D. Wall et al.   GENETICS

Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium

(2013) P.-R. Loh et al.   GENETICS

A conservation plan for Atlantic salmon (Salmo salar) and anadromous brown trout (Salmo trutta) in a region with intensive industrial use of aquatic habitats, the Hardangerfjord, western Norway

(2013) Øystein Skaala et al.   Marine Biology Research

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

Analyses of genetic ancestry enable key insights for molecular ecology

(2013) Zachariah Gompert et al.   MOLECULAR ECOLOGY

Genotyping-by-sequencing in ecological and conservation genomics

(2013) Shawn R. Narum et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation

(2013) Philip W. Hedrick   MOLECULAR ECOLOGY

Inferring Demographic History from a Spectrum of Shared Haplotype Lengths

(2013) Kelley Harris et al.   PLoS Genetics

Conservation Genomics of Threatened Animal Species

(2013) Cynthia C. Steiner et al.   Annual Review of Animal Biosciences

Population Genetics Models of Local Ancestry

(2012) S. Gravel   GENETICS

Dynamics of introgressive hybridization assessed by SNP population genomics of coding genes in stocked brook charr (Salvelinus fontinalis)

(2012) FABIEN C. LAMAZE et al.   MOLECULAR ECOLOGY

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns

(2011) Sigbjørn Lien et al.   BMC GENOMICS

Genomic toolboxes for conservation biologists

(2011) Francesco Angeloni et al.   Evolutionary Applications

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Genomics and the future of conservation genetics

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

Compromising genetic diversity in the wild: unmonitored large-scale release of plants and animals

(2010) Linda Laikre 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

Admixture analysis of stocked brown trout populations using mapped microsatellite DNA markers: indigenous trout persist in introgressed populations

(2009) M. M. Hansen et al.   Biology Letters

Hybridization rapidly reduces fitness of a native trout in the wild

(2009) C. C. Muhlfeld et al.   Biology Letters

Where are we in conservation genetics and where do we need to go?

(2009) Richard Frankham   CONSERVATION GENETICS

Fast model-based estimation of ancestry in unrelated individuals

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

Long-term changes in the fine-scale population structure of coho salmon populations (Oncorhynchus kisutch) subject to extensive supportive breeding

(2009) W H Eldridge et al.   HEREDITY

Sixty years of anthropogenic pressure: a spatio-temporal genetic analysis of brown trout populations subject to stocking and population declines

(2009) MICHAEL M. HANSEN et al.   MOLECULAR ECOLOGY

Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations

(2009) Alkes L. Price et al.   PLoS Genetics

Inference of Historical Changes in Migration Rate From the Lengths of Migrant Tracts

(2008) J. E. Pool et al.   GENETICS

Admixture as the basis for genetic mapping

(2008) C. Alex Buerkle et al.   TRENDS IN ECOLOGY & EVOLUTION

Detecting hybridization between wild species and their domesticated relatives

(2007) ETTORE RANDI   MOLECULAR ECOLOGY