| 1. |
|
|
| 2. |
- Allendorf, Fred W, et al.
(författare)
-
Genetic effects of harvest on wild animal populations.
- 2008
-
Ingår i: Trends Ecol Evol. - 0169-5347. ; 23:6, s. 327-37
-
Tidskriftsartikel (refereegranskat)abstract
- Human harvest of animals in the wild occurs in terrestrial and aquatic habitats throughout the world and is often intense. Harvest has the potential to cause three types of genetic change: alteration of population subdivision, loss of genetic variation, and selective genetic changes. To sustain the productivity of harvested populations, it is crucial to incorporate genetic considerations into management. Nevertheless, it is not necessary to disentangle genetic and environmental causes of phenotypic changes to develop management plans for individual species. We recommend recognizing that some genetic change due to harvest is inevitable. Management plans should be developed by applying basic genetic principles combined with molecular genetic monitoring to minimize harmful genetic change.
|
|
| 3. |
- Allendorf, Fred W., et al.
(författare)
-
So long to genetic diversity, and thanks for all the fish
- 2014
-
Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 23:1, s. 23-25
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The world faces a global fishing crisis. Wild marine fisheries comprise nearly 15% of all animal protein in the human diet, but, according to the U.N. Food and Agriculture Organization, nearly 60% of all commercially important marine fish stocks are overexploited, recovering, or depleted (FAO 2012; Fig. 1). Some authors have suggested that the large population sizes of harvested marine fish make even collapsed populations resistant to the loss of genetic variation by genetic drift (e. g. Beverton 1990). In contrast, others have argued that the loss of alleles because of overfishing may actually be more dramatic in large populations than in small ones (Ryman et al. 1995). In this issue, Pinsky & Palumbi (2014) report that overfished populations have approximately 2% lower heterozygosity and 12% lower allelic richness than populations that are not overfished. They also performed simulations which suggest that their estimates likely underestimate the actual loss of rare alleles by a factor of three or four. This important paper shows that the harvesting of marine fish can have genetic effects that threaten the long-term sustainability of this valuable resource.
|
|
| 4. |
- Andersson, Anastasia, et al.
(författare)
-
Complex genetic diversity patterns of cryptic, sympatric brown trout (Salmo trutta) populations in tiny mountain lakes
- 2017
-
Ingår i: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 18:5, s. 1213-1227
-
Tidskriftsartikel (refereegranskat)abstract
- Intraspecific genetic variation can have similar effects as species diversity on ecosystem function; understanding such variation is important, particularly for ecological key species. The brown trout plays central roles in many northern freshwater ecosystems, and several cases of sympatric brown trout populations have been detected in freshwater lakes based on apparent morphological differences. In some rare cases, sympatric, genetically distinct populations lacking visible phenotypic differences have been detected based on genetic data alone. Detecting such cryptic sympatric populations without prior grouping of individuals based on phenotypic characteristics is more difficult statistically, though. The aim of the present study is to delineate the spatial connectivity of two cryptic, sympatric genetic clusters of brown trout discovered in two interconnected, tiny subarctic Swedish lakes. The structures were detected using allozyme markers, and have been monitored over time. Here, we confirm their existence for almost three decades and report that these cryptic, sympatric populations exhibit very different connectivity patterns to brown trout of nearby lakes. One of the clusters is relatively isolated while the other one shows high genetic similarity to downstream populations. There are indications of different spawning sites as reflected in genetic structuring among parr from different creeks. We used > 3000 SNPs on a subsample and find that the SNPs largely confirm the allozyme pattern but give considerably lower F (ST) values, and potentially indicate further structuring within populations. This type of complex genetic substructuring over microgeographical scales might be more common than anticipated and needs to be considered in conservation management.
|
|
| 5. |
- Andersson, Anastasia, 1987-
(författare)
-
Hidden biodiversity in an alpine freshwater top predator : Existence, characteristics, and temporal dynamics of cryptic, sympatric brown trout populations
- 2021
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Intraspecific genetic diversity is imperative to the survival of species in a changing environment, and it plays a vital role in ecosystem function. Since this type of diversity can be difficult to detect it is sometimes referred to as “hidden biodiversity”. When separate and genetically distinct populations of the same species coexist within the same habitat, without apparent barriers to migration and obvious phenotypic divergence, this form of hidden biodiversity is called cryptic sympatry. Knowledge of cryptic sympatry is limited, however, and the aim of this thesis is to increase our understanding of this phenomenon by focusing on a species group where several cases of sympatry have been documented – the salmonids.Using the brown trout (Salmo trutta) as a model, I characterized two previously reported cases of cryptic sympatry occurring in small Swedish alpine lakes with respect to both phenotypic and genetic characteristics. I explored the hypothesis that cryptic sympatry is more common than currently recognized by reviewing literature documenting sympatry, as well as by assessing the statistical power to detect sympatric populations with varying degrees of divergence using commonly applied sample sizes for loci and individuals. Further, I performed a large-scale search for sympatric populations in alpine lakes in central Sweden.I found that cryptic, sympatric populations can coexist while apparently utilizing the same food resources and exhibiting the same adaptive plasticity to their shared environment (Paper I). In one of the empirical cases there were indications that the populations used different creeks for spawning, suggesting that segregation in spawning location contributes to the maintenance of sympatry (Paper II). Further, I found that differences between cryptic, sympatric populations of the same lake may be large with respect to levels of genetic diversity, inbreeding, and connectivity with populations in nearby lakes (Papers II and III). I found support for the hypothesis that cryptic sympatry is more common than generally acknowledged (Papers IV and V). In the literature, cryptic sympatry is rarely reported and typically associated with higher divergence levels than between sympatric populations that differ phenotypically. My results suggest that this to a large extent may be due to limited statistical power when commonly used sample sizes in terms of individuals and loci are applied and the amount of divergence between populations is small (Paper IV). Cryptic sympatry was observed in over 40% of the screened localities (27 lakes), and was shown to be temporally stable over at least 40 years (Paper V).
|
|
| 6. |
- Andersson, Anastasia, et al.
(författare)
-
Lack of trophic polymorphism despite substantial genetic differentiation in sympatric brown trout (Salmo trutta) populations
- 2017
-
Ingår i: Ecology of Freshwater Fish. - : Wiley. - 0906-6691 .- 1600-0633. ; 26:4, s. 643-652
-
Tidskriftsartikel (refereegranskat)abstract
- Sympatric populations occur in many freshwater fish species; such populations are typically detected through morphological distinctions that are often coupled to food niche and genetic separations. In salmonids, trophic and genetically separate sympatric populations have been reported in landlocked Arctic char, whitefish and brown trout. In Arctic char and brown trout rare cases of sympatric, genetically distinct populations have been detected based on genetic data alone, with no apparent morphological differences, that is cryptic structuring. It remains unknown whether such cryptic, sympatric structuring can be coupled to food niche separation. Here, we perform an extensive screening for trophic divergence of two genetically divergent, seemingly cryptic, sympatric brown trout populations documented to remain in stable sympatry over several decades in two interconnected, tiny mountain lakes in a nature reserve in central Sweden. We investigate body shape, body length, gill raker metrics, breeding status and diet (stomach content analysis and stable isotopes) in these populations. We find small significant differences for body shape, body size and breeding status, and no evidence of food niche separation between these two populations. In contrast, fish in the two lakes differed in body shape, diet, and nitrogen and carbon isotope signatures despite no genetic difference between lakes. These genetically divergent populations apparently coexist using the same food resources and showing the same adaptive plasticity to the local food niches of the two separate lakes. Such observations have not been reported previously but may be more common than recognised as genetic screenings are necessary to detect the structures.
|
|
| 7. |
|
|
| 8. |
- Andersson, Anastasia, 1987-, et al.
(författare)
-
Monitoring genetic diversity with new indicators applied to an alpine freshwater top predator
- 2022
-
Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 31:24, s. 6422-6439
-
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.
|
|
| 9. |
- André, Carl, 1958, et al.
(författare)
-
Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus) : direct, simultaneous evaluation of neutral vs putatively selected loci
- 2011
-
Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 106:2, s. 270-280
-
Tidskriftsartikel (refereegranskat)abstract
- In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers to detect population structure in Atlantic herring (Clupea harengus), a migratory pelagic species with large effective population sizes. We compared the spatial and temporal patterns of divergence and statistical power of three traditional genetic marker types, microsatellites, allozymes and mitochondrial DNA, with one microsatellite locus, Cpa112, previously shown to be influenced by divergent selection associated with salinity, and one locus located in the major histocompatibility complex class IIA (MHC-IIA) gene, using the same individuals across analyses. Samples were collected in 2002 and 2003 at two locations in the North Sea, one location in the Skagerrak and one location in the low-saline Baltic Sea. Levels of divergence for putatively neutral markers were generally low, with the exception of single outlier locus/sample combinations; microsatellites were the most statistically powerful markers under neutral expectations. We found no evidence of selection acting on the MHC locus. Cpa112, however, was highly divergent in the Baltic samples. Simulations addressing the statistical power for detecting population divergence showed that when using Cpa112 alone, compared with using eight presumed neutral microsatellite loci, sample sizes could be reduced by up to a tenth while still retaining high statistical power. Our results show that the loci influenced by selection can serve as powerful markers for detecting population structure in high gene-flow marine fish species.
|
|
| 10. |
- Bekkevold, D., et al.
(författare)
-
Genetic mixed-stock analysis of Atlantic herring populations in a mixed feeding area
- 2011
-
Ingår i: Marine Ecology Progress Series. - : Inter-Research Science Center. - 0171-8630 .- 1616-1599. ; 442, s. 187-199
-
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.
|
|
| 11. |
- Charlier, Johan, et al.
(författare)
-
Census (NC) and genetically effective (Ne) population size in a lake-resident population of brown trout Salmo trutta
- 2011
-
Ingår i: Journal of Fish Biology. - : Wiley. - 0022-1112 .- 1095-8649. ; 79:7, s. 2074-2082
-
Tidskriftsartikel (refereegranskat)abstract
- 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
|
|
| 12. |
- Charlier, Johan, et al.
(författare)
-
Genetic monitoring reveals temporal stability over 30 years in a small, lake-resident brown trout population
- 2012
-
Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 109:4, s. 246-253
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
| 13. |
- Charlier, Johan, et al.
(författare)
-
Genetic structure and evidence of a local bottleneck in moose in Sweden
- 2008
-
Ingår i: Journal of Wildlife Management. - : Wiley. - 0022-541X .- 1937-2817. ; 72:2, s. 411-415
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
| 14. |
- Charlier, Johan, 1977-
(författare)
-
Monitoring gene level biodiversity - aspects and considerations in the context of conservation
- 2011
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- 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.
|
|
| 15. |
- Dussex, Nicolas, et al.
(författare)
-
Moose genomes reveal past glacial demography and the origin of modern lineages
- 2020
-
Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 21:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America.Results: We found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines.Conclusions: Taken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies.
|
|
| 16. |
- Dussex, Nicolas, et al.
(författare)
-
Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose
- 2023
-
Ingår i: Communications Biology. - 2399-3642. ; 6:1
-
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.
|
|
| 17. |
- Hadzihalilovic-Numanovic, Amra, 1963-
(författare)
-
Genetic Variation and Relatedness of Freshwater Pearl Mussel Margaritifera margaritifera L. populations
- 2005
-
Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The two papers presented in this thesis focus on population genetic study on freshwater pearl mussel populations in Sweden, using RAPD method. In paper I, I examine genetic variation within and between 5 populations in a single drainage area in south western Sweden. In paper II, I study the evolutionary relationship, and how genetic variation is related to population size, age structure and geographic isolation in 14 populations of freshwater pearl mussel in south central Sweden. In both papers I and II, I found that genetic variation was larger than found in previous studies using other techniques, and variation was larger between than within populations. I did not found any correlation between geographic and genetic distance, which indicates that mussel populations have been adapted locally to environmental factors in a relatively short time. In paper I, I found that genetic distance between populations was greater than found in other studies, despite small geographic distances. In paper II, I found that populations were highly differentiated indicating little gene flow between them. There was no significant positive relation between genetic variation and population size or age structure but there was a significant positive relation between mean age and population size indicating that many populations have gone through bottlenecks recently.
|
|
| 18. |
- Hössjer, Ola, et al.
(författare)
-
A new general analytical approach for modeling patterns of genetic differentiation and effective size of subdivided populations over time
- 2014
-
Ingår i: Mathematical Biosciences. - : Elsevier BV. - 0025-5564 .- 1879-3134. ; 258, s. 113-133
-
Tidskriftsartikel (refereegranskat)abstract
- The main purpose of this paper is to develop a theoretical framework for assessing effective population size and genetic divergence in situations with structured populations that consist of various numbers of more or less interconnected subpopulations. We introduce a general infinite allele model for a diploid, monoecious and subdivided population, with subpopulation sizes varying overtime, including local subpopulation extinction and recolonization, bottlenecks, cyclic census size changes or exponential growth. Exact matrix analytic formulas are derived for recursions of predicted (expected) gene identities and gene diversities, identity by descent and coalescence probabilities, and standardized variances of allele frequency change. This enables us to compute and put into a general framework a number of different types of genetically effective population sizes (N-e) including variance, inbreeding, nucleotide diversity, and eigenvalue effective size. General expressions for predictions (g(ST)) of the coefficient of gene differentiation G(ST) are also derived. We suggest that in order to adequately describe important properties of a subdivided population with respect to allele frequency change and maintenance of genetic variation over time, single values of g(ST) and N-e are not enough. Rather, the temporal dynamic patterns of these properties are important to consider. We introduce several schemes for weighting subpopulations that enable effective size and expected genetic divergence to be calculated and described as functions of time, globally for the whole population and locally for any group of subpopulations. The traditional concept of effective size is generalized to situations where genetic drift is confounded by external sources, such as immigration and mutation. Finally, we introduce a general methodology for state space reduction, which greatly decreases the computational complexity of the matrix analytic formulas.
|
|
| 19. |
- Hössjer, Ola, 1964-, et al.
(författare)
-
Assessment of the Global Variance Effective Size of Subdivided Populations, and Its Relation to Other Effective Sizes
- 2023
-
Ingår i: Acta Biotheoretica. - 0001-5342 .- 1572-8358. ; 71:3
-
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.
|
|
| 20. |
- Hössjer, Ola, et al.
(författare)
-
Effective sizes and time to migration-drift equilibrium in geographically subdivided populations
- 2016
-
Ingår i: Theoretical Population Biology. - : Elsevier BV. - 0040-5809 .- 1096-0325. ; 112, s. 139-156
-
Tidskriftsartikel (refereegranskat)abstract
- Many versions of the effective population size (N-e) exist, and they are important in population genetics in order to quantify rates of change of various characteristics, such as inbreeding, heterozygosity, or allele frequencies. Traditionally, N-e was defined for single, isolated populations, but we have recently presented a mathematical framework for subdivided populations. In this paper we focus on diploid populations with geographic subdivision, and present new theoretical results. We compare the haploid and diploid versions of the inbreeding effective size (N-ei) with novel expression for the variance effective size (N-ev), and conclude that for local populations N-ev is often much smaller than both versions of Nei, whenever they exist. Global N(ev)of the metapopulation, on the other hand, is close to the haploid Net and much larger than the diploid Nei. We introduce a new effective size, the additive genetic variance effective size Neill', which is of particular interest for long term protection of species. It quantifies the rate at which additive genetic variance is lost and we show that this effective size is closely related to the haploid version of Nei. Finally, we introduce a new measure of a population's deviation from migration-drift equilibrium, and apply it to quantify the time it takes to reach this equilibrium. Our findings are of importance for understanding the concept of effective population size in substructured populations and many of the results have applications in conservation biology.
|
|
| 21. |
- Hössjer, Ola, et al.
(författare)
-
Metapopulation inbreeding dynamics, effective size and subpopulation differentiation-A general analytical approach for diploid organisms
- 2015
-
Ingår i: Theoretical Population Biology. - : Elsevier BV. - 0040-5809 .- 1096-0325. ; 102, s. 40-59
-
Tidskriftsartikel (refereegranskat)abstract
- Motivated by problems in conservation biology we study genetic dynamics in structured populations of diploid organisms (monoecious or dioecious). Our analysis provides an analytical framework that unifies substantial parts of previous work in terms of exact identity by descent (IBD) and identity by state (IBS) recursions. We provide exact conditions under which two structured haploid and diploid populations are equivalent, and some sufficient conditions under which a dioecious diploid population can be treated as a monoecious diploid one. The IBD recursions are used for computing local and metapopulation inbreeding and coancestry effective population sizes and for predictions of several types of fixation indices over different time horizons.
|
|
| 22. |
- Hössjer, Ola, et al.
(författare)
-
Quasi equilibrium approximations of the fixation index under neutrality : The finite and infinite island models
- 2013
-
Ingår i: Theoretical Population Biology. - : Elsevier BV. - 0040-5809 .- 1096-0325. ; 84, s. 9-24
-
Tidskriftsartikel (refereegranskat)abstract
- The fixation index FST and the coefficient of gene differentiation GST are analyzed for the finite island model under short time spans, ignoring mutations. Dividing the reproduction cycle into the three steps–gamete formation, fertilization, and migration–we develop a new approach for computing quasi equilibrium formulas for FST (and GST). Our formulas generalize earlier ones and reveal that the equilibrium value of FST is influenced not only by the migration rate and local effective population size, Ne, but also by the local census size N, particularly so when the migration rate is high. The order of migration and fertilization is found to have a smaller effect on FST. A major advantage compared to previous approaches is that stochastic allele frequency of migrants is easily accommodated, thereby avoiding underestimation of FST for large migration rates.
|
|
| 23. |
|
|
| 24. |
- Hössjer, Ola, et al.
(författare)
-
Quasi equilibrium, variance effective size and fixation index for populations with substructure
- 2014
-
Ingår i: Journal of Mathematical Biology. - : Springer Science and Business Media LLC. - 0303-6812 .- 1432-1416. ; 69:5, s. 1057-1128
-
Tidskriftsartikel (refereegranskat)abstract
- In this paper, we develop a method for computing the variance effective size , the fixation index and the coefficient of gene differentiation of a structured population under equilibrium conditions. The subpopulation sizes are constant in time, with migration and reproduction schemes that can be chosen with great flexibility. Our quasi equilibrium approach is conditional on non-fixation of alleles. This is of relevance when migration rates are of a larger order of magnitude than the mutation rates, so that new mutations can be ignored before equilibrium balance between genetic drift and migration is obtained. The vector valued time series of subpopulation allele frequencies is divided into two parts; one corresponding to genetic drift of the whole population and one corresponding to differences in allele frequencies among subpopulations. We give conditions under which the first two moments of the latter, after a simple standardization, are well approximated by quantities that can be explicitly calculated. This enables us to compute approximations of the quasi equilibrium values of , and . Our findings are illustrated for several reproduction and migration scenarios, including the island model, stepping stone models and a model where one subpopulation acts as a demographic reservoir. We also make detailed comparisons with a backward approach based on coalescence probabilities.
|
|
| 25. |
- Jonsson, B. G., et al.
(författare)
-
Skogspolitiken hotar biologiska mångfalden
- 2008
-
Ingår i: Dagens Nyheter. ; 14 april
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Ledande svenska forskare varnar för att det nationella naturarvet äventyras: Vi skäms över våra beslutsfattares likgiltighet för miljön. Den svenska skogen har förvandlats till en jättelik odlingsyta. Där förr otaliga arter levde samman i harmoni dominerar numera helt gran, tall och inplanterade främmande trädslag. Denna skogsodling utgör ett hot mot den biologiska mångfalden vilket strider mot riksdagens miljökvalitetsmål. Den svenska skogspolitiken vilar officiellt på att produktion av skogsråvara och miljö är likvärdiga mål. Men i praktiken har produktionen satts i första rummet. Bortåt 2 000 skogslevande arters överlevnad hotas på grund av den förda politiken. Vi är djupt oroade och skäms över att det rika Sverige inte arbetar effektivt för att nå nationella och internationella miljömål. Det skriver 14 ledande forskare i bland annat växtekologi, ekologisk zoologi och botanik.
|
|
| 26. |
|
|
| 27. |
|
|
| 28. |
- Jorde, Per Erik, et al.
(författare)
-
Are we underestimating the occurrence of sympatric populations?
- 2018
-
Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 27:20, s. 4011-4025
-
Tidskriftsartikel (refereegranskat)abstract
- Sympatric populations are conspecific populations that coexist spatially. They are of interest in evolutionary biology by representing the potential first steps of sympatric speciation and are important to identify and monitor in conservation management. Reviewing the literature pertaining to sympatric populations, we find that most cases of sympatry appear coupled to phenotypic divergence, implying ease of detection. In comparison, phenotypically cryptic, sympatric populations seem rarely documented. We explore the statistical power for detecting population mixtures from genetic marker data, using commonly applied tests for heterozygote deficiency (i.e., Wahlund effect) and the structure software, through computer simulations. We find that both tests are efficient at detecting population mixture only when genetic differentiation is high, sample size and number of genetic markers are reasonable and the sympatric populations happen to occur in similar proportions in the sample. We present an approximate expression based on these experimental factors for the lower limit of F-ST, beyond which power for structure collapses and only the heterozygote-deficiency tests retain some, although low, power. The findings suggest that cases of cryptic sympatry may have passed unnoticed in population genetic screenings using number of loci typical of the pre-genomics era. Hence, cryptic sympatric populations may be more common than hitherto thought, and we urge more attention being diverted to their detection and characterization.
|
|
| 29. |
- Jorde, Per Erik, et al.
(författare)
-
Unbiased estimator for genetic drift and effective population size
- 2007
-
Ingår i: Genetics. - : Oxford University Press (OUP). - 1943-2631. ; 177, s. 927-935
-
Tidskriftsartikel (refereegranskat)abstract
- Amounts of genetic drift and the effective size of populations can be estimated from observed temporal shifts in sample allele frequencies. Bias in this so-called temporal method has been noted in cases of small sample sizes and when allele frequencies are highly skewed. We characterize bias in commonly applied estimators under different sampling plans and propose an alternative estimator for genetic drift and effective size that weights alleles differently. Numerical evaluations of exact probability distributions and computer simulations verify that this new estimator yields unbiased estimates also when based on a modest number of alleles and loci. At the cost of a larger standard deviation, it thus eliminates the bias associated with earlier estimators. The new estimator should be particularly useful for microsatellite loci and panels of SNPs, representing a large number of alleles, many of which will occur at low frequencies.
|
|
| 30. |
- Karlsson, Sten, et al.
(författare)
-
A genetic marker for the maternal identification of Atlantic salmon x brown trout hybrids
- 2013
-
Ingår i: Conservation Genetics Resources. - : Springer Science and Business Media LLC. - 1877-7252 .- 1877-7260. ; 5:1, s. 47-49
-
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.
|
|
| 31. |
|
|
| 32. |
|
|
| 33. |
- Kurland, Sara, 1989-, et al.
(författare)
-
Effects of subpopulation extinction on effective size (Ne) of metapopulations
- 2023
-
Ingår i: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 24:4, s. 417-433
-
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.
|
|
| 34. |
- Kurland, Sara, et al.
(författare)
-
Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species
- 2019
-
Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 9, s. 11448-11463
-
Tidskriftsartikel (refereegranskat)abstract
- Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool-seq data to generate a de novo genome assembly for mining exons, upon which Pool-seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual-based single nucleotide polymorphisms [SNPs]) and from mapping the Pool-seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F-ST) between the two introduced populations exceeds that of the naturally sympatric populations (F-ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ (pi over bar approximate to 0.002 and pi over bar approximate to 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high-quality reference assembly from a divergent species. We conclude that the Pool-seq-only approach can be suitable for detecting and quantifying genome-wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.
|
|
| 35. |
- Kurland, Sara, et al.
(författare)
-
Genomic dynamics of brown trout populations released to a novel environment
- 2022
-
Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 12:7
-
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.
|
|
| 36. |
- Kurland, Sara, et al.
(författare)
-
Genomic dynamics of brown trout (Salmo trutta) populations released to a novel environment
- 2024
-
Annan publikation (övrigt vetenskapligt/konstnärligt)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 genomic effects of population translocations. In 1979, fish from each of two genetically and ecologically separate populations were released at one point in time to the same lake system. Whole-genome sequencing data is used to characterize diversity within and divergence between introduced fish from different source populations and fish inhabiting two lakes down-stream of the release sites, sampled 30 years later (c. 5 generations). Diversity and divergence among introduced populations and fish sampled in the wild c. 5 generations later suggest extensive hybridization. Introduced fish are unequally represented in the lakes down-stream of the release sites, with fish from one population mainly contributing to the lake closest to the release site, and the fish from the other dominating the lake further downstream. We also identify genomic regions putatively under directional selection in the new lake system, where genes from one of the introduced populations, regulating metabolism, appear advantageous. Our results demonstrate that genetic effects of population translocations e.g., establishment, hybridization, and adaptation can be rapid after release into novel environments – even for a species with relatively small local effective population sizes and a large, complex genome. This is an important contribution to understanding the microevolutionary effects population translocations have on intraspecific diversity.
|
|
| 37. |
- Kurland, Sara, 1989-, et al.
(författare)
-
New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data
- 2024
-
Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 33:2
-
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.
|
|
| 38. |
- Laikre, Linda, et al.
(författare)
-
Compromising genetic diversity in the wild : unmonitored large-scale release of plants and animals
- 2010
-
Ingår i: Trends in Ecology & Evolution. - : Elsevier BV. - 0169-5347 .- 1872-8383. ; 25:9, s. 520-529
-
Tidskriftsartikel (refereegranskat)abstract
- Large-scale exploitation of wild animals and plants through fishing, hunting and logging often depends on augmentation through releases of translocated or captively raised individuals. Such releases are performed worldwide in vast numbers. Augmentation can be demographically and economically beneficial but can also cause four types of adverse genetic change to wild populations: (1) loss of genetic variation, (2) loss of adaptations, (3) change of population composition, and (4) change of population structure. While adverse genetic impacts are recognized and documented in fisheries, little effort is devoted to actually monitoring them. In forestry and wildlife management, genetic risks associated with releases are largely neglected. We outline key features of programs to effectively monitor consequences of such releases on natural populations.
|
|
| 39. |
|
|
| 40. |
- Laikre, Linda, et al.
(författare)
-
Effekter av spridning av genetiskt främmande populationer : En kartläggning av förutsättningarna för uppföljande studier av utsättningar av djur och växter i Sverige
- 2008
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Förord Spridning av främmande arter utgör ett av de stora hoten mot biologisk mångfald. En viktig del i arbetet med att verkställa Förenta nationernas konvention om biologisk mångfald (Convention on Biological Diversity – CBD) är därför att öka kunskapen kring, och förhindra fortsatt spridning av, sådana arter. Begreppet ”art” har en vid definition inom konventionsarbetet – även lägre taxonomiska enheter så som underarter och genetiskt särpräglade populationer omfattas. Spridning av genetiskt främmande populationer utgör alltså ett internationellt erkänt hot mot biologisk mångfald. Framför allt är det diversiteten på gennivå som kan drabbas negativt av sådan spridning. Vetenskapliga rådet för biologisk mångfald utses av Sveriges regering och ska bistå regeringen med råd i samband med internationellt och nationellt arbete med frågor som rör biologisk mångfald. Rådet har länge påtalat vikten av att öka kunskapen kring den genetiska nivån av biologisk mångfald och inte minst effekterna på denna mångfald av storskaliga utsättningar av genetiskt främmande populationer. Sådana utsättningar är vanliga inom skogsbruket, fiskevården och viltvården. Från min egen mångåriga erfarenhet av fiskevårdsfrågor har jag praktisk erfarenhet av att introduktion och spridning av främmande arter och populationer kan få högst påtagliga negativa konsekvenser.Vetenskapliga rådet för biologisk mångfald har i samband med konventionens tillämpning tagit upp frågor med koppling till den genetiska variationens betydelse – särskilt de vetenskapliga aspekterna kring detta. Rådet har också arrangerat en workshop som för första gången samlade experter och intressenter från de tre områden inom vilka storskaliga utsättningar bedrivs (skogsbruket, fisk- och viltvården). De intressanta och givande diskussionerna finns refererade i Rapport 5683 i Naturvårdsverkets serie. I den nu föreliggande rapporten fortsätter kartläggningen av vad vi egentligen vet om de storskaliga utsättningarna i Sverige och vilka effekter de har på biologisk mångfald. Ett gediget arbete har gjorts för att försöka bringa reda i detta område där dokumentation till stora delar saknas. Bristen på registrering och uppföljning av dessa stora spridningar, som riskerar att förändra den genetiska sammansättning som under årtusenden mejslats fram hos våra vilda fisk-, träd- och fågelpopulationer, är skrämmande. Här behövs en snabb och påtaglig förändring. Vetenskapliga rådet för biologisk mångfald kommer att fortsätta ägna denna fråga stor uppmärksamhet. Det är angeläget att Sverige bedriver ett starkt och engagerat arbete som ligger i internationell framkant när det gäller att slå vakt om den grundläggande, och för fortsatt evolution nödvändiga, mångfalden på gennivå. Stockholm den 10 september 2008 Per Wramner Professor i tillämpad miljövetenskap Ordförande för Vetenskapliga rådet för biologisk mångfald Förord 2 Utsättning av främmande populationer eller provenienser av växter och djur sker i stor skala i svenska marker och vattendrag. Spridningen av främmande populationer har stora ekonomiska värden men vi vet väldigt lite om vilka effekter den har på biologisk mångfald. Etablering av främmande genotyper kan leda till förlust och förändringar av, i första hand, mångfalden på gennivå hos mottagande naturliga populationer. I förlängningen kan sådana effekter även drabba art- och ekosystemnivåerna negativt. Det är mycket angeläget att öka kunskaperna inom detta område. Regeringen har uppdragit åt naturvårdsverket att ta fram en nationell strategi och handlingsplan för främmande arter och genotyper. Denna rapport utgör ett underlag i detta arbete. Uppdraget gavs med anledning av uppföljningen av miljökvalitetsmålen och implementering av artikel 8 h i Konventionen om biologisk mångfald som särskilt berör främmande arter och populationer och deras effekter på biologisk mångfalden. Rapporten utgör en uppföljning av den första kartläggningen av spridning av genetiskt främmande populationer inom fiske- och viltvården samt skogsbruk i Sverige som genomfördes under 2004–2005. Syftet med rapporten är en fördjupad granskning av den information som är möjlig att få fram när det gäller spridningen av främmande populationer eller genotyper i Sverige, samt i vilken utsträckning effekterna av sådana utsättningar kan kartläggas. Författarna är ensamma ansvariga för rapportens innehåll.Stockholm den 7 oktober 2008Naturvårdsverket
|
|
| 41. |
- Laikre, Linda, et al.
(författare)
-
Hunting Effects on Favourable Conservation Status of Highly Inbred Swedish Wolves
- 2013
-
Ingår i: Conservation Biology. - : Wiley. - 0888-8892 .- 1523-1739. ; 27:2, s. 248-253
-
Tidskriftsartikel (refereegranskat)abstract
- The wolf (Canis lupus) is classified as endangered in Sweden by the Swedish Species Information Centre, which is the official authority for threat classification. The present population, which was founded in the early 1980s, descends from 5 individuals. It is isolated and highly inbred, and on average individuals are more related than siblings. Hunts have been used by Swedish authorities during 2010 and 2011 to reduce the population size to its upper tolerable level of 210 wolves. European Union (EU) biodiversity legislation requires all member states to promote a concept called “favourable conservation status” (FCS) for a series of species including the wolf. Swedish national policy stipulates maintenance of viable populations with sufficient levels of genetic variation of all naturally occurring species. Hunting to reduce wolf numbers in Sweden is currently not in line with national and EU policy agreements and will make genetically based FCS criteria less achievable for this species. We suggest that to reach FCS for the wolf in Sweden the following criteria need to be met: (1) a well-connected, large, subdivided wolf population over Scandinavia, Finland, and the Russian Karelia-Kola region should be reestablished, (2) genetically effective size (Ne) of this population is in the minimum range of Ne = 500–1000, (3) Sweden harbors a part of this total population that substantially contributes to the total Ne and that is large enough to not be classified as threatened genetically or according to IUCN criteria, and (4) average inbreeding levels in the Swedish population are <0.1.
|
|
| 42. |
- Laikre, Linda, et al.
(författare)
-
Importance of Genetics in the Interpretation of Favourable Conservation Status
- 2009
-
Ingår i: Conservation Biology. - : Wiley. - 0888-8892 .- 1523-1739. ; 23, s. 1378-1381
-
Tidskriftsartikel (refereegranskat)abstract
- “Favourable Conservation Status” (FCS) is a central concept in the biodiversity conservation legislation of the European Union (EU). Here, we highlight the importance of incorporating aspects of conservation genetics in interpretation of this concept. Recent documents from the EU Commission indicate that knowledge of conservation genetics has so far been lacking among those who have tried to employ the concept. We think it is crucial that aspects of conservation genetics be incorporated in discussion of this concept and that this be done before the EU Court of Justice takes a position on the legal interpretation of FCS.
|
|
| 43. |
- Laikre, Linda, et al.
(författare)
-
Metapopulation effective size and conservation genetic goals for the Fennoscandian wolf (Canis lupus) population
- 2016
-
Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 117:4, s. 279-289
-
Tidskriftsartikel (refereegranskat)abstract
- The Scandinavian wolf population descends from only five individuals, is isolated, highly inbred and exhibits inbreeding depression. To meet international conservation goals, suggestions include managing subdivided wolf populations over Fennoscandia as a metapopulation; a genetically effective population size of N-e >= 500, in line with the widely accepted long-term genetic viability target, might be attainable with gene flow among subpopulations of Scandinavia, Finland and Russian parts of Fennoscandia. Analytical means for modeling N-e of subdivided populations under such non-idealized situations have been missing, but we recently developed new mathematical methods for exploring inbreeding dynamics and effective population size of complex metapopulations. We apply this theory to the Fennoscandian wolves using empirical estimates of demographic parameters. We suggest that the long-term conservation genetic target for metapopulations should imply that inbreeding rates in the total system and in the separate subpopulations should not exceed Delta f = 0.001. This implies a meta-Ne of N-eMeta >= 500 and a realized effective size of each subpopulation of N-eRx >= 500. With current local effective population sizes and one migrant per generation, as recommended by management guidelines, the meta-Ne that can be reached is similar to 250. Unidirectional gene flow from Finland to Scandinavia reduces meta-N-e to similar to 130. Our results indicate that both local subpopulation effective sizes and migration among subpopulations must increase substantially from current levels to meet the conservation target. Alternatively, immigration from a large (N-e >= 500) population in northwestern Russia could support the Fennoscandian metapopulation, but immigration must be substantial (5-10 effective immigrants per generation) and migration among Fennoscandian subpopulations must nevertheless increase.
|
|
| 44. |
|
|
| 45. |
- Laikre, Linda, 1960-, et al.
(författare)
-
Planned cull endangers Swedish wolf population
- 2022
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 377:6602
-
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).
|
|
| 46. |
- Laikre, Linda, et al.
(författare)
-
Potentials for monitoring gene level biodiversity : using Sweden as an example
- 2008
-
Ingår i: Biodiversity and Conservation. - : Springer Science and Business Media LLC. - 0960-3115 .- 1572-9710. ; 17:4, s. 893-910
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
| 47. |
- Laikre, Linda, et al.
(författare)
-
Release of alien populations in Sweden
- 2006
-
Ingår i: Ambio. - 0044-7447 .- 1654-7209. ; 35:5, s. 255-261
-
Tidskriftsartikel (refereegranskat)abstract
- Introduction of alien species is a major threat to biological diversity. Although public attention typically focuses on the species level, guidelines from the Convention of Biological Diversity define alien species to include entities below species level. This inclusion recognizes that release of nonlocal populations of native species may also result in negative effects on biodiversity. In practice, little is known about the extent, degree of establishment, or the effects on natural gene pools of such releases. Existing information on the releases in Sweden shows that alien populations are spread to a great extent. The most commonly released species include brown trout, Atlantic salmon, Arctic char, common whitefish, Scots pine, Norway spruce, mallard duck, gray partridge, and pheasant. Although millions of forest trees, fish, and birds are released annually, poor documentation makes the geographic and genetic origin of these populations, as well as the sites where they have been released, largely unclear. We provide recommendations for urgently needed first steps relating to the risks and problems associated with release of alien populations.
|
|
| 48. |
- Laikre, Linda, et al.
(författare)
-
Spatial genetic structure of northern pike (Esox lucius) in the Baltic Sea
- 2005
-
Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 14:7, s. 1955-1964
-
Tidskriftsartikel (refereegranskat)abstract
- The genetic relationships among 337 northern pike (Esox lucius) collected from the coastal zone of the central Baltic region and the Finnish islands of Åland were analysed using five microsatellite loci. Spatial structure was delineated using both traditional F-statistics and individually based approaches including spatial autocorrelation analysis. Our results indicate that the observed genotypic distribution is incompatible with that of a single, panmictic population. Isolation by distance appears important for shaping the genetic structure of pike in this region resulting in a largely continuous genetic change over the study area. Spatial autocorrelation analysis (Moran’s I) of individual pairwise genotypic data show significant positive genetic correlation among pike collected within geographical distances of less than c. 100–150 km (genetic patch size). We suggest that the genetic patch size may be used as a preliminary basis for identifying management units for pike in the Baltic Sea.
|
|
| 49. |
- Lamichhaney, Sangeet, 1984-, et al.
(författare)
-
Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean
- 2017
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 114:17, s. E3452-E3461
-
Tidskriftsartikel (refereegranskat)abstract
- Atlantic herring is an excellent species for studying the genetic basis of adaptation in geographically distant populations because of its characteristically large population sizes and low genetic drift. In this study we compared whole-genome resequencing data of Atlantic herring populations from both sides of the Atlantic Ocean. An important finding was the very low degree of genetic differentiation among geographically distant populations (fixation index = 0.026), suggesting lack of reproductive isolation across the ocean. This feature of the Atlantic herring facilitates the detection of genetic factors affecting adaptation because of the sharp contrast between loci showing genetic differentiation resulting from natural selection and the low background noise resulting from genetic drift. We show that genetic factors associated with timing of reproduction are shared between genetically distinct and geographically distant populations. The genes for thyroid-stimulating hormone receptor (TSHR), the SOX11 transcription factor (SOX11), calmodulin (CALM), and estrogen receptor 2 (ESR2A), all with a significant role in reproductive biology, were among the loci that showed the most consistent association with spawning time throughout the species range. In fact, the same two SNPs located at the 5' end of TSHR showed the most significant association with spawning time in both the east and west Atlantic. We also identified unexpected haplotype sharing between spring-spawning oceanic herring and autumn-spawning populations across the Atlantic Ocean and the Baltic Sea. The genomic regions showing this pattern are unlikely to control spawning time but may be involved in adaptation to ecological factor(s) shared among these populations.
|
|
| 50. |
- Lamichhaney, Sangeet, et al.
(författare)
-
Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring
- 2012
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 109:47, s. 19345-19350
-
Tidskriftsartikel (refereegranskat)abstract
- The Atlantic herring (Clupea harengus), one of the most abundant marine fishes in the world, has historically been a critical food source in Northern Europe. It is one of the few marine species that can reproduce throughout the brackish salinity gradient of the Baltic Sea. Previous studies based on few genetic markers have revealed a conspicuous lack of genetic differentiation between geographic regions, consistent with huge population sizes and minute genetic drift. Here, we present a cost-effective genome-wide study in a species that lacks a genome sequence. We first assembled amuscle transcriptome and then aligned genomic reads to the transcripts, creating an "exome assembly," capturing both exons and flanking sequences. We then resequenced pools of fish from a wide geographic range, including the Northeast Atlantic, as well as different regions in the Baltic Sea, aligned the reads to the exome assembly, and identified 440,817 SNPs. The great majority of SNPs showed no appreciable differences in allele frequency among populations; however, several thousand SNPs showed striking differences, some approaching fixation for different alleles. The contrast between low genetic differentiation at most loci and striking differences at others implies that the latter category primarily reflects natural selection. A simulation study confirmed that the distribution of the fixation index F-ST deviated significantly from expectation for selectively neutral loci. This study provides insights concerning the population structure of an important marine fish and establishes the Atlantic herring as a model for population genetic studies of adaptation and natural selection.
|
|
