Biology subjects

Slotte, T.

Publications and source records attributed to Slotte, T..

16 recordsLinked to original sources

bioRxiv2026

Evolutionary consequences of repeated loss of distyly in Linum

The breakdown of distyly, a polymorphism that promotes disassortative pollination between two floral morphs, is often assumed to increase self-fertilization, reducing the efficacy of selection and challenging long-term species persistence. We tested whether repeated losses of distyly Linum were associated with genomic signatures of selfing by 1) testing for relaxed selective pressure in homostylous relative to distylous lineages, and 2) by characterising population genomic patterns of the homostylous Linum leonii in comparison to its distylous close relative Linum perenne. We generated whole-genome sequences and target-capture data from sixteen Linum species, and additionally built a high-quality genome assembly and acquired population-level whole-genome sequencing data for L. leonii (n=20). We reconstructed plastome phylogenies, estimated selective pressure for chloroplast and nuclear genes, inferred ancestral floral morph states, and tested for signatures of selfing in homostylous lineages. Compared to theoretical expectations, results were mixed, with partial identification of relaxed selective pressure in homostyles. Population genomic analyses of L. leonii revealed a moderate selfing rate of 0.32, suggesting that loss of distyly was associated with mixed mating rather than selfing, contrary to previous results on loss of distyly. Reduced nucleotide diversity and evidence for relaxed selection efficacy in L. leonii were instead consistent with a historical bottleneck. In Linum, the genomic consequences are more heterogeneous than generally assumed, and likely depend on species-specific evo-demographic history. This study highlights the complex evolutionary dynamics associated with the breakdown of distyly and emphasizes the need for comparative population genomic studies to clarify how such transitions shape evolutionary processes. Significance statementPlant mating system variation is central to evolution as it shapes genetic diversity, adaptability and fitness. Loss of distyly, an iconic example of a complex mating system favouring cross-pollination, can drive shifts from outcrossing to selfing, with potentially severe evolutionary consequences for the long-term persistence of the species in which it occurs. Using high-quality genome assembly and omic data for multiple Linum species, we tested for relaxed selective pressure in homostylous compared to distylous lineages, and tested for a population genomic signature of selfing in homostylous Linum leonii compared to the closely related distylous Linum perenne. Contrary to theoretical expectations, evidence for relaxation of selection was mixed in Linum homostyles and L. leonii did not exhibit a genomic signature of selfing. Our study reveals multiple evolutionary pathways following the loss of distyly, and highlights how mating system transitions, together with complex demographic processes, shape plant genetic diversity and evolution.

evolutionary biology↗

bioRxiv2025

Universal Hyb-Seq kits capture considerable intraspecific variation: Less is more in herbarium-inclusive molecular ecology

Target capture sequencing has enhanced the study of plant evolution and molecular ecology, particularly through the access to degraded DNA from herbarium specimens. Universal "off-the-shelf" kits, such as Angiosperms-353, are cheap and readily available but are considered to expose insufficient variation below the species level, because they are designed to target highly conserved regions. However, this remains to be tested in a direct comparison with customised approaches below the species level. In this study, near-identical genotypes from both herbarium and fresh material of the common dandelion (apomictic lineages in Taraxacum officinale F.H.Wigg.) are characterised with customised and universal approaches of target capture sequencing. An RNA-bait panel was designed to capture (i) highly variable loci normally obtained with a Genotyping-by-Sequencing (GBS) approach customised for dandelions; (ii) custom selected genes with potential for environmental adaptation, likely to harbour intraspecific genetic variation; (iii) conserved exons from universal kits (Angiosperms-353; Compositae-COS). Although exons from universal kits yield considerably less intraspecific genetic variation than both customised approaches, they still provided sufficient genetic variation to discriminate between near-identical genotypes of the same apomictic lineage. Given that universal kits save time, money, and the need for genomic reference data, this approach is recommended to increase the number of samples under budgetary constraints while still capturing considerable levels of intraspecific genetic variation.

genomics↗

bioRxiv2025

Genomic studies in Linum shed light on the evolution of the distyly supergene and the molecular basis of convergent floral evolution

O_LIDistyly, an example of convergent evolution, is governed by a supergene called the S- locus. Recent studies highlight similar genetic architectures of independently evolved S-loci, but whether similar regulatory pathways underlie convergent evolution of distyly remains unclear. C_LIO_LIWe examined the evolution of supergenes and mechanisms underlying distyly in Linum species that diverged [~]33 Mya. Using haplotype-resolved genomes and population genomics, we identified and characterized the S-loci of Linum perenne (distylous) and Linum grandiflorum (style length dimorphic), and compared them to that of Linum tenue (distylous). We then tested for a conserved hormonal mechanism regulating style length polymorphism in Linum. C_LIO_LIHemizygosity in short-styled individuals is a shared feature of the Linum S-locus supergene, though its size, gene content, repeat elements, and extent of recombination suppression vary greatly among species. Two distyly candidate genes, TSS1 (style length) and WDR-44 (anther height/pollen self-incompatibility) are conserved at the C_LIO_LIS-locus. Consistent with a brassinosteroid-dependent role of TSS1, epibrassinolide treatment revealed a conserved, morph-specific effect on style length. C_LIO_LIS-locus genetic architecture, key S-locus genes and mechanisms regulating style length remain conserved >30 Mya in Linum. In combination with findings from other systems, our results suggest that the brassinosteroid pathway frequently contributes to style length polymorphism. C_LI

evolutionary biology↗

bioRxiv2025

Whole-genome duplication increases genetic diversity and load in outcrossing Arabidopsis

Genetic variation underpins evolutionary change, but accumulation of slightly deleterious mutations also increases mutation load. There are multiple factors affecting the extent of load such as population size and breeding system, yet other potential determinants remain unexplored. A common macromutation, whole-genome duplication (WGD) occurs broadly across Eukaryotes, yet we lack a clear understanding of how WGD impacts neutral and selective processes within a population. Using forward simulations and empirical analysis of 632 short- and 16 long-read sequenced individuals of Arabidopsis arenosa (23 diploid and 42 natural autotetraploid populations), we test for the effects of WGD on genome-wide diversity and mutation load. Our simulations show how genetic variation gradually rises in autotetraploids due to increase of mutational target size. Moreover, mutation load increases due to relaxed purifying selection when deleterious mutations are masked by additional chromosome copies. Empirical data confirm these patterns, showing significant increase in nucleotide diversity, ratios of non-synonymous to synonymous SNPs, and number of indels and large structural variants in A. arenosa autotetraploids. However, a rather modest increase in load proxies together with a broad distribution and niche of autotetraploids suggests load accumulation has not (yet) limited their successful expansion. Overall, we demonstrate a complex interplay between neutral processes and purifying selection in shaping genetic variation following WGD and highlight ploidy as an important determinant of genetic diversity and mutation load in natural populations.

evolutionary biology↗

bioRxiv2023

Genomic analyses elucidate the causes and consequences of breakdown of distyly in Linum trigynum

Distyly is an iconic floral polymorphism governed by a supergene, which promotes efficient pollen transfer and outcrossing through reciprocal differences in the position of sexual organs in flowers, often coupled with heteromorphic self-incompatibility (SI). Distyly has evolved convergently in multiple flowering plant lineages, but has also broken down repeatedly, often resulting in homostylous, self-compatible populations with elevated rates of self-fertilization. Here, we aimed to study the genetic causes and genomic consequences of the shift to homostyly in Linum trigynum, which is closely related to distylous Linum tenue. Building on a high-quality genome assembly, we show that L. trigynum harbors a genomic region homologous to the dominant haplotype of the distyly supergene conferring long stamens and short styles in L. tenue, suggesting that loss of distyly first occurred in a short-styled individual. In contrast to homostylous Primula and Fagopyrum, L. trigynum harbors no fixed loss-of-function mutations in coding sequences of S-linked distyly candidate genes. Instead, floral gene expression analyses and controlled crosses suggest that mutations downregulating the S-linked LtWDR-44 candidate gene for male SI and/or anther height could underlie homostyly and self-compatibility (SC) in L. trigynum. Population genomic analyses of 224 whole-genome sequences further demonstrate that L. trigynum is highly self-fertilizing, exhibits significantly lower genetic diversity genome-wide, and is experiencing relaxed purifying selection and less frequent positive selection on nonsynonymous mutations relative to L. tenue. Our analyses shed light on the loss of distyly in L. trigynum, and advance our understanding of a common evolutionary transition in flowering plants.

evolutionary biology↗

bioRxiv2022

Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level

Supergenes govern balanced polymorphisms in a wide range of systems. The reciprocal placement of stigmas and anthers in pin and thrum floral morphs of distylous species constitutes an iconic example of a balanced polymorphism governed by a supergene, the distyly S-locus. Recent studies have shown that the Primula and Turnera distyly supergenes are both hemizygous in thrums, but it remains unknown if hemizygosity is pervasive among distyly S-loci. Here we have characterized the genetic architecture and evolution of the distyly supergene in Linum by generating a chromosome-level genome assembly of Linum tenue, followed by the identification of the S-locus using population genomic data. We show that hemizygosity and thrum-specific expression of S-linked genes, including a pistil-expressed candidate gene for style length, are major features of the Linum S-locus. Structural variation is likely instrumental for recombination suppression, and although the non-recombining dominant haplotype has accumulated transposable elements, S-linked genes are not under relaxed purifying selection. Our findings reveal remarkable convergence in the genetic architecture and evolution of independently derived distyly supergenes. The chromosome-level genome assembly and detailed characterization of the distyly S-locus in L. tenue will facilitate elucidation of molecular mechanisms underlying the different forms of flowers described by Darwin.

evolutionary biology↗

bioRxiv2021

What can the cold-induced transcriptomes of Arctic Brassicaceae tell us about the evolution of cold tolerance?

O_LILittle is known about the evolution of cold tolerance in polar plant species and how they differ from their temperate relatives. To gain insight into their biology and the evolution of cold tolerance, we compared the molecular basis of cold response in three Arctic Brassicaceae species. C_LIO_LIWe conducted a comparative time series experiment to examine transcriptional responses to low temperature. RNA was sampled at 22 {degrees}C, and after 3h, 6h, and 24h at 2 {degrees}C. We then identified sets of genes that were differentially expressed in response to cold and compared them between species, as well as to published data from the temperate Arabidopsis thaliana. C_LIO_LIMost differentially expressed genes were species-specific, but a significant portion of the cold response was also shared among species. Among thousands of differentially expressed genes, [~]200 were shared among the three Arctic species and A. thaliana, while [~]100 were exclusively shared among the three Arctic species. C_LIO_LIOur results show that cold response differs markedly between Arctic Brassicaceae species, but likely builds on a conserved basis found across the family. They also confirm that highly polygenic traits such as cold tolerance may show little repeatability in their patterns of adaptation. C_LI

evolutionary biology↗

bioRxiv2021

Supergene degeneration opposes polymorphism: The curious case of balanced lethals

Supergenes offer some of the most spectacular examples of long-term balancing selection in nature but their origin and maintenance remain a mystery. A critical aspect of supergenes is reduced recombination between arrangements. Reduced recombination protects adaptive multi-trait phenotypes, but can also lead to degeneration through mutation accumulation. Mutation accumulation can stabilize the system through the emergence of associative overdominance (AOD), destabilize the system, or lead to new evolutionary outcomes. One such outcome is the formation of balanced lethal systems, a maladaptive system where both supergene arrangements have accumulated deleterious mutations to the extent that both homozygotes are inviable, leaving only heterozygotes to reproduce. Here, we perform a simulation study to understand the conditions under which these different outcomes occur, assuming a scenario of introgression after allopatric divergence. We found that AOD aids the invasion of a new supergene arrangement and the establishment of a polymorphism. However, this polymorphism is easily destabilized by further mutation accumulation. While degradation may strengthen AOD, thereby stabilizing the supergene polymorphism, it is often asymmetric, which is the key disrupter of the quasi-equilibrium state of the polymorphism. Furthermore, mechanisms that accelerate degeneration also tend to amplify asymmetric mutation accumulation between the supergene arrangements and vice versa. As the evolution of a balanced lethal system requires symmetric degradation of both arrangements, this leaves highly restricted conditions under which such a system could evolve. We show that small population size and low dominance coefficients are critical factors, as these reduce the efficacy of selection. The dichotomy between the persistence of a polymorphism and degradation of supergene arrangements likely underlies the rarity of balanced lethal systems in nature.

evolutionary biology↗

bioRxiv2021

Genomic signatures of sexual selection on pollen-expressed genes in Arabis alpina

Fertilization in angiosperms involves the germination of pollen on the stigma, followed by the extrusion of a pollen tube that elongates through the style and delivers two sperm cells to the embryo sac. Sexual selection could occur throughout this process when male gametophytes compete for fertilization. The strength of sexual selection during pollen competition should be affected by the number of genotypes deposited on the stigma. As increased self-fertilization reduces the number of mating partners, and the genetic diversity and heterozygosity of populations, it should thereby reduce the intensity of sexual selection during pollen competition. Despite the prevalence of mating system shifts, few studies have directly compared the molecular signatures of sexual selection during pollen competition in populations with different mating systems. Here we analyzed whole-genome sequences from natural populations of Arabis alpina, a species showing mating system variation across its distribution, to test whether shifts from cross- to self-fertilization result in molecular signatures consistent with sexual selection on genes involved in pollen competition. We found evidence for efficient purifying selection on genes expressed in vegetative pollen, and overall weaker selection on sperm-expressed genes. This pattern was robust when controlling for gene expression level and specificity. In agreement with the expectation that sexual selection intensifies under cross-fertilization, we found that the efficacy of purifying selection on male gametophyte-expressed genes was significantly stronger in genetically more diverse and outbred populations. Our results show that intra-sexual competition shapes the evolution of pollen-expressed genes, and that its strength fades with increasing self-fertilization rates.

evolutionary biology↗

bioRxiv2021

Genome assemblies of three closely related leaf beetle species (Galerucella spp).

Galerucella (Coleoptera: Chrysomelidae) is a leaf beetle genus that has been extensively used for ecological and evolutionary studies. It has also been used as biological control agent against invading purple loosestrife in North America, with large effects on biodiversity. Here we report genome assembly and annotation of three closely related Galerucella species: G. calmariensis, G. pusilla and G. tenella. The three assemblies have a genome size ranging from 460Mb to 588Mb, with N50 from 31,588kb to 79.674kb, containing 29,202 to 40,929 scaffolds. Using an ab initio evidence-driven approach, 30,302 to 33,794 protein-coding genes were identified and functionally annotated. These draft genomes will contribute to the understanding of host-parasitoid interactions, evolutionary comparisons of leaf beetle species and future population genomics studies.

genomics↗

bioRxiv2020

Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm

Hybridization of closely related plant species is frequently connected to endosperm arrest and seed failure, for reasons that remain to be identified. In this study, we investigated the molecular events accompanying seed failure in hybrids of the closely related species pair Capsella rubella and C. grandiflora. Mapping of QTLs for the underlying cause of hybrid incompatibility in Capsella revealed three QTLs that were close to pericentromeric regions. This prompted us to investigate whether there are specific changes in heterochromatin associated with interspecific hybridizations. Indeed, we found that chromatin was less condensed in the endosperm, while the embryo was not affected. Loss of chromosome condensation was connected with a strong loss of CHG and CHH methylation and mitotic abnormalities. Genome-wide sequencing of hybrid endosperm revealed that the chromosome loss was random and was likely a consequence of reduced chromatin condensation. Consistent with reduced DNA methylation in hybrid endosperm, we found a disproportionate deregulation of genes located close to pericentromeric regions. Among those deregulated genes there were many potential targets of the AGAMOUS-LIKE transcription factor PHERES1, suggesting that reduced DNA methylation allows PHERES1 to hyperactivate its targets. Since the identified QTLs were also associated with pericentromeric regions, we conclude that relaxation of heterochromatin in response to interspecies hybridization exposes and activates loci leading to hybrid seed failure.

evolutionary biology↗

bioRxiv2020

Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives

Parallel adaptation provides valuable insight into the predictability of evolutionary change through replicated natural experiments. A steadily increasing number of studies have demonstrated genomic parallelism, yet the magnitude of this parallelism varies depending on whether populations, species or genera are compared. This led us to hypothesize that the magnitude of genomic parallelism scales with genetic divergence between lineages, but whether this is the case and the underlying evolutionary processes remain unknown. Here, we resequenced seven parallel lineages of two Arabidopsis species which repeatedly adapted to challenging alpine environments. By combining genome-wide divergence scans with model-based approaches we detected a suite of 151 genes that show parallel signatures of positive selection associated with alpine colonization, involved in response to cold, high radiation, short season, herbivores and pathogens. We complemented these parallel candidates with published gene lists from five additional alpine Brassicaceae and tested our hypothesis on a broad scale spanning ~ 0.02 to 18 million years of divergence. Indeed, we found quantitatively variable genomic parallelism whose extent significantly decreased with increasing divergence between the compared lineages. We further modeled parallel evolution over the Arabidopsis candidate genes and showed that a decreasing probability of repeated selection of the same standing or introgressed alleles drives the observed pattern of divergence-dependent parallelism. We therefore conclude that genetic divergence between populations, species and genera, affecting the pool of shared variants, is an important factor in the predictability of genome evolution. Significance statementRepeated evolution tends to be more predictable. The impressive spectrum of recent reports on genomic parallelism, however, revealed that the fraction of the genome that evolves in parallel largely varies, possibly reflecting different evolutionary scales investigated. Here, we demonstrate divergence-dependent parallelism using a comprehensive genome-wide dataset comprising 12 cases of parallel alpine adaptation and identify decreasing probability of adaptive re-use of genetic variation as the major underlying cause. This finding empirically demonstrates that evolutionary predictability is scale dependent and suggests that availability of pre-existing variation drives parallelism within and among populations and species. Altogether, our results inform the ongoing discussion about the (un)predictability of evolution, relevant for applications in pest control, nature conservation, or the evolution of pathogen resistance.

evolutionary biology↗

bioRxiv2018

Long-term balancing selection drives evolution of immunity genes in Capsella

Genetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genus Capsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. Our data point to long term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck.

evolutionary biology↗

bioRxiv2018

Genetic basis and timing of a major mating system shift in Capsella

Shifts from outcrossing to self-fertilisation have occurred repeatedly in many different lineages of flowering plants, and often involve the breakdown of genetic outcrossing mechanisms. In the Brassicaceae, self-incompatibility (SI) allows plants to ensure outcrossing by recognition and rejection of self-pollen on the stigma. This occurs through the interaction of female and male specificity components, consisting of a pistil based receptor and a pollen-coat protein, both of which are encoded by tightly linked genes at the S-locus. When benefits of selfing are higher than costs of inbreeding, theory predicts that loss-of-function mutations in the male (pollen) SI component should be favoured, especially if they are dominant. However, it remains unclear whether mutations in the male component of SI are predominantly responsible for shifts to self-compatibility, and testing this prediction has been difficult due to the challenges of sequencing the highly polymorphic and repetitive ~100 kbp S-locus. The crucifer genus Capsella offers an excellent opportunity to study multiple transitions from outcrossing to self-fertilization, but so far, little is known about the genetic basis and timing of loss of SI in the self-fertilizing diploid Capsella orientalis. Here, we show that loss of SI in C. orientalis occurred within the past 2.6 Mya and maps as a dominant trait to the S-locus. Using targeted long-read sequencing of multiple complete S-haplotypes, we identify a frameshift deletion in the male specificity gene SCR that is fixed in C. orientalis, and we confirm loss of male SI specificity. We further analyze RNA sequencing data to identify a conserved, S-linked small RNA (sRNA) that is predicted to cause dominance of self-compatibility. Our results suggest that degeneration of pollen SI specificity in dominant S-alleles is important for shifts to self-fertilization in the Brassicaceae.\n\nAuthor SummaryAlready Darwin was fascinated by the widely varying modes of plant reproduction. The shift from outcrossing to self-fertilization is considered one of the most frequent evolutionary transitions in flowering plants, yet we still know little about the genetic basis of these shifts. In the Brassicaceae, outcrossing is enforced by a self-incompatibility (SI) system that enables the recognition and rejection of self pollen. This occurs through the action of two tightly linked genes at the S-locus, that encode a receptor protein located on the stigma (female component) and a pollen ligand protein (male component), respectively. Nevertheless, SI has frequently been lost, and theory predicts that mutations in the male component should have an advantage during the loss of SI, especially if they are dominant. To test this hypothesis, we mapped the loss of SI in a selfing species from the genus Capsella, a model system for evolutionary genomics. We found that loss of SI mapped to the S-locus, which harbored a dominant loss-of-function mutation in the male SI protein, and as expected, we found that male specificity was indeed lost in C. orientalis. Our results suggest that transitions to selfing often involve parallel genetic changes.

evolutionary biology↗

bioRxiv2018

Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa

Ploidy-variable species allow direct inference of the effects of chromosome copy number on fundamental evolutionary processes. While an abundance of theoretical work suggests polyploidy should leave distinct population genomic signatures, empirical data remains sparse. We sequenced [~]300 individuals from 39 populations of Arabidopsis arenosa, a naturally diploid-autotetraploid species. We find the impacts of polyploidy on population genomic processes are subtle yet pervasive, including reduced efficiency on linked and purifying selection as well as rampant gene flow from diploids. Initial masking of deleterious mutations, faster rates of nucleotide substitution, and interploidy introgression all conspire to shape the evolutionary potential of polyploids.

evolutionary biology↗

bioRxiv2017

Demography And Mating System Shape The Genome-Wide Impact Of Purifying Selection In Arabis alpina

Plant mating systems have profound effects on levels and structuring of genetic variation, and can affect the impact of natural selection. While theory predicts that intermediate outcrossing rates may allow plants to prevent accumulation of deleterious alleles, few studies have empirically tested this prediction using genomic data. Here, we study the effect of mating system on purifying selection by conducting population genomic analyses on whole-genome resequencing data from 38 European individuals of the arctic-alpine crucifer Arabis alpina. We find that outcrossing and mixed-mating populations maintain genetic diversity at similar levels, whereas highly self-fertilizing Scandinavian A. alpina show a strong reduction in genetic diversity, most likely as a result of a postglacial colonization bottleneck. We further find evidence for accumulation of genetic load in highly self-fertilizing populations, whereas the genome-wide impact of purifying selection does not differ greatly between mixed-mating and outcrossing populations. Our results demonstrate that intermediate levels of outcrossing may allow efficient selection against harmful alleles whereas demographic effects can be important for relaxed purifying selection in highly selfing populations. Thus, both mating system and demography shape the impact of purifying selection on genomic variation in A. alpina. These results are important for an improved understanding of the evolutionary consequences of mating system variation and the maintenance of mixed-mating strategies.\n\nSignificanceIntermediate outcrossing rates are theoretically predicted to maintain effective selection against harmful alleles, but few studies have empirically tested this prediction using genomic data. We used whole-genome resequencing data from alpine rock-cress to study how genetic variation and purifying selection vary with mating system. We find that populations with intermediate outcrossing rates have similar levels of genetic diversity as outcrossing populations, and that purifying selection against harmful alleles is efficient in mixed-mating populations. In contrast, self-fertilizing populations from Scandinavia have strongly reduced genetic diversity, and accumulate harmful mutations, likely as a result of demographic effects of postglacial colonization. Our results suggest that mixed-mating populations can avoid the negative evolutionary consequences of high self-fertilization rates.

evolutionary biology↗