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James, J., Kastally, C., Budde, K. B., Gonzalez-Martinez, S. C., Milesi, P., Pyhajarvi, T. & Lascoux, M. (2023). Between but Not Within-Species Variation in the Distribution of Fitness Effects. Molecular biology and evolution, 40(11), Article ID msad228.
Open this publication in new window or tab >>Between but Not Within-Species Variation in the Distribution of Fitness Effects
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2023 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 40, no 11, article id msad228Article in journal (Refereed) Published
Abstract [en]

New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is, therefore, of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, that is whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterized the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence, and genetic background. We find statistical support for the presence of variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and those evolutionarily recent events, such as demographic changes and local adaptation, have little impact.

Place, publisher, year, edition, pages
Oxford University Press, 2023
Keywords
DFE, deleterious mutations, population structure, forest trees
National Category
Genetics Botany Other Environmental Engineering
Identifiers
urn:nbn:se:uu:diva-518769 (URN)10.1093/molbev/msad228 (DOI)001100887100002 ()37832225 (PubMedID)
Available from: 2023-12-22 Created: 2023-12-22 Last updated: 2023-12-22Bibliographically approved
Tiret, M., Olsson, L., Grahn, T., Karlsson, B., Milesi, P., Lascoux, M., . . . García‐Gil, M. R. (2023). Divergent selection predating the Last Glacial Maximum mainly acted on macro‐phenotypes in Norway spruce. Evolutionary Applications, 16(1), 163-172
Open this publication in new window or tab >>Divergent selection predating the Last Glacial Maximum mainly acted on macro‐phenotypes in Norway spruce
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2023 (English)In: Evolutionary Applications, E-ISSN 1752-4571, Vol. 16, no 1, p. 163-172Article in journal (Refereed) Published
Abstract [en]

The current distribution and population structure of many species were, to a large extent, shaped by cycles of isolation in glacial refugia and subsequent population expansions. Isolation in and postglacial expansion through heterogeneous environments led to either neutral or adaptive divergence. Norway spruce is no exception, and its current distribution is the consequence of a constant interplay between evolutionary and demographic processes. We investigated population differentiation and adaptation of Norway spruce for juvenile growth, diameter of the stem, wood density, and tracheid traits at breast height. Data from 4461 phenotyped and genotyped Norway spruce from 396 half-sib families in two progeny tests were used to test for divergent selection in the framework of QST vs. FST. We show that the macroscopic resultant trait (stem diameter), unlike its microscopic components (tracheid dimensions) and juvenile growth, was under divergent selection that predated the Last Glacial Maximum. Altogether, the current variation in these phenotypic traits in Norway spruce is better explained by local adaptation to ancestral environments than to current ones, where populations were partly preadapted, mainly through growth-related traits.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
National Category
Ecology
Identifiers
urn:nbn:se:uu:diva-492268 (URN)10.1111/eva.13519 (DOI)000901493100001 ()36699125 (PubMedID)
Funder
Swedish University of Agricultural SciencesUppsala University
Available from: 2023-01-03 Created: 2023-01-03 Last updated: 2023-10-24Bibliographically 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
Leal, L. J., Milesi, P., Salojarvi, J. & Lascoux, M. (2023). Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences. Systematic Biology, 72(2), 372-390
Open this publication in new window or tab >>Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences
2023 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 72, no 2, p. 372-390Article in journal (Refereed) Published
Abstract [en]

Phylogenetic analysis of polyploid hybrid species has long posed a formidable challenge as it requires the ability to distinguish between alleles of different ancestral origins in order to disentangle their individual evolutionary history. This problem has been previously addressed by conceiving phylogenies as reticulate networks, using a two-step phasing strategy that first identifies and segregates homoeologous loci and then, during a second phasing step, assigns each gene copy to one of the subgenomes of an allopolyploid species. Here, we propose an alternative approach, one that preserves the core idea behind phasing-to produce separate nucleotide sequences that capture the reticulate evolutionary history of a polyploid-while vastly simplifying its implementation by reducing a complex multistage procedure to a single phasing step. While most current methods used for phylogenetic reconstruction of polyploid species require sequencing reads to be pre-phased using experimental or computational methods-usually an expensive, complex, and/or time-consuming endeavor-phasing executed using our algorithm is performed directly on the multiple-sequence alignment (MSA), a key change that allows for the simultaneous segregation and sorting of gene copies. We introduce the concept of genomic polarization that, when applied to an allopolyploid species, produces nucleotide sequences that capture the fraction of a polyploid genome that deviates from that of a reference sequence, usually one of the other species present in the MSA. We show that if the reference sequence is one of the parental species, the polarized polyploid sequence has a close resemblance (high pairwise sequence identity) to the second parental species. This knowledge is harnessed to build a new heuristic algorithm where, by replacing the allopolyploid genomic sequence in the MSA by its polarized version, it is possible to identify the phylogenetic position of the polyploid's ancestral parents in an iterative process. The proposed methodology can be used with long-read and short-read high-throughput sequencing data and requires only one representative individual for each species to be included in the phylogenetic analysis. In its current form, it can be used in the analysis of phylogenies containing tetraploid and diploid species. We test the newly developed method extensively using simulated data in order to evaluate its accuracy. We show empirically that the use of polarized genomic sequences allows for the correct identification of both parental species of an allotetraploid with up to 97% certainty in phylogenies with moderate levels of incomplete lineage sorting (ILS) and 87% in phylogenies containing high levels of ILS. We then apply the polarization protocol to reconstruct the reticulate histories of Arabidopsis kamchatica and Arabidopsis suecica, two allopolyploids whose ancestry has been well documented. [Allopolyploidy; Arabidopsis; genomic polarization; homoeologs; incomplete lineage sorting; phasing; polyploid phylogenetics; reticulate evolution.]

Place, publisher, year, edition, pages
Oxford University Press, 2023
National Category
Evolutionary Biology Biological Systematics
Identifiers
urn:nbn:se:uu:diva-511328 (URN)10.1093/sysbio/syad009 (DOI)000980207200001 ()36932679 (PubMedID)
Funder
Swedish Research Council Formas, 2016-00780Swedish Research Council Formas, 2020-01456Swedish Research Council, 2020-01456Vinnova, 2020-01456
Available from: 2023-09-12 Created: 2023-09-12 Last updated: 2023-09-12Bibliographically approved
Ament-Velásquez, S. L., Vogan, A. A., Granger-Farbos, A., Bastiaans, E., Martinossi-Allibert, I., Saupe, S. J., . . . Johannesson, H. (2022). Allorecognition genes drive reproductive isolation in Podospora anserina. Nature Ecology & Evolution, 6(7), 910-923
Open this publication in new window or tab >>Allorecognition genes drive reproductive isolation in Podospora anserina
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2022 (English)In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 6, no 7, p. 910-923Article in journal (Refereed) Published
Abstract [en]

Allorecognition, the capacity to discriminate self from conspecific non-self, is a ubiquitous organismal feature typically governed by genes evolving under balancing selection. Here, we show that in the fungus Podospora anserina, allorecognition loci controlling vegetative incompatibility (het genes), define two reproductively isolated groups through pleiotropic effects on sexual compatibility. These two groups emerge from the antagonistic interactions of the unlinked loci het-r (encoding a NOD-like receptor) and het-v (encoding a methyltransferase and an MLKL/HeLo domain protein). Using a combination of genetic and ecological data, supported by simulations, we provide a concrete and molecularly defined example whereby the origin and coexistence of reproductively isolated groups in sympatry is driven by pleiotropic genes under balancing selection.

Place, publisher, year, edition, pages
Springer Nature, 2022
Keywords
Podospora, Genetics, Speciation, Reproductive isolation, allorecognition, heterokaryon incompatibility genes, vegetative incompatibility, balancing selection, selfing
National Category
Evolutionary Biology
Research subject
Biology with specialization in Systematics; Biology with specialization in Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-406878 (URN)10.1038/s41559-022-01734-x (DOI)000794102000002 ()35551248 (PubMedID)
Funder
Swedish National Infrastructure for Computing (SNIC), 2017/1-567Swedish National Infrastructure for Computing (SNIC), 2019/8-371EU, European Research Council, ERC-2014-CoGEU, European Research Council, 648143Swedish Research Council, 2015-04649Stiftelsen Anna Maria Lundins stipendiefond
Available from: 2020-03-27 Created: 2020-03-27 Last updated: 2022-09-22Bibliographically 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
Fu, R., Zhu, Y., Liu, Y., Feng, Y., Lu, R.-S., Li, Y., . . . Chen, J. (2022). Genome-wide analyses of introgression between two sympatric Asian oak species. Nature Ecology & Evolution, 6(7), 924-+
Open this publication in new window or tab >>Genome-wide analyses of introgression between two sympatric Asian oak species
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2022 (English)In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 6, no 7, p. 924-+Article in journal (Refereed) Published
Abstract [en]

Introgression can be an important source of new alleles for adaption under rapidly changing environments, perhaps even more important than standing variation. Though introgression has been extensively studied in many plants and animals, key questions on the underlying mechanisms of introgression still remain unanswered. In particular, we are yet to determine the genomic distribution of introgressed regions along the genome; whether the extent and patterns of introgression are influenced by ecological factors; and when and how introgression contributes to adaptation. Here, we generated high-quality genomic resources for two sympatric widespread Asian oak species, Quercus acutissima and Q. variabilis, sampled in multiple forests to study introgression between them. We show that introgressed regions are broadly distributed across the genome. Introgression was affected by genetic divergence between pairs of populations and by the similarity of the environments in which they live-populations occupying similar ecological sites tended to share the same introgressed regions. Introgressed genomic footprints of adaptation were preferentially located in regions with suppressed recombination rate. Introgression probably confers adaptation in these oak populations by introducing allelic variation in cis-regulatory elements, in particular through transposable element insertions, thereby altering the regulation of genes related to stress. Our results provide new avenues of research for uncovering mechanisms of adaptation due to hybridization in sympatric species. Introgression is an important source of genetic variation. Analysing genomes of two sympatric widespread Asian oak species, the authors find introgression across the genome and signatures of adaptive introgression in regions with suppressed recombination rate.

Place, publisher, year, edition, pages
Springer Nature, 2022
National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-485710 (URN)10.1038/s41559-022-01754-7 (DOI)000791115700003 ()35513577 (PubMedID)
Available from: 2022-09-27 Created: 2022-09-27 Last updated: 2022-09-27Bibliographically approved
Saleh, D., Chen, J., Leple, J.-C., Leroy, T., Truffaut, L., Dencausse, B., . . . Kremer, A. (2022). Genome-wide evolutionary response of European oaks during the Anthropocene. Evolution Letters, 6(1), 4-20
Open this publication in new window or tab >>Genome-wide evolutionary response of European oaks during the Anthropocene
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2022 (English)In: Evolution Letters, E-ISSN 2056-3744, Vol. 6, no 1, p. 4-20Article in journal (Refereed) Published
Abstract [en]

The pace of tree microevolution during Anthropocene warming is largely unknown. We used a retrospective approach to monitor genomic changes in oak trees since the Little Ice Age (LIA). Allelic frequency changes were assessed from whole-genome pooled sequences for four age-structured cohorts of sessile oak (Quercus petraea) dating back to 1680, in each of three different oak forests in France. The genetic covariances of allelic frequency changes increased between successive time periods, highlighting genome-wide effects of linked selection. We found imprints of parallel linked selection in the three forests during the late LIA, and a shift of selection during more recent time periods of the Anthropocene. The changes in allelic covariances within and between forests mirrored the documented changes in the occurrence of extreme events (droughts and frosts) over the last 300 years. The genomic regions with the highest covariances were enriched in genes involved in plant responses to pathogens and abiotic stresses (temperature and drought). These responses are consistent with the reported sequence of frost (or drought) and disease damage ultimately leading to the oak dieback after extreme events. They provide support for adaptive evolution of long-lived species during recent climatic changes. Although we acknowledge that other sources (e.g., gene flow, generation overlap) may have contributed to temporal covariances of allelic frequency changes, the consistent and correlated response across the three forests lends support to the existence of a systematic driving force such as natural selection.

Place, publisher, year, edition, pages
John Wiley & Sons, 2022
Keywords
Anthropocene, evolution, linked selection, Little Ice Age, Quercus petraea
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-485714 (URN)10.1002/evl3.269 (DOI)000746496700001 ()35127134 (PubMedID)
Funder
EU, European Research Council, FP7-339728
Available from: 2022-09-27 Created: 2022-09-27 Last updated: 2023-01-03Bibliographically 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
Projects
Sustainable biological resources management in the genomic era: reconstructing the past to predict the future [2007-00433_Formas]; Uppsala UniversityHow predictable is genetic evolution at the species and population levels? On the effects of polyploidy and history [2012-04999_VR]; Uppsala UniversityLife at the Edge: Evolutionary Conservation Biology of the Euphrates poplar (Populus euphratica) along North African riparian systems [2014-04322_VR]; Uppsala UniversityIs adaptive evolution pervasive? On the effects of levels of biological integration and polyploidy [2015-03797_VR]; Uppsala UniversityHow to survive a macromutation: evolution of gene expression and the burden of deleterious mutations during an allopolyploid hop [2019-03503_VR]; Uppsala UniversitySetting the stage for genomic selection in birch in a changing climate [2020-01456_Formas]; Uppsala UniversityThe evolution of the genetic architecture of an allopolyploid and the genetic basis of the selfing syndrome [2023-03904_VR]; Uppsala University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-1699-9042

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