Journal ArticleDOI
SNP-array reveals genome-wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar).
Vincent Bourret,Matthew Peter Kent,Craig R. Primmer,Anti Vasemägi,Anti Vasemägi,Sten Karlsson,Kjetil Hindar,Philip McGinnity,Eric Verspoor,Louis Bernatchez,Sigbjørn Lien +10 more
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TLDR
The development of a medium‐density Atlantic salmon single nucleotide polymorphism (SNP) array based on expressed sequence tags (ESTs) and genomic sequencing is described and the potential for the array to disentangle neutral and putative adaptive divergence of SNP allele frequencies across populations and among regional groups is assessed.Abstract:
Atlantic salmon (Salmo salar) is one of the most extensively studied fish species in the world due to its significance in aquaculture, fisheries and ongoing conservation efforts to protect declining populations Yet, limited genomic resources have hampered our understanding of genetic architecture in the species and the genetic basis of adaptation to the wide range of natural and artificial environments it occupies In this study, we describe the development of a medium-density Atlantic salmon single nucleotide polymorphism (SNP) array based on expressed sequence tags (ESTs) and genomic sequencing The array was used in the most extensive assessment of population genetic structure performed to date in this species A total of 6176 informative SNPs were successfully genotyped in 38 anadromous and freshwater wild populations distributed across the species natural range Principal component analysis clearly differentiated European and North American populations, and within Europe, three major regional genetic groups were identified for the first time in a single analysis We assessed the potential for the array to disentangle neutral and putative adaptive divergence of SNP allele frequencies across populations and among regional groups In Europe, secondary contact zones were identified between major clusters where endogenous and exogenous barriers could be associated, rendering the interpretation of environmental influence on potentially adaptive divergence equivocal A small number of markers highly divergent in allele frequencies (outliers) were observed between (multiple) freshwater and anadromous populations, between northern and southern latitudes, and when comparing Baltic populations to all others We also discuss the potential future applications of the SNP array for conservation, management and aquacultureread more
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Journal ArticleDOI
Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon
Nicola J. Barson,Tutku Aykanat,Kjetil Hindar,Matthew Baranski,Geir H. Bolstad,Peder Fiske,Celeste Jacq,Arne Jensen,Susan E. Johnston,Sten Karlsson,Matthew Peter Kent,Thomas Moen,Eero Niemelä,Torfinn Nome,Tor F. Næsje,Panu Orell,Atso Romakkaniemi,Harald Sægrov,Kurt Urdal,Jaakko Erkinaro,Sigbjørn Lien,Craig R. Primmer +21 more
TL;DR: This work identifies a large effect locus controlling age at maturity in Atlantic salmon, an important fitness trait in which selection favours earlier maturation in males than females, and shows it is a clear example of sex-dependent dominance that reduces intralocus sexual conflict and maintains adaptive variation in wild populations.
Journal ArticleDOI
Drivers of population genetic differentiation in the wild: isolation by dispersal limitation, isolation by adaptation and isolation by colonization
TL;DR: A method is proposed to detect whether IBDL, IBA and M shape genetic differentiation in natural landscapes by studying patterns of variation at neutral and non‐neutral markers as well as at ecologically relevant traits and reinterpret a representative number of studies by associating patterns to processes.
Journal ArticleDOI
Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools.
TL;DR: For advancing the field of polyploid population genetics, most priority should be given to development of new molecular approaches that allow efficient dosage determination, and to further development of analytical approaches to circumvent dosage uncertainty and to accommodate ‘flexible’ modes of inheritance.
Environmental biology of fishes
C.D. Becker,D.A. Neitzel +1 more
TL;DR: The primary conditions in the gravel that influence survival during dewatering are residual flow, moisture retention, temperature, gravel composition, dissolved oxygen, alevin behavior, and species characteristics as discussed by the authors.
Journal ArticleDOI
Texture and Structure Measurements and Analyses for Evaluation of Fish and Fillet Freshness Quality: A Review.
TL;DR: This review aims to present recent advances of texture and structure measurements and analyses, including sensory evaluation and instrumental methods, for indicating and evaluating fish freshness quality.
References
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Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more
TL;DR: In this paper, a different approach to problems of multiple significance testing is presented, which calls for controlling the expected proportion of falsely rejected hypotheses -the false discovery rate, which is equivalent to the FWER when all hypotheses are true but is smaller otherwise.
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Estimating F-statistics for the analysis of population structure.
Bruce S. Weir,C. Clark Cockerham +1 more
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Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows
TL;DR: The main innovations of the new version of the Arlequin program include enhanced outputs in XML format, the possibility to embed graphics displaying computation results directly into output files, and the implementation of a new method to detect loci under selection from genome scans.
Journal ArticleDOI
Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps
TL;DR: It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.
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