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Exploring a Pool-se...
Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species
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- Kurland, Sara (författare)
- Stockholms universitet,Zoologiska institutionen,Stockholm Univ, Dept Zool, Div Populat Genet, SE-10691 Stockholm, Sweden
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- Wheat, Christopher W. (författare)
- Stockholms universitet,Zoologiska institutionen,Stockholm Univ, Dept Zool, Div Populat Genet, SE-10691 Stockholm, Sweden
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- Celorio Mancera, Maria de la Paz (författare)
- Stockholms universitet,Zoologiska institutionen,Stockholm Univ, Dept Zool, Div Populat Genet, SE-10691 Stockholm, Sweden
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- Kutschera, Verena E. (författare)
- Stockholms universitet,Science for Life Laboratory (SciLifeLab),Institutionen för biokemi och biofysik,Stockholm Univ, Sci Life Lab, Solna, Sweden;Stockholm Univ, Dept Biochem & Biophys, Solna, Sweden
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- Hill, Jason (författare)
- Stockholms universitet,Zoologiska institutionen,Stockholm Univ, Dept Zool, Div Populat Genet, SE-10691 Stockholm, Sweden
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- Andersson, Anastasia (författare)
- Stockholms universitet,Zoologiska institutionen,Stockholm Univ, Dept Zool, Div Populat Genet, SE-10691 Stockholm, Sweden
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- Rubin, Carl-Johan (författare)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi
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- Andersson, Leif (författare)
- Uppsala universitet,Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics,Uppsala University,Texas A&M University,Institutionen för medicinsk biokemi och mikrobiologi,Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden;Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX USA
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- Ryman, Nils (författare)
- Stockholms universitet,Zoologiska institutionen,Stockholm Univ, Dept Zool, Div Populat Genet, SE-10691 Stockholm, Sweden
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- Laikre, Linda (författare)
- Stockholms universitet,Zoologiska institutionen,Stockholm Univ, Dept Zool, Div Populat Genet, SE-10691 Stockholm, Sweden
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(creator_code:org_t)
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- 2019-09-26
- 2019
- Engelska.
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 9, s. 11448-11463
- Relaterad länk:
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https://doi.org/10.1...
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https://onlinelibrar...
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https://uu.diva-port... (primary) (Raw object)
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https://urn.kb.se/re...
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https://doi.org/10.1...
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https://res.slu.se/i...
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool-seq data to generate a de novo genome assembly for mining exons, upon which Pool-seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual-based single nucleotide polymorphisms [SNPs]) and from mapping the Pool-seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F-ST) between the two introduced populations exceeds that of the naturally sympatric populations (F-ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ (pi over bar approximate to 0.002 and pi over bar approximate to 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high-quality reference assembly from a divergent species. We conclude that the Pool-seq-only approach can be suitable for detecting and quantifying genome-wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.
Ämnesord
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Evolutionsbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Evolutionary Biology (hsv//eng)
Nyckelord
- genetic diversity
- genome sequencing
- population genomics
- Salmo trutta
- salmonid
- single nucleotide polymorphism
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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Kurland, Sara
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Wheat, Christoph ...
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Celorio Mancera, ...
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Kutschera, Veren ...
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Hill, Jason
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Andersson, Anast ...
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Rubin, Carl-Joha ...
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Andersson, Leif
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Ryman, Nils
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Laikre, Linda
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NATURVETENSKAP
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Ecology and Evol ...
- Av lärosätet
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Stockholms universitet
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Sveriges Lantbruksuniversitet
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Uppsala universitet