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Statistical power for detecting genetic divergence–organelle versus nuclear markers
Stockholm University, Faculty of Science, Department of Zoology.
Stockholm University, Faculty of Science, Department of Zoology.
Stockholm University, Faculty of Science, Department of Zoology.ORCID iD: 0000-0001-9286-3361
Stockholm University, Faculty of Science, Department of Zoology.ORCID iD: 0000-0003-3342-8479
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.

Place, publisher, year, edition, pages
2009. Vol. 10, no 5, 1255-1264 p.
Keyword [en]
Genetic differentiation, Detecting heterogeneity, Mitochondrial DNA, Chloroplast DNA
National Category
Zoology
Research subject
Population Genetics
Identifiers
URN: urn:nbn:se:su:diva-25648DOI: 10.1007/s10592-008-9693-zOAI: oai:DiVA.org:su-25648DiVA: diva2:200120
Available from: 2008-11-27 Created: 2008-11-20 Last updated: 2017-12-13Bibliographically approved
In thesis
1. Disentangling small genetic differences in large Atlantic herring populations: comparing genetic markers and statistical power
Open this publication in new window or tab >>Disentangling small genetic differences in large Atlantic herring populations: comparing genetic markers and statistical power
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
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:nbn:se:su:diva-8338 (URN)978-91-7155-780-3 (ISBN)
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
2. Monitoring gene level biodiversity - aspects and considerations in the context of conservation
Open this publication in new window or tab >>Monitoring gene level biodiversity - aspects and considerations in the context of conservation
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The objectives of this thesis relate to questions needed to be addressed in the context of genetic monitoring for implementing the Convention on Biological Diversity for the gene level. Genetic monitoring is quantifying temporal changes in population genetic metrics. Specific goals of this thesis include i) synthesizing existing information relevant to genetic monitoring of Swedish species, ii) providing a genetic baseline for the Swedish moose, iii) evaluating the relative performance of nuclear versus organelle genetic markers for detecting population divergence, iv) actually monitoring the genetic composition, structure, level of variation, and effective population size (Ne) and assessing the relation between Ne and the actual number of individuals for an unexploited brown trout population.

The concept of conservation genetic monitoring is defined and Swedish priority species for such monitoring are identified; they include highly exploited organisms such as moose, salmonid fishes, Norway spruce, Atlantic cod, and Atlantic herring. Results indicate that the Swedish moose might be more genetically divergent than previously anticipated and appears to be divided into at least three different subpopulations, representing a southern, a central, and a northern population.

The relative efficiency of nuclear and organelle markers depends on the relationship between the degree of genetic differentiation at the two types of markers. In turn, this relates to how far the divergence process has progressed.

For the monitored brown trout population no indication of systematic change of population structure or allele frequencies was observed over 30 years. Significant genetic drift was found, though, translating into an overall Ne-estimate of ~75. The actual number of adult fish (NC) was assessed as ~600, corresponding to an Ne/NC ratio of 0.13. In spite of the relatively small effective population size monitoring did not reveal loss of genetic variation.

Place, publisher, year, edition, pages
Stockholm: Department of Zoology, Stockholm University, 2011. 60 p.
Keyword
brown trout, conservation genetics, genetic drift, genetic monitoring, effective population size, moose, one-sample approach, spatial genetic structure, statistical power, temporal data
National Category
Zoology
Research subject
Population Genetics
Identifiers
urn:nbn:se:su:diva-62796 (URN)978-91-7447-353-7 (ISBN)
Public defence
2011-12-09, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Available from: 2011-11-17 Created: 2011-09-30 Last updated: 2011-11-09Bibliographically approved

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Larsson, Lena C.Charlier, JohanLaikre, LindaRyman, Nils
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