| 1. |
- 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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| 2. |
- 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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| 3. |
- Kurland, Sara, 1989-
(författare)
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Genomic dynamics over contemporary time frames in wild salmonid populations
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Genetic diversity is the foundation of all biological variation. An approach for sustainable use and protection of genetic diversity is continuous sampling over space and time, i.e. monitoring. It is important to consider genetic changes over contemporary time frames, since most human perturbations have occurred within the last century. Modern molecular tools now enable genome-wide diversity monitoring, also in non-model species.The work included in this thesis utilizes theoretical and molecular tools to monitor genomic diversity over microevolutionary time frames using salmonid fishes as models. First, the capacity for substructured populations to retain genetic variation following population extinctions was theoretically assessed. Models of effective population size (Ne) relevant to salmonids were used. Further, spatio-temporal genetic patterns of the highly substructured brown trout (Salmo trutta) were empirically estimated. Wild populations were studied using whole-genome sequencing, primarily of pools of individuals (Pool-seq). The brown trout is characterized by a large and complex genome, and genomic resources have, until recently, been lacking. One central aim of this thesis was therefore to evaluate the benefit of using Pool-seq data for monitoring genetic diversity in this species. To this end, disparate natural populations were studied that are, in part, previously described using classic genetic markers. First, I hypothesized that a Pool-seq-only approach developed for non-model species that lack reference genomes could be used to detect population differentiation between two scenarios of coexisting populations. In a second step, two different cases of populations in the wild – one experimental release and one case of protected populations – were monitored over nearly four decades (5-6 brown trout generations) using Pool-seq data. I asked what the levels of diversity and divergence among populations are, whether changes could be detected over contemporary time and if they could be attributed to adaptation.Paper I demonstrates that the effect of extinction on the rate of diversity change in population systems is more complex than previously recognized. Diversity loss is most prominent when migration within the population system is limited, which suggests that highly substructured population systems, e.g., many salmonids, are particularly vulnerable to population extinction. The utility of Pool-seq for monitoring brown trout populations over contemporary time is demonstrated for the three different cases of brown trout populations (Papers II-IV). Paper II confirms the ability of a Pool-seq-only approach to detect subtle population differentiation. Paper III identifies genome-wide levels of hybridization between populations introduced to a new environment and signs of adaptation in genes putatively involved in metabolism. Paper IV detects significant allele frequency shifts over a limited number of generations. Potentially adaptive change is also identified, with regions containing genes possibly associated to immunity, skin pigmentation, and reproduction (Paper IV).This thesis demonstrates the benefit of modern theoretical and molecular tools for monitoring diversity in highly substructured population systems. These tools are relevant for advancing population genetic knowledge, as well as for sustainable management and conservation of a wide range of species.
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| 4. |
- 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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| 5. |
- 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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