39 results on '"Olofsson, Jill K."'
Search Results
2. Long-term anti-tumor effects following both conventional radiotherapy and FLASH in fully immunocompetent animals with glioblastoma
- Author
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Liljedahl, Emma, Konradsson, Elise, Gustafsson, Emma, Jonsson, Karolina Förnvik, Olofsson, Jill K., Ceberg, Crister, and Redebrandt, Henrietta Nittby
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- 2022
- Full Text
- View/download PDF
3. Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species
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Bianconi, Matheus E., Dunning, Luke T., Curran, Emma V., Hidalgo, Oriane, Powell, Robyn F., Mian, Sahr, Leitch, Ilia J., Lundgren, Marjorie R., Manzi, Sophie, Vorontsova, Maria S., Besnard, Guillaume, Osborne, Colin P., Olofsson, Jill K., and Christin, Pascal-Antoine
- Published
- 2020
4. Morphological and genetic evidence suggest gene flow among native and naturalized mint species
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Olofsson, Jill K., Tyler, Torbjörn, Dunning, Luke T., Hjertson, Mats, Rühling, Åke, Hansen, Anders J., Olofsson, Jill K., Tyler, Torbjörn, Dunning, Luke T., Hjertson, Mats, Rühling, Åke, and Hansen, Anders J.
- Abstract
Premise: Cultivation and naturalization of plants beyond their natural range can bring previously geographically isolated taxa together, increasing the opportunity for hybridization, the outcomes of which are not predictable. Here, we explored the phenotypic and genomic effects of interspecific gene flow following the widespread cultivation of Mentha spicata (spearmint), M. longifolia, and M. suaveolens. Methods: We morphologically evaluated 155 herbarium specimens of three Mentha species and sequenced the genomes of a subset of 93 specimens. We analyzed the whole genomes in a population and the phylogenetic framework and associated genomic classifications in conjunction with the morphological assessments. Results: The allopolyploid M. spicata, which likely evolved in cultivation, had altered trichome characters, that is possibly a product of human selection for a more palatable plant or a byproduct of selection for essential oils. There were signs of genetic admixture between mints, including allopolyploids, indicating that the reproductive barriers between Mentha species with differences in ploidy are likely incomplete. Still, despite gene flow between species, we found that genetic variants associated with the cultivated trichome morphology continue to segregate. Conclusions: Although hybridization, allopolyploidization, and human selection during cultivation can increase species richness (e.g., by forming hybrid taxa), we showed that unless reproductive barriers are strong, these processes can also result in mixing of genes between species and the potential loss of natural biodiversity.
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- 2024
5. Frequent fires prime plant developmental responses to burning
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Simpson, Kimberley J., Olofsson, Jill K., Ripley, Brad S., and Osborne, Colin P.
- Published
- 2019
6. Lateral transfers of large DNA fragments spread functional genes among grasses
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Dunning, Luke T., Olofsson, Jill K., Parisod, Christian, Choudhury, Rimjhim Roy, Moreno-Villena, Jose J., Yang, Yang, Dionora, Jacqueline, Quick, W. Paul, Park, Minkyu, Bennetzen, Jeffrey L., Besnard, Guillaume, Nosil, Patrik, Osborne, Colin P., and Christin, Pascal-Antoine
- Published
- 2019
7. Assembling genetic structure of Gardenia remyi, a critically endangered tree endemic to the Hawaiian Islands
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Hansen, Kristina Egholm, primary, Opgenorth, Mike, additional, Flynn, Tim, additional, Kennedy, Barbara, additional, Rønsted, Nina, additional, Olofsson, Jill K., additional, and Barnes, Christopher J., additional
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- 2023
- Full Text
- View/download PDF
8. Assembling genetic structure of Gardenia remyi, a critically endangered tree endemic to the Hawaiian Islands
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Hansen, Kristina Egholm, Opgenorth, Mike, Flynn, Tim, Kennedy, Barbara, Rønsted, Nina, Olofsson, Jill K., Barnes, Christopher J., Hansen, Kristina Egholm, Opgenorth, Mike, Flynn, Tim, Kennedy, Barbara, Rønsted, Nina, Olofsson, Jill K., and Barnes, Christopher J.
- Abstract
Conservation and restoration planning of extremely rare species relies on an understanding of the genetic diversity and population dynamics within a species to overcome potential inbreeding depression. Nānū or Nāʻū (Gardenia remyi H. Mann.) is an endemic tree native to the Hawaiian Islands and is one of more than 200 endangered plant species in Hawaiʻi with less than 50 individuals remaining in the wild. Efforts to understand the genetic diversity and connectivity between wild populations are foundational to conservation management plans, however little is known of the population structure of the species. In this study we utilize double digest restriction-site associated sequencing (ddRADSeq) on both historical herbarium specimens and samples from living ex situ collections to: (1) Test the hypothesis that we can capture genetic diversity in herbarium material of G. remyi using ddRADSeq, and (2) test the hypothesis that there are genetically distinct populations or subpopulation units among different Hawaiian islands. Usable sequencing data from thirty-seven samples of herbarium specimens collected between 1952 and 2017 and twenty wild sourced living collection samples were obtained representing all four islands where G. remyi is known to occur. Phylogenetic and population structure analysis revealed a monophyletic ingroup and a clear division between G. remyi samples of the northern island of Kauaʻi and those from the more southeastern younger islands of Molokaʻi, Maui and Hawaiʻi islands. The Kauaʻi samples were further split into a subpopulation from Southern Kauaʻi and the subpopulations from Northern Kauaʻi. Some admixed samples were detected. Our results are consistent with subpopulations of G. remyi, which needs to be considered in future conservation planning and breeding efforts to minimize inbreeding depression.
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- 2023
9. Additional file 1 of Combined anti-C1-INH and radiotherapy against glioblastoma
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Liljedahl, Emma, Konradsson, Elise, Gustafsson, Emma, Jonsson, Karolina Förnvik, Olofsson, Jill K., Osther, Kurt, Ceberg, Crister, and Redebrandt, Henrietta Nittby
- Abstract
Additional file 1.
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- 2023
- Full Text
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10. High Y‐chromosomal Differentiation Among Ethnic Groups of Dir and Swat Districts, Pakistan
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Ullah, Inam, Olofsson, Jill K., Margaryan, Ashot, Ilardo, Melissa, Ahmad, Habib, Sikora, Martin, Hansen, Anders J., Shahid Nadeem, Muhammad, Fazal, Numan, Ali, Murad, Buchard, Anders, Hemphill, Brian E., Willerslev, Eske, and Allentoft, Morten E.
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- 2017
- Full Text
- View/download PDF
11. Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia
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Dunning, Luke T., Olofsson, Jill K., Papadopulos, Alexander S. T., Hibdige, Samuel G.S., Hidalgo, Oriane, Leitch, Ilia J., Baleeiro, Paulo C., Ntshangase, Sinethemba, Barker, Nigel, Jobson, Richard W., Dunning, Luke T., Olofsson, Jill K., Papadopulos, Alexander S. T., Hibdige, Samuel G.S., Hidalgo, Oriane, Leitch, Ilia J., Baleeiro, Paulo C., Ntshangase, Sinethemba, Barker, Nigel, and Jobson, Richard W.
- Abstract
Ecotypes are distinct populations within a species that are adapted to specific environmental conditions. Understanding how these ecotypes become established, and how they interact when reunited, is fundamental to elucidating how ecological adaptations are maintained. This study focuses on Themeda triandra, a dominant grassland species across Asia, Africa and Australia. It is the most widespread plant in Australia, where it has distinct ecotypes that are usually restricted to either wetter and cooler coastal regions or the drier and hotter interior. We generate a reference genome for T. triandra and use whole genome sequencing for over 80 Themeda accessions to reconstruct the evolutionary history of T. triandra and related taxa. Organelle phylogenies confirm that Australia was colonized by T. triandra twice, with the division between ecotypes predating their arrival in Australia. The nuclear genome provides evidence of differences in the dominant ploidal level and gene-flow among the ecotypes. In northern Queensland there appears to be a hybrid zone between ecotypes with admixed nuclear genomes and shared chloroplast haplotypes. Conversely, in the cracking claypans of Western Australia, there is cytonuclear discordance with individuals possessing the coastal chloroplast and interior clade nuclear genome. This chloroplast capture is potentially a result of adaptive introgression, with selection detected in the rpoC2 gene which is associated with water use efficiency. The reason that T. triandra is the most widespread plant in Australia appears to be a result of distinct ecotypic genetic variation and genome duplication, with the importance of each depending on the geographic scale considered.
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- 2022
12. Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia
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Australian Biological Resources Study, Rio Tinto, Natural Environment Research Council (UK), National Research Foundation (South Africa), Dunning, Luke T., Olofsson, Jill K., Papadopulos, Alexander S.T., Hibdige, Samuel G.S., Hidalgo, Oriane, Leitch, Ilia J., Baleeiro, Paulo C., Ntshangase, Sinethemba, Barker, Nigel, Jobson, Richard W., Australian Biological Resources Study, Rio Tinto, Natural Environment Research Council (UK), National Research Foundation (South Africa), Dunning, Luke T., Olofsson, Jill K., Papadopulos, Alexander S.T., Hibdige, Samuel G.S., Hidalgo, Oriane, Leitch, Ilia J., Baleeiro, Paulo C., Ntshangase, Sinethemba, Barker, Nigel, and Jobson, Richard W.
- Abstract
Ecotypes are distinct populations within a species that are adapted to specific environmental conditions. Understanding how these ecotypes become established, and how they interact when reunited, is fundamental to elucidating how ecological adaptations are maintained. This study focuses on Themeda triandra, a dominant grassland species across Asia, Africa and Australia. It is the most widespread plant in Australia, where it has distinct ecotypes that are usually restricted to either wetter and cooler coastal regions or the drier and hotter interior. We generate a reference genome for T. triandra and use whole genome sequencing for over 80 Themeda accessions to reconstruct the evolutionary history of T. triandra and related taxa. Organelle phylogenies confirm that Australia was colonized by T. triandra twice, with the division between ecotypes predating their arrival in Australia. The nuclear genome provides evidence of differences in the dominant ploidal level and gene-flow among the ecotypes. In northern Queensland there appears to be a hybrid zone between ecotypes with admixed nuclear genomes and shared chloroplast haplotypes. Conversely, in the cracking claypans of Western Australia, there is cytonuclear discordance with individuals possessing the coastal chloroplast and interior clade nuclear genome. This chloroplast capture is potentially a result of adaptive introgression, with selection detected in the rpoC2 gene which is associated with water use efficiency. The reason that T. triandra is the most widespread plant in Australia appears to be a result of distinct ecotypic genetic variation and genome duplication, with the importance of each depending on the geographic scale considered.
- Published
- 2022
13. Supplementary Matrial from Hybridization boosts dispersal of two contrasted ecotypes in a grass species
- Author
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Curran, Emma V., Scott, Matilda S., Olofsson, Jill K., Nyirenda, Florence, Sotelo, Graciela, Bianconi, Matheus E., Manzi, Sophie, Besnard, Guillaume, Pereira, Lara, and Christin, Pascal-Antoine
- Abstract
Combined pdf containing nine supplementary figures and three supplementary tables
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- 2022
- Full Text
- View/download PDF
14. Hybridization boosts dispersal of two contrasted ecotypes in a grass species
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Curran, Emma V., primary, Scott, Matilda S., additional, Olofsson, Jill K., additional, Nyirenda, Florence, additional, Sotelo, Graciela, additional, Bianconi, Matheus E., additional, Manzi, Sophie, additional, Besnard, Guillaume, additional, Pereira, Lara, additional, and Christin, Pascal-Antoine, additional
- Published
- 2022
- Full Text
- View/download PDF
15. A Revised Phylogeny of the Mentha spicata Clade Reveals Cryptic Species
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Heylen, Olivier C. G., Debortoli, Nicolas, Marescaux, Jonathan, Olofsson, Jill K., Heylen, Olivier C. G., Debortoli, Nicolas, Marescaux, Jonathan, and Olofsson, Jill K.
- Abstract
The genus Mentha is taxonomically and phylogenetically challenging due to complex genomes, polyploidization and an extensive historical nomenclature, potentially hiding cryptic taxa. A straightforward interpretation of phylogenetic relationships within the section Mentha is further hindered by dominant but outdated concepts on historically identified hybrid taxa. Mentha spicata is traditionally considered to be of hybrid origin, but the evidence for this is weak. Here, we aim to understand the phylogenetic relationships within the section Mentha using large sample sizes and to revisit the hybrid status and identity of M. spicata. We show that two of three traditional species in the subsection Spicatae are polyphyletic, as is the subsection as a whole, while the real number of cryptic species was underestimated. Compared to previous studies we present a fundamentally different phylogeny, with a basal split between M. spicata s.s. and M. longifolia s.s. Cluster analyses of morphological and genotypic data demonstrate that there is a dissociation between morphologically and genotypically defined groups of samples. We did not find any evidence that M. spicata is of hybrid origin, and we conclude its taxonomic status should be revised. The combination of genetic and phenotypic information is essential when evaluating hyperdiverse taxonomic groups.
- Published
- 2021
16. Low dispersal and ploidy differences in a grass maintain photosynthetic diversity despite gene flow and habitat overlap
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European Research Council, Natural Environment Research Council (UK), Royal Society (UK), Olofsson, Jill K., Curran, Emma V., Nyirenda, Florence, Bianconi, Matheus E., Dunning, Luke T., Milenkovic, Vanja, Sotelo, Graciela, Hidalgo, Oriane, Powell, Robyn F., Lundgren, Marjorie R., Leitch, Ilia J., Nosil, Patrik, Osborne, Colin P., Christin, Pascal-Antoine, European Research Council, Natural Environment Research Council (UK), Royal Society (UK), Olofsson, Jill K., Curran, Emma V., Nyirenda, Florence, Bianconi, Matheus E., Dunning, Luke T., Milenkovic, Vanja, Sotelo, Graciela, Hidalgo, Oriane, Powell, Robyn F., Lundgren, Marjorie R., Leitch, Ilia J., Nosil, Patrik, Osborne, Colin P., and Christin, Pascal-Antoine
- Abstract
Geographical isolation facilitates the emergence of distinct phenotypes within a single species, but reproductive barriers or selection are needed to maintain the polymorphism after secondary contact. Here, we explore the processes that maintain intraspecific variation of C4 photosynthesis, a complex trait that results from the combined action of multiple genes. The grass Alloteropsis semialata includes C4 and non-C4 populations, which have coexisted as a polyploid series for more than 1 million years in the miombo woodlands of Africa. Using population genomics, we show that there is genome-wide divergence for the photosynthetic types, but the current geographical distribution does not reflect a simple habitat displacement scenario as the genetic clusters overlap, being occasionally mixed within a given habitat. Despite evidence of recurrent introgression between non-C4 and C4 groups, in both diploids and polyploids, the distinct genetic lineages retain their identity, potentially because of selection against hybrids. Coupled with strong isolation by distance within each genetic group, this selection created a geographical mosaic of photosynthetic types. Diploid C4 and non-C4 types never grew together, and the C4 type from mixed populations constantly belonged to the hexaploid lineage. By limiting reproductive interactions between photosynthetic types, the ploidy difference probably allows their co-occurrence, reinforcing the functional diversity within this species. Together, these factors enabled the persistence of divergent physiological traits of ecological importance within a single species despite gene flow and habitat overlap.
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- 2021
17. Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species: Intraspecific dispersal of C4 physiology
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Bianconi, Matheus E., Dunning, Luke T., Curran, Emma V., Hidalgo, Oriane, Powell, Robyn F., Mian, Sahr, Leitch, Ilia J., Lundgren, Marjorie R., Manzi, Sophie, Vorontsova, Maria S., Besnard, Guillaume, Osborne, Colin P., Olofsson, Jill K., Christin, Pascal-Antoine, European Research Council, Royal Society (UK), Agence Nationale de la Recherche (France), and Labex TULIP
- Abstract
C 4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C 4 and non-C 4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata. We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C 4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C 4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C 4 physiology away from its region of origin., This study was funded by the European Research Council (grant no. ERC-2014-STG-638333), the Royal Society (grant no. RGF\EA\181050) and has benefited from ‘Investissements d'Avenir' grants managed by the Agence Nationale de la Recherche (CEBA, ref. ANR-10-LABX-25-01 and TULIP, ref. ANR-10-LABX-41). Edinburgh Genomics, which contributed to the sequencing, is partly supported through core grants from the NERC (grant no. R8/H10/ 56), MRC (grant no. MR/K001744/1) and BBSRC (grant no. BB/ J004243/1). P.A.C. is funded by a Royal Society University Research Fellowship (grant no. URF\R\180022)., 1. Introduction 2. Materials and methods (a) Sampling, sequencing and data filtering (b) Genome sizing and carbon isotope analyses (c) Assembly of organelle genomes and molecular dating (d) Phylogenetic analyses of the nuclear genome (e) Genetic structure (f) Genome composition 3. Results (a) Genome sizes (b) Time-calibrated organelle phylogenies (c) Nuclear phylogeny (d) Population structure and genome composition 4. Discussion (a) Limited seed dispersal in the region of origin (b) Widespread pollen flow and sweep of the C4 nuclear genome (c) Recurrent hybridization and polyploidization 5. Concluding remarks Data accessibility Authors' contributions Competing interests Funding Acknowledgements Footnotes
- Published
- 2020
18. A Revised Phylogeny of the Mentha spicata Clade Reveals Cryptic Species
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Heylen, Olivier C. G., primary, Debortoli, Nicolas, additional, Marescaux, Jonathan, additional, and Olofsson, Jill K., additional
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- 2021
- Full Text
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19. Supplementary Information from Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species
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Matheus E. Bianconi, Dunning, Luke T., Curran, Emma V., Hidalgo, Oriane, Powell, Robyn F., Sahr Mian, Leitch, Ilia J., Lundgren, Marjorie R., Manzi, Sophie, Vorontsova, Maria S., Besnard, Guillaume, Osborne, Colin P., Olofsson, Jill K., and Christin, Pascal-Antoine
- Subjects
ComputingMethodologies_DOCUMENTANDTEXTPROCESSING - Abstract
Single pdf containing six figures and one table.
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- 2020
- Full Text
- View/download PDF
20. Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species: Intraspecific dispersal of C4 physiology
- Author
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European Research Council, Royal Society (UK), Agence Nationale de la Recherche (France), Labex TULIP, Bianconi, Matheus E., Dunning, Luke T., Curran, Emma V., Hidalgo, Oriane, Powell, Robyn F., Mian, Sahr, Leitch, Ilia J., Lundgren, Marjorie R., Manzi, Sophie, Vorontsova, Maria S., Besnard, Guillaume, Osborne, Colin P., Olofsson, Jill K., Christin, Pascal-Antoine, European Research Council, Royal Society (UK), Agence Nationale de la Recherche (France), Labex TULIP, Bianconi, Matheus E., Dunning, Luke T., Curran, Emma V., Hidalgo, Oriane, Powell, Robyn F., Mian, Sahr, Leitch, Ilia J., Lundgren, Marjorie R., Manzi, Sophie, Vorontsova, Maria S., Besnard, Guillaume, Osborne, Colin P., Olofsson, Jill K., and Christin, Pascal-Antoine
- Abstract
C 4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C 4 and non-C 4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata. We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C 4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C 4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C 4 physiology away from its region of origin.
- Published
- 2020
21. Population-Specific Selection on Standing Variation Generated by Lateral Gene Transfers in a Grass
- Author
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Olofsson, Jill K., primary, Dunning, Luke T., additional, Lundgren, Marjorie R., additional, Barton, Henry J., additional, Thompson, John, additional, Cuff, Nicholas, additional, Ariyarathne, Menaka, additional, Yakandawala, Deepthi, additional, Sotelo, Graciela, additional, Zeng, Kai, additional, Osborne, Colin P., additional, Nosil, Patrik, additional, and Christin, Pascal-Antoine, additional
- Published
- 2019
- Full Text
- View/download PDF
22. Population-Specific Selection on Standing Variation Generated by Lateral Gene Transfers in a Grass
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Olofsson, Jill K., Dunning, Luke T., Lundgren, Marjorie, Barton, Henry, Thompson, John, Cuff, Nicholas, Ariyarathne, Menaka, Yakandawala, Deepthi, Sotelo, Graciela, Zeng, Kai, Osborne, Colin P., Nosil, Patrik, Christin, Pascal-Antoine, Olofsson, Jill K., Dunning, Luke T., Lundgren, Marjorie, Barton, Henry, Thompson, John, Cuff, Nicholas, Ariyarathne, Menaka, Yakandawala, Deepthi, Sotelo, Graciela, Zeng, Kai, Osborne, Colin P., Nosil, Patrik, and Christin, Pascal-Antoine
- Abstract
Evidence of eukaryote-to-eukaryote lateral gene transfer (LGT) has accumulated in recent years, but the selective pressures governing the evolutionary fate of these genes within recipient species remain largely unexplored. Among non-parasitic plants, successful LGT has been reported between different grass species. Here, we use the grass Alloteropsis semialata, a species that possesses multigene LGT fragments that were acquired recently from distantly related grass species, to test the hypothesis that the successful LGT conferred an advantage and were thus rapidly swept into the recipient species. Combining whole-genome and population-level RAD sequencing, we show that the multigene LGT fragments were rapidly integrated in the recipient genome, likely due to positive selection for genes encoding proteins that added novel functions. These fragments also contained physically linked hitchhiking protein-coding genes, and subsequent genomic erosion has generated gene presence-absence polymorphisms that persist in multiple geographic locations, becoming part of the standing genetic variation. Importantly, one of the hitchhiking genes underwent a secondary rapid spread in some populations. This shows that eukaryotic LGT can have a delayed impact, contributing to local adaptation and intraspecific ecological diversification. Therefore, while short-term LGT integration is mediated by positive selection on some of the transferred genes, physically linked hitchhikers can remain functional and augment the standing genetic variation with delayed adaptive consequences.
- Published
- 2019
23. Key changes in gene expression identified for different stages of C4 evolution in Alloteropsis semialata
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Dunning, Luke T., Moreno-Villena, Jose J., Lundgren, Marjorie Ruth, Dionora, Jacqueline, Salazar, Paolo, Adams, Claire, Nyirenda, Florence, Olofsson, Jill K., Mapaura, Anthony, Grundy, Isla, Kayombo, Canisius, Dunning, Lucy, Kentatchime, Fabrice, Ariyarathne, Menaka, Yakandawala, Deepthi, Besnard, Guillaume, Quick, W. Paul, Brautigam, Andrea, Osborne, Colin P., Christin, Pascal-Antoine, Dunning, Luke T., Moreno-Villena, Jose J., Lundgren, Marjorie Ruth, Dionora, Jacqueline, Salazar, Paolo, Adams, Claire, Nyirenda, Florence, Olofsson, Jill K., Mapaura, Anthony, Grundy, Isla, Kayombo, Canisius, Dunning, Lucy, Kentatchime, Fabrice, Ariyarathne, Menaka, Yakandawala, Deepthi, Besnard, Guillaume, Quick, W. Paul, Brautigam, Andrea, Osborne, Colin P., and Christin, Pascal-Antoine
- Abstract
C4 photosynthesis is a complex trait that boosts productivity in tropical conditions. Compared to C3 species, the C4 state seems to require numerous novelties, but species comparisons can be confounded by long divergence times. Here, we exploit the photosynthetic diversity that exists within a single species, the grass Alloteropsis semialata, to detect changes in gene expression associated with different photosynthetic phenotypes. Phylogenetically-informed comparative transcriptomics show that intermediates with a weak C4 cycle are separated from the C3 phenotype by increases in the expression of 58 genes (0.22% of genes expressed in the leaves), including those encoding just three core C4 enzymes: ASP-AT, PCK, and PEPC. The subsequent transition to full C4 physiology was accompanied by increases in another 15 genes (0.06%), including only the core C4 enzyme PPDK. These changes likely created a rudimentary C4 physiology, and isolated populations subsequently improved this emerging C4 physiology, resulting in a patchwork of expression for some C4-accessory genes. Our work shows how C4 assembly in A. semialata happened in incremental steps, each requiring few alterations over the previous one. These create short bridges across adaptive landscapes that likely facilitated the recurrent origins of C4 photosynthesis through a gradual process of evolution.
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- 2019
24. C4 anatomy can evolve via a single developmental change
- Author
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Lundgren, Marjorie Ruth, Dunning, Luke T., Olofsson, Jill K., Moreno-Villena, Jose J., Bouvier, Jacques W., Sage, Tammy, Khoshravesh, Roxana, Sultmanis, Stefanie, Stata, Matt, Ripley, Brad S., Vorontsova, Maria S., Besnard, Guillaume, Adams, Claire, Cuff, Nicholas, Mapaura, Anthony, Bianconi, Matheus, Long, Christine M., Christin, Pascal-Antoine, Osborne, Colin P., Lundgren, Marjorie Ruth, Dunning, Luke T., Olofsson, Jill K., Moreno-Villena, Jose J., Bouvier, Jacques W., Sage, Tammy, Khoshravesh, Roxana, Sultmanis, Stefanie, Stata, Matt, Ripley, Brad S., Vorontsova, Maria S., Besnard, Guillaume, Adams, Claire, Cuff, Nicholas, Mapaura, Anthony, Bianconi, Matheus, Long, Christine M., Christin, Pascal-Antoine, and Osborne, Colin P.
- Abstract
C4 photosynthesis is a complex trait that boosts productivity in warm environments. Paradoxically, it evolved independently in numerous plant lineages, despite requiring specialised leaf anatomy. The anatomical modifications underlying C4 evolution have previously been evaluated through interspecific comparisons, which capture numerous changes besides those needed for C4 functionality. Here, we quantify the anatomical changes accompanying the transition between non‐C4 and C4 phenotypes by sampling widely across the continuum of leaf anatomical traits in the grass Alloteropsis semialata. Within this species, the only trait that is shared among and specific to C4 individuals is an increase in vein density, driven specifically by minor vein development that yields multiple secondary effects facilitating C4 function. For species with the necessary anatomical preconditions, developmental proliferation of veins can therefore be sufficient to produce a functional C4 leaf anatomy, creating an evolutionary entry point to complex C4 syndromes that can become more specialised.
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- 2019
25. Lateral transfers of large DNA fragments spread functional genes among grasses
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Dunning, Luke T, Olofsson, Jill K, Parisod, Christian, Choudhury, Rimjhim Roy, Moreno-Villena, Jose J, Yang, Yang, Dionora, Jacqueline, Quick, W Paul, Park, Minkyu, Bennetzen, Jeffrey L, Besnard, Guillaume, Nosil, Patrik, Osborne, Colin P, Christin, Pascal-Antoine, Dunning, Luke T, Olofsson, Jill K, Parisod, Christian, Choudhury, Rimjhim Roy, Moreno-Villena, Jose J, Yang, Yang, Dionora, Jacqueline, Quick, W Paul, Park, Minkyu, Bennetzen, Jeffrey L, Besnard, Guillaume, Nosil, Patrik, Osborne, Colin P, and Christin, Pascal-Antoine
- Abstract
A fundamental tenet of multicellular eukaryotic evolution is that vertical inheritance is paramount, with natural selection acting on genetic variants transferred from parents to offspring. This lineal process means that an organism's adaptive potential can be restricted by its evolutionary history, the amount of standing genetic variation, and its mutation rate. Lateral gene transfer (LGT) theoretically provides a mechanism to bypass many of these limitations, but the evolutionary importance and frequency of this process in multicellular eukaryotes, such as plants, remains debated. We address this issue by assembling a chromosome-level genome for the grass Alloteropsis semialata, a species surmised to exhibit two LGTs, and screen it for other grass-to-grass LGTs using genomic data from 146 other grass species. Through stringent phylogenomic analyses, we discovered 57 additional LGTs in the A. semialata nuclear genome, involving at least nine different donor species. The LGTs are clustered in 23 laterally acquired genomic fragments that are up to 170 kb long and have accumulated during the diversification of Alloteropsis. The majority of the 59 LGTs in A. semialata are expressed, and we show that they have added functions to the recipient genome. Functional LGTs were further detected in the genomes of five other grass species, demonstrating that this process is likely widespread in this globally important group of plants. LGT therefore appears to represent a potent evolutionary force capable of spreading functional genes among distantly related grass species.
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- 2019
26. Key changes in gene expression identified for different stages of C4 evolution in Alloteropsis semialata
- Author
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Dunning, Luke T, primary, Moreno-Villena, Jose J, additional, Lundgren, Marjorie R, additional, Dionora, Jacqueline, additional, Salazar, Paolo, additional, Adams, Claire, additional, Nyirenda, Florence, additional, Olofsson, Jill K, additional, Mapaura, Anthony, additional, Grundy, Isla M, additional, Kayombo, Canisius J, additional, Dunning, Lucy A, additional, Kentatchime, Fabrice, additional, Ariyarathne, Menaka, additional, Yakandawala, Deepthi, additional, Besnard, Guillaume, additional, Quick, W Paul, additional, Bräutigam, Andrea, additional, Osborne, Colin P, additional, and Christin, Pascal-Antoine, additional
- Published
- 2019
- Full Text
- View/download PDF
27. C4 anatomy can evolve via a single developmental change
- Author
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Lundgren, Marjorie R., primary, Dunning, Luke T., additional, Olofsson, Jill K., additional, Moreno‐Villena, Jose J., additional, Bouvier, Jacques W., additional, Sage, Tammy L., additional, Khoshravesh, Roxana, additional, Sultmanis, Stefanie, additional, Stata, Matt, additional, Ripley, Brad S., additional, Vorontsova, Maria S., additional, Besnard, Guillaume, additional, Adams, Claire, additional, Cuff, Nicholas, additional, Mapaura, Anthony, additional, Bianconi, Matheus E., additional, Long, Christine M., additional, Christin, Pascal‐Antoine, additional, and Osborne, Colin P., additional
- Published
- 2018
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- View/download PDF
28. The recent and rapid spread of Themeda triandra
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Dunning, Luke T., Anne-Lise Liabot, Olofsson, Jill K., Smith, Emma K., Vorontsova, Maria S., Besnard, Guillaume, Simpson, Kimberley J., Lundgren, Marjorie R., Addicott, Eda, Gallagher, Rachael V., Yingying Chu, R. Toby Pennington, Pascal-Antoine Christin, Lehmann, Caroline E. R., and Centre National de la Recherche Scientifique (CNRS)
- Subjects
[SDV]Life Sciences [q-bio] ,[SDE]Environmental Sciences ,parasitic diseases ,ComputingMilieux_MISCELLANEOUS - Abstract
Tropical savannas cover over 20% of land surface. They sustain a high diversity of mammalian herbivores and promote frequent fires, both of which are dependent on the underlying grass composition. These habitats are typically dominated by relatively few taxa, and the evolutionary origins of the dominant grass species are largely unknown. Here, we trace the origins of the genus Themeda, which contains a number of widespread grass species dominating tropical savannas. Complete chloroplast genomes were assembled for seven samples and supplemented with chloroplast and nuclear ITS markers for 71 samples representing 18 of the 27 Themeda species. Phylogenetic analysis supports a South Asian origin for both the genus and the widespread dominant T. triandra. This species emerged ~1.5 Ma from a group that had lived in the savannas of Asia for several million years. It migrated to Australia ~1.3 Ma and to mainland Africa ~0.5 Ma, where it rapidly spread in pre-existing savannas and displaced other species. Themeda quadrivalvis, the second most widespread Themeda species, is nested within T. triandra based on whole chloroplast genomes, and may represent a recent evolution of an annual growth form that is otherwise almost indistinguishable from T. triandra. The recent spread and modern-day dominance of T. triandra highlight the dynamism of tropical grassy biomes over millennial time-scales that has not been appreciated, with dramatic shifts in species dominance in recent evolutionary times. The ensuing species replacements likely had profound effects on fire and herbivore regimes across tropical savannas.
- Published
- 2017
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29. Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait
- Author
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Olofsson, Jill K., Bianconi, Matheus, Besnard, Guillaume, Dunning, Luke T., Lundgren, Marjorie R., Holota, Helene, Vorontsova, Maria S., Hidalgo, Oriane, Leitch, Ilia J., Nosil, Patrik, Osborne, Colin P., and Christin, Pascal‐Antoine
- Published
- 2016
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- View/download PDF
30. Key changes in gene expression identified for different stages of C 4 evolution in Alloteropsis semialata.
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Dunning, Luke T, Moreno-Villena, Jose J, Lundgren, Marjorie R, Dionora, Jacqueline, Salazar, Paolo, Adams, Claire, Nyirenda, Florence, Olofsson, Jill K, Mapaura, Anthony, Grundy, Isla M, Kayombo, Canisius J, Dunning, Lucy A, Kentatchime, Fabrice, Ariyarathne, Menaka, Yakandawala, Deepthi, Besnard, Guillaume, Quick, W Paul, Bräutigam, Andrea, Osborne, Colin P, and Christin, Pascal-Antoine
- Subjects
GENE expression ,TROPICAL conditions ,PHYSIOLOGY ,BIOLOGICAL evolution ,ASPARTATE aminotransferase ,PHENOTYPES - Abstract
C
4 photosynthesis is a complex trait that boosts productivity in tropical conditions. Compared with C3 species, the C4 state seems to require numerous novelties, but species comparisons can be confounded by long divergence times. Here, we exploit the photosynthetic diversity that exists within a single species, the grass Alloteropsis semialata , to detect changes in gene expression associated with different photosynthetic phenotypes. Phylogenetically informed comparative transcriptomics show that intermediates with a weak C4 cycle are separated from the C3 phenotype by increases in the expression of 58 genes (0.22% of genes expressed in the leaves), including those encoding just three core C4 enzymes: aspartate aminotransferase, phosphoenolpyruvate carboxykinase, and phosphoenolpyruvate carboxylase. The subsequent transition to full C4 physiology was accompanied by increases in another 15 genes (0.06%), including only the core C4 enzyme pyruvate orthophosphate dikinase. These changes probably created a rudimentary C4 physiology, and isolated populations subsequently improved this emerging C4 physiology, resulting in a patchwork of expression for some C4 accessory genes. Our work shows how C4 assembly in A. semialata happened in incremental steps, each requiring few alterations over the previous step. These create short bridges across adaptive landscapes that probably facilitated the recurrent origins of C4 photosynthesis through a gradual process of evolution. [ABSTRACT FROM AUTHOR]- Published
- 2019
- Full Text
- View/download PDF
31. C4 anatomy can evolve via a single developmental change.
- Author
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Lundgren, Marjorie R., Dunning, Luke T., Olofsson, Jill K., Moreno‐Villena, Jose J., Bouvier, Jacques W., Sage, Tammy L., Khoshravesh, Roxana, Sultmanis, Stefanie, Stata, Matt, Ripley, Brad S., Vorontsova, Maria S., Besnard, Guillaume, Adams, Claire, Cuff, Nicholas, Mapaura, Anthony, Bianconi, Matheus E., Long, Christine M., Christin, Pascal‐Antoine, Osborne, Colin P., and Pannell, John
- Subjects
PHOTOSYNTHESIS ,CARBON fixation ,PLANT photorespiration ,CARBON dioxide ,MESOPHYLL tissue - Abstract
C4 photosynthesis is a complex trait that boosts productivity in warm environments. Paradoxically, it evolved independently in numerous plant lineages, despite requiring specialised leaf anatomy. The anatomical modifications underlying C4 evolution have previously been evaluated through interspecific comparisons, which capture numerous changes besides those needed for C4 functionality. Here, we quantify the anatomical changes accompanying the transition between non‐C4 and C4 phenotypes by sampling widely across the continuum of leaf anatomical traits in the grass Alloteropsis semialata. Within this species, the only trait that is shared among and specific to C4 individuals is an increase in vein density, driven specifically by minor vein development that yields multiple secondary effects facilitating C4 function. For species with the necessary anatomical preconditions, developmental proliferation of veins can therefore be sufficient to produce a functional C4 leaf anatomy, creating an evolutionary entry point to complex C4 syndromes that can become more specialised. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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- View/download PDF
32. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci
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Purps, Josephine, Siegert, Sabine, Willuweit, Sascha, Nagy, Marion, Alves, Cintia, Salazar, Renato, Angustia, Sheila M. T., Santos, Lorna H., Anslinger, Katja, Bayer, Birgit, Ayub, Qasim, Wei, Wei, Xue, Yali, Tyler-Smith, Chris, Bafalluy, Miriam Baeta, Martinez-Jarreta, Begona, Egyed, Balazs, Balitzki, Beate, Tschumi, Sibylle, Ballard, David, Court, Denise Syndercombe, Barrantes, Xinia, Bassler, Gerhard, Wiest, Tina, Berger, Burkhard, Niederstaetter, Harald, Parson, Walther, Davis, Carey, Budowle, Bruce, Burri, Helen, Borer, Urs, Koller, Christoph, Carvalho, Elizeu F., Domingues, Patricia M., Chamoun, Wafaa Takash, Coble, Michael D., Hill, Carolyn R., Corach, Daniel, Caputo, Mariela, D'Amato, Maria E., Davison, Sean, Decorte, Ronny, Larmuseau, Maarten H. D., Ottoni, Claudio, Rickards, Olga, Lu, Di, Jiang, Chengtao, Dobosz, Tadeusz, Jonkisz, Anna, Frank, William E., Furac, Ivana, Gehrig, Christian, Castella, Vincent, Grskovic, Branka, Haas, Cordula, Wobst, Jana, Hadzic, Gavrilo, Drobnic, Katja, Honda, Katsuya, Hou, Yiping, Zhou, Di, Li, Yan, Hu, Shengping, Chen, Shenglan, Immel, Uta-Dorothee, Lessig, Rudiger, Jakovski, Zlatko, Ilievska, Tanja, Klann, Anja E., Garcia, Cristina Cano, de Knijff, Peter, Kraaijenbrink, Thirsa, Kondili, Aikaterini, Miniati, Penelope, Vouropoulou, Maria, Kovacevic, Lejla, Marjanovic, Damir, Lindner, Iris, Mansour, Issam, Al-Azem, Mouayyad, El Andari, Ansar, Marino, Miguel, Furfuro, Sandra, Locarno, Laura, Martin, Pablo, Luque, Gracia M., Alonso, Antonio, Miranda, Luis Souto, Moreira, Helena, Mizuno, Natsuko, Iwashima, Yasuki, Moura Neto, Rodrigo S., Nogueira, Tatiana L. S., Silva, Rosane, Nastainczyk-Wulf, Marina, Edelmann, Jeanett, Kohl, Michael, Nie, Shengjie, Wang, Xianping, Cheng, Baowen, Nunez, Carolina, Martinez de Pancorbo, Marian, Olofsson, Jill K., Morling, Niels, Onofri, Valerio, Tagliabracci, Adriano, Pamjav, Horolma, Volgyi, Antonia, Barany, Gusztav, Pawlowski, Ryszard, Maciejewska, Agnieszka, Pelotti, Susi, Pepinski, Witold, Abreu-Glowacka, Monica, Phillips, Christopher, Cardenas, Jorge, Rey-Gonzalez, Danel, Salas, Antonio, Brisighelli, Francesca, Capelli, Cristian, Toscanini, Ulises, Piccinini, Andrea, Piglionica, Marilidia, Baldassarra, Stefania L., Ploski, Rafal, Konarzewska, Magdalena, Jastrzebska, Emila, Robino, Carlo, Sajantila, Antti, Palo, Jukka U., Guevara, Evelyn, Salvador, Jazelyn, Corazon De Ungria, Maria, Russell Rodriguez, Jae Joseph, Schmidt, Ulrike, Schlauderer, Nicola, Saukko, Pekka, Schneider, Peter M., Sirker, Miriam, Shin, Kyoung-Jin, Oh, Yu Na, Skitsa, Iulia, Ampati, Alexandra, Smith, Tobi-Gail, de Calvit, Lina Solis, Stenzl, Vlastimil, Capal, Thomas, Tillmar, Andreas, Nilsson, Helena, Turrina, Stefania, De Leo, Domenico, Verzeletti, Andrea, Cortellini, Venusia, Wetton, Jon H., Gwynne, Gareth M., Jobling, Mark A., Whittle, Martin R., Sumita, Denilce R., Wolanska-Nowak, Paulina, Yong, Rita Y. Y., Krawczak, Michael, Nothnagel, Michael, Roewer, Lutz, Purps, Josephine, Siegert, Sabine, Willuweit, Sascha, Nagy, Marion, Alves, Cintia, Salazar, Renato, Angustia, Sheila M. T., Santos, Lorna H., Anslinger, Katja, Bayer, Birgit, Ayub, Qasim, Wei, Wei, Xue, Yali, Tyler-Smith, Chris, Bafalluy, Miriam Baeta, Martinez-Jarreta, Begona, Egyed, Balazs, Balitzki, Beate, Tschumi, Sibylle, Ballard, David, Court, Denise Syndercombe, Barrantes, Xinia, Bassler, Gerhard, Wiest, Tina, Berger, Burkhard, Niederstaetter, Harald, Parson, Walther, Davis, Carey, Budowle, Bruce, Burri, Helen, Borer, Urs, Koller, Christoph, Carvalho, Elizeu F., Domingues, Patricia M., Chamoun, Wafaa Takash, Coble, Michael D., Hill, Carolyn R., Corach, Daniel, Caputo, Mariela, D'Amato, Maria E., Davison, Sean, Decorte, Ronny, Larmuseau, Maarten H. D., Ottoni, Claudio, Rickards, Olga, Lu, Di, Jiang, Chengtao, Dobosz, Tadeusz, Jonkisz, Anna, Frank, William E., Furac, Ivana, Gehrig, Christian, Castella, Vincent, Grskovic, Branka, Haas, Cordula, Wobst, Jana, Hadzic, Gavrilo, Drobnic, Katja, Honda, Katsuya, Hou, Yiping, Zhou, Di, Li, Yan, Hu, Shengping, Chen, Shenglan, Immel, Uta-Dorothee, Lessig, Rudiger, Jakovski, Zlatko, Ilievska, Tanja, Klann, Anja E., Garcia, Cristina Cano, de Knijff, Peter, Kraaijenbrink, Thirsa, Kondili, Aikaterini, Miniati, Penelope, Vouropoulou, Maria, Kovacevic, Lejla, Marjanovic, Damir, Lindner, Iris, Mansour, Issam, Al-Azem, Mouayyad, El Andari, Ansar, Marino, Miguel, Furfuro, Sandra, Locarno, Laura, Martin, Pablo, Luque, Gracia M., Alonso, Antonio, Miranda, Luis Souto, Moreira, Helena, Mizuno, Natsuko, Iwashima, Yasuki, Moura Neto, Rodrigo S., Nogueira, Tatiana L. S., Silva, Rosane, Nastainczyk-Wulf, Marina, Edelmann, Jeanett, Kohl, Michael, Nie, Shengjie, Wang, Xianping, Cheng, Baowen, Nunez, Carolina, Martinez de Pancorbo, Marian, Olofsson, Jill K., Morling, Niels, Onofri, Valerio, Tagliabracci, Adriano, Pamjav, Horolma, Volgyi, Antonia, Barany, Gusztav, Pawlowski, Ryszard, Maciejewska, Agnieszka, Pelotti, Susi, Pepinski, Witold, Abreu-Glowacka, Monica, Phillips, Christopher, Cardenas, Jorge, Rey-Gonzalez, Danel, Salas, Antonio, Brisighelli, Francesca, Capelli, Cristian, Toscanini, Ulises, Piccinini, Andrea, Piglionica, Marilidia, Baldassarra, Stefania L., Ploski, Rafal, Konarzewska, Magdalena, Jastrzebska, Emila, Robino, Carlo, Sajantila, Antti, Palo, Jukka U., Guevara, Evelyn, Salvador, Jazelyn, Corazon De Ungria, Maria, Russell Rodriguez, Jae Joseph, Schmidt, Ulrike, Schlauderer, Nicola, Saukko, Pekka, Schneider, Peter M., Sirker, Miriam, Shin, Kyoung-Jin, Oh, Yu Na, Skitsa, Iulia, Ampati, Alexandra, Smith, Tobi-Gail, de Calvit, Lina Solis, Stenzl, Vlastimil, Capal, Thomas, Tillmar, Andreas, Nilsson, Helena, Turrina, Stefania, De Leo, Domenico, Verzeletti, Andrea, Cortellini, Venusia, Wetton, Jon H., Gwynne, Gareth M., Jobling, Mark A., Whittle, Martin R., Sumita, Denilce R., Wolanska-Nowak, Paulina, Yong, Rita Y. Y., Krawczak, Michael, Nothnagel, Michael, and Roewer, Lutz
- Abstract
In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent. (C) 2014 The Authors. Published by Elsevier Ireland Ltd.
- Published
- 2014
33. Supplementary Materials for Simpson et al 'Frequent fires prime plant developmental responses to burning'
- Author
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Simpson, Kimberley J., Olofsson, Jill K., Ripley, Brad S., and Osborne, Colin P.
- Subjects
food and beverages ,15. Life on land - Abstract
Tables S1-S6, Figures S1-S4. Proceedings of the Royal Society B, DOI - 10.1098/rspb.2019.1315. Coping with temporal variation in fire requires plants to have plasticity in traits that promote persistence, but how plastic responses to current conditions are affected by past fire exposure remains unknown. We investigate phenotypic divergence between populations of four resprouting grasses exposed to differing experimental fire regimes (annually-burnt or unburnt for >35 years), and test whether divergence persists after plants are grown in a common environment for one year. Traits relating to flowering and biomass allocation were measured before plants were experimentally burnt, and their regrowth was tracked. Genetic differentiation between populations was investigated for a subset of individuals. Historic fire frequency influenced traits relating to flowering and below-ground investment. Previously burnt plants produced more inflorescences and invested proportionally more biomass below ground, suggesting greater capacity for recruitment and resprouting than unburnt individuals. Tiller-scale regrowth rate did not differ between treatments, but prior fire exposure enhanced total regrown biomass in two species. We found no consistent genetic differences between populations suggesting trait differences arose from developmental plasticity. Grass development is influenced by prior fire exposure, independent of current environmental conditions. This priming response to fire, resulting in adaptive trait changes, may produce communities more resistant to future fire regime changes.
34. Supplementary Materials for Simpson et al 'Frequent fires prime plant developmental responses to burning'
- Author
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Simpson, Kimberley J., Olofsson, Jill K., Ripley, Brad S., and Osborne, Colin P.
- Subjects
food and beverages ,15. Life on land - Abstract
Tables S1-S6, Figures S1-S4. Proceedings of the Royal Society B, DOI - 10.1098/rspb.2019.1315. Coping with temporal variation in fire requires plants to have plasticity in traits that promote persistence, but how plastic responses to current conditions are affected by past fire exposure remains unknown. We investigate phenotypic divergence between populations of four resprouting grasses exposed to differing experimental fire regimes (annually-burnt or unburnt for >35 years), and test whether divergence persists after plants are grown in a common environment for one year. Traits relating to flowering and biomass allocation were measured before plants were experimentally burnt, and their regrowth was tracked. Genetic differentiation between populations was investigated for a subset of individuals. Historic fire frequency influenced traits relating to flowering and below-ground investment. Previously burnt plants produced more inflorescences and invested proportionally more biomass below ground, suggesting greater capacity for recruitment and resprouting than unburnt individuals. Tiller-scale regrowth rate did not differ between treatments, but prior fire exposure enhanced total regrown biomass in two species. We found no consistent genetic differences between populations suggesting trait differences arose from developmental plasticity. Grass development is influenced by prior fire exposure, independent of current environmental conditions. This priming response to fire, resulting in adaptive trait changes, may produce communities more resistant to future fire regime changes.
35. Contrasting phylogeographic structures between freshwater lycopods and angiosperms in the British Isles
- Author
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Wood, Daniel P., Olofsson, Jill K., McKenzie, Scott W., and Dunning, Luke T.
- Subjects
fungi ,6. Clean water - Abstract
Aquatic plants face many novel challenges compared to their terrestrial counterparts. The habitat they occupy is typically highly fragmented, with isolated water bodies surrounded by swathes of “dry desert”. This can result in reduced gene flow, inbreeding, and potentially local extinction. The level of gene flow and degree of genetic structure in these species is also likely to be influenced by the mating system they adopt. To test this hypothesis we compare the phylogeographic structure of two freshwater plants in the British Isles, the largely clonal angiosperm Littorella uniflora, and the heterosporous lycopod Isoetes lacustris. We sampled both plants from lakes where they co-occur, and used restriction site-associated DNA sequencing (RAD-Seq) to infer their relationships. Genetic structure among lakes is higher in the angiosperm, which we associate with reduced sexual reproduction, and hence lower levels of gene flow between lakes. Furthermore, we found evidence of lineage-specific association to certain lake nutrient types in L. uniflora, which might result from environmental filtering of specific ecotypes. Overall, we conclude that the reproductive system of lycopods, which is less specialized to terrestrial conditions, provides an advantage following the secondary colonization of aquatic habitats by enabling frequent genetic exchanges between populations and potentially facilitating faster adaptation.
36. Contrasting phylogeographic structures between freshwater lycopods and angiosperms in the British Isles
- Author
-
Wood, Daniel P., Olofsson, Jill K., McKenzie, Scott W., and Dunning, Luke T.
- Subjects
fungi ,6. Clean water - Abstract
Aquatic plants face many novel challenges compared to their terrestrial counterparts. The habitat they occupy is typically highly fragmented, with isolated water bodies surrounded by swathes of “dry desert”. This can result in reduced gene flow, inbreeding, and potentially local extinction. The level of gene flow and degree of genetic structure in these species is also likely to be influenced by the mating system they adopt. To test this hypothesis we compare the phylogeographic structure of two freshwater plants in the British Isles, the largely clonal angiosperm Littorella uniflora, and the heterosporous lycopod Isoetes lacustris. We sampled both plants from lakes where they co-occur, and used restriction site-associated DNA sequencing (RAD-Seq) to infer their relationships. Genetic structure among lakes is higher in the angiosperm, which we associate with reduced sexual reproduction, and hence lower levels of gene flow between lakes. Furthermore, we found evidence of lineage-specific association to certain lake nutrient types in L. uniflora, which might result from environmental filtering of specific ecotypes. Overall, we conclude that the reproductive system of lycopods, which is less specialized to terrestrial conditions, provides an advantage following the secondary colonization of aquatic habitats by enabling frequent genetic exchanges between populations and potentially facilitating faster adaptation.
37. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci
- Author
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Thomas Capal, Marian M. de Pancorbo, Birgit Bayer, Sheila M.T. Angustia, Francesca Brisighelli, Andrea Piccinini, Lutz Roewer, Yali Xue, Aikaterini Kondili, Alexandra Ampati, Katja Anslinger, Mouayyad Al-Azem, Witold Pepinski, Harald Niederstätter, Jae Joseph Russell B. Rodriguez, Katja Drobnič, Denise Syndercombe Court, Jana Wobst, David Ballard, Danel Rey-González, Marina Nastainczyk-Wulf, Christopher Phillips, Magdalena Konarzewska, Evelyn K. Guevara, Jill K. Olofsson, Maria Eugenia D’Amato, Natsuko Mizuno, Ansar El Andari, Yiping Hou, G.M. Luque, Carolyn R. Hill, Antti Sajantila, Cordula Haas, Tobi Gail Smith, Christian Gehrig, Andreas O. Tillmar, Marilidia Piglionica, Anja E. Klann, M. Sirker, Jazelyn M. Salvador, Jukka U. Palo, Rita Y.Y. Yong, Antonio Alonso, Xinia Barrantes, Bruce Budowle, Helen Burri, Xianping Wang, Baowen Cheng, Paulina Wolańska-Nowak, Peter de Knijff, Renato Salazar, Thirsa Kraaijenbrink, Shenglan Chen, Susi Pelotti, Tatiana Lúcia Santos Nogueira, Mark A. Jobling, Iulia Skitsa, Issam Mansour, Jeanett Edelmann, Urs V. Borer, Stefania Lonero Baldassarra, Maria Corazon A. De Ungria, Di Zhou, William E. Frank, Jon H. Wetton, Begoña Martínez-Jarreta, Sheng-Ping Hu, Marion Nagy, Andrea Verzeletti, Rodrigo Soares de Moura Neto, Martin R. Whittle, Anna Jonkisz, Ryszard Pawłowski, Cristian Capelli, Yu Na Oh, Emila Jastrzebska, Helena Nilsson, Agnieszka Maciejewska, M. Kohl, Cristina Cano García, Miguel Marino, Michael D. Coble, Elizeu Fagundes de Carvalho, Gareth M. Gwynne, Michael Nothnagel, Chengtao Jiang, Tadeusz Dobosz, Gavrilo Hadzic, Burkhard Berger, Sascha Willuweit, Branka Grskovic, Katsuya Honda, Tanja Ilievska, Rüdiger Lessig, Zlatko Jakovski, Antonio Salas, Balázs Egyed, Laura Locarno, Christoph Koller, Helena Moreira, Sibylle Tschumi, Carolina Núñez, Luís Souto Miranda, Nicola Schlauderer, Patrícia Domingues, Yasuki Iwashima, Di Lu, V. Cortellini, Antónia Völgyi, Monica Abreu-Głowacka, Mariela Caputo, Maarten Larmuseau, Peter M. Schneider, Wafaa Takash Chamoun, Gerhard Bäßler, Pekka Saukko, Cíntia Alves, Lejla Kovacevic, Maria Vouropoulou, Walther Parson, Stefania Turrina, Chris Tyler-Smith, Lina Solis De Calvit, D.R. Sumita, Qasim Ayub, T. Wiest, Iris Lindner, Jorge Cárdenas, Kyoung Jin Shin, Daniel Corach, Claudio Ottoni, Carlo Robino, Sabine Siegert, Ivana Furač, Miriam Baeta Bafalluy, Uta Dorothee Immel, Domenico De Leo, Ronny Decorte, Sandra Furfuro, Niels Morling, Valerio Onofri, Adriano Tagliabracci, Rosane Silva, Beate Balitzki, Ulises Toscanini, Olga Rickards, Michael Krawczak, Sean Davison, Ulrike Schmidt, Wei Wei, Pablo Martín, Vincent Castella, Yan Li, P. Miniati, Rafał Płoski, Gusztáv Bárány, Vlastimil Stenzl, Shengjie Nie, Horolma Pamjav, Carey Davis, Josephine Purps, Lorna H. Santos, Damir Marjanović, Hjelt Institute (-2014), Forensic Medicine, PaleOmics Laboratory, Purps, Josephine, Siegert, Sabine, Willuweit, Sascha, Nagy, Marion, Alves, Cíntia, Salazar, Renato, Angustia, Sheila M.T., Santos, Lorna H., Anslinger, Katja, Bayer, Birgit, Ayub, Qasim, Wei, Wei, Xue, Yali, Tyler-Smith, Chri, Bafalluy, Miriam Baeta, Martínez-Jarreta, Begoña, Egyed, Balaz, Balitzki, Beate, Tschumi, Sibylle, Ballard, David, Court, Denise Syndercombe, Barrantes, Xinia, Bäßler, Gerhard, Wiest, Tina, Berger, Burkhard, Niederstätter, Harald, Parson, Walther, Davis, Carey, Budowle, Bruce, Burri, Helen, Borer, Ur, Koller, Christoph, Carvalho, Elizeu F., Domingues, Patricia M., Chamoun, Wafaa Takash, Coble, Michael D., Hill, Carolyn R., Corach, Daniel, Caputo, Mariela, D'Amato, Maria E., Davison, Sean, Decorte, Ronny, Larmuseau, Maarten H.D., Ottoni, Claudio, Rickards, Olga, Lu, Di, Jiang, Chengtao, Dobosz, Tadeusz, Jonkisz, Anna, Frank, William E., Furac, Ivana, Gehrig, Christian, Castella, Vincent, Grskovic, Branka, Haas, Cordula, Wobst, Jana, Hadzic, Gavrilo, Drobnic, Katja, Honda, Katsuya, Hou, Yiping, Zhou, Di, Li, Yan, Hu, Shengping, Chen, Shenglan, Immel, Uta-Dorothee, Lessig, Rüdiger, Jakovski, Zlatko, Ilievska, Tanja, Klann, Anja E., García, Cristina Cano, De Knijff, Peter, Kraaijenbrink, Thirsa, Kondili, Aikaterini, Miniati, Penelope, Vouropoulou, Maria, Kovacevic, Lejla, Marjanovic, Damir, Lindner, Iri, Mansour, Issam, Al-Azem, Mouayyad, Andari, Ansar El, Marino, Miguel, Furfuro, Sandra, Locarno, Laura, Martín, Pablo, Luque, Gracia M., Alonso, Antonio, Miranda, Luís Souto, Moreira, Helena, Mizuno, Natsuko, Iwashima, Yasuki, Neto, Rodrigo S. Moura, Nogueira, Tatiana L.S., Silva, Rosane, Nastainczyk-Wulf, Marina, Edelmann, Jeanett, Kohl, Michael, Nie, Shengjie, Wang, Xianping, Cheng, Baowen, Núñez, Carolina, Pancorbo, Marian Martínez De, Olofsson, Jill K., Morling, Niel, Onofri, Valerio, Tagliabracci, Adriano, Pamjav, Horolma, Volgyi, Antonia, Barany, Gusztav, Pawlowski, Ryszard, Maciejewska, Agnieszka, Pelotti, Susi, Pepinski, Witold, Abreu-Glowacka, Monica, Phillips, Christopher, Cárdenas, Jorge, Rey-Gonzalez, Danel, Salas, Antonio, Brisighelli, Francesca, Capelli, Cristian, Toscanini, Ulise, Piccinini, Andrea, Piglionica, Marilidia, Baldassarra, Stefania L., Ploski, Rafal, Konarzewska, Magdalena, Jastrzebska, Emila, Robino, Carlo, Sajantila, Antti, Palo, Jukka U., Guevara, Evelyn, Salvador, Jazelyn, Ungria, Maria Corazon De, Rodriguez, Jae Joseph Russell, Schmidt, Ulrike, Schlauderer, Nicola, Saukko, Pekka, Schneider, Peter M., Sirker, Miriam, Shin, Kyoung-Jin, Oh, Yu Na, Skitsa, Iulia, Ampati, Alexandra, Smith, Tobi-Gail, Calvit, Lina Solis De, Stenzl, Vlastimil, Capal, Thoma, Tillmar, Andrea, Nilsson, Helena, Turrina, Stefania, De Leo, Domenico, Verzeletti, Andrea, Cortellini, Venusia, Wetton, Jon H., Gwynne, Gareth M., Jobling, Mark A., Whittle, Martin R., Sumita, Denilce R., Wolańska-Nowak, Paulina, Yong, Rita Y.Y., Krawczak, Michael, Nothnagel, Michael, and Roewer, Lutz
- Subjects
Forensic Genetics ,Population structure ,RECOMBINATION ,Forensic Genetic ,purl.org/becyt/ford/1 [https] ,AMOVA, Database, Discriminatory power, Gene diversity, Population structure ,Genética y Herencia ,0302 clinical medicine ,MARKERS ,Haplotype ,POPULATION ,Allele ,Genetics ,0303 health sciences ,education.field_of_study ,Medicine (all) ,Gene diversity ,319 Forensic science and other medical sciences ,16. Peace & justice ,Gene diversity, Discriminatory power, AMOVA, Population structure, Database ,Str loci ,Microsatellite Repeat ,AMOVA, Database, Discriminatory power, Gene diversity, Population structure, Genetics, Forensic Medicine ,ALLELE FREQUENCIES ,Discriminatory power ,CIENCIAS NATURALES Y EXACTAS ,Human ,AMOVA ,Population ,Settore BIO/08 - ANTROPOLOGIA ,Biology ,Settore BIO/08 ,SEQUENCE ,Article ,Pathology and Forensic Medicine ,EVENTS ,Ciencias Biológicas ,Database ,03 medical and health sciences ,Genetic ,Settore MED/43 - Medicina Legale ,Humans ,030216 legal & forensic medicine ,education ,purl.org/becyt/ford/1.6 [https] ,Allele frequency ,Alleles ,030304 developmental biology ,Chromosomes, Human, Y ,ta1184 ,DELETION ,Null (mathematics) ,AZFA REGION ,ta3121 ,Haplotypes ,3111 Biomedicine ,SYSTEM ,Microsatellite Repeats - Abstract
In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent. Fil: Corach, Daniel. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Servicio de Huellas Digitales Genéticas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Caputo, Mariela. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Servicio de Huellas Digitales Genéticas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Marino, Miguel Eduardo. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Laboratorio de Analisis de ADN; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Purps, Josephine. Charité-Universitätsmedizin; Alemania Fil: Siegert, Sabine. University of Cologne; Alemania Fil: Willuweit, Sascha. Charité-Universitätsmedizin; Alemania Fil: Nagy, Marion. Charité-Universitätsmedizin; Alemania Fil: Alves, Cíntia. Universidad de Porto; Portugal Fil: Salazar, Renato. Universidad de Porto; Portugal Fil: Angustia, Sheila M. T.. Philippine National Police Crime Laboratory; Filipinas Fil: Santos, Lorna H.. Philippine National Police Crime Laboratory; Filipinas Fil: Anslinger, Katja. Universitat Genzentrum Der Ludwing-maximilians; Alemania Fil: Bayer, Birgit. Universitat Genzentrum Der Ludwing-maximilians; Alemania Fil: Ayub, Qasim. The Wellcome Trust Sanger Institute; Reino Unido Fil: Wei, Wei. The Wellcome Trust Sanger Institute; Reino Unido Fil: Xue, Yali. The Wellcome Trust Sanger Institute; Reino Unido Fil: Tyler Smith, Chris. The Wellcome Trust Sanger Institute; Reino Unido Fil: Baeta Bafalluy, Miriam. Universidad de Zaragoza; España Fil: Martínez Jarreta, Begoña. Universidad de Zaragoza; España Fil: Egyed, Balazs. Eotvos University, Budapest; Argentina Fil: Balitzki, Beate. Universidad de Basilea; Suiza Fil: Tschumi, Sibylle. Universidad de Basilea; Suiza Fil: Ballard, David. King; Reino Unido Fil: Syndercombe Court, Denise. King; Reino Unido Fil: Barrantes, Xinia. Poder Judicial, Forensic Sciences Department; Costa Rica Fil: Bäßler, Gerhard. Landeskriminalamt Baden-Württemberg; Alemania Fil: Berger, Burkhard. Universidad de Innsbruck; Austria Fil: Niederstätter, Haral. Universidad de Innsbruck; Austria Fil: Parson, Walther. Universidad de Innsbruck; Austria. University Park; Estados Unidos Fil: Davis, Carey. Department of Molecular and Medical Genetics; Estados Unidos. Institute of Applied Genetics; Estados Unidos Fil: Furfuro, Sandra. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Laboratorio de Análisis de ADN; Argentina Fil: Locarno, Laura. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Laboratorio de Análisis de ADN; Argentina
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38. Hybridization boosts dispersal of two contrasted ecotypes in a grass species.
- Author
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Curran EV, Scott MS, Olofsson JK, Nyirenda F, Sotelo G, Bianconi ME, Manzi S, Besnard G, Pereira L, and Christin PA
- Subjects
- Alleles, Gene Flow, Hybridization, Genetic, Ecotype, Poaceae genetics
- Abstract
Genetic exchanges between closely related groups of organisms with different adaptations have well-documented beneficial and detrimental consequences. In plants, pollen-mediated exchanges affect the sorting of alleles across physical landscapes and influence rates of hybridization. How these dynamics affect the emergence and spread of novel phenotypes remains only partially understood. Here, we use phylogenomics and population genomics to retrace the origin and spread of two geographically overlapping ecotypes of the African grass Alloteropsis angusta . In addition to an ecotype inhabiting wetlands, we report the existence of a previously undescribed ecotype inhabiting Miombo woodlands and grasslands. The two ecotypes are consistently associated with different nuclear groups, which represent an advanced stage of divergence with secondary low-level gene flow. However, the seed-transported chloroplast genomes are consistently shared by distinct ecotypes inhabiting the same region. These patterns suggest that the nuclear genome of one ecotype can enter the seeds of the other via occasional pollen movements with sorting of nuclear groups in subsequent generations. The contrasting ecotypes of A. angusta can thus use each other as a gateway to new locations across a large part of Africa, showing that hybridization can facilitate the geographical dispersal of distinct ecotypes of the same grass species.
- Published
- 2022
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39. C 4 anatomy can evolve via a single developmental change.
- Author
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Lundgren MR, Dunning LT, Olofsson JK, Moreno-Villena JJ, Bouvier JW, Sage TL, Khoshravesh R, Sultmanis S, Stata M, Ripley BS, Vorontsova MS, Besnard G, Adams C, Cuff N, Mapaura A, Bianconi ME, Long CM, Christin PA, and Osborne CP
- Subjects
- Plant Leaves anatomy & histology, Plants, Photosynthesis, Poaceae
- Abstract
C
4 photosynthesis is a complex trait that boosts productivity in warm environments. Paradoxically, it evolved independently in numerous plant lineages, despite requiring specialised leaf anatomy. The anatomical modifications underlying C4 evolution have previously been evaluated through interspecific comparisons, which capture numerous changes besides those needed for C4 functionality. Here, we quantify the anatomical changes accompanying the transition between non-C4 and C4 phenotypes by sampling widely across the continuum of leaf anatomical traits in the grass Alloteropsis semialata. Within this species, the only trait that is shared among and specific to C4 individuals is an increase in vein density, driven specifically by minor vein development that yields multiple secondary effects facilitating C4 function. For species with the necessary anatomical preconditions, developmental proliferation of veins can therefore be sufficient to produce a functional C4 leaf anatomy, creating an evolutionary entry point to complex C4 syndromes that can become more specialised., (© 2018 The Authors Ecology Letters published by CNRS and John Wiley & Sons Ltd.)- Published
- 2019
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