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- Leebens-Mack, James H., et al.
(author)
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One thousand plant transcriptomes and the phylogenomics of green plants
- 2019
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In: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
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Journal article (peer-reviewed)abstract
- Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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- Hietala, H., et al.
(author)
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The Challenges and Rewards of Running a Geospace Environment Modeling Challenge
- 2020
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In: Journal of Geophysical Research - Space Physics. - 2169-9380 .- 2169-9402. ; 125:3
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Journal article (other academic/artistic)abstract
- Geospace Environment Modeling (GEM) is a community-driven, National Science Foundation-sponsored research program investigating the physics of the Earth's magnetosphere and its coupling to the solar wind and the atmosphere. This commentary provides an introduction to a Special Issue collating recent studies related to a GEM Challenge on kinetic plasma processes in the dayside magnetosphere during southward interplanetary magnetic field conditions. We also recount our experiences of organizing such a collaborative activity, where modelers and observers compare their results, that is, of the human side of bringing researchers together. We give suggestions on planning, managing, funding, and documenting these activities, which provide valuable opportunities to advance the field. Plain Language Summary Geospace Environment Modeling (GEM) is a community-driven, National Science Foundation-sponsored research program investigating the physics of the Earth's magnetosphere and its coupling to the solar wind and the atmosphere. An integral part of the program is the so-called "Challenges", which bring people together to compare models and observations in order to advance our understanding of the near-Earth space environment. This commentary provides an introduction to a Special Issue collating recent studies related to one such collaborative effort. We also share our experiences as early-career scientists organizing such an activity, to aid those who might take part in such endeavors in the future. We give suggestions on planning, managing, funding, and documenting the activities.
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