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Population-scale se...
Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring
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- Lamichhaney, Sangeet (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
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- Barrio, Alvaro Martinez (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
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- Rafati, Nima (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
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- Sundström, Görel (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
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- Rubin, Carl-Johan (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
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- Gilbert, Elizabeth R. (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
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- Berglund, Jonas (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
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Wetterbom, Anna (author)
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- Laikre, Linda (author)
- Stockholms universitet,Zoologiska institutionen
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- Webster, Matthew T. (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
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- Grabherr, Manfred (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
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- Ryman, Nils (author)
- Stockholms universitet,Zoologiska institutionen
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- Andersson, Leif (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics,Uppsala University
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(creator_code:org_t)
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- 2012-11-07
- 2012
- English.
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 109:47, s. 19345-19350
- Related links:
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https://www.pnas.org...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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https://urn.kb.se/re...
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https://res.slu.se/i...
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Abstract
Subject headings
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- The Atlantic herring (Clupea harengus), one of the most abundant marine fishes in the world, has historically been a critical food source in Northern Europe. It is one of the few marine species that can reproduce throughout the brackish salinity gradient of the Baltic Sea. Previous studies based on few genetic markers have revealed a conspicuous lack of genetic differentiation between geographic regions, consistent with huge population sizes and minute genetic drift. Here, we present a cost-effective genome-wide study in a species that lacks a genome sequence. We first assembled amuscle transcriptome and then aligned genomic reads to the transcripts, creating an "exome assembly," capturing both exons and flanking sequences. We then resequenced pools of fish from a wide geographic range, including the Northeast Atlantic, as well as different regions in the Baltic Sea, aligned the reads to the exome assembly, and identified 440,817 SNPs. The great majority of SNPs showed no appreciable differences in allele frequency among populations; however, several thousand SNPs showed striking differences, some approaching fixation for different alleles. The contrast between low genetic differentiation at most loci and striking differences at others implies that the latter category primarily reflects natural selection. A simulation study confirmed that the distribution of the fixation index F-ST deviated significantly from expectation for selectively neutral loci. This study provides insights concerning the population structure of an important marine fish and establishes the Atlantic herring as a model for population genetic studies of adaptation and natural selection.
Subject headings
- NATURVETENSKAP -- Biologi -- Zoologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Zoology (hsv//eng)
- LANTBRUKSVETENSKAPER -- Bioteknologi med applikationer på växter och djur -- Genetik och förädling inom lantbruksvetenskap (hsv//swe)
- AGRICULTURAL SCIENCES -- Agricultural Biotechnology -- Genetics and Breeding in Agricultural Sciences (hsv//eng)
Keyword
- Baltic herring
- genetics
- population biology
- populationsgenetik
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Lamichhaney, San ...
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Barrio, Alvaro M ...
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Rafati, Nima
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Sundström, Görel
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Rubin, Carl-Joha ...
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Gilbert, Elizabe ...
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show more...
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Berglund, Jonas
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Wetterbom, Anna
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Laikre, Linda
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Webster, Matthew ...
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Grabherr, Manfre ...
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Ryman, Nils
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Andersson, Leif
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Zoology
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- AGRICULTURAL SCIENCES
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AGRICULTURAL SCI ...
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and Agricultural Bio ...
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and Genetics and Bre ...
- Articles in the publication
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Proceedings of t ...
- By the university
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Uppsala University
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Stockholm University
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Swedish University of Agricultural Sciences
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Karolinska Institutet