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Tenaillon, M. I., Burban, E., Huynh, S., Wojcik, A., Thuillet, A.-C., Manicacci, D., . . . Glemin, S. (2023). Crop domestication as a step toward reproductive isolation. American Journal of Botany, 110(7), Article ID e16173.
Open this publication in new window or tab >>Crop domestication as a step toward reproductive isolation
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2023 (English)In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 110, no 7, article id e16173Article in journal (Refereed) Published
Place, publisher, year, edition, pages
Wiley-Blackwell, 2023
Keywords
adaptive introgression, crop vulnerability, domestication load, genetic incompatibilities, genomic divergence, hybrid breakdown, mating system, speciation gene flow
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-512582 (URN)10.1002/ajb2.16173 (DOI)000997762200001 ()37087742 (PubMedID)
Available from: 2023-09-28 Created: 2023-09-28 Last updated: 2023-09-28Bibliographically approved
Duan, T., Sicard, A., Glémin, S. & Lascoux, M. (2023). Expression pattern of resynthesized allotetraploid Capsella is determined by hybridization, not whole genome duplication. New Phytologist, 237(1), 339-353
Open this publication in new window or tab >>Expression pattern of resynthesized allotetraploid Capsella is determined by hybridization, not whole genome duplication
2023 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 237, no 1, p. 339-353Article in journal (Refereed) Published
Abstract [en]
  • Polyploidization, the process leading to the increase in chromosome sets, is a major evolutionary transition in plants. Whole-genome duplication (WGD) within the same species gives rise to autopolyploids, whereas allopolyploids result from a compound process with two distinct components: WGD and interspecific hybridization.
  • To dissect the instant effects of WGD and hybridization on gene expression and phenotype, we created a series of synthetic hybrid and polyploid Capsella plants, including diploid hybrids, autotetraploids of both parental species, and two kinds of resynthesized allotetraploids with different orders of WGD and hybridization.
  • Hybridization played a major role in shaping the relative expression pattern of the neo-allopolyploids, whereas WGD had almost no immediate effect on relative gene expression pattern but, nonetheless, still affected phenotypes. No transposable element-mediated genomic shock scenario was observed in either neo-hybrids or neo-polyploids. Finally, WGD and hybridization interacted and the distorting effects of WGD were less strong in hybrids. Whole-genome duplication may even improve hybrid fertility.
  • In summary, while the initial relative gene expression pattern in neo-allotetraploids was almost entirely determined by hybridization, WGD only had trivial effects on relative expression patterns, both processes interacted and had a strong impact on physical attributes and meiotic behaviors.
Place, publisher, year, edition, pages
John Wiley & Sons, 2023
Keywords
Capsella bursa-pastoris, Gene expression, Hybridization, Neopolyploid lines, Polyploidy
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-487259 (URN)10.1111/nph.18542 (DOI)000879474700001 ()36254103 (PubMedID)
Funder
Swedish Research Council, 2019-00806Stiftelsen Akademiens Nilsson-Ehle medaljRoyal Physiographic Society in LundErik Philip-Sörensens stiftelseSven och Lilly Lawskis fond för naturvetenskaplig forskningSwedish National Infrastructure for Computing (SNIC)Swedish Research Council, 2018-05973
Available from: 2022-10-26 Created: 2022-10-26 Last updated: 2023-03-09Bibliographically approved
Anderson, B., Pannell, J., Billiard, S., Burgarella, C., de Boer, H., Dufay, M., . . . Glemin, S. (2023). Opposing effects of plant traits on diversification. iScience, 26(4), Article ID 106362.
Open this publication in new window or tab >>Opposing effects of plant traits on diversification
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2023 (English)In: iScience, E-ISSN 2589-0042, Vol. 26, no 4, article id 106362Article in journal (Refereed) Published
Abstract [en]

Species diversity can vary dramatically across lineages due to differences in speciation and extinction rates. Here, we explore the effects of several plant traits on diversification, finding that most traits have opposing effects on diversification. For example, outcrossing may increase the efficacy of selection and adaptation but also decrease mate availability, two processes with contrasting effects on lineage persistence. Such opposing trait effects can manifest as differences in diversification rates that depend on ecological context, spatiotemporal scale, and associations with other traits. The complexity of pathways linking traits to diversification suggests that the mechanistic underpinnings behind their correlations may be difficult to interpret with any certainty, and context dependence means that the effects of specific traits on diversification are likely to differ across multiple lineages and timescales. This calls for taxonomically and context-controlled approaches to studies that correlate traits and diversification.

Place, publisher, year, edition, pages
Cell Press, 2023
Keywords
Biological sciences, Evolutionary biology, Evolutionary theories, Plant biology, Plant population biology
National Category
Evolutionary Biology Ecology
Identifiers
urn:nbn:se:uu:diva-502637 (URN)10.1016/j.isci.2023.106362 (DOI)001016421700001 ()37034980 (PubMedID)
Funder
EU, Horizon 2020, 839643
Available from: 2023-05-29 Created: 2023-05-29 Last updated: 2024-01-16Bibliographically approved
Helmstetter, A. J., Zenil‐Ferguson, R., Sauquet, H., Otto, S. P., Méndez, M., Vallejo‐Marín, M., . . . Käfer, J. (2023). Trait‐dependent diversification in angiosperms: Patterns, models and data. Ecology Letters, 26(4), 640-657
Open this publication in new window or tab >>Trait‐dependent diversification in angiosperms: Patterns, models and data
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2023 (English)In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 26, no 4, p. 640-657Article in journal (Refereed) Published
Abstract [en]

Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous, and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about their relative importance and how they interact. Here, we synthesised data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, SSE model results were correlated to data set properties - trees that were larger, older or less well-sampled tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species' ecology, demography and genetics.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
National Category
Ecology Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-499137 (URN)10.1111/ele.14170 (DOI)000939689500001 ()36829296 (PubMedID)
Available from: 2023-03-23 Created: 2023-03-23 Last updated: 2023-05-26Bibliographically approved
Orsucci, M., Yang, X., Vanikiotis, T., Guerrina, M., Duan, T., Lascoux, M. & Glemin, S. (2022). Competitive ability depends on mating system and ploidy level across Capsella species. Annals of Botany, 129(6), 697-708
Open this publication in new window or tab >>Competitive ability depends on mating system and ploidy level across Capsella species
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2022 (English)In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 129, no 6, p. 697-708Article in journal (Refereed) Published
Abstract [en]

Background and Aims: Self-fertilization is often associated with ecological traits corresponding to the ruderal strategy, and selfers are expected to be less competitive than outcrossers, either because of a colonization/competition trade-off or because of the deleterious genetic effects of selfing. Range expansion could reduce further competitive ability while polyploidy could mitigate the effects of selfing. If pollinators are not limited, individual fitness is thus expected to be higher in outcrossers than in selfers and, within selfers, in polyploids than in diploids. Although often proposed in the botanical literature and also suggested by meta-analyses, these predictions have not been directly tested yet.

Methods: In order to compare fitness and the competitive ability of four Capsella species with a different mating system and ploidy level, we combined two complementary experiments. First, we carried out an experiment outdoors in north-west Greece, i.e. within the range of the obligate outcrossing species, C. grandiflora, where several life history traits were measured under two different disturbance treatments, weeded plots vs. unweeded plots. To better control competition and to remove potential effects of local adaptation of the outcrosser, we also performed a similar competition experiment but under growth chamber conditions.

Key Results: In the outdoor experiment, disturbance of the environment did not affect the phenotype in any of the four species. For most traits, the obligate outcrossing species performed better than all selfing species. In contrast, polyploids did not survive or reproduce better than diploids. Under controlled conditions, as in the field experiment, the outcrosser had a higher fitness than selfing species and was less affected by competition. Finally, contrary to the outdoor experiment where the two behaved identically, polyploid selfers were less affected by competition than diploid selfes.

Conclusions: In the Capsella genus, selfing induces lower fitness than outcrossing and can also reduce competitive ability. The effect of polyploidy is, however, unclear. These results highlight the possible roles of ecological context in the evolution of selfing species.

Place, publisher, year, edition, pages
Oxford University Press (OUP), 2022
Keywords
Mating system, ploidy, life history traits, environmental disturbance
National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-476186 (URN)10.1093/aob/mcac044 (DOI)000796693200002 ()35325927 (PubMedID)
Funder
Swedish Research Council, VR 2019-03503Swedish Research Council, 2018-05973Swedish National Infrastructure for Computing (SNIC), SNIC 2021/22-291
Note

De två första författarna delar förstaförfattarskapet

Available from: 2022-06-08 Created: 2022-06-08 Last updated: 2022-06-08Bibliographically approved
Brazier, T. & Glémin, S. (2022). Diversity and determinants of recombination landscapes in flowering plants. PLOS Genetics, 18(8), Article ID e1010141.
Open this publication in new window or tab >>Diversity and determinants of recombination landscapes in flowering plants
2022 (English)In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 18, no 8, article id e1010141Article in journal (Refereed) Published
Abstract [en]

During meiosis, crossover rates are not randomly distributed along the chromosome and their location may have a strong impact on the functioning and evolution of the genome. To date, the broad diversity of recombination landscapes among plants has rarely been investigated and a formal comparative genomic approach is still needed to characterize and assess the determinants of recombination landscapes among species and chromosomes. We gathered genetic maps and genomes for 57 flowering plant species, corresponding to 665 chromosomes, for which we estimated large-scale recombination landscapes. We found that the number of crossover per chromosome spans a limited range (between one to five/six) whatever the genome size, and that there is no single relationship across species between genetic map length and chromosome size. Instead, we found a general relationship between the relative size of chromosomes and recombination rate, while the absolute length constrains the basal recombination rate for each species. At the chromosome level, we identified two main patterns (with a few exceptions) and we proposed a conceptual model explaining the broad-scale distribution of crossovers where both telomeres and centromeres play a role. These patterns correspond globally to the underlying gene distribution, which affects how efficiently genes are shuffled at meiosis. These results raised new questions not only on the evolution of recombination rates but also on their distribution along chromosomes.

Place, publisher, year, edition, pages
Public Library of Science (PLoS), 2022
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-489596 (URN)10.1371/journal.pgen.1010141 (DOI)000886644100003 ()36040927 (PubMedID)
Available from: 2022-12-02 Created: 2022-12-02 Last updated: 2023-04-04Bibliographically approved
Trickovic, B. & Glemin, S. (2022). Establishment of local adaptation in partly self-fertilizing populations. Genetics, 220(2), Article ID iyab201.
Open this publication in new window or tab >>Establishment of local adaptation in partly self-fertilizing populations
2022 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 220, no 2, article id iyab201Article in journal (Refereed) Published
Abstract [en]

Populations often inhabit multiple ecological patches and thus experience divergent selection, which can lead to local adaptation if migration is not strong enough to swamp locally adapted alleles. Conditions for the establishment of a locally advantageous allele have been studied in randomly mating populations. However, many species reproduce, at least partially, through self-fertilization, and how selfing affects local adaptation remains unclear and debated. Using a two-patch branching process formalism, we obtained a closed-form approximation under weak selection for the probability of establishment of a locally advantageous allele (P) for arbitrary selfing rate and dominance level, where selection is allowed to act on viability or fecundity, and migration can occur via seed or pollen dispersal. This solution is compared to diffusion approximation and used to investigate the consequences of a shift in a mating system on P, and the establishment of protected polymorphism. We find that selfing can either increase or decrease P, depending on the patterns of dominance in the two patches, and has conflicting effects on local adaptation. Globally, selfing favors local adaptation when locally advantageous alleles are (partially) recessive, when selection between patches is asymmetrical and when migration occurs through pollen rather than seed dispersal. These results establish a rigorous theoretical background to study heterogeneous selection and local adaptation in partially selfing species. Trickovic and Glemin obtain a closed-form solution for the establishment probability (P) of a locally advantageous allele under an arbitrary population selfing rate, different modes of selection (viability or fecundity selection), and migration (seed or pollen). They investigate the conditions under which selfing facilitates or impedes the establishment of an allele and the protected polymorphism.

Place, publisher, year, edition, pages
Oxford University Press (OUP), 2022
Keywords
branching process, local adaptation, migration-selection balance, protected polymorphism, selfing
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-470966 (URN)10.1093/genetics/iyab201 (DOI)000761458000013 ()34791199 (PubMedID)
Available from: 2022-04-01 Created: 2022-04-01 Last updated: 2022-04-01Bibliographically approved
Zhang, Z., Kryvokhyzha, D., Orsucci, M., Glemin, S., Milesi, P. & Lascoux, M. (2022). How broad is the selfing syndrome? Insights from convergent evolution of gene expression across species and tissues in the Capsella genus. New Phytologist, 236(6), 2344-2357
Open this publication in new window or tab >>How broad is the selfing syndrome? Insights from convergent evolution of gene expression across species and tissues in the Capsella genus
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2022 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 236, no 6, p. 2344-2357Article in journal (Refereed) Published
Abstract [en]

The shift from outcrossing to selfing is one of the main evolutionary transitions in plants. It is accompanied by profound effects on reproductive traits, the so-called selfing syndrome. Because the transition to selfing also implies deep genomic and ecological changes, one also expects to observe a genomic selfing syndrome. We took advantage of the three independent transitions from outcrossing to selfing in the Capsella genus to characterize the overall impact of mating system change on RNA expression, in flowers but also in leaves and roots. We quantified the extent of both selfing and genomic syndromes, and tested whether changes in expression corresponded to adaptation to selfing or to relaxed selection on traits that were constrained in outcrossers. Mating system change affected gene expression in all three tissues but more so in flowers than in roots and leaves. Gene expression in selfing species tended to converge in flowers but diverged in the two other tissues. Hence, convergent adaptation to selfing dominates in flowers, whereas genetic drift plays a more important role in leaves and roots. The effect of mating system transition is not limited to reproductive tissues and corresponds to both adaptation to selfing and relaxed selection on previously constrained traits.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2022
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-492292 (URN)10.1111/nph.18477 (DOI)000861911600001 ()36089898 (PubMedID)
Funder
Swedish Research Council, 2019‐03502Swedish National Infrastructure for Computing (SNIC)Swedish Research Council, 2018-05973
Note

De två sista författarna delar sistaförfattarskapet.

Available from: 2023-01-03 Created: 2023-01-03 Last updated: 2023-10-31Bibliographically approved
Chen, J., Bataillon, T., Glemin, S. & Lascoux, M. (2022). Hunting for Beneficial Mutations: Conditioning on SIFT Scores When Estimating the Distribution of Fitness Effect of New Mutations. Genome Biology and Evolution, 14(1)
Open this publication in new window or tab >>Hunting for Beneficial Mutations: Conditioning on SIFT Scores When Estimating the Distribution of Fitness Effect of New Mutations
2022 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 14, no 1Article in journal (Refereed) Published
Abstract [en]

The distribution of fitness effects (DFE) of new mutations is a key parameter of molecular evolution. The DFE can in principle be estimated by comparing the site frequency spectra (SFS) of putatively neutral and functional polymorphisms. Unfortunately, the DFE is intrinsically hard to estimate, especially for beneficial mutations because these tend to be exceedingly rare. There is therefore a strong incentive to find out whether conditioning on properties of mutations that are independent of the SFS could provide additional information. In the present study, we developed a new measure based on SIFT scores. SIFT scores are assigned to nucleotide sites based on their level of conservation across a multispecies alignment: the more conserved a site, the more likely mutations occurring at this site are deleterious, and the lower the SIFT score. If one knows the ancestral state at a given site, one can assign a value to new mutations occurring at the site based on the change of SIFT score associated with the mutation. We called this new measure delta. We show that properties of the DFE as well as the flux of beneficial mutations across classes covary with delta and, hence, that SIFT scores are informative when estimating the fitness effect of new mutations. In particular, conditioning on SIFT scores can help to characterize beneficial mutations.

Place, publisher, year, edition, pages
Oxford University Press (OUP), 2022
Keywords
SIFT, DFE, beneficial mutations
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-467400 (URN)10.1093/gbe/evab151 (DOI)000747583400003 ()34180988 (PubMedID)
Funder
Swedish Research Council
Available from: 2022-02-18 Created: 2022-02-18 Last updated: 2022-02-18Bibliographically approved
Marie-Orleach, L., Brochmann, C. & Glemin, S. (2022). Mating system and speciation I: Accumulation of genetic incompatibilities in allopatry. PLOS Genetics, 18(12), Article ID e1010353.
Open this publication in new window or tab >>Mating system and speciation I: Accumulation of genetic incompatibilities in allopatry
2022 (English)In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 18, no 12, article id e1010353Article in journal (Refereed) Published
Abstract [en]

Self-fertilisation is widespread among hermaphroditic species across the tree of life. Selfing has many consequences on the genetic diversity and the evolutionary dynamics of populations, which may in turn affect macroevolutionary processes such as speciation. On the one hand, because selfing increases genetic drift and reduces migration rate among populations, it may be expected to promote speciation. On the other hand, because selfing reduces the efficacy of selection, it may be expected to hamper ecological speciation. To better understand under which conditions and in which direction selfing affects the build-up of reproductive isolation, an explicit population genetics model is required. Here, we focus on the interplay between genetic drift, selection and genetic linkage by studying speciation without gene flow. We test how fast populations with different rates of selfing accumulate mutations leading to genetic incompatibilities. When speciation requires populations to pass through a fitness valley caused by underdominant and compensatory mutations, selfing reduces the depth and/or breadth of the valley, and thus overall facilitates the fixation of incompatibilities. When speciation does not require populations to pass through a fitness valley, as for Bateson-Dobzhanzky-Muller incompatibilities (BDMi), the lower effective population size and higher genetic linkage in selfing populations both facilitate the fixation of incompatibilities. Interestingly, and contrary to intuitive expectations, local adaptation does not always accelerate the fixation of incompatibilities in outcrossing relative to selfing populations. Our work helps to clarify how incompatibilities accumulate in selfing vs. outcrossing lineages, and has repercussions on the pace of speciation as well as on the genetic architecture of reproductive isolation.

Place, publisher, year, edition, pages
PUBLIC LIBRARY SCIENCE, 2022
National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-498156 (URN)10.1371/journal.pgen.1010353 (DOI)000924505200007 ()36520924 (PubMedID)
Funder
The Research Council of Norway, 274607
Available from: 2023-03-15 Created: 2023-03-15 Last updated: 2023-03-15Bibliographically approved
Projects
Tackling the Lewontin´s paradox in plants [2022-03099_VR]; Uppsala University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-7260-4573

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