| 1. |
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| 2. |
- Andersson, Anastasia, 1987-, et al.
(författare)
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Monitoring genetic diversity with new indicators applied to an alpine freshwater top predator
- 2022
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 31:24, s. 6422-6439
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Tidskriftsartikel (refereegranskat)abstract
- Genetic diversity is the basis for population adaptation and long-term survival, yet rarely considered in biodiversity monitoring. One key issue is the need for useful and straightforward indicators of genetic diversity. We monitored genetic diversity over 40 years (1970–2010) in metapopulations of brown trout (Salmo trutta) inhabiting 27 small mountain lakes representing 10 lake systems in central Sweden using >1200 fish per time point. We tested six newly proposed indicators; three were designed for broad, international use in the UN Convention on Biological Diversity (CBD) and are currently applied in several countries. The other three were recently elaborated for national use by a Swedish science-management effort and applied for the first time here. The Swedish indicators use molecular genetic data to monitor genetic diversity within and between populations (indicators ΔH and ΔFST, respectively) and assess the effective population size (Ne-indicator). We identified 29 genetically distinct populations, all retained over time. Twelve of the 27 lakes harboured more than one population indicating that brown trout biodiversity hidden as cryptic, sympatric populations are more common than recognized. The Ne indicator showed values below the threshold (Ne ≤ 500) in 20 populations with five showing Ne < 100. Statistically significant genetic diversity reductions occurred in several populations. Metapopulation structure appears to buffer against diversity loss; applying the indicators to metapopulations suggest mostly acceptable rates of change in all but one system. The CBD indicators agreed with the Swedish ones but provided less detail. All these indicators are appropriate for managers to initiate monitoring of genetic biodiversity.
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| 3. |
- Bekkevold, D., et al.
(författare)
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Genetic mixed-stock analysis of Atlantic herring populations in a mixed feeding area
- 2011
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Ingår i: Marine Ecology Progress Series. - : Inter-Research Science Center. - 0171-8630 .- 1616-1599. ; 442, s. 187-199
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Tidskriftsartikel (refereegranskat)abstract
- Determining spatio-temporal distributions of fish populations is of interest to marine ecology, in general, and to fisheries science in particular. Genetic mixed-stock analysis is routinely applied in several anadromous fishes for determining migratory routes and timing but has rarely been used for marine fishes, for which population differentiation is commonly weak and the method presumably less powerful. We used microsatellite information for Northeast Atlantic herring Clupea harengus L. populations and mixed stocks to address 2 questions. We used simulated mixture samples and 3 different statistical approaches to determine whether mixed stock composition could be determined with accuracy. Simulations showed that the applied approaches and mixture samples of 100 individuals enabled detailed composition analyses on a regional level, with resolution for tracing the ecologically dominant Rügen (Greifswalder Bodden) herring population. We then estimated spatio-temporal variation in herring migratory behaviour in the Skagerrak from 17 mixed samples collected over 2 seasons and 2 yr, and identified hitherto undescribed differences in distributions among populations that feed and winter in the area.
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| 4. |
- Dussex, Nicolas, et al.
(författare)
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Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose
- 2023
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Ingår i: Communications Biology. - 2399-3642. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Ungulate species have experienced severe declines over the past centuries through overharvesting and habitat loss. Even if many game species have recovered thanks to strict hunting regulation, the genome-wide impacts of overharvesting are still unclear. Here, we examine the temporal and geographical differences in genome-wide diversity in moose (Alces alces) over its whole range in Sweden by sequencing 87 modern and historical genomes. We found limited impact of the 1900s near-extinction event but local variation in inbreeding and load in modern populations, as well as suggestion of a risk of future reduction in genetic diversity and gene flow. Furthermore, we found candidate genes for local adaptation, and rapid temporal allele frequency shifts involving coding genes since the 1980s, possibly due to selective harvesting. Our results highlight that genomic changes potentially impacting fitness can occur over short time scales and underline the need to track both deleterious and selectively advantageous genomic variation.
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| 5. |
- Hössjer, Ola, 1964-, et al.
(författare)
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Assessment of the Global Variance Effective Size of Subdivided Populations, and Its Relation to Other Effective Sizes
- 2023
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Ingår i: Acta Biotheoretica. - 0001-5342 .- 1572-8358. ; 71:3
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Tidskriftsartikel (refereegranskat)abstract
- The variance effective population size (N-eV) is frequently used to quantify the expected rate at which a population's allele frequencies change over time. The purpose of this paper is to find expressions for the global N-eV of a spatially structured population that are of interest for conservation of species. Since N-eV depends on allele frequency change, we start by dividing the cause of allele frequency change into genetic drift within subpopulations (I) and a second component mainly due to migration between subpopulations (II). We investigate in detail how these two components depend on the way in which subpopulations are weighted as well as their dependence on parameters of the model such a migration rates, and local effective and census sizes. It is shown that under certain conditions the impact of II is eliminated, and N-eV of the metapopulation is maximized, when subpopulations are weighted proportionally to their long term reproductive contributions. This maximal N-eV is the sought for global effective size, since it approximates the gene diversity effective size N-eGD, a quantifier of the rate of loss of genetic diversity that is relevant for conservation of species and populations. We also propose two novel versions of N-eV, one of which (the backward version of N-eV) is most stable, exists for most populations, and is closer to N-eGD than the classical notion of N-eV. Expressions for the optimal length of the time interval for measuring genetic change are developed, that make it possible to estimate any version of N-eV with maximal accuracy.
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| 6. |
- Karlsson, Sten, et al.
(författare)
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A genetic marker for the maternal identification of Atlantic salmon x brown trout hybrids
- 2013
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Ingår i: Conservation Genetics Resources. - : Springer Science and Business Media LLC. - 1877-7252 .- 1877-7260. ; 5:1, s. 47-49
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Tidskriftsartikel (refereegranskat)abstract
- Interspecific hybridization between Atlantic salmon and brown trout is well documented, but why it should vary so much among populations is not clear. Determining the maternal origin of hybrids can provide insights into the mechanisms underlying interspecific hybridization, but this information is lacking in many studies. Here we present a species-specific mitochondrial DNA marker for the identification of the maternal origin of hybrids. This marker involves only one PCR step followed by fragment analysis, can be integrated within PCR multiplexing for existing nuclear markers for hybrid identification, and is therefore faster and more cost-effective than previous methods.
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| 7. |
- Kurland, Sara, 1989-, et al.
(författare)
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Effects of subpopulation extinction on effective size (Ne) of metapopulations
- 2023
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Ingår i: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 24:4, s. 417-433
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Tidskriftsartikel (refereegranskat)abstract
- Population extinction is ubiquitous in all taxa. Such extirpations can reduce intraspecific diversity, but the extent to which genetic diversity of surviving populations are affected remains largely unclear. A key concept in this context is the effective population size (Ne), which quantifies the rate at which genetic diversity within populations is lost. Ne was developed for single, isolated populations while many natural populations are instead connected to other populations via gene flow. Recent analytical approaches and software permit modelling of Ne of interconnected populations (metapopulations). Here, we apply such tools to investigate how extinction of subpopulations affects Ne of the metapopulation (NeMeta) and of separate surviving subpopulations (NeRx) under different rates and patterns of genetic exchange between subpopulations. We assess extinction effects before and at migration-drift equilibrium. We find that the effect of extinction on NeMeta increases with reduced connectivity, suggesting that stepping stone models of migration are more impacted than island-migration models when the same number of subpopulations are lost. Furthermore, in stepping stone models, after extinction and before a new equilibrium has been reached, NeRx can vary drastically among surviving subpopulations and depends on their initial spatial position relative to extinct ones. Our results demonstrate that extinctions can have far more complex effects on the retention of intraspecific diversity than typically recognized. Metapopulation dynamics need heightened consideration in sustainable management and conservation, e.g., in monitoring genetic diversity, and are relevant to a wide range of species in the ongoing extinction crisis.
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| 8. |
- Kurland, Sara, et al.
(författare)
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Genomic dynamics of brown trout populations released to a novel environment
- 2022
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 12:7
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Tidskriftsartikel (refereegranskat)abstract
- Population translocations occur for a variety of reasons, from displacement due to climate change to human-induced transfers. Such actions have adverse effects on genetic variation and understanding their microevolutionary consequences requires monitoring. Here, we return to an experimental release of brown trout (Salmo trutta) in order to monitor the genomic effects of population translocations. In 1979, fish from each of two genetically (F-ST = 0.16) and ecologically separate populations were simultaneously released, at one point in time, to a lake system previously void of brown trout. Here, whole-genome sequencing of pooled DNA (Pool-seq) is used to characterize diversity within and divergence between the introduced populations and fish inhabiting two lakes downstream of the release sites, sampled 30 years later (c. 5 generations). Present results suggest that while extensive hybridization has occurred, the two introduced populations are unequally represented in the lakes downstream of the release sites. One population, which is ecologically resident in its original habitat, mainly contributes to the lake closest to the release site. The other population, migratory in its natal habitat, is genetically more represented in the lake further downstream. Genomic regions putatively under directional selection in the new habitat are identified, where allele frequencies in both established populations are more similar to the introduced population stemming from a resident population than the migratory one. Results suggest that the microevolutionary consequences of population translocations, for example, hybridization and adaptation, can be rapid and that Pool-seq can be used as an initial tool to monitor genome-wide effects.
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| 9. |
- Kurland, Sara, 1989-, et al.
(författare)
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New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data
- 2024
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 33:2
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Tidskriftsartikel (refereegranskat)abstract
- International policy recently adopted commitments to maintain genetic diversity in wild populations to secure their adaptive potential, including metrics to monitor temporal trends in genetic diversity – so-called indicators. A national programme for assessing trends in genetic diversity was recently initiated in Sweden. Relating to this effort, we systematically assess contemporary genome-wide temporal trends (40 years) in wild populations using the newly adopted indicators and whole genome sequencing (WGS). We use pooled and individual WGS data from brown trout (Salmo trutta) in eight alpine lakes in protected areas. Observed temporal trends in diversity metrics (nucleotide diversity, Watterson's ϴ and heterozygosity) lie within proposed acceptable threshold values for six of the lakes, but with consistently low values in lakes above the tree line and declines observed in these northern-most lakes. Local effective population size is low in all lakes, highlighting the importance of continued protection of interconnected systems to allow genetic connectivity for long-term viability of these populations. Inbreeding (FROH) spans 10%–30% and is mostly represented by ancient (<1 Mb) runs of homozygosity, with observations of little change in mutational load. We also investigate adaptive dynamics over evolutionarily short time frames (a few generations); identifying putative parallel selection across all lakes within a gene pertaining to skin pigmentation as well as candidates of selection unique to specific lakes and lake systems involved in reproduction and immunity. We demonstrate the utility of WGS for systematic monitoring of natural populations, a priority concern if genetic diversity is to be protected.
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| 10. |
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| 11. |
- Laikre, Linda, 1960-, et al.
(författare)
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Planned cull endangers Swedish wolf population
- 2022
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 377:6602
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Tidskriftsartikel (refereegranskat)abstract
- In May, the Swedish Parliament announced a goal to reduce the Swedish wolf population from about 400 to about 200 individuals (1). This action further threatens this highly endangered population, which is genetically isolated and inbred. Scientific advice for improvements has not been implemented (2, 3).The Swedish Parliament proposed this drastic cull at a time when biodiversity is a global focus. The 50-year anniversary of the first UN conference on the environment was celebrated in June, and the UN Convention on Biological Diversity (CBD) will soon finalize its global biodiversity framework for 2020 to 2050. Sweden’s actions are inconsistent with the country’s obligations under the CBD and European Union law.Few wild populations are as well studied as the Scandinavian wolf. Genetic monitoring has provided a full pedigree since the population was reestablished in the 1980s after extinction, and the data confirm persisting genetic isolation (4–6). Hunting, conducted both legally and illegally, has prevented population expansion and the influx of genetic variation.Three founders comprised the population’s genetic origin until 2007, and only three more wolves have subsequently contributed genetically to the present population (6). The genetic base is thus extremely narrow, and genomic erosion has been confirmed (7, 8). The average level of inbreeding is similar to the level found in the offspring of two full siblings (6). Inbreeding in this population has been shown to reduce litter size (4). Also, high frequencies of anatomical defects (9) and male reproductive disorders (10) have been observed.To make this population viable, population size and immigration must increase. So far, the population has been too small, and limited immigration followed by inbreeding could lead to extinction, similar to the Isle Royale wolf population (11). The goal should be to recreate a well-connected metapopulation spanning Scandinavia and Finland with a genetically effective population size of over 500, in line with the proposed CBD indicator (12). Considerably more genetic exchange than the current one-migrant-per-generation aim is needed (3).
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| 12. |
- Olsson, Jens, et al.
(författare)
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Genetic population structure of perch Perca fluviatilis along the Swedish coast of the Baltic Sea
- 2011
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Ingår i: Journal of Fish Biology. - : Wiley. - 0022-1112 .- 1095-8649. ; 79:1, s. 122-137
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Tidskriftsartikel (refereegranskat)abstract
- In this study, the genetic variation of perch Perca fluviatilis from 18 different sites along the Swedish coast of the Baltic Sea was assessed. There was a relative strong support for isolation by distance and the results suggest an overall departure from panmixia. The level of genetic divergence was moderate (global FST = 0·04) and indications of differences in the population genetic structure between the two major basins (central Baltic Sea and Gulf of Bothnia) in the Baltic Sea were found. There was a higher level of differentiation in the central Baltic Sea compared to the Gulf of Bothnia, and the results suggest that stretches of deep water might act as barriers to gene flow in the species. On the basis of the estimation of genetic patch size, the results corroborate previous mark–recapture studies and suggest that this is a species suitable for local management. In all, the findings of this study emphasize the importance of considering regional differences even when strong isolation by distance characterize the genetic population structure of species.
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| 13. |
- Olsson, Jens, et al.
(författare)
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Genetic structure of whitefish (Coregonus maraena) in the Baltic Sea
- 2012
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Ingår i: Eustarine, Coastal and Shelf Science. - : Elsevier BV. - 0272-7714 .- 1096-0015. ; 97, s. 104-113
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Tidskriftsartikel (refereegranskat)abstract
- Stocks of whitefish (Coregonus maraena) in the northern part of the Baltic Sea have in many areas declined drastically during recent years. Causes for the decline are yet not fully understood, but knowledge on the genetic population structure of the species is pivotal for future conservation measures. In this study we analyse the genetic variation at seven microsatellite loci for whitefish from 18 different sites along the Swedish coast of the Baltic Sea. We found a strong dependence of isolation by distance (R = 0.73), and a week but rather fine scaled genetic structure. In addition, there were differences between more northern and southern sites in the population genetic structure, where the degree of differentiation appears to be stronger in the north compared to the south. The results suggest that whitefish is a species suitable for local management with a regional context of the management strategy. In addition, the findings corroborate what is previously known for other coastal fish species in the Baltic Sea, such as perch and pike, suggesting that the majority of gene flow occurs between adjacent areas. Finally, our results highlight the potential for genetic subdivision even when the dependence of isolation by distance is strong.
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| 14. |
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| 15. |
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| 16. |
- Ryman, Nils, 1943-, et al.
(författare)
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Variance effective population size is affected by census size in sub-structured populations
- 2023
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Ingår i: Molecular Ecology Resources. - 1755-098X .- 1755-0998. ; 23:6, s. 1334-1347
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Tidskriftsartikel (refereegranskat)abstract
- Measurement of allele frequency shifts between temporally spaced samples has long been used for assessment of effective population size (N-e), and this 'temporal method' provides estimates of N-e referred to as variance effective size (N-eV). We show that N-eV of a local population that belongs to a sub-structured population (a metapopulation) is determined not only by genetic drift and migration rate (m), but also by the census size (N-c). The realized N-eV of a local population can either increase or decrease with increasing m, depending on the relationship between N-e and N-c in isolation. This is shown by explicit mathematical expressions for the factors affecting N-eV derived for an island model of migration. We verify analytical results using high-resolution computer simulations, and show that the phenomenon is not restricted to the island model migration pattern. The effect of N-c on the realized N-eV of a local subpopulation is most pronounced at high migration rates. We show that N-c only affects local N-eV, whereas N-eV for the metapopulation as a whole, inbreeding (N-eI), and linkage disequilibrium (N-eLD) effective size are all independent of N-c. Our results provide a possible explanation to the large variation of N-e/N-c ratios reported in the literature, where N-e is frequently estimated by N-eV. They are also important for the interpretation of empirical N-e estimates in genetic management where local N-eV is often used as a substitute for inbreeding effective size, and we suggest an increased focus on metapopulation N-eV as a proxy for N-eI.
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| 17. |
- Saha, Atal, et al.
(författare)
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Monitoring genome-wide diversity over contemporary time with new indicators applied to Arctic charr populations
- 2024
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Ingår i: Conservation Genetics. - 1566-0621 .- 1572-9737. ; 25, s. 513-531
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Tidskriftsartikel (refereegranskat)abstract
- Genetic diversity is fundamental to the adaptive potential and survival of species. Although its importance has long been recognized in science, it has a history of neglect within policy, until now. The new Global Biodiversity Framework recently adopted by the Convention on Biological Diversity, states that genetic diversity must be maintained at levels assuring adaptive potential of populations, and includes metrics for systematic monitoring of genetic diversity in so called indicators. Similarly, indicators for genetic diversity are being developed at national levels. Here, we apply new indicators for Swedish national use to one of the northernmost salmonid fishes, the Arctic charr (Salvelinus alpinus). We sequence whole genomes to monitor genetic diversity over four decades in three landlocked populations inhabiting protected alpine lakes in central Sweden. We find levels of genetic diversity, inbreeding and load to differ among lakes but remain stable over time. Effective population sizes are generally small (< 500), suggesting a limited ability to maintain adaptive variability if genetic exchange with nearby populations became eliminated. We identify genomic regions potentially shaped by selection; SNPs exhibiting population divergence exceeding expectations under drift and a putative selective sweep acting within one lake to which the competitive brown trout (Salmo trutta) was introduced during the sampling period. Identified genes appear involved in immunity and salinity tolerance. Present results suggest that genetically vulnerable populations of Arctic charr have maintained neutral and putatively adaptive genetic diversity despite small effective sizes, attesting the importance of continued protection and assurance of gene flow among populations.
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