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- Cortés, Andrés J., 1989-
(författare)
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On The Big Challenges of a Small Shrub : Ecological Genetics of Salix herbacea L
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The response of plants to climate change is among the main questions in ecology and evolution. Faced with changing conditions, populations may respond by adapting, going extinct or migrating. Fine-scale environmental variation offers a unique mosaic to explore these alternatives. In this thesis, I used ecological surveys, field experiments and molecular methods to study the range of possible responses at a very local scale in the alpine dwarf willow Salix herbacea L. Since gene flow may impact the potential for adaptation and migration, I first explored whether phenological divergence driven by snowmelt patterns impacts gene flow. I found that sites with late snowmelt work as sinks of the genetic diversity, as compared to sites with early snowmelt. I also used a combined approach that looked at the selection, heritability and genomic architecture of ecologically-relevant traits, as well as genomic divergence across the snowmelt mosaic. In this way, I was able to understand which genomic regions may relate to phenological, growth and fitness traits, and which regions in the genome harbor genetic variation associated with late- and early- snowmelt sites. I found that most of the genomic divergence driven by snowmelt is novel and is localized in few regions. Also, Salix herbacea has a strong female bias. Sex bias may matter for adaptation to climate change because different sexes of many dioecious species differ in several functions that may fluctuate with changing conditions. I found that the bias is uniform across environments and is already present at seeds and seedlings. A polygenic sex determination system together with transmission distortion may be maintaining the bias. Overall, fast-evolving microhabitat-driven genomic divergence and, at the same time, genetically-based trait variation at a larger scale may play a role for the ability of S. herbacea to persist in diverse and variable conditions.
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| 2. |
- Liu, Xiaodong, et al.
(författare)
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Evolution of barrier loci at an intermediate stage of speciation with gene flow
- 2024
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Understanding the origin of new species is a central goal in evolutionary biology. Diverging lineages often evolve highly heterogeneous patterns of differentiation; however, the underlying mechanisms are not well understood. We used an integrated approach to investigate evolutionary processes governing genetic differentiation between the hybridizing campions (Silene dioica (L.) Clairv. and S. latifolia Poiret). Demographic modeling indicated that the two species diverged with continuous gene flow. The best-supported scenario with heterogeneity in both migration rate and effective population size suggested that 5% of the loci evolved without gene flow. Differentiation (FST) and sequence divergence (dXY) were correlated and both tended to peak in the middle of most linkage groups, consistent with reduced gene flow at highly differentiated loci. Highly differentiated loci further exhibited signatures of selection and differentiation was significantly elevated around previously identified QTLs associated with assortative mating. In between-species population pairs, isolation by distance was stronger for genomic regions with low between-species differentiation than for highly differentiated regions that may contain barrier loci. Moreover, differentiation landscapes within and between species were only weakly correlated suggesting that the interplay of background selection and conserved genomic features is not the dominant determinant of genetic differentiation in these lineages. Instead, our results suggest that divergent selection drove the evolution of barrier loci played and the genomic landscape of differentiation between the two species, consistent with predictions for speciation in the face of gene flow.
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| 3. |
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| 4. |
- Liu, Xiaodong
(författare)
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Mechanisms of speciation in Silene
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- A fundamental question in the field of evolutionary biology is how new species originate. Investigating speciation benefits from an integrated approach, which requires a solid understanding of ecology, reproductive biology, geographical distribution, underlying genetic architecture of reproductive isolation (RI), demographic history and genomic divergence. In this thesis, I studied the evolution of reproductive isolation in the sister species Silene dioica (L.) Clairv. and S. latifolia Poiret. The aims of the thesis are to investigate (1) the individual and cumulative contributions of extrinsic and intrinsic reproductive barriers between S. dioica and S. latifolia, (2) the genetic architecture of traits associated with reproductive barriers (3) the demographic history of lineage-split between the two species, (4) genomic patterns of divergence between the species.I found that multiple extrinsic pre- and postzygotic barriers resulting from ecological differentiation contributed most to total RI, while intrinsic barriers had substantial individual strength but contributed weakly to total RI. QTL mapping revealed evidence for genetic coupling of QTLs controlling traits associated with RI, although QTLs were overall widely distributed. QTLs related to sexually dimorphic traits were located on or near the pseudo-autosomal region of the sex chromosomes. The best-supported demographic model suggests heterogeneous population size and migration rates among genome-wide loci and points to the presence of barrier loci. Genomic divergence (measured using FST and dXY) was commonly accentuated around the middle of linkage groups and near QTLs for traits associated with reproductive barriers.In summary, the results in my thesis indicate that the speciation process is driven by multiple interacting and complex reproductive barriers. The genomic divergence landscape is shaped by interplay of the magnitude of gene flow, the strength and timing of selection, and other confounding factors such as genomic features.
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| 5. |
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| 6. |
- Söderquist, Linus, et al.
(författare)
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Genetic differentiation and diversity do not explain variation in heterosis or inbreeding depression
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Assisted gene flow can restore genetic diversity when genetic drift has driven deleterious alleles to high frequencies in small, isolated populations. Previous crosses among 20 populations of Gymnadenia conopsea documented the strongest heterosis and the weakest inbreeding depression in sparse and small populations, consistent with fixation of mildly deleterious alleles by genetic drift. We genotyped the populations used for crosses for 1,728 SNPs and tested the following predictions: 1) heterosis increases with genetic differentiation (FST) to donor populations and decreases with genetic diversity in the recipient population, 2) inbreeding depression increases with genetic diversity, and 3) genetic diversity increases, and mean FST to other populations decreases, with population size and density. Pairwise FST ranged from very low to moderate (0.005-0.20) and genetic diversity varied moderately among populations (proportion of polymorphic loci=0.52-0.75). However, neither FST between populations, nor genetic diversity in the recipient population, was related to the strength of heterosis. There was also no association between genetic diversity and the strength of inbreeding depression. Genetic diversity increased and mean FST decreased with population size, consistent with reduced diversity and increased differentiation of small populations by genetic drift. The results indicate that the loci conferring heterosis are not mirrored by overall population differentiation, and limited additional information on potential source populations for genetic rescue is gained by the genetic data. Instead, controlled crosses can directly reveal positive effects of introducing new genetic material, and is a simple method with high potential in conservation.
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| 7. |
- Söderquist, Linus, et al.
(författare)
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Genetic structure and diversity of the declining orchid Gymnadenia conopsea in Scandinavia: implications for conservation and management
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Understanding how historical versus contemporary processes shape population genetic structure and variation is important to design effective management actions for threatened species. To unravel population structure, connectivity, and genetic variation in the declining Gymnadenia conopsea, we genotyped 1,834 SNPs in 1,120 individuals in 110 populations, in three different habitats (fen, meadow, coastal) across Scandinavia. We further tested if genetic diversity increases with census population size, and is higher in core habitats (fen and meadow) than in marginal, coastal habitats. We identified three main genetic clusters and pronounced isolation by distance, consistent with two independent colonization routes after last glacial maximum, followed by admixture. Estimates of effective migration using EEMS indicated reduced gene flow between coastal and inland populations, suggesting that the complex topography of the fjord landscape constitutes a dispersal barrier. Genetic diversity increased with census population size. The highest genetic diversity was found in core habitats, in meadows in southern Sweden and in inland fens along the Scandes mountains, while the lowest genetic diversity was found on the Atlantic coast and in a few populations scattered across Scandinavia. Genetic diversity did not vary significantly among habitat types. In conclusion, current genetic structure suggests a strong legacy of historical events, and the high genetic diversity documented in the main Scandinavian range indicates that both current viability and future adaptation potential is high. To maintain genetic diversity and connectivity, it is particularly important to preserve southern meadow populations, which depend on traditional land use, along with central fen populations.
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| 8. |
- Söderquist, Linus
(författare)
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Population size, viability and genetic diversity in the orchid Gymnadenia conopsea
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis, I combined controlled crosses with genetic and demographic data to examine how a main conservation value indicator, population size, was associated with estimates of population viability. I focused on the still common, but decreasing, perennial orchid Gymnadenia conopsea at two spatial scales—locally on the island Öland, in SE Sweden, and regionally across Scandinavia. I aimed to determine whether: (1) population size or density could predict the strength of heterosis and inbreeding depression, (2) local density variation within populations affected self-pollen transfer and relatedness of individuals, (3) genetic diversity increased with population size or density, and genetic differentiation and diversity predicted the strength of heterosis, (4) population growth rate increased with population size and genetic diversity, and (5) large-scale genetic structure indicated several independent colonization events in Scandinavia, with clear genetic groups and genetic diversity hotspots.I found heterosis to decrease and inbreeding depression to increase with local density in Öland populations. The proportion of deposited self-pollen decreased with local density, but established individuals located in sparse patches were not more related than those in dense ones, possibly due to high inbreeding depression at early life stages. Genetic diversity increased with population size, but neither population genetic differentiation or within population genetic diversity was related to the strength of heterosis or inbreeding depression. I found the majority of Öland populations to be declining, and population growth rate to increase with population size. This relationship was driven by higher survival in large populations, and most likely reflects that population size was positively associated with local habitat quality and stability. Population growth rate was not related to the amount of genetic diversity within the population, suggesting declines are not driven by genetic erosion. At the Scandinavian scale, I identified three genetic groups, consistent with two independent post-glacial colonizations followed by admixture. High genetic diversity was found in southern and central populations, while low diversity was seen in marginal populations along the Atlantic coast.In conclusion, population size was associated with both genetic diversity and population viability at the Öland scale. Genetic diversity was not related to the strength of heterosis or population viability, suggesting that demographic metrics can be more informative than genetic metrics, regarding conservation priority.
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