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Disentangling small genetic differences in large Atlantic herring populations: comparing genetic markers and statistical power
Stockholm University, Faculty of Science, Department of Zoology.
2008 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Genes are the foundation of evolution and biodiversity. The genetic structure of natural populations needs to be understood to maintain exploited resources rationally. This thesis focuses on genetic variability and methods to determine spatial and temporal genetic heterogeneities. Intense human exploitation generates particular challenges to conserve genetic diversity of fishes since it has genetic effects. My research concerns one of our most valuable fish species: the Atlantic herring (Clupea harengus).

I analyzed Atlantic herring samples from the North and Baltic Seas. The objectives were to determine: 1) spatial genetic structure, 2) whether allozymes and microsatellites provide similar descriptions of the differentiation pattern, or 3) if they are influenced by selection, 4) factors affecting statistical power when testing for genetic differentiation, and 5) the temporal stability of the genetic structure.

The results show: 1) very low levels of spatial genetic differentiation in Atlantic herring; a major component is a difference between the Baltic and North Seas, 2) a concordant pattern with allozymes and microsatellites, 3) that selection influences a microsatellite locus, which can be a low salinity adaptation, 4) that statistical power is substantial for frequently used sample sizes and markers; the difference in power between organelle and nuclear loci is partly dependent on the populations’ stage of divergence, and 5) no changes in amount of genetic variation or spatial genetic structure over a 24-year period; the selection pattern in one microsatellite locus remained.

The notion that the large population sizes make herring unlikely to lose genetic diversity may be disputed. I found small local effective population sizes, and the evidence of selection hints of a distinct evolutionary lineage in the Baltic. When Atlantic herring is managed as very large units, there can be detrimental genetic effects if certain population segments are excessively harvested.

Place, publisher, year, edition, pages
Stockholm: Zoologiska institutionen , 2008. , 45 p.
Keyword [en]
conservation genetics, marine fish, spatial and temporal genetic variation, molecular marker comparison, allozyme, microsatellite, selection, fisheries management
National Category
Biological Sciences
Research subject
Population Genetics
Identifiers
URN: urn:nbn:se:su:diva-8338ISBN: 978-91-7155-780-3 (print)OAI: oai:DiVA.org:su-8338DiVA: diva2:200122
Public defence
2008-12-19, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 12 A, Stockholm, 10:00
Opponent
Supervisors
Available from: 2008-11-27 Created: 2008-11-20Bibliographically approved
List of papers
1. Power for detecting genetic divergence: Differences between statistical methods and marker loci
Open this publication in new window or tab >>Power for detecting genetic divergence: Differences between statistical methods and marker loci
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2006 In: Molecular Ecology, ISSN 0962-1083, Vol. 15, no 8, 2031-2045 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-25645 (URN)
Note
Part of urn:nbn:se:su:diva-8338Available from: 2008-11-27 Created: 2008-11-20Bibliographically approved
2. Concordance of allozyme and microsatellite differentiation in a marine fish, but evidence of selection at a microsatellite locus
Open this publication in new window or tab >>Concordance of allozyme and microsatellite differentiation in a marine fish, but evidence of selection at a microsatellite locus
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2007 In: Molecular Ecology, ISSN 0962-1083, Vol. 16, no 6, 1135-1147 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-25646 (URN)000244602500003 ()
Note
Part of urn:nbn:se:su:diva-8338Available from: 2008-11-27 Created: 2008-11-20Bibliographically approved
3. Biocomplexity in a highly migratory pelagic marine fish, Atlantic herring
Open this publication in new window or tab >>Biocomplexity in a highly migratory pelagic marine fish, Atlantic herring
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2006 In: Proceedings of the Royal Society B: Biological Sciences, ISSN 0962-8452, Vol. 273, no 1593, 1459-1464 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-25647 (URN)
Note
Part of urn:nbn:se:su:diva-8338Available from: 2008-11-27 Created: 2008-11-20Bibliographically approved
4. Statistical power for detecting genetic divergence–organelle versus nuclear markers
Open this publication in new window or tab >>Statistical power for detecting genetic divergence–organelle versus nuclear markers
2009 (English)In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 10, no 5, 1255-1264 p.Article in journal (Refereed) Published
Abstract [en]

Statistical power is critical in conservation for detecting genetic differences in space or time from allele frequency data. Organelle and nuclear genetic markers have fundamentally different transmission dynamics; the potential effect of these differences on power to detect divergence have been speculated on but not investigated. We examine, analytically and with computer simulations, the relative performance of organelle and nuclear markers under basic, ideal situations. We conclude that claims of a generally higher resolving power of either marker type are not correct. The ratio R = FST,organelle/FST,nuclear varies between 1 and 4 during differentiation and this greatly affects the power relationship. When nuclear FST is associated with organelle differentiation four times higher, the power of the organelle marker is similar to two nuclear loci with the same allele frequency distribution. With large sample sizes (n C 50) and several populations or many alleles per locus (C5), the power difference may typically be disregarded when nuclear FST[0.05. To correctly interpret observed patterns of genetic differentiation in practical situations, the expected FSTs and the statistical properties (i.e., power analysis) of the genetic markers used should be evaluated, taking the observed allele frequency distributions into consideration.

Keyword
Genetic differentiation, Detecting heterogeneity, Mitochondrial DNA, Chloroplast DNA
National Category
Zoology
Research subject
Population Genetics
Identifiers
urn:nbn:se:su:diva-25648 (URN)10.1007/s10592-008-9693-z (DOI)
Available from: 2008-11-27 Created: 2008-11-20 Last updated: 2014-10-13Bibliographically approved
5. Temporally stable genetic structure of Atlantic herring (Clupea harengus) in Swedish waters but indications of small local effective population size
Open this publication in new window or tab >>Temporally stable genetic structure of Atlantic herring (Clupea harengus) in Swedish waters but indications of small local effective population size
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Manuscript (Other academic)
Identifiers
urn:nbn:se:su:diva-25649 (URN)
Note
Part of urn:nbn:se:su:diva-8338Available from: 2008-11-27 Created: 2008-11-20 Last updated: 2010-01-13Bibliographically approved

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