| 1. |
- Andersson, Anastasia, 1987-
(author)
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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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Doctoral thesis (other academic/artistic)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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| 2. |
- Charlier, Johan, 1977-
(author)
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Monitoring gene level biodiversity - aspects and considerations in the context of conservation
- 2011
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Doctoral thesis (other academic/artistic)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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| 3. |
- Gilchrist, Ciaran
(author)
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Hopeful monsters: The role of hybrids in adaptation : The impact of hybridisation and genetic diversity on adaptation to stressful and novel environments
- 2022
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Doctoral thesis (other academic/artistic)abstract
- Adaptation to novel environments can only occur if natural selection has the raw material to act upon. But small, endangered populations are often genetically depleted, and the acquisition of beneficial de novo mutations often takes too long when population face quick and extreme environmental change. An alternative source for new variation is hybridisation and the genomic reshuffling and structural chromosomal changes accompanying it. In this thesis, I use yeast, experimental evolution, and comparative genomics to investigate the impact of different sources of genetic variation in adaptation to stressful environments - standing genetic variation, de novo mutations, and hybridisation.In Chapter I, I investigate the role of aneuploidy in the adaptation of microbial eukaryotes and the genetic mechanisms causing erroneous chromosome segregation, using a meta-analysis. I found that smaller chromosomes are more often aneuploid and that the frequency of segregation errors during cell division is higher in genomes with higher initial ploidy. I also propose that the co-occurrence of hybridisation and aneuploidy may provide an adaptive advantage in stressful environments.Traditionally, microbial experimental evolution studies start with clonal populations, relying on adaptation from de novo mutations alone. In the wild, this is an unlikely scenario. In Chapter II, I evolved genetically diverse founder populations for up to 1000 generations in 4 distinct environments and tracked adaptation dynamics at the phenotypic and genomic level. Almost all populations rapidly increased in fitness but the underlying allele frequency changes were surprisingly diverse and environment-specific. While in some populations all ancestral variation went to fixation in < 30 generations, others maintained genetic diversity across hundreds of generations. I found stunning parallelism of de novo mutations at the gene and pathway level and detected potentially adaptive aneuploidies.Hybridisation drastically boosts the genetic diversity of populations, which can allow for transgressive hybrids (hopeful monsters) with selective advantages in novel environments. In Chapter III, I made hybrid crosses at increasing parental divergence (using divergently evolved populations from Chapter II) and measured how much heterosis and transgressive segregation occurred in F1 and F2 hybrids when exposing them to 50 new, stressful environments. I found that both heterosis and transgression increased as a function of parental divergence, confirming predictions of quantitative genetics theory. Some hybrids were even able to survive in arsenic concentrations lethal for both parents.Anthropogenic climate change drives up rates of hybridisation between natural populations, yet the potential benefits and risks of hybridisation for the long-term conservation of populations are often unknown. In Chapter IV, I compared the survivability of hybrid populations to their parents under deteriorating environmental conditions. I found that hybrids avoided extinction for a significantly longer time than their parents, at all levels of parental divergence. The more divergent the parents the more similar were the responses of replicate crosses, likely due to the erosion of standing genetic variation in the parental populations.In summary, my thesis provides a better understanding of the impact of different sources of genetic diversity in determining a population’s capacity to adapt to environmental change.
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| 4. |
- Jansson, Mija, 1979-
(author)
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Assessing inbreeding and loss of genetic variation in canids, domestic dog (Canis familiaris) and wolf (Canis lupus), using pedigree data
- 2014
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Doctoral thesis (other academic/artistic)abstract
- Genetic variation is necessary to maintain the ability of wild and domestic populations to genetically adapt to changed selective pressures. When relationships among individuals are known, conservation genetic management can be based on statistical pedigree analysis. Such approaches have traditionally focused on wild animal conservation breeding in captivity. In this thesis, I apply pedigree-based techniques to domestic and wild animal populations, focusing on two canids – the domestic dog and the wild wolf.Main objectives include to 1) develop a means for making any pedigree fit the input requirements of the software Population Management x (PMx) and to use this program to 2) investigate rate of inbreeding and loss of genetic variation in dog breeds, including possible correlations between recent inbreeding and health problems, 3) estimate effects on inbreeding of the 2010 hunt of the endangered Swedish wolf population, and to 4) evaluate the potential to genetically support this wolf population through cross-fostering releases of zoo bred pups from a conservation breeding program.Results include successfully developing the converter program mPed (Paper I) and applying both mPed and PMx to dog and wolf pedigrees. I found extensive loss of genetic variation and moderate rates of recent inbreeding in 26 dog breeds, but no major difference in these parameters between breeds classified as “healthy” vs. “unhealthy“ (Paper II). I found average inbreeding coefficients to more than double (from F=0.03 to 0.07) and founder genetic variation to decrease by c. 30 percent over the past few decades in traditional Swedish dog breeds identified as being of conservation concern (Paper IV). Hunting will make it less likely to reach genetically based Favourable Conservation Status criteria for the Swedish wild wolf population (Paper III), but release of zoo bred wolves through cross-fostering may potentially almost double founder genetic variation of this population (Paper V).
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| 5. |
- Kurland, Sara, 1989-
(author)
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Genomic dynamics over contemporary time frames in wild salmonid populations
- 2022
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Doctoral thesis (other academic/artistic)abstract
- Genetic diversity is the foundation of all biological variation. An approach for sustainable use and protection of genetic diversity is continuous sampling over space and time, i.e. monitoring. It is important to consider genetic changes over contemporary time frames, since most human perturbations have occurred within the last century. Modern molecular tools now enable genome-wide diversity monitoring, also in non-model species.The work included in this thesis utilizes theoretical and molecular tools to monitor genomic diversity over microevolutionary time frames using salmonid fishes as models. First, the capacity for substructured populations to retain genetic variation following population extinctions was theoretically assessed. Models of effective population size (Ne) relevant to salmonids were used. Further, spatio-temporal genetic patterns of the highly substructured brown trout (Salmo trutta) were empirically estimated. Wild populations were studied using whole-genome sequencing, primarily of pools of individuals (Pool-seq). The brown trout is characterized by a large and complex genome, and genomic resources have, until recently, been lacking. One central aim of this thesis was therefore to evaluate the benefit of using Pool-seq data for monitoring genetic diversity in this species. To this end, disparate natural populations were studied that are, in part, previously described using classic genetic markers. First, I hypothesized that a Pool-seq-only approach developed for non-model species that lack reference genomes could be used to detect population differentiation between two scenarios of coexisting populations. In a second step, two different cases of populations in the wild – one experimental release and one case of protected populations – were monitored over nearly four decades (5-6 brown trout generations) using Pool-seq data. I asked what the levels of diversity and divergence among populations are, whether changes could be detected over contemporary time and if they could be attributed to adaptation.Paper I demonstrates that the effect of extinction on the rate of diversity change in population systems is more complex than previously recognized. Diversity loss is most prominent when migration within the population system is limited, which suggests that highly substructured population systems, e.g., many salmonids, are particularly vulnerable to population extinction. The utility of Pool-seq for monitoring brown trout populations over contemporary time is demonstrated for the three different cases of brown trout populations (Papers II-IV). Paper II confirms the ability of a Pool-seq-only approach to detect subtle population differentiation. Paper III identifies genome-wide levels of hybridization between populations introduced to a new environment and signs of adaptation in genes putatively involved in metabolism. Paper IV detects significant allele frequency shifts over a limited number of generations. Potentially adaptive change is also identified, with regions containing genes possibly associated to immunity, skin pigmentation, and reproduction (Paper IV).This thesis demonstrates the benefit of modern theoretical and molecular tools for monitoring diversity in highly substructured population systems. These tools are relevant for advancing population genetic knowledge, as well as for sustainable management and conservation of a wide range of species.
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| 6. |
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| 7. |
- Larsson, Lena C., 1965-
(author)
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Disentangling small genetic differences in large Atlantic herring populations: comparing genetic markers and statistical power
- 2008
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Doctoral thesis (other academic/artistic)abstract
- Genes are the foundation of evolution and biodiversity. The genetic structure of natural populations needs to be understood to maintain exploited resources rationally. This thesis focuses on genetic variability and methods to determine spatial and temporal genetic heterogeneities. Intense human exploitation generates particular challenges to conserve genetic diversity of fishes since it has genetic effects. My research concerns one of our most valuable fish species: the Atlantic herring (Clupea harengus).I analyzed Atlantic herring samples from the North and Baltic Seas. The objectives were to determine: 1) spatial genetic structure, 2) whether allozymes and microsatellites provide similar descriptions of the differentiation pattern, or 3) if they are influenced by selection, 4) factors affecting statistical power when testing for genetic differentiation, and 5) the temporal stability of the genetic structure.The results show: 1) very low levels of spatial genetic differentiation in Atlantic herring; a major component is a difference between the Baltic and North Seas, 2) a concordant pattern with allozymes and microsatellites, 3) that selection influences a microsatellite locus, which can be a low salinity adaptation, 4) that statistical power is substantial for frequently used sample sizes and markers; the difference in power between organelle and nuclear loci is partly dependent on the populations’ stage of divergence, and 5) no changes in amount of genetic variation or spatial genetic structure over a 24-year period; the selection pattern in one microsatellite locus remained.The notion that the large population sizes make herring unlikely to lose genetic diversity may be disputed. I found small local effective population sizes, and the evidence of selection hints of a distinct evolutionary lineage in the Baltic. When Atlantic herring is managed as very large units, there can be detrimental genetic effects if certain population segments are excessively harvested.
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| 8. |
- Palmé, Anna, 1975-
(author)
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Assessing and monitoring genetic patterns for conservation purposes with special emphasis on Scandinavia
- 2010
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Doctoral thesis (other academic/artistic)abstract
- Genetic variation is essential for biological evolution, for maintaining viability of populations, and to ensure ecosystem resilience. Increased human exploitation and environmental change result in rapid loss of biological variation, including genetic diversity. Measures to halt this trend require that biological diversity is assessed and monitored. Assessment of biodiversity includes identifying patterns of distribution of genetic variation within individual species. This thesis focuses on spatial genetic structure and assessment of units for conservation in continuous environments without apparent migration barriers. Empirical data refer to Scandinavia and the model species are northern pike (Esox lucius), brown trout (Salmo trutta), and harbour porpoise (Phocoena phocoena). Questions regarding monitoring genetic diversity and releases of alien populations are also addressed. The spatial genetic structure of the northern pike in the Baltic Sea is characterized by isolation by distance and continuous genetic change. Positive genetic correlation was found among pike within geographical distances of less than 150 km. This distance may be used to suggest management units in this area. For the brown trout, genetic monitoring identified two sympatric populations within a small mountain lake system. The situation is characterized by a clear genetic but no apparent phenotypic dichotomy. Scientific support for a genetically distinct Baltic harbour porpoise population is limited, and the spatial genetic structure of the harbour porpoise in Swedish waters needs to be clarified. Data for launching conservation genetic monitoring programs is available for only a few Swedish species. Millions of forest trees, fish, and birds are released annually in Sweden and the documentation on these releases is poor. To meet responsibilities of safeguarding biodiversity and surveying biological effects of releases, there is an urgent need for studies aimed at evaluating genetic diversity.
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| 9. |
- Wennerström, Lovisa, 1983-
(author)
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Population genetic patterns in continuous environments in relation to conservation management
- 2016
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Doctoral thesis (other academic/artistic)abstract
- Genetic variation is a prerequisite for the viability and evolution of species. Information on population genetic patterns on spatial and temporal scales is therefore important for effective management and for protection of biodiversity. However, incorporation of genetics into management has been difficult, even though the need has been stressed for decades. In this thesis population genetic patterns in continuous environments are described, compared among species, and related to conservation management. The model systems are moose (Alces alces) in Sweden and multiple species in the Baltic Sea, with particular focus on the Northern pike (Esox lucius). The spatial scope of the studies is large, and much focus is dedicated towards comprehensive sampling over large geographic areas. The moose population in Sweden is shown to be divided into two major subpopulations, a northern and a southern one. Both subpopulations show genetic signals of major population bottlenecks, which coincide with known population reductions due to high hunting pressure (Paper I). The Northern pike in the Baltic Sea shows relatively weak, but temporally stable population genetic structure. An isolation by distance pattern suggests that gene flow primarily takes place among neighboring populations, either over shortest waterway distance or along the mainland coast, with island populations acting as stepping stones (Paper III). In a comparative study of seven Baltic Sea species no shared genetic patterns were found, either in terms of genetic divergence among or genetic diversity within geographic regions. These results complicate the incorporation of genetic data into management, because it suggests that no generalization can be made among species in the Baltic Sea, but that species-specific management is needed (Paper II). Over the last 50 years, 61 species in the Baltic Sea have been studied with respect to spatial genetic patterns. For over 20 of these species information of direct relevance for management is available. Relevant information is synthesized into management recommendations (Paper IV). This thesis provides vital information on spatial and temporal genetic structure for a number of ecologically and socio-economically important species. It shows that such information is important to consider species by species and that both local and metapopulation approaches are needed to effectively manage genetic diversity in e.g. moose and pike. Further, it identifies for which organisms in the Baltic Sea genetic information exists, how it can be used, and where important information is lacking. In order to successfully make use of genetic data in management, effective communication channels between academia and policy-makers are needed.
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