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A simple route to single-nucleotide polymorphisms in a nonmodel species: identification and characterization of SNPs in the Artic ringed seal (Pusa hispida hispida)
Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
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2011 (English)In: Molecular Ecology Resources, ISSN 1755-098X, Vol. 11, 9-19 p.Article in journal (Refereed) Published
Abstract [en]

Although single-nucleotide polymorphisms (SNPs) have become the marker of choice in the field of human genetics, these markers are only slowly emerging in ecological, evolutionary and conservation genetic analyses of nonmodel species. This is partly because of difficulties associated with the discovery and characterization of SNP markers. Herein, we adopted a simple straightforward approach to identifying SNPs, based on screening of a random genomic library. In total, we identified 768 SNPs in the ringed seal, Pusa hispida hispida, in samples from Greenland and Svalbard. Using three seal samples, SNPs were discovered at a rate of one SNP per 402 bp, whereas re-sequencing of 96 seals increased the density to one SNP per 29 bp. Although applicable to any species of interest, the approach is especially well suited for SNP discovery in nonmodel organisms and is easily implemented in any standard genetics laboratory, circumventing the need for prior genomic data and use of next-generation sequencing facilities.

Place, publisher, year, edition, pages
2011. Vol. 11, 9-19 p.
Keyword [en]
Arctic, discovery, genomics, natural populations, single-nucleotide polymorphism
National Category
Biochemistry and Molecular Biology Ecology Evolutionary Biology
URN: urn:nbn:se:su:diva-67939DOI: 10.1111/j.1755-0998.2010.02941.xISI: 000287485100002OAI: diva2:471665
authorCount :8 Available from: 2012-01-02 Created: 2012-01-02 Last updated: 2012-01-30Bibliographically approved
In thesis
1. Molecular ecology of marine mammals
Open this publication in new window or tab >>Molecular ecology of marine mammals
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Marine mammals comprise a paraphyletic group of species whose current abundance and distribution has been greatly shaped by past environmental changes and anthropogenic impacts. This thesis describes molecular ecological approaches to answer questions regarding habitat requirements, genetic differentiation, and life-history trade-offs in three species of marine mammals. 

The annual sea-ice dynamics of the Arctic may have large effects on the abundance and distribution of Arctic species such as the pagophilic ringed seal (Pusa hispida). Paper I describes and applies a simple molecular method for isolating and characterizing a relatively large set of single nucleotide polymorphisms (SNPs) in the ringed seal. These SNPs have been genotyped in a yet-to-be-analysed dataset which will form the basis in an assessment of the micro-evolutionary effects of annual sea-ice dynamics on ringed seal. 

Current management efforts directed towards the North Atlantic fin whale (Balaenoptera physalus) are hampered by an unclear understanding of population structure. Paper II investigates the DNA basis for the high levels of genetic differentiation that have been reported in allozyme studies of the North Atlantic fin whale. We find that additional processes (at the organismal level) may have contributed to shaping the phenotype of the underlying allozyme variation.

Telomeres may potentially serve as markers for determining the chronological and biological age of animals where other means of inference is difficult. Paper III describes the application and evaluation of four qPCR assays for telomere length estimation in humpback whales (Megaptera novaeangliae), finding that reliable telomere length estimates require extensive quality control. Paper IV applies the best performing qPCR assay to test whether telomeres may provide a method for genetic determination of chronological age in whales and concludes that the biological and experimental variation in telomere length estimates is too large to determine age with sufficient resolution. Finally, because telomere length and rate of telomere loss also may be affected by other cellular and organismal processes, such as resource allocation among self-maintenance mechanisms, growth and reproduction, Paper V describes the correlations between individual telomere length and rate of telomere loss, and sex, maturity status and female reproductive output. We found that the costs of reproduction in terms of telomere loss are higher in mature humpback whales than in juveniles; that reproductive costs are higher in males than females; and that differences among females tend to correlate with reproductive output.

Place, publisher, year, edition, pages
Stockholm: Department of Genetics, Microbiology and Toxicology, Stockholm University, 2012. 86 p.
Marine mammals, molecular ecology, life history, environmental change, phenotypic plasticity, SNPs, telomeres
National Category
Research subject
Molecular Genetics
urn:nbn:se:su:diva-71166 (URN)978-91-7447-403-9 (ISBN)
Public defence
2012-02-29, Nordenskiöldsalen, Geovetenskapens hus, Svante Arrheniusväg 12, Stockholm, 10:00 (English)
At the time of doctoral defence the following papers were unpublished and had a status as follows: Paper 2: Submitted; Paper 3:Submitted; Paper 4: Manuscript; Paper 5:ManuscriptAvailable from: 2012-02-07 Created: 2012-01-26 Last updated: 2012-01-30Bibliographically approved

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Olsen, Morten TangeBerube, MartinePalsbøll, Per
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