| 1. |
- Andersson, Anastasia, et al.
(författare)
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Complex genetic diversity patterns of cryptic, sympatric brown trout (Salmo trutta) populations in tiny mountain lakes
- 2017
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Ingår i: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 18:5, s. 1213-1227
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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.
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| 2. |
- Andersson, Anastasia, 1987-
(författare)
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Hidden biodiversity in an alpine freshwater top predator : Existence, characteristics, and temporal dynamics of cryptic, sympatric brown trout populations
- 2021
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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).
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| 3. |
- Andersson, Anastasia, et al.
(författare)
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Lack of trophic polymorphism despite substantial genetic differentiation in sympatric brown trout (Salmo trutta) populations
- 2017
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Ingår i: Ecology of Freshwater Fish. - : Wiley. - 0906-6691 .- 1600-0633. ; 26:4, s. 643-652
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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.
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| 4. |
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| 5. |
- 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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| 6. |
- André, Carl, 1958, et al.
(författare)
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Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus) : direct, simultaneous evaluation of neutral vs putatively selected loci
- 2011
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Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 106:2, s. 270-280
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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.
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| 7. |
- Charlier, Johan, et al.
(författare)
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Census (NC) and genetically effective (Ne) population size in a lake-resident population of brown trout Salmo trutta
- 2011
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Ingår i: Journal of Fish Biology. - : Wiley. - 0022-1112 .- 1095-8649. ; 79:7, s. 2074-2082
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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
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| 8. |
- Charlier, Johan, et al.
(författare)
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Genetic monitoring reveals temporal stability over 30 years in a small, lake-resident brown trout population
- 2012
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Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 109:4, s. 246-253
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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.
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| 9. |
- Charlier, Johan, et al.
(författare)
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Genetic structure and evidence of a local bottleneck in moose in Sweden
- 2008
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Ingår i: Journal of Wildlife Management. - : Wiley. - 0022-541X .- 1937-2817. ; 72:2, s. 411-415
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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.
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| 10. |
- Charlier, Johan, 1977-
(författare)
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Monitoring gene level biodiversity - aspects and considerations in the context of conservation
- 2011
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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.
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