Mimmi C. Eriksson

University of Vienna

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Ovidiu Paun

University of Vienna

Thomas M. Wolfe

University of Vienna

Stephen Wright

Clemson University

Mikael Hedrén

Lund University

Tianlin Duan

Science for Life Laboratory

Dmytro Kryvokhyzha

Lund University

Katie Emelianova

UK Dementia Research Institute

Sylvain Glémin

Centre National de la Recherche Scientifique

Julia M. Kreiner

University of Chicago

Martin Lascoux

Uppsala University

Cooperative Institutions

University of Vienna

Institut de Biologia Evolutiva

Science for Life Laboratory

Uppsala University

Swedish University of Agricultural Sciences

University of Toronto

Royal Botanic Gardens, Kew

Czech Academy of Sciences, Biology Centre

University of Sheffield

Australian National University

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Current research frontiers in plant epigenetics: an introduction to a Virtual Issue

New Phytologist (2020)

Mimmi C. Eriksson Aglaia Szukala Bin Tian Ovidiu Paun

Link to the Virtual Special Issue

10.1111/nph.16493

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Citations (30)

Parental legacy, demography, and introgression influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)

bioRxiv (Cold Spring Harbor Laboratory) (2017)

Dmytro Kryvokhyzha Adriana Salcedo Mimmi C. Eriksson Tianlin Duan Nilesh R. Tawari

Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species and how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (Cg) and the other one from the selfing and genetically depauperate Capsella orientalis (Co). For each subgenome, we assessed its relationship with the diploid relatives, temporal change of effective population size N e , signatures of positive and negative selection, and gene expression patterns. Introgression between C. bursa-pastoris and its diploid relatives was widespread and the two subgenomes were impacted differentially depending on geographic region. In all three regions, Ne of the two subgenomes decreased gradually and the Co subgenome accumulated more deleterious changes than Cg. Selective sweeps were more common on the Cg subgenome in Europe and the Middle East, and on the Co subgenome in Asia. In contrast, differences in expression were limited with the Cg subgenome slightly more expressed than Co in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy and were differentially affected by introgression and selection.

Introgression

Selfing

Outcrossing

Polyploid

10.1101/234096

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Citations (3)

Small RNAs regulation and genomic harmony: insights into allopolyploid evolution in marsh orchids (Dactylorhiza)

bioRxiv (Cold Spring Harbor Laboratory) (2024)

Mimmi C. Eriksson Matthew E. Thornton Emiliano Trucchi Thomas M. Wolfe Francisco Balao

Hybridization and polyploidy are prevalent drivers of speciation, with novel ecological properties potentially arising, among other mechanisms, through changes in gene regulation by small RNAs (smRNAs), linked to transposable element (TE) dynamics. With a common garden set-up, we comparatively investigated smRNA abundance in two young, but widely distributed, ecologically divergent sibling allotetraploid marsh orchids ( Dactylorhiza majalis and D. traunsteineri ) and their diploid parents. Despite independent origins, the allopolyploids appear to share a substantial portion of smRNA targeting, with transgressive smRNA targeting consistently overexpressed in both, related to key genes regulating transcription, cell division, and biotic and abiotic stress responses. TE-targeting smRNAs also display shared patterns between the sibling allopolyploids, with 20-23 nt smRNAs following the maternal and smaller genome, whereas 24 nt smRNAs targeting typically resembling the level of the paternal and larger genome. However, differences between the allopolyploids are also evident, with the older allopolyploid D. majalis often showing higher regulation by smRNAs, appearing more focused on fine-tuning gene copy regulation, whereas its younger sibling D. traunsteineri exhibits stronger non-additive expression, more prominently reflecting an apparent ongoing resolution of post-polyploidization meiotic/mitotic challenges. These findings highlight shared and species-specific smRNA dynamics, revealing how allopolyploids balance genomic instability and adaptive regulation during their evolutionary trajectories. In this system, the younger D. traunsteineri seems to prioritize stabilizing its genome, while the older D. majalis shifted towards optimizing gene expression. Together, this study emphasizes the role of smRNAs in facilitating ecological novelty and speciation during post-polyploidization evolution, providing insights into molecular mechanisms and adaptive evolution.

Evolutionary Dynamics

10.1101/2024.11.29.626004

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Ecological divergence of sibling allopolyploid marsh orchids is associated with species specific plasticity and distinct fungal communities

The Plant Journal (2025)

Katie Emelianova Anna‐Sophie Hawranek Mimmi C. Eriksson Thomas M. Wolfe Ovidiu Paun

SUMMARY Phenotypic plasticity, the dynamic adjustment of traits to environmental variations, is crucial for enabling species to exploit broader niches and withstand suboptimal conditions. This adaptability is particularly relevant for newly formed allopolyploids, which possess redundant gene copies and must become established in diverse environments distinct from their parents and other relatives. By evaluating gene expression and root mycobiome among two ecologically divergent sibling allopolyploid marsh orchids ( Dactylorhiza majalis and D. traunsteineri ) in reciprocal transplants at localities where both species are native, we aimed to understand the drivers of species persistence in the face of interspecific gene flow. Despite consistent abiotic differences characterising the alternative environments at each locality, the majority of gene expression differences between the allopolyploids appears to be plastic. Ecologically relevant processes, such as photosynthesis and transmembrane transport, include some genes that are differentially expressed between the two orchids regardless of the environment, while others change their activity plastically in one species or the other. This suggests that although plasticity helps define the specific ecological range of each sibling allopolyploid, it also mediates gene flow between them, thereby preventing differentiation. Extending our investigations to the root mycobiome, we uncover more diverse fungal communities for either species when grown in the environment with nutrient‐poor soils, indicating that both abiotic and biotic factors drive the distribution of sibling marsh orchids. Altogether, our results indicate that plasticity can simultaneously promote diversification and homogenisation of lineages, influencing the establishment and persistence of recurrently formed allopolyploid species.

10.1111/tpj.70001

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Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)

PLoS Genetics (2019)

Dmytro Kryvokhyzha Adriana Salcedo Mimmi C. Eriksson Tianlin Duan Nilesh R. Tawari

Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species nor how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe, and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (CbpCg) and the other one from the selfing and genetically depauperate Capsella orientalis (CbpCo). For each subgenome, we assessed its relationship with the diploid relatives, temporal changes of effective population size (Ne), signatures of positive and negative selection, and gene expression patterns. In all three regions, Ne of the two subgenomes decreased gradually over time and the CbpCo subgenome accumulated more deleterious changes than CbpCg. There were signs of widespread admixture between C. bursa-pastoris and its diploid relatives. The two subgenomes were impacted differentially depending on geographic region suggesting either strong interploidy gene flow or multiple origins of C. bursa-pastoris. Selective sweeps were more common on the CbpCg subgenome in Europe and the Middle East, and on the CbpCo subgenome in Asia. In contrast, differences in expression were limited with the CbpCg subgenome slightly more expressed than CbpCo in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy but their evolutionary trajectory strongly varied across geographic regions.

Selfing

Outcrossing

Polyploid

10.1371/journal.pgen.1007949

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Citations (50)

Ecological divergence is marked by species specific plastic gene expression and distinct rhizosphere among sibling allopolyploid marsh orchids (Dactylorhiza)

bioRxiv (Cold Spring Harbor Laboratory) (2024)

Katie Emelianova Anna‐Sophie Hawranek Mimmi C. Eriksson Thomas M. Wolfe Ovidiu Paun

Abstract Phenotypic plasticity, the dynamic adjustment of traits to environmental variations, is pivotal to enabling species to exploit broader niches and withstand suboptimal conditions. This adaptability is expected to be particularly relevant for newly formed allopolyploids, which have redundant gene copies and must establish themselves in diverse environments, distinct from their parents and other relatives. Here we investigate ecologically divergent sibling allopolyploid marsh orchids ( Dactylorhiza ) through reciprocal transplantation experiments at two localities to understand the drivers of ecological divergence and species persistence in the face of interspecific gene flow. Although consistent abiotic differences characterise the alternative environments, the great majority of gene expression differences between the sibling allopolyploids is plastic. Few genes exhibit fixed expression differences, suggesting that despite ecological divergence, plasticity may mediate gene flow between sibling allopolyploids, thereby preventing differentiation. Extending our investigations to the rhizosphere, we uncover a much more diverse root mycobiome for either species when growing in the environment with nutrient-poor soils. Our finding suggests that both biotic and abiotic factors contribute to the distribution and delimitation of Dactylorhiza sibling allopolyploids. Altogether, our results indicate that plasticity can simultaneously promote diversification and homogenization of lineages, influencing the establishment and persistence of recurrently formed allopolyploid species. Plain language summary A duplicated genome can enhance plasticity in polyploids, widening their environmental tolerance, but the long term effects of this plasticity remain unclear. Studying ecologically distinct marsh orchids, we show that sibling allopolyploids exhibit high plasticity with only very few fixed transcriptomic differences. Instead, we observe divergent mycobiomes associated with each orchid’s environment, revealing a complex interplay in polyploid speciation.

Divergence (linguistics)

Sibling species

10.1101/2024.04.24.590886

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Repeat Dynamics across Timescales: A Perspective from Sibling Allotetraploid Marsh Orchids (Dactylorhiza majalis s.l.)

Molecular Biology and Evolution (2022)

Mimmi C. Eriksson Terezie Mandáková Jamie McCann Eva M. Temsch Mark W. Chase

Abstract To provide insights into the fate of transposable elements (TEs) across timescales in a post-polyploidization context, we comparatively investigate five sibling Dactylorhiza allotetraploids (Orchidaceae) formed independently and sequentially between 500 and 100K generations ago by unidirectional hybridization between diploids D. fuchsii and D. incarnata. Our results first reveal that the paternal D. incarnata genome shows a marked increased content of LTR retrotransposons compared to the maternal species, reflected in its larger genome size and consistent with a previously hypothesized bottleneck. With regard to the allopolyploids, in the youngest D. purpurella both genome size and TE composition appear to be largely additive with respect to parents, whereas for polyploids of intermediate ages we uncover rampant genome expansion on a magnitude of multiple entire genomes of some plants such as Arabidopsis. The oldest allopolyploids in the series are not larger than the intermediate ones. A putative tandem repeat, potentially derived from a non-autonomous miniature inverted-repeat TE (MITE) drives much of the genome dynamics in the allopolyploids. The highly dynamic MITE-like element is found in higher proportions in the maternal diploid, D. fuchsii, but is observed to increase in copy number in both subgenomes of the allopolyploids. Altogether, the fate of repeats appears strongly regulated and therefore predictable across multiple independent allopolyploidization events in this system. Apart from the MITE-like element, we consistently document a mild genomic shock following the allopolyploidizations investigated here, which may be linked to their relatively large genome sizes, possibly associated with strong selection against further genome expansions.

10.1093/molbev/msac167

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Citations (7)