| 1. |
- Bachmann, Jörg A., et al.
(author)
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Genetic basis and timing of a major mating system shift in Capsella
- 2019
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In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 224:1, s. 505-517
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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.
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| 2. |
- Désamorè, Aurélie, et al.
(author)
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Early burst in body size evolution is uncoupled from species diversification in diving beetles (Dytiscidae)
- 2018
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In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 27:4, s. 979-993
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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.
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| 3. |
- Desamore, Aurelie, et al.
(author)
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High migration rates shape the postglacial history of amphi-Atlantic bryophytes
- 2016
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In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 25:21, s. 5568-5584
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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.
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| 4. |
- Gil-Lopez, Manuel J., et al.
(author)
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Different historical backgrounds determine contrasting phylogeographical patterns in two co-distributed Erica species (Ericaceae) across the Strait of Gibraltar
- 2017
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In: Botanical journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4074 .- 1095-8339. ; 185:3, s. 359-375
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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.
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| 5. |
- Gutiérrez-Valencia, Juanita, 1991-, et al.
(author)
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Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum
- 2024
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In: Molecular biology and evolution. - 0737-4038 .- 1537-1719. ; 41:5
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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.
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| 6. |
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| 7. |
- Gutiérrez-Valencia, Juanita, et al.
(author)
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Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level
- 2022
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In: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 32:20, s. 4360-4371, 4371.e1-4371.e6
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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.
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| 8. |
- Gutiérrez-Valencia, Juanita, et al.
(author)
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Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina
- 2022
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In: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 39:1
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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.
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| 9. |
- Laenen, Benjamin, et al.
(author)
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Evolutionary origin of the latitudinal diversity gradient in liverworts
- 2018
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In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 127, s. 606-612
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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.
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| 10. |
- Laenen, Benjamin, et al.
(author)
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Geographical range in liverworts : does sex really matter?
- 2016
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In: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 43:3, s. 627-635
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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.
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