Showing papers by "Tanja Slotte published in 2018"
TL;DR: It is proposed that variation in transposable element insertions, the resulting differences in PEG number and divergence in their expression level form one component of the effective ploidy variation between species of different breeding system histories, and, as a consequence, allow the establishment of endosperm-based hybridization barriers.
Abstract: Hybrid seed lethality is a widespread type of reproductive barrier among angiosperm taxa(1,2) that contributes to species divergence by preventing gene flow between natural populations(3,4). Beside ...
59 citations
TL;DR: It is found 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.
Abstract: Plant mating systems have profound effects on levels and structuring of genetic variation and can affect the impact of natural selection. Although 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, 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.
54 citations
TL;DR: In this article, the authors present the metagenomic data set of Hasseldala Port with a special focus on the abundance and biodiversity of Archaea, which allows reconstructing for the first time the temporal succession of major Archaea groups between 13.9 and 10.8 ka BP by using ancient environmental DNA metagenomics and fossil archaeal cell membrane lipids.
36 citations
TL;DR: 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.
Abstract: 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
24 citations
TL;DR: It is suggested that degeneration of pollen SI specificity in dominant S-alleles is important for shifts to self-fertilization in the Brassicaceae, and a conserved, S-linked small RNA (sRNA) that is predicted to cause dominance of self-compatibility is identified.
Abstract: 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.
14 citations
TL;DR: The objective of this study was to evaluate the phytochemical properties of polyploidy in response to the presence of E.coli in the E. coli O157:H2O 2.1.
Abstract: 1. Polyploidy is associated with a plethora of phenotypic and genetic changes yielding transformative effects on species' life-history and ecology. These biological attributes can contribute to the ...
12 citations
TL;DR: The results show that, until de novo assembly of multiple individuals using long-read sequencing becomes feasible, targeted long- read sequencing of loci under balancing selection is a viable option with low error rates for single nucleotide polymorphisms or structural variation.
Abstract: Rapid advances in short-read DNA sequencing technologies have revolutionized population genomic studies, but there are genomic regions where this technology reaches its limits. Limitations mostly arise due to the difficulties in assembly or alignment to genomic regions of high sequence divergence and high repeat content, which are typical characteristics for loci under strong long-term balancing selection. Studying genetic diversity at such loci therefore remains challenging. Here, we investigate the feasibility and error rates associated with targeted long-read sequencing of a locus under balancing selection. For this purpose, we generated bacterial artificial chromosomes (BACs) containing the Brassicaceae S-locus, a region under strong negative frequency-dependent selection which has previously proven difficult to assemble in its entirety using short reads. We sequence S-locus BACs with single-molecule long-read sequencing technology and conduct de novo assembly of these S-locus haplotypes. By comparing repeated assemblies resulting from independent long-read sequencing runs on the same BAC clone we do not detect any structural errors, suggesting that reliable assemblies are generated, but we estimate an indel error rate of 5.7×10-5 A similar error rate was estimated based on comparison of Illumina short-read sequences and BAC assemblies. Our results show that, until de novo assembly of multiple individuals using long-read sequencing becomes feasible, targeted long-read sequencing of loci under balancing selection is a viable option with low error rates for single nucleotide polymorphisms or structural variation. We further find that short-read sequencing is a valuable complement, allowing correction of the relatively high rate of indel errors that result from this approach.
11 citations
TL;DR: It is found 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.
Abstract: 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.
4 citations
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TL;DR: In the Brassicaceae, many studies on the population genetic, gene regulatory and genomic effects of selfing have centered on the model plant Arabidopsis thaliana and the crucifer genus Capsella as discussed by the authors.
Abstract: Many plants harbor complex mechanisms that promote outcrossing and efficient pollen transfer. These include floral adaptations as well as genetic mechanisms, such as molecular self-incompatibility (SI) systems. The maintenance of such systems over long evolutionary timescales suggests that outcrossing is favorable over a broad range of conditions. Conversely, SI has repeatedly been lost, often in association with transitions to self-fertilization (selfing). This transition is favored when the short-term advantages of selfing outweigh the costs, primarily inbreeding depression. The transition to selfing is expected to have major effects on population genetic variation and adaptive potential, as well as on genome evolution. In the Brassicaceae, many studies on the population genetic, gene regulatory and genomic effects of selfing have centered on the model plant Arabidopsis thaliana and the crucifer genus Capsella. The accumulation of population genomics datasets have allowed detailed investigation of where, when and how the transition to selfing occurred. Future studies will take advantage of the development of population genetics theory on the impact of selfing, especially regarding positive selection. Furthermore, investigation of systems including recent transitions to selfing, mixed mating populations and/or multiple independent replicates of the same transition will facilitate dissecting the effects of mating system variation from processes driven by demography.
2 citations