Browsing by Subject "effective population size"

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  • Partanen, Reeta-Maria (Helsingin yliopisto, 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.
  • Fabritius, Henna (Helsingfors universitet, 2010)
    Genetic variation is vital for both contemporary and long-term wellbeing of populations. Whereas heterozygosity (Ho) and allelic richness (A) are commonly used to measure the level of genetic diversity in a population, effective population size (Ne) describes the speed of loss of genetic variation. Various effective population sizes are proposed as standards for safe retention of genetic variation in a Minimum Viable Population (MVP). Since the 1940s, several types of effective population size estimators have been developed. Earlier estimators relied on demographic parameters, whereas genetic estimators are based on the analysis of either one or two genetic samples from a population. All Ne estimators have their unique sensitivities and limiting assumptions, which complicate the choice of estimator, comparison of results of different studies and the assessment of the reliability of the results. Ne estimators have recently been used e.g. in the monitoring of many aquatic populations, but their reliability and comparability has not often been tested with extensive ecological and genetic data, and it is not well established how much added value they bring to the conservation of easily observable species. I tested this with an extensive dataset on the Siberian jays (Perisoreus infaustus) living in Suupohja, Finland (62°22'N, 21°30'E). The Suupohja Siberian jays form one of the few isolates of Siberian jays in Southern Finland. I utilised three demographic and three genetic Ne estimators to estimate the Ne and the Ne/N ratio in the Suupohja Siberian jays, and compared the findings to the Ho and A estimates calculated with the same data, and to various suggested MVP standards. The results showed that the ratio of effective and census population sizes (Ne/N) is close to 0.6 in the Suupohja Siberian jays. Uneven survival of offspring and population size fluctuations are the main factors in the formation of this ratio. The average genetic Ne estimate would, then, suggest a census population size of 44 % higher than the average N in the Suupohja study area. This result is probably connected to the high proportion of breeding immigrants in the data, which would cause the Ne estimates to reflect a larger genetic neighbourhood than the study area. The genetic Ne estimates also suggest that the Suupohja Siberian jays might not be able to maintain their genetic diversity in the long term if gene flow would cease due to further isolation, especially if isolation would also cause a faster demographic decline. Conservation attempts should aim at ensuring gene flow to the remaining Siberian jay isolates in Southern Finland, in order to protect them from increasing genetic uniformity and inbreeding. It is possible that while the average dispersal distances in the Siberian jay are short, occasional long-distance dispersal events have an important role in the pretention of genetic structuring in a Siberian jay population. Ne estimation based on demographic data was laborious in the case of the Suupohja Siberian jays, whereas the genetic Ne estimates showed large variation depending on year and estimation method used. Reliable estimation of Ne with genetic methods would have required information on the large-scale genetic structure of the population. In any case, Ne estimates gave a clearer picture on the genetic viability of the Suupohja Siberian jays than the Ho and A estimates, which did not indicate any decrease of genetic diversity during the study period.
  • Paakala, Elina (Helsingfors universitet, 2011)
    The aim of this master’s thesis was to study genetic diversity within and between ten dog breeds. The original data was produced by Finnzymes Oy and it contained raw data files that were used to genotype microsatellite markers. The final data contained information from 395 dogs belonging to ten fairly different dog breeds. The amount of dogs per breed was from 31 to 53. The data was genotyped with 18 microsatellite markers. A llelic richness varied between 2,0 – 9,9. The most variable microsatellite locus was AHT137 and the least variable AHTk211. Over all loci allelic richness was highest in Jack Russell Terrier and lowest in Cavalier King Charles Spaniel. S c hipperke had the largest amount of microsatellite loci that were not in Hardy- Weinberg equilibrium. In Coton de Tulear, German Shepherd Dog and Finnish Lapphund all microsatellite loci were in Hardy-Weinberg equilibrium. The lowest overall heterozygosity was in Cavalier King Charles Spaniel (0,50) and highest in Finnish Lapphund (0,73). The only statistically significant FIS-values were in Schipperke in locus INU030 (0,39) and over all loci (0,11). The most distant breeds according to FST-value were Cavalier King Charles Spaniel and Rough Collie (0,34) and the closest breeds were Chihuahua and Coton de Tulear (0,07). Overall between breeds diversity was 17,7 %. On the grounds of these results the ten breeds are distinct populations. Coton de Tulear had clearly the highest amount of allele pairs in linkage disequilibrium (94) and Tibetan Spaniel the lowest amount (15). Effective population size was lowest in Rough Collie (35) and highest in Chihuahua (86). Based on many population genetic measures Cavalier King Charles Spaniel, Rough Collie and Schipperke seem to have the lowest genetic diversity and Chihuahua, Jack Russel Terrier and Finnish Lapphound the highest. Reasons for different levels of genetic diversity can be found on histories of these dog breeds.