| 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. |
- Andersson, Anastasia, et al.
(författare)
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Two shades of boldness : novel object and anti-predator behavior reflect different personality dimensions in domestic rabbits
- 2014
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Ingår i: Journal of ethology. - : Springer Science and Business Media LLC. - 0289-0771 .- 1439-5444. ; 32:3, s. 123-136
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Tidskriftsartikel (refereegranskat)abstract
- It is increasingly common to quantify and describe behavioral variation in domestic and wild animals in terms of personality. Correlating behavioral traits are referred to as personality dimensions or factors and different dimensions have been reported in different species. Boldness is a well-described personality dimension in several species, although some issues remain unclear. Previous models of boldness include both novelty and risk taking, but recent studies indicate that these types of behaviors may reflect separate personality dimensions. In this study, we developed a behavioral test battery for domestic rabbits, and recorded behaviors of 61 individuals in four different situations (novel object, novel arena, social, and predator interactions). We used domestic rabbits as a model because behavioral variation in rabbits has rarely been quantified in terms of personality dimensions, although rabbit behavior is described. We also wanted to investigate behavioral variation in a Swedish rabbit breed of conservation concern - the Gotland rabbit. Factor analysis of the behavioral test measures suggested three personality dimensions: exploration, boldness, and anxiety. Novel object scores clustered in the exploration and boldness factors, whereas scores associated with predator interactions were explained by anxiety, indicating that novel object and anti-predator behavior reflect different personality dimensions in rabbits.
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| 7. |
- Jorde, Per Erik, et al.
(författare)
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Are we underestimating the occurrence of sympatric populations?
- 2018
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 27:20, s. 4011-4025
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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.
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| 8. |
- Kurland, Sara, et al.
(författare)
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Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species
- 2019
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 9, s. 11448-11463
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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.
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| 9. |
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| 10. |
- Saha, Atal, et al.
(författare)
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Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes
- 2022
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 31:2, s. 498-511
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Tidskriftsartikel (refereegranskat)abstract
- The sympatric existence of genetically distinguishable populations of the same species remains a puzzle in ecology. Coexisting salmonid fish populations are known from over 100 freshwater lakes. Most studies of sympatric populations have used limited numbers of genetic markers making it unclear if genetic divergence involves certain parts of the genome. We returned to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (coding for lactate dehydrogenase A) in brown trout in the small Lakes Bunnersjöarna, Sweden. First, we verified the existence of the two coexisting demes using a 96-SNP fluidigm array. We then applied whole-genome resequencing of pooled DNA to explore genome-wide diversity within and between these demes; nucleotide diversity was higher in deme I than in deme II. Strong genetic divergence is observed with genome-wide FST ≈ 0.2. Compared with data from populations of similar small lakes, this divergence is of similar magnitude as that between reproductively isolated populations. Individual whole-genome resequencing of two individuals per deme suggests higher inbreeding in deme II versus deme I, indicating different degree of isolation. We located two gene-copies for LDH-A and found divergence between demes in a regulatory section of one of these genes. However, we did not find a perfect fit between the sequence data and previous allozyme results, and this will require further research. Our data demonstrates genome-wide divergence governed mostly by genetic drift but also by diversifying selection in coexisting populations. This type of hidden biodiversity needs consideration in conservation management.
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