Browsing by Author "Partanen, Reeta-Maria"
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Partanen, Reeta-Maria (2020)There is a naturally reproducing Atlantic salmon population in the River Teno in northern Norway and Finland. The Teno population has a strong population structure and up to 28 subpopulations have been recognized. Estimation of effective population size is important in conservation of the subpopulations. Effective population size tells about genetic variation of a population and is among the most important concepts in conservation genetics. In this study, current and past effective population sizes of 28 subpopulations were estimated from high density SNP-data for 1137 individuals in total. The estimation was done with the linkage disequilibrium method and the effects of using different assumptions were studied. Current estimated effective population sizes in subpopulations were generally low and ranged from around nine to 272 individuals. Only four populations had a current effective population size bigger than 50 individuals. Past effective population sizes showed a clear declining trend from the most distant generations in all populations. The choice between physical and linkage map as well as female, male or average linkage map had an effect to estimates. Also, different sample size corrections resulted in different estimates. Furthermore, effective population size was estimated with temporal method in three populations. It was detected that the estimates from temporal and linkage disequilibrium method were different from each other. The results of this study suggest that Teno Atlantic salmon subpopulations have declined over the past 150 generations and are in risk of losing genetic variation due to current low effective population size. This should be taken into account in conservation plans.
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Tehollisen populaatiokoon genominen vaihtelu suomalaisessa maatiais- ja yorkshire-sikapopulaatiossa Partanen, Reeta-Maria (2018)Effective population size is one of the most important concepts in population genetics. Large enough effective population size is important in maintaining genetic variation in populations. The aim of the study was to estimate effective population size in Landrace and Yorkshire populations and to find out if there is variation in the effective population size between chromosomes and chromosome segments. Effective population sizes were estimated using changes in allele frequencies across generations. Estimation was done from a SNP-genotype data consisting of 1020 Landrace and 1824 Yorkshire boars born in 1996-2013. Average effective population size in Landrace was approximately 40 individuals when estimated at chromosome level and approximately 47 individuals when estimated from chromosome segments. In Yorkshire, the respective estimates were around 37 and 46 individuals. It was noticed that there is variation in the estimated effective population size in both Landrace and Yorkshire populations. In Landrace, the largest chromosome-wise estimates of the effective population size were four times larger than the smallest estimates. The largest chromosome segment based estimates were 21 times larger than the smallest estimates. In Yorkshire, the largest estimates of chromosome-wise effective population size were three times larger and the largest estimates of chromosome segment based effective population size as much as 35 times larger than the smallest ones. The estimates of average effective population size in this study were clearly smaller in both breeds than the estimates of effective population sizes in previous studies that were based on pedigrees or linkage disequilibrium between SNPs. Chromosome-wise or chromosome segment based estimates of effective population size can be utilized in maintaining genetic variation in populations and in optimizing breeding programs.
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