| 1. |
- Bachmann, Jörg A., et al.
(författare)
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Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella
- 2018
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Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 8:4, s. 1327-1333
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Tidskriftsartikel (refereegranskat)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 5.7x10(-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.
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| 2. |
- Désamorè, Aurélie, et al.
(författare)
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Early burst in body size evolution is uncoupled from species diversification in diving beetles (Dytiscidae)
- 2018
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 27:4, s. 979-993
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Tidskriftsartikel (refereegranskat)abstract
- Changes in morphology are often thought to be linked to changes in species diversification,which is expected to leave a signal of early burst (EB) in phenotypic traits.However, such signal is rarely recovered in empirical phylogenies, even for groupswith well-known adaptive radiation. Using a comprehensive phylogenetic approachin Dytiscidae, which harbours ~4,300 species with as much as 50-fold variation inbody size among them, we ask whether pattern of species diversification correlateswith morphological evolution. Additionally, we test whether the large variation inbody size is linked to habitat preference and whether the latter influences speciesturnover. We found, in sharp contrast to most animal groups, that Dytiscidae bodysize evolution follows an early-burst model with subsequent high phylogenetic conservatism.However, we found no evidence for associated shifts in species diversification,which point to an uncoupled evolution of morphology and speciesdiversification. We recovered the ancestral habitat of Dytiscidae as lentic (standingwater), with many transitions to lotic habitat (running water) that are concomitantto a decrease in body size. Finally, we found no evidence for difference in net diversificationrates between habitats nor difference in turnover in lentic and lotic species.This result, together with recent findings in dragonflies, contrasts with sometheoretical expectations of the habitat stability hypothesis. Thus, a thoroughreassessment of the impact of dispersal, gene flow and range size on the speciationprocess is needed to fully encompass the evolutionary consequences of the lentic–lotic divide for freshwater fauna.
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| 3. |
- Laenen, Benjamin, et al.
(författare)
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Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina
- 2018
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 115:4, s. 816-821
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Tidskriftsartikel (refereegranskat)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.
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| 4. |
- Laenen, Benjamin, et al.
(författare)
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Evolutionary origin of the latitudinal diversity gradient in liverworts
- 2018
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 127, s. 606-612
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Tidskriftsartikel (refereegranskat)abstract
- A latitudinal diversity gradient towards the tropics appears as one most recurrent patterns in ecology, but the mechanisms underlying this pattern remain an area of controversy. In angiosperms, the tropical conservatism hypothesis proposes that most groups originated in the tropics and are adapted to a tropical climatic regime, and that relatively few species have evolved physiological adaptations to cold, dry or unpredictable climates. This mechanism is, however, unlikely to apply across land plants, and in particular, to liverworts, a group of about 7500 species, whose ability to withstand cold much better than their tracheophyte counterparts is at odds with the tropical conservatism hypothesis. Molecular dating, diversification rate analyses and ancestral area reconstructions were employed to explore the evolutionary mechanisms that account for the latitudinal diversity gradient in liverworts. As opposed to angiosperms, tropical liverwort genera are not older than their extratropical counterparts (median stem age of tropical and extra-tropical liverwort genera of 24.35 +/- 39.65 Ma and 39.57 +/- 49.07 Ma, respectively), weakening the `time for speciation hypothesis'. Models of ancestral area reconstructions with equal migration rates between tropical and extra-tropical regions outperformed models with asymmetrical migration rates in either direction. The symmetry and intensity of migrations between tropical and extra-tropical regions suggested by the lack of resolution in ancestral area reconstructions towards the deepest nodes are at odds with the tropical niche conservatism hypothesis. In turn, tropical genera exhibited significantly higher net diversification rates than extra-tropical ones, suggesting that the observed latitudinal diversity gradient results from either higher extinction rates in extra-tropical lineages or higher speciation rates in the tropics. We discuss a series of experiments to help deciphering the underlying evolutionary mechanisms.
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