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Monitoring gene level biodiversity - aspects and considerations in the context of conservation
Stockholm University, Faculty of Science, Department of Zoology.
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 [en]
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: urn:nbn:se:su:diva-62796ISBN: 978-91-7447-353-7 (print)OAI: oai:DiVA.org:su-62796DiVA: diva2:453179
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
List of papers
1. Potentials for monitoring gene level biodiversity: using Sweden as an example
Open this publication in new window or tab >>Potentials for monitoring gene level biodiversity: using Sweden as an example
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2008 (English)In: Biodiversity and Conservation, ISSN 0960-3115, E-ISSN 1572-9710, Vol. 17, no 4, 893-910 p.Article in journal (Refereed) Published
Abstract [en]

Programs for monitoring biological diversity over time are needed to detect changes that can constitute threats to biological resources. The convention on biological diversity regards effective monitoring as necessary to halt the ongoing erosion of biological variation, and such programs at the ecosystem and species levels are enforced in several countries. However, at the level of genetic biodiversity, little has been accomplished, and monitoring programs need to be developed. We define “conservation genetic monitoring” to imply the systematic, temporal study of genetic variation within particular species/populations with the aim to detect changes that indicate compromise or loss of such diversity. We also (i) identify basic starting points for conservation genetic monitoring, (ii) review the availability of such information using Sweden as an example, (iii) suggest categories of species for pilot monitoring programs, and (iv) identify some scientific and logistic issues that need to be addressed in the context of conservation genetic monitoring. We suggest that such programs are particularly warranted for species subject to large scale enhancement and harvest—operations that are known to potentially alter the genetic composition and reduce the variability of populations.

Keyword
Conservation genetic monitoring, Genetic diversity, Human induced genetic change, Release of alien populations, Spatial genetic structure, Stocking, Temporal genetic variability
National Category
Zoology
Research subject
Population Genetics
Identifiers
urn:nbn:se:su:diva-42937 (URN)10.1007/s10531-008-9335-2 (DOI)000254360200017 ()
Available from: 2010-09-20 Created: 2010-09-20 Last updated: 2017-12-12Bibliographically approved
2. Genetic structure and evidence of a local bottleneck in moose in Sweden
Open this publication in new window or tab >>Genetic structure and evidence of a local bottleneck in moose in Sweden
2008 (English)In: Journal of Wildlife Management, ISSN 0022-541X, Vol. 72, no 2, 411-415 p.Article in journal (Refereed) Published
Abstract [en]

The moose (Alces alces) is the most intensely managed game species in Sweden. Despite the biological and socioeconomical importance of moose, little is known of its population genetic structure. We analyzed 132 individuals from 4 geographically separate regions in Sweden for genetic variability at 6 microsatellite loci. We found evidence of strong substructuring and restricted levels of gene flow in this potentially mobile mammal. FST values were around 10%, and assignment tests indicated 3 genetically distinct populations over the study area. Spatial autocorrelation analysis provided a genetic patch size of approximately 420 km, implying that moose less than this distance apart are genetically more similar than 2 random individuals. Allele and genotype frequency distributions suggested a recent bottleneck in southern Sweden. Results indicate that moose may be more genetically divergent than currently anticipated, and therefore, the strong hunting pressure that is maintained over all of Sweden may have considerable local effects on genetic diversity. Sustainable moose hunting requires identification of spatial genetic structure to ensure that separate, genetically distinct subpopulations are not overharvested.

Keyword
Alces alces, bottleneck, conservation genetics, game species, genetic variation, spatial autocorrelation, spatial genetic structure
National Category
Zoology
Research subject
Population Genetics
Identifiers
urn:nbn:se:su:diva-12863 (URN)10.2193/2007-122 (DOI)000253210200011 ()
Available from: 2008-02-15 Created: 2008-02-15 Last updated: 2014-10-13Bibliographically approved
3. 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
4. Census (NC) and genetically effective (Ne) population size in a lake-resident population of brown trout Salmo trutta
Open this publication in new window or tab >>Census (NC) and genetically effective (Ne) population size in a lake-resident population of brown trout Salmo trutta
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2011 (English)In: Journal of Fish Biology, ISSN 0022-1112, E-ISSN 1095-8649, Vol. 79, no 7, 2074-2082 p.Article in journal (Refereed) Published
Abstract [en]

Census (NC) and effective population size (Ne) were estimated for a lake-resident population of brown trout Salmo trutta as 576 and 63, respectively. The point estimate of the ratio of effective to census population size (Ne:NC) for this population is 0·11 with a range of 0·06–0·26, suggesting that Ne:NC ratio for lake-resident populations agree more with estimates for fishes with anadromous life histories than the small ratios observed in many marine fishes

Keyword
abundance, conservation genetics, fishery management, genetic monitoring, mark- recapture
National Category
Zoology
Research subject
Population Genetics
Identifiers
urn:nbn:se:su:diva-62794 (URN)10.1111/j.1095-8649.2011.03124.x (DOI)000298014800027 ()
Available from: 2011-09-30 Created: 2011-09-30 Last updated: 2017-12-08Bibliographically approved
5. Genetic monitoring reveals temporal stability over 30 years in a small, lake-resident brown trout population
Open this publication in new window or tab >>Genetic monitoring reveals temporal stability over 30 years in a small, lake-resident brown trout population
2012 (English)In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 109, no 4, 246-253 p.Article in journal (Refereed) Published
Abstract [en]

Knowledge of the degree of temporal stability of population genetic structure and composition is important for understanding microevolutionary processes and addressing issues of human impact of natural populations. We know little about how representative single samples in time are to reflect population genetic constitution, and we explore the temporal genetic variability patterns over a 30-year period of annual sampling of a lake-resident brown trout (Salmo trutta) population, covering 37 consecutive cohorts and five generations. Levels of variation remain largely stable over this period, with no indication of substructuring within the lake. We detect genetic drift, however, and the genetically effective population size (Ne) was assessed from allele-frequency shifts between consecutive cohorts using an unbiased estimator that accounts for the effect of overlapping generation. The overall mean Ne is estimated as 74. We find indications that Ne varies over time, but there is no obvious temporal trend. We also estimated Ne using a one-sample approach based on linkage disequilibrium (LD) that does not account for the effect of overlapping generations. Combining one-sample estimates for all years gives an Ne estimate of 76. This similarity between estimates may be coincidental or reflecting a general robustness of the LD approach to violations of the discrete generations assumption. In contrast to the observed genetic stability, body size and catch per effort have increased over the study period. Estimates of annual effective number of breeders (Nb) correlated with catch per effort, suggesting that genetic monitoring can be used for detecting fluctuations in abundance.

Keyword
temporal genetic variation, effective population size, spatio-temporal structure, temporal method, linkage disequilibrium, one-sample approach
National Category
Zoology
Research subject
Population Genetics
Identifiers
urn:nbn:se:su:diva-62795 (URN)10.1038/hdy.2012.36 (DOI)000309109700007 ()
Available from: 2011-09-30 Created: 2011-09-30 Last updated: 2017-12-08Bibliographically approved

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