Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species
Stockholm Univ, Dept Zool, Div Populat Genet, SE-10691 Stockholm, Sweden.ORCID iD: 0000-0002-5370-1236
Stockholm Univ, Dept Zool, Div Populat Genet, SE-10691 Stockholm, Sweden.
Stockholm Univ, Dept Zool, Div Populat Genet, SE-10691 Stockholm, Sweden.
Stockholm Univ, Sci Life Lab, Solna, Sweden;Stockholm Univ, Dept Biochem & Biophys, Solna, Sweden.
Show others and affiliations
2019 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 9, no 19, p. 11448-11463Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
WILEY , 2019. Vol. 9, no 19, p. 11448-11463
Keywords [en]
genetic diversity, genome sequencing, population genomics, Salmo trutta, salmonid, single nucleotide polymorphism
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-399013DOI: 10.1002/ece3.5646ISI: 000487783000001PubMedID: 31641485OAI: oai:DiVA.org:uu-399013DiVA, id: diva2:1378515
Funder
Swedish Research Council FormasKnut and Alice Wallenberg Foundation, 2014.0278Carl Tryggers foundation Swedish Agency for Marine and Water ManagementAvailable from: 2019-12-13 Created: 2019-12-13 Last updated: 2019-12-13Bibliographically approved

Open Access in DiVA

fulltext(1391 kB)18 downloads
File information
File name FULLTEXT01.pdfFile size 1391 kBChecksum SHA-512
6c7f76ec10a11d016839070aab68bc2b5821e69802bbd1d3f4f0c4efce01a48744bf75bc0e6bd11245a12528671738532f4654487fa2b5fde3efd7cdecf3353a
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Kurland, SaraRubin, Carl-JohanAndersson, LeifRyman, NilsLaikre, Linda
By organisation
Department of Medical Biochemistry and Microbiology
In the same journal
Ecology and Evolution
Evolutionary Biology

Search outside of DiVA

GoogleGoogle Scholar
Total: 18 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 16 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf