| 1. |
- Wang, Baosheng, 1983-
(författare)
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Hybridization and Evolution in the Genus Pinus
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Gene flow and hybridization are pervasive in nature, and can lead to different evolutionary outcomes. They can either accelerate divergence and promote speciation or reverse differentiation. The process of divergence and speciation are strongly influenced by both neutral and selective forces. Disentangling the interplay between these processes in natural systems is important for understanding the general importance of interspecific gene flow in generating novel biodiversity in plants. This thesis first examines the importance of introgressive hybridization in the evolution of the genus Pinus as a whole, and then focusing on specific pine species, investigates the role of geographical, environmental and demographical factors in driving divergence and adaptation.By examining the distribution of cytoplasmic DNA variation across the wide biogeographic range of the genus Pinus, I revealed historical introgression and mtDNA capture events in several groups of different pine species. This finding suggests that introgressive hybridization was common during past species’ range contractions and expansions and thus has played an important role in the evolution of the genus. To understand the cause and process of hybrid speciation, I focused on the significant case of hybrid speciation in Pinus densata. I established the hybridization, colonization and differentiation processes that defined the origin of this species. I found P. densata originated via multiple hybridization events in the late Miocene. The direction and intensity of introgression with two parental species varied among geographic regions of this species. During the colonization on Tibetan Plateau from the ancestral hybrid zone, consecutive bottlenecks and surfing of rare alleles caused a significant reduction in genetic diversity and strong population differentiation. Divergence within P. densata started from the late Pliocene onwards, induced by regional topographic changes and Pleistocene glaciations. To address the role of neutral and selective forces on genetic divergence, I examined the association of ecological and geographical distance with genetic distance in Pinus yunnanensis populations. I found both neutral and selective forces have contributed to population structure and differentiation in P. yunnanensis, but their relative contributions varied across the complex landscape. Finally, I evaluated genetic diversity in the Vietnamese endemic Pinus krempfii. I found extremely low genetic diversity in this species, which is explained by a small ancestral population, short-term population expansion and recent population decline and habitat fragmentation.These findings highlight the role of hybridization in generating novel genetic diversity and the different mechanisms driving divergence and adaptation in the genus Pinus.
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| 2. |
- Wang, Xi, 1990-
(författare)
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The roles of demography and natural selection in shaping genome-wide variation of Norway spruce
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Understanding the relative contribution of genetic drift, natural selection, and mutation to genetic variation, and quantifying adaptive evolution and the effects of natural selection in species are enduring goals of evolutionary genetics. Norway spruce (Picea abies) is one of the most important conifer species that dominates from both an ecological and economical point of view in many boreal ecosystems. Recently published reference genome of Norway spruce makes it possible to perform population genomic studies to understand the basis of genetic variation and evolutionary effects of natural selection in P. abies by using next-generation sequencing (NGS) data. We create an ultra-dense genetic linkage map for Norway spruce using sequence capture data. The consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups (LGs). We also demonstrate, however, that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors. By performing population genetic analyses using the genomic regions anchored to LGs, our genetic linkage map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.In order to understand how different evolutionary forces have shaped patterns of nucleotide diversity in Norway spruce, we perform population genomic analyses using whole-genome resequencing data. We find that genetic diversity is low across a number of populations in spite of a very wide geographic distribution of P. abies. The demographic history of several reoccurring bottlenecks with concomitant decreases in effective population size, the recurrent natural selection (both purifying and positive selection), and the low overall mutation rates seen in conifers, together make contribute to the loss of genome-wide nucleotide diversity in Norway spruce.We quantify adaptive evolution and the effects of natural selection across the Norway spruce whole genome. The results show that negative selection is very limited in coding regions, while positive selection is rare in coding regions but very strong in non-coding regions, suggesting the great importance of regulatory changes in evolutionary history of P. abies. We further find a positive correlation between adaptive rate with recombination rate and a negative correlation between adaptive rate and gene density, suggesting a widespread influence from Hill-Robertson interference to efficiency of protein adaptation in P. abies. The distinct population statistics between genomic regions under either positive or balancing selection with that under neutral regions indicate impact from natural selection to genomic architecture of Norway spruce.
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| 3. |
- Andersson, Bea Angelica, 1992-
(författare)
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Finding fitness : empirical and theoretical explorations of inferring fitness effects from population-level SNP data
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The distribution of fitness effects (DFE) describes the likelihood that a new mutation has a specific effect on the fitness of an individual in a given population. The shape of the DFE is a result of several factors such as population size, mating system and selective environment, and can in turn influence the evolutionary potential of a species. The DFE has long been a field of intense research, but particularly since molecular methods enabled us to study of genetic variation in organisms empirically. This research has led to the development of several statistical methods that use population-level frequencies of single nucleotide polymorphisms (SNPs) to infer the DFE. However, these methods rely on assumptions about the data and the organism itself, which could potentially affect the accuracy of the inferences. In this thesis, I describe how two major factors – data quality and inbreeding – can affect the accuracy of DFE inferences. I also show how and when to (and when not to) use DFE inference methods based on SNP frequencies.All genomic datasets contain inaccuracies and some level of uncertainty. The data sets are therefore often treated to remove the gaps or less reliable information, such as genotypes with low coverage. Some data sets need heavy filtering, which could reduce the amount of data available for analysis. We show that the choice of filter method affects the size of the final data set and the accuracy of the estimated DFE.Many DFE estimation software assumes random mating within the study population. Unfortunately, this assumption induces some error when trying to estimate the DFE in inbred or selfing species. Some have assumed that this is a result of high rates of homozygosity in the data, and should only be a problem in populations with very high rates of selfing (>99%). We show that accuracy of the estimated DFE decreases already at relatively low rates of selfing (70%) and that removing homozygosity does not improve the accuracy, implying that another mechanism could be causing the error.
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| 4. |
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| 5. |
- Eklöf, Helena, 1989-
(författare)
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Genetic diversity and differentiation in natural and managed stands of Norway spruce (Picea abies)
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Being one of Sweden’s most important tree species, both as a keystone species and for the forest industry, it is important that we keep our stands of Norway spruce (Picea abies (L.) Karst.) as healthy as possible. With an unclear starting point of existing genetic diversity in natural forests we need to both evaluate what levels of natural diversity we have to begin with and how modern forestry practices might affect this. Previous studies have used relatively few markers to study this or similar situation before. We proved that both capture probes and genotyping by sequencing (GBS) show similar results in common diversity measurements and offers many SNPs, although capture probes showed slightly more diversity in the results, we choose to use PoolSeq and GBS together to examine a large number of planted and natural stands of Norwegian spruce in northern Sweden. In line with previous results on the subject we did not find any large differences between our young, planted forests and our old forests, suggesting that today’s re-planting methods have not affected the general diversity in different stands. However, we did find a difference in the variance of our summary statistics on a stand level between planted and old stands, an indicator that there is a possibility that forestry can cause long-term effects. This becomes even more important in the light of possible clonal deployment of Norway spruce. I believe that more research is needed over both larger geographical areas and with a focus on within stand variation. Using mitochondrial and chloroplast DNA to discern finer details of spatial distribution within stands and looking closer at the genotypic diversity within natural and planted stands. An effort should also be put into examine how these possible differences are affecting the rest of the ecosystem, living with and among Norway spruce.
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| 6. |
- Heuchel, Alisa, 1990-
(författare)
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Game of crops : genetic composition and adaptation of seed orchard crops
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Orchard populations are artificial and intensively managed populations of elite, best-performing trees that are established for mass production of genetically improved seeds. Seed orchards connect cycles of selection, breeding, and testing of plus-trees with the deployment of the improved seeds at the operational plantations. Long reproductive cycles and rotation age, irregular flowering of trees pose serious threats to the economic success of tree breeding and urge efficiency monitoring. This thesis describes genetic functioning of Swedish seed orchard of Scots pine and Norway spruce, diversity levels of orchard crops, their performance in the field in connection with their genetic background, and possible ways to stimulate flowering. It is especially relevant now when molecular technologies became more affordable and allow more intensive sampling and genome coverage.We detected differences between the two species in all genetic parameters and higher diversity levels in Scots pine crops. Crop diversity was at acceptable level though slightly reduced compared to reference population. We detected great variation in flowering in orchard parents, and the influence of linear deployment strategy on diversity, reproductive success, and effective number of orchard parents. Frost tolerance of a crop depended on the origin of orchard parents but up to a smaller extent than was previously expected.Seedlings orchard crops perform well in the field, and do not suffer from increased mortality while their counterparts from controlled crosses have variable performance and tend to form G-by-E interactions. Overall, selected seed sources perform better than forest seed lots, and this superiority is independent from the silvicultural methods at the between-sites level. Site preparation methods and planting positions play a larger role at each location and may enhance survival and growth. Seed weight correlates positively with height, while diameter is more affected by the planting position.Topgrafting showed varying degree of success but efficiently reduced time to flowering to 1 year after the grafting procedure. The extent of male and female flowering was dramatically different, and for satisfactory cone crops, there is a great need in the application of flowering stimulation methods.This is a first systematic attempt to analyse genetic background of mating and population structure of several crops from different orchards of the two species. It describes the success of Swedish tree breeding strategy in conserving genetic diversity, improving survival and economic traits, and provides the assessment of linear deployment strategy with the advanced molecular techniques. We emphasize the urgent need to efficiently stimulate flowering in both species for securing orchard production and balanced genetic composition.
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| 7. |
- Ninnes, Sofia, 1984-
(författare)
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Molecular analysis of lake-sediment organic matter : long-term dynamics and environmental implications in boreal lakes
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Lake sediment organic matter is material composed of residues from plants, algae, animals, fungi and bacteria. Its molecular composition is dependent on the sources as well as secondary biotic and abiotic transformations, which combined generates a highly complex matrix. Considering that organic matter plays a key role in carbon and nitrogen cycle, and its composition affects many different biogeochemical reactions, paleolimnologic studies have payed proportionately little attention to the organic matter composition compared with the other sediment fractions, even though organic matter makes up 20–60 % of the dry sediment mass in boreal and subarctic lakes. This thesis therefore primarily aims to explore and evaluate two methods; pyrolysis-gas chromatography/mass spectrometry (Pyrolysis-GC/MS) and diffuse reflectance Fourier-transform infrared spectroscopy (DRIFTS) for characterisation of bulk organic matter at the molecular level, both which have been extensively used for soils and peat and which balances the need for cost and time-effective analysis and for analytical detail.With pyrolysis-GC/MS the organic matter composition and long-term dynamics in two neighbouring boreal lakes is explored and compared with the conventional bulk carbon and nitrogen contents and their stable isotopes. Both pyrolysis data and conventional data capture the timing of organic matter compositional changes, but only pyrolysis provides detailed information on how the composition changes, which allows for a deeper understanding of the processes behind the changes. The same two lakes are also analysed with DRIFTS and with this approach information on the major organic compound groups aromatics, lignin, aliphatics, proteins and polysaccharides is extracted. In combination with the rapid analysis time and low cost, DRIFTS emerges as a very useful tool for rapid yet informative organic matter analysis. DRIFTS is then evaluated as a stand-alone tool for sediment characterisation in four mountain lakes. The four lakes all have different sediment composition and as a result of the multi-fraction information obtained with DRIFTS compositional differences can be related and explained in terms of their individual lake and landscape settings. The importance of landscape setting is further highlighted in the synthesis of the long-term dynamics of lake-water quality in seven lakes where development trajectories and responses to different types of disturbances are connected to the extent of peatlands within the lake catchments. This thesis demonstrates the advantages of two different approaches for more detailed lake sediment organic matter characterisation and advances our understanding of the molecular organic matter composition in boreal lakes over the Holocene, and how landscape setting affects both the organic matter composition and the sensitivity of lakes to disturbance.
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| 8. |
- Olajos, Fredrik, 1987-
(författare)
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Using environmental DNA to unravel aquatic ecosystem dynamics
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Human-induced climate change has led to unprecedented declines in Earth's biodiversity and significant habitat loss. Aquatic ecosystems areespecially at risk, facing pollution, overexploitation, and destruction. Consequently, monitoring biodiversity is critical. Traditional monitoring methods are often low in detection rates, time-consuming, invasive, and harmful to species, which hampers comprehensive biodiversity assessments. Environmental DNA (eDNA) offers a rapid alternative fortaxonomic identification, extracting genetic material from soil, sediments, or water without capturing living organisms, proving useful where traditional methods fall short. However, its integration into aquatic ecology is hampered by unresolved methodological issues.This thesis demonstrates how eDNA can help reconstruct fish colonization histories in lakes post-glacial retreat. I employed species-specific primers with digital droplet PCR and metagenomic shotgun sequencing on ancient DNA from Holocene lake sediments. My findings show the detectability of DNA from ancient fish populations. However, each method exhibited technical limitations that led to varying degrees offalse negatives and false positive results. Additionally, I examined how Northern pike (Esox Lucius) affects ecological speciation in Europeanwhitefish (Coregonus lavaretus), promoting a shift from insectivorous to piscivorous states, enhancing predator biodiversity and biomass. Dietan alyses of piscivorous birds through digital droplet PCR revealed that smaller whitefish support a larger, more diverse bird community. Finally, I compared two molecular techniques for quantifying bird diets from fecal DNA, finding that metabarcoding with a universal fish primer and digital droplet PCR yielded similar results. This research enhances ourunderstanding of the potential and limitations of molecular tools forspecies identification and aids the integration of eDNA into aquatic ecology.
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| 9. |
- Sullivan, Alexis R., 1988-
(författare)
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A forest dark : an evolutionary history of Norway spruce
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Embedded within the relationships among species is a dense forest of gene trees, each with a potentially unique and discordant history. Such widespread genealogical heterogeneity is expected, but embracing this hierarchy of discordance while reconstructing the histories of populations and species remains a major challenge.In this thesis, I studied the history of the genes and genomes contained within Norway spruce (Picea abies: Pinaceae), a forest tree distributed throughout boreal and montane Europe. I sequenced plastid genomes from all the commonly-recognized Picea species and developed a novel strategy to assemble the bacterial-sized mitochondrial genome of Norway spruce. Using multispecies coalescent network models, I reconstructed the relationships among populations of Norway spruce and the parapatric Siberian spruce (P. obovata) and distinguished between drift and hybridization as sources of phylogenetic discord.Norway spruce holds heterogenous histories at multiple levels of organization. Although organelle genomes are expected to be clonal and uniparentally inherited, the chloroplast genome held by Norway spruce originated after sexual recombination between two divergent lineages. In the mitochondrial genome, recombination creates a diverse population of genome arrangements subjected to drift and selection within individuals and populations. Genetic diversity among populations is shaped in nearly equal measure by divergence and hybridization. Norway spruce is discordance distilled.
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| 10. |
- Tan, Biyue, 1986-
(författare)
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Genomic selection and genome-wide association studies to dissect quantitative traits in forest trees
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The convergence of quantitative genetics of complex traits with genomic technologies is quickly becoming an innovative approach to explore fundamental genetic questions and also have practical consequences for implementations in tree breeding. In this thesis, I used genomic selection and genome-wide association studies (GWAS) to dissect the genetic basis of quantitative traits, i.e. growth, phenology and wood property traits. I also assessed the importance of dominance and epistatic effects in hybrid Eucalyptus. Both dominance and epistasis are important in hybrids, as they are the likely contributing to the genetic basis of heterosis. To successfully implement genomic selection models, several important factors have to be considered. I found that for a good model establishment, both the size and composition of the training population, as well as the number of SNPs to be important considered. Based on the optimal models, additive, dominance and epistasis genetic effects of growth and wood traits have been estimated to evaluate genetic parameters and how these influence the prediction accuracy, which can be used in selecting elite breeding individuals or clones. I also addressed the advantage of genotyping-based analyses by showing that we could accurately correct pedigree information errors. More importantly, genotyping-based analyses capture both Mendelian segregation variation within full-sib families and cryptic genetic links through unknown common ancestors, which are not available from traditional pedigree data. GWAS were used to analyse growth and phenology related traits. Using a single-trait GWAS method, we identified a region strongly associated with the timing of bud set in Populus tremula, a trait with high heritability. For the growth related traits, we found that a multi-traits GWAS approach was more powerful than single-trait analyses as it identified more associated SNPs in hybrid Eucalyptus. Moreover, many more novel associated SNPs were identified from considering over-dominance effects in the GWAS analyses. After annotating the associated SNPs I show that these functional candidate genes were related to growth and responding to abiotic and biotic stress. In summary, the results of genomic selection and GWAS provided a deeper understanding of the genetic backgrounds of quantitative traits in forest trees.
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