SwePub - search: WFRF:(Laenen Benjamin)

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1.	Bachmann, Jörg A., et al. (author) Genetic basis and timing of a major mating system shift in Capsella 2019 In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 224:1, s. 505-517 Journal article (peer-reviewed)abstract A crucial step in the transition from outcrossing to self-fertilization is the loss of genetic self-incompatibility (SI). In the Brassicaceae, SI involves the interaction of female and male specificity components, encoded by the genes SRK and SCR at the self-incompatibility locus (S-locus). Theory predicts that S-linked mutations, and especially dominant mutations in SCR, are likely to contribute to loss of SI. However, few studies have investigated the contribution of dominant mutations to loss of SI in wild plant species. Here, we investigate the genetic basis of loss of SI in the self-fertilizing crucifer species Capsella orientalis, by combining genetic mapping, long-read sequencing of complete S-haplotypes, gene expression analyses and controlled crosses. We show that loss of SI in C. orientalis occurred S-locus. We identify a fixed frameshift deletion in the male specificity gene SCR and confirm loss of male SI specificity. We further identify an S-linked small RNA that is predicted to cause dominance of self-compatibility. Our results agree with predictions on the contribution of dominant S-linked mutations to loss of SI, and thus provide new insights into the molecular basis of mating system transitions.
2.	Bachmann, Jörg A., et al. (author) Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella 2018 In: G3. - : Oxford University Press (OUP). - 2160-1836. ; 8:4, s. 1327-1333 Journal article (peer-reviewed)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.
3.	Bohutínská, Magdalena, et al. (author) Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives 2021 In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 118:21 Journal article (peer-reviewed)abstract 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 My 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 on 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.
4.	Désamorè, Aurélie, et al. (author) Early burst in body size evolution is uncoupled from species diversification in diving beetles (Dytiscidae) 2018 In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 27:4, s. 979-993 Journal article (peer-reviewed)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.
5.	Desamore, Aurelie, et al. (author) High migration rates shape the postglacial history of amphi-Atlantic bryophytes 2016 In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 25:21, s. 5568-5584 Journal article (peer-reviewed)abstract Paleontological evidence and current patterns of angiosperm species richness suggest that European biota experienced more severe bottlenecks than North American ones during the last glacial maximum. How well this pattern fits other plant species is less clear. Bryophytes offer a unique opportunity to contrast the impact of the last glacial maximum in North America and Europe because about 60% of the European bryoflora is shared with North America. Here, we use population genetic analyses based on approximate Bayesian computation on eight amphi-Atlantic species to test the hypothesis that North American populations were less impacted by the last glacial maximum, exhibiting higher levels of genetic diversity than European ones and ultimately serving as a refugium for the postglacial recolonization of Europe. In contrast with this hypothesis, the best-fit demographic model involved similar patterns of population size contractions, comparable levels of genetic diversity and balanced migration rates between European and North American populations. Our results thus suggest that bryophytes have experienced comparable demographic glacial histories on both sides of the Atlantic. Although a weak, but significant genetic structure was systematically recovered between European and North American populations, evidence for migration from and towards both continents suggests that amphi-Atlantic bryophyte population may function as a metapopulation network. Reconstructing the biogeographic history of either North American or European bryophyte populations therefore requires a large, trans-Atlantic geographic framework.
6.	Dziasek, Katarzyna, et al. (author) Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm 2021 In: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 17:2 Journal article (peer-reviewed)abstract 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 QTL for the underlying cause of hybrid incompatibility in Capsella identified three QTL that were close to pericentromeric regions. We investigated whether there are specific changes in heterochromatin associated with interspecific hybridizations and found a strong reduction of chromatin condensation in the endosperm, connected with a strong loss of CHG and CHH methylation and random loss of a single chromosome. Consistent with reduced DNA methylation in the hybrid endosperm, we found a disproportionate deregulation of genes located close to pericentromeric regions, suggesting that reduced DNA methylation allows access of transcription factors to targets located in heterochromatic regions. Since the identified QTL were also associated with pericentromeric regions, we propose that relaxation of heterochromatin in response to interspecies hybridization exposes and activates loci leading to hybrid seed failure.
7.	Gil-Lopez, Manuel J., et al. (author) Different historical backgrounds determine contrasting phylogeographical patterns in two co-distributed Erica species (Ericaceae) across the Strait of Gibraltar 2017 In: Botanical journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4074 .- 1095-8339. ; 185:3, s. 359-375 Journal article (peer-reviewed)abstract Erica australis and Erica arborea are morphologically and ecologically similar heather species. Erica australis is restricted to the western Mediterranean Basin where it overlaps with the westernmost distribution of E. arborea. Here we investigate the role of the Strait of Gibraltar (SG) as a potential biogeographical barrier to dispersal and/or as glacial refugium in these two Erica spp. in the western Mediterranean (WMed) region with contrasting geographical origins and distributions. Samples were collected from 55 and 54 populations of E. australis and E. arborea, respectively. One individual each of 52 and 45 populations of E. australis and E. arborea, respectively, were sequenced for plastid DNA regions, and 1304 and 1214 individuals from 44 and 42 populations of E. australis and E. arborea, respectively, were genotyped using nuclear microsatellites (SSRs). Plastid DNA sequences were used to estimate divergence time of lineages and to construct haplotype networks. SSR data helped to infer population genetic diversity and fixation indices and genetic structure patterns through Bayesian analysis, analysis of molecular variance and isolation by distance. Plastid haplotype diversity of E. australis was higher in the SG than in the WMed area, whereas the opposite was found in E. arborea. SSRs revealed high genetic diversity within populations of both species and population genetic structure patterns were consistent with those retrieved from plastid DNA. The SG was identified as the likely area of origin and diversification for E. australis in the late Pliocene-Pleistocene, where it survived the Last Glacial Maximum (LGM) and expanded northwards into the western Iberian Peninsula. In contrast, two separate evolutionary lineages were found for E. arborea in the Iberian Peninsula. The SG and southern WMed areas represent the western Mediterranean expansion limit of an E. arborea lineage from East Africa/Arabia in the late Pliocene-Pleistocene, whereas the northern WMed populations were relicts from an older refugium that survived LGM in north-western Iberia. This study illustrates how geographical range and origin explain differences in the phylogeographical structure of co-distributed Mediterranean plants and highlights the role of the SG as a Pleistocene refugium and biogeographical crossroads in the Mediterranean.
8.	Gutiérrez-Valencia, Juanita, 1991-, et al. (author) Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum 2024 In: Molecular biology and evolution. - 0737-4038 .- 1537-1719. ; 41:5 Journal article (peer-reviewed)abstract 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. 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 self-incompatibility and/or anther height could underlie homostyly and self-compatibility 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.
9.	Gutiérrez-Valencia, Juanita, 1991-, et al. (author) Genomic analyses of the breakdown of distyly in Linum trigynum Other publication (other academic/artistic)
10.	Gutiérrez-Valencia, Juanita, et al. (author) Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level 2022 In: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 32:20, s. 4360-4371, 4371.e1-4371.e6 Journal article (peer-reviewed)abstract Supergenes govern multi-trait-balanced polymorphisms in a wide range of systems; however, our understanding of their origins and evolution remains incomplete. 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 whether hemizygosity is pervasive among distyly S-loci. As hemizygosity has major consequences for supergene evolution and loss, clarifying whether this genetic architecture is shared among distylous species is critical. 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, provide a counterexample to classic inversion-based supergenes, and shed new light on the origin and maintenance of an iconic floral polymorphism.
11.	Gutiérrez-Valencia, Juanita, et al. (author) Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina 2022 In: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 39:1 Journal article (peer-reviewed)abstract 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.
12.	Hatorangan, Marcelinus Rocky, et al. (author) Rapid Evolution of Genomic Imprinting in Two Species of the Brassicaceae 2016 In: The Plant Cell. - : Oxford University Press (OUP). - 1040-4651 .- 1532-298X. ; 28:8, s. 1815-1827 Journal article (peer-reviewed)abstract Genomic imprinting is an epigenetic phenomenon occurring in mammals and flowering plants that causes genes to adopt a parent-of-origin-specific mode of expression. While the imprinting status of genes is well conserved in mammals, clear estimates for the degree of conservation were lacking in plants. We therefore analyzed the genome-wide imprinting status of Capsella rubella, which shared a common recent ancestor with Arabidopsis thaliana similar to 10 to 14 million years ago. However, only similar to 14% of maternally expressed genes (MEGs) and similar to 29% of paternally expressed genes (PEGs) in C. rubella were commonly imprinted in both species, revealing that genomic imprinting is a rapidly evolving phenomenon in plants. Nevertheless, conserved PEGs exhibited signs of selection, suggesting that a subset of imprinted genes play an important functional role and are therefore maintained in plants. Like in Arabidopsis, PEGs in C. rubella are frequently associated with the presence of transposable elements that preferentially belong to helitron and MuDR families. Our data further reveal that MEGs and PEGs differ in their targeting by 24-nucleotide small RNAs and asymmetric DNA methylation, suggesting different mechanisms establishing DNA methylation at MEGs and PEGs.
13.	Hedenäs, Lars, et al. (author) Three species for theprice of one within the moss Homalotheciumsericeum s.l. 2014 In: Taxon. - : Wiley. - 0040-0262 .- 1996-8175. ; 63, s. 249-257 Journal article (peer-reviewed)
14.	Horvath, Robert, et al. (author) Single-cell expression noise and gene-body methylation in Arabidopsis thaliana 2019 In: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 123:2, s. 81-91 Journal article (peer-reviewed)abstract Gene-body methylation (gbM) refers to an increased level of methylated cytosines specifically in a CG sequence context within genes. gbM is found in plant genes with intermediate expression level, which evolve slowly, and is often broadly conserved across millions of years of evolution. Intriguingly however, some plants lack gbM, and thus it remains unclear whether gbM has a function. In animals, there is support for a role of gbM in reducing erroneous transcription and transcription noise, but so far most studies in plants have tested for an effect of gbM on expression level, not noise. Here, we therefore tested whether gbM was associated with reduced expression noise in Arabidopsis thaliana, using single-cell transcriptome sequencing data from root quiescent centre cells. We find that gbM genes have lower expression noise levels than unmethylated genes. However, an analysis of covariance revealed that, if other genomic features are taken into account, this association disappears. Nonetheless, gbM genes were more consistently expressed across single-cell samples, supporting previous inference that gbM genes are constitutively expressed. Finally, we observed that fewer RNAseq reads map to introns of gbM genes than to introns of unmethylated genes, which indicates that gbM might be involved in reducing erroneous transcription by reducing intron retention.
15.	Laenen, Benjamin, et al. (author) Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina 2018 In: 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 Journal article (peer-reviewed)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.
16.	Laenen, Benjamin, et al. (author) Evolutionary origin of the latitudinal diversity gradient in liverworts 2018 In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 127, s. 606-612 Journal article (peer-reviewed)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.
17.	Laenen, Benjamin, et al. (author) Geographical range in liverworts : does sex really matter? 2016 In: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 43:3, s. 627-635 Journal article (peer-reviewed)abstract AimWhy some species exhibit larger geographical ranges than others remains a fundamental, but largely unanswered, question in ecology and biogeography. In plants, a relationship between range size and mating system was proposed over a century ago and subsequently formalized in Baker's Law. Here, we take advantage of the extensive variation in sexual systems of liverworts to test the hypothesis that dioecious species compensate for limited fertilization by producing vegetative propagules more commonly than monoecious species. As spores are assumed to contribute to random long-distance dispersal, whereas vegetative propagules contribute to colony maintenance and frequent short-distance dispersal, we further test the hypothesis that monoecious species exhibit larger geographical ranges than dioecious ones. LocationWorldwide. MethodsWe used comparative phylogenetic methods to assess the correlation between range size and life history traits related to dispersal, including mating systems, spore size and production of specialized vegetative propagules. ResultsNo significant correlation was found between dioecy and production of vegetative propagules. However, production of vegetative propagules is correlated with the size of geographical ranges across the liverwort tree of life, whereas sexuality and spores size are not. Moreover, variation in sexual systems did not have an influence on the correlation between geographical range and production of asexual propagules. Main conclusionsOur results challenge the long-held notion that spores, and not vegetative propagules, are involved in long-distance dispersal. Asexual reproduction seems to play a major role in shaping the global distribution patterns of liverworts, so that monoecious species do not tend to display, on average, broader distribution ranges than dioecious ones. Our results call for further investigation on the spatial genetic structure of bryophyte populations at different geographical scales depending on their mating systems to assess the dispersal capacities of spores and asexual propagules and determine their contribution in shaping species distribution ranges.
18.	Laenen, Benjamin, et al. (author) Increased diversification rates follow shifts to bisexuality in liverworts 2016 In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 210:3, s. 1121-1129 Journal article (peer-reviewed)abstract Shifts in sexual systems are one of the key drivers of species diversification. In contrast to angiosperms, unisexuality prevails in bryophytes. Here, we test the hypotheses that bisexuality evolved from an ancestral unisexual condition and is a key innovation in liverworts. We investigate whether shifts in sexual systems influence diversification using hidden state speciation and extinction analysis (HiSSE). This new method compares the effects of the variable of interest to the best-fitting latent variable, yielding robust and conservative tests. We find that the transitions in sexual systems are significantly biased toward unisexuality, even though bisexuality is coupled with increased diversification. Sexual systems are strongly conserved deep within the liverwort tree but become much more labile toward the present. Bisexuality appears to be a key innovation in liverworts. Its effects on diversification are presumably mediated by the interplay of high fertilization rates, massive spore production and long-distance dispersal, which may separately or together have facilitated liverwort speciation, suppressed their extinction, or both. Importantly, shifts in liverwort sexual systems have the opposite effect when compared to angiosperms, leading to contrasting diversification patterns between the two groups. The high prevalence of unisexuality among liverworts suggests, however, a strong selection for sexual dimorphism.
19.	Ledent, A., et al. (author) No borders during the post-glacial assembly of European bryophytes 2019 In: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 22:6, s. 973-986 Journal article (peer-reviewed)abstract Climatic fluctuations during the Last Glacial Maximum (LGM) exerted a profound influence on biodiversity patterns, but their impact on bryophytes, the second most diverse group of land plants, has been poorly documented. Approximate Bayesian computations based on coalescent simulations showed that the post-glacial assembly of European bryophytes involves a complex history from multiple sources. The contribution of allochthonous migrants was 95-100% of expanding populations in about half of the 15 investigated species, which is consistent with the globally balanced genetic diversities and extremely low divergence observed among biogeographical regions. Such a substantial contribution of allochthonous migrants in the post-glacial assembly of Europe is unparalleled in other plants and animals. The limited role of northern micro-refugia, which was unexpected based on bryophyte life-history traits, and of southern refugia, is consistent with recent palaeontological evidence that LGM climates in Eurasia were much colder and drier than what palaeoclimatic models predict.
20.	Ledent, Alice, et al. (author) What do tropical cryptogams reveal? Strong genetic structure in Amazonian bryophytes 2020 In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 228:2, s. 640-650 Journal article (peer-reviewed)abstract Lowland tropical bryophytes have been perceived as excellent dispersers. In such groups, the inverse isolation hypothesis proposes that spatial genetic structure is erased beyond the limits of short-distance dispersal. Here, we determine the influence of environmental variation and geographic barriers on the spatial genetic structure of a widely dispersed and phylogenetically independent sample of Amazonian bryophytes. Single nucleotide polymorphism data were produced from a restriction site-associated DNA sequencing protocol for 10 species and analyzed through F-statistics and Mantel tests. Neither isolation-by-environment nor the impact of geographic barriers were recovered from the analyses. However, significant isolation-by-distance patterns were observed for 8 out of the 10 investigated species beyond the scale of short-distance dispersal (> 1 km), offering evidence contrary to the inverse isolation hypothesis. Despite a cadre of life-history traits and distributional patterns suggesting that tropical bryophytes are highly vagile, our analyses reveal spatial genetic structures comparable to those documented for angiosperms, whose diaspores are orders of magnitude larger. Dispersal limitation for tropical bryophytes flies in the face of traditional assumptions regarding their dispersal potential, and suggests that the plight of this component of cryptic biodiversity is more dire than previously considered in light of accelerated forest fragmentation in the Amazon.
21.	Mattila, Tiina M., et al. (author) Impact of demography on linked selection in two outcrossing Brassicaceae species 2019 In: Ecology and Evolution. - : Wiley. - 2045-7758. ; 9:17, s. 9532-9545 Journal article (peer-reviewed)abstract Genetic diversity is shaped by mutation, genetic drift, gene flow, recombination, and selection. The dynamics and interactions of these forces shape genetic diversity across different parts of the genome, between populations and species. Here, we have studied the effects of linked selection on nucleotide diversity in outcrossing populations of two Brassicaceae species, Arabidopsis lyrata and Capsella grandiflora, with contrasting demographic history. In agreement with previous estimates, we found evidence for a modest population size expansion thousands of generations ago, as well as efficient purifying selection in C. grandiflora. In contrast, the A. lyrata population exhibited evidence for very recent strong population size decline and weaker efficacy of purifying selection. Using multiple regression analyses with recombination rate and other genomic covariates as explanatory variables, we can explain 47% of the variance in neutral diversity in the C. grandiflora population, while in the A. lyrata population, only 11% of the variance was explained by the model. Recombination rate had a significant positive effect on neutral diversity in both species, suggesting that selection at linked sites has an effect on patterns of neutral variation. In line with this finding, we also found reduced neutral diversity in the vicinity of genes in the C. grandiflora population. However, in A. lyrata no such reduction in diversity was evident, a finding that is consistent with expectations of the impact of a recent bottleneck on patterns of neutral diversity near genes. This study thus empirically demonstrates how differences in demographic history modulate the impact of selection at linked sites in natural populations.
22.	Monnahan, Patrick, et al. (author) Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa 2019 In: Nature Ecology & Evolution. - : Springer Science and Business Media LLC. - 2397-334X. ; 3:3, s. 457-468 Journal article (peer-reviewed)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 similar to 300 individuals from 39 populations of Arabidopsis arenosa, a naturally diploidautotetraploid species. We find that the impacts of polyploidy on population genomic processes are subtle yet pervasive, such as reduced efficiency of purifying selection, differences in linked selection and rampant gene flow from diploids. Initial masking of deleterious mutations, faster rates of nucleotide substitution and interploidy introgression likely conspire to shape the evolutionary potential of polyploids.
23.	Patino, Jairo, et al. (author) Range size heritability and diversification patterns in the liverwort genus Radula 2017 In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 106, s. 73-85 Journal article (peer-reviewed)abstract Why some species exhibit larger geographical ranges than others, and to what extent does variation in range size affect diversification rates, remains a fundamental, but largely unanswered question in ecology and evolution. Here, we implement phylogenetic comparative analyses and ancestral area estimations in Radula, a liverwort genus of Cretaceous origin, to investigate the mechanisms that explain differences in geographical range size and diversification rates among lineages. Range size was phylogenetically constrained in the two sub-genera characterized by their almost complete Australasian and Neotropical endemicity, respectively. The congruence between the divergence time of these lineages and continental split suggests that plate tectonics could have played a major role in their present distribution, suggesting that a strong imprint of vicariance can still be found in extant distribution patterns in these highly mobile organisms. Amentuloradula, Volutoradula and Metaradula species did not appear to exhibit losses of dispersal capacities in terms of dispersal life-history traits, but evidence for significant phylogenetic signal in macroecological niche traits suggests that niche conservatism accounts for their restricted geographic ranges. Despite their greatly restricted distribution to Australasia and Neotropics respectively, Amentuloradula and Volutoradula did not exhibit significantly lower diversification rates than more widespread lineages, in contrast with the hypothesis that the probability of speciation increases with range size by promoting geographic isolation and increasing the rate at which novel habitats are encountered. We suggest that stochastic long-distance dispersal events may balance allele frequencies across large spatial scales, leading to low genetic structure among geographically distant areas or even continents, ultimately decreasing the diversification rates in highly mobile, widespread lineages.
24.	Sim-Sim, Manuela, et al. (author) Integrative taxonomy reveals too extensive lumping and a new species in the moss genus Amphidium (Bryophyta) 2017 In: Systematics and Biodiversity. - : Informa UK Limited. - 1477-2000 .- 1478-0933. ; 15:5, s. 451-463 Journal article (peer-reviewed)abstract An integrative taxonomic approach, including molecular phylogenetic reconstructions based on plastid rps4-trnF and nuclear ITS sequences, statistical analysis of morphological-anatomical characters, and classical taxonomy, indicates that the reduction of 13 Amphidium species to three in a recent morphological revision represents a case of too extensive lumping. Instead, six Amphidium species can be distinguished based on molecular and morphological data, the widespread Amphidium lapponicum, A. mougeotii, and A. tortuosum, as well as the Macaronesian endemic A. curvipes, the North American endemic A. californicum, and a newly discovered species from Central Asia (southern Siberia and northern Mongolia), A. asiaticum sp. nov. Diagnostic morphological characters for all six species are discussed. The present data confirm that species diversity of Amphidium is highest in the Holarctic, where all six species occur.
25.	Steige, Kim A., et al. (author) Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora 2017 In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 114:5, s. 1087-1092 Journal article (peer-reviewed)abstract Understanding the causes of cis-regulatory variation is a long-standing aim in evolutionary biology. Although cis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants, and selective forces shaping cis-regulatory variation in the outcrossing plant Capsella grandiflora. We first identified a set of 1,010 genes with common cis-regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with common cis-regulatory variation (i) are underweaker purifying selection and (ii) undergo less frequent positive selection than other genes. We further identified genomic determinants of cis-regulatory variation. Gene body methylation (gbM) was a major factor constraining cis-regulatory variation, whereas presence of nearby transposable elements (TEs) and tissue specificity of expression increased the odds of ASE. Our results suggest that most common cis-regulatory variation in C. grandiflora is under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance of cis-regulatory variation than genome-scale variation in the intensity of selection. Our results agree with previous findings that suggest TE silencing affects nearby gene expression, and provide evidence for a link between gbM and cis-regulatory constraint, possibly reflecting greater dosage sensitivity of body-methylated genes. Given the extensive conservation of gbM in flowering plants, this suggests that gbM could be an important predictor of cis-regulatory variation in a wide range of plant species.
26.	Steige, Kim A., et al. (author) The impact of natural selection on the distribution of cis-regulatory variation across the genome of an outcrossing plant Other publication (other academic/artistic)
27.	Vanderpoorten, Alain, et al. (author) To what extent are bryophytes efficient dispersers? 2019 In: Journal of Ecology. - : Wiley. - 0022-0477 .- 1365-2745. ; 107:5, s. 2149-2154 Journal article (peer-reviewed)abstract 1. Bryophytes are typically seen as extremely efficient dispersers. Experimental evidence suggests that efficient short-distance dispersal coupled with random long-distance dispersal (LDD) leads to an inverse isolation effect. Under the latter, a higher genetic diversity of colonizing propagules is expected with increasing isolation, counteracting differentiation beyond the range of short-distance dispersal. 2. This expectation is tested from a review of evidence on spatial genetic structure and analyses of isolation-by-distance (IBD) at different scales. 3. A decay of the IBD signal, characterized by non-significant slopes between kinship coefficients and geographic distance was observed beyond 100 m. A second slope shift was observed at distances larger than 1 km, with a proportion of significant slopes in more than one third of the datasets. 4. The decay of the IBD signal beyond 100 m, which reflects efficient LDD, is consistent with the inverse isolation hypothesis. Persistence of a significant IBD signal at medium ranges in one third of the analysed cases suggests, however, that the inverse isolation effect is not a rule in bryophyte spore dispersal. Furthermore, the higher proportion of significant IBD patterns observed at scales over 100 km likely marks the limits of regional dispersal, beyond which an increasingly smaller proportion of spores travel. 5. Synthesis. We discuss the differences between experimental and genetic estimates of spore dispersal and conclude that geographic distance remains a significant proxy of spore colonization rates, with major consequences for our understanding of actual migration capacities in bryophytes, and hence, our capacity to model range shifts in a changing world.

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