| 1. |
- 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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| 2. |
- Abbafati, Cristiana, et al.
(author)
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- 2020
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Journal article (peer-reviewed)
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| 3. |
- Frohlich, Michael W., et al.
(author)
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Molecular phylogenetics of Euploca (Boraginaceae) : homoplasy in many characters, including the C-4 photosynthetic pathway
- 2022
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In: Botanical journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4074 .- 1095-8339. ; 199:2, s. 497-537
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Journal article (peer-reviewed)abstract
- We present a phylogenetic analysis using plastid (matK, rbcL) and nuclear (nrITS) DNA for diverse Euploca spp. (formerly Heliotropium section Orthostachys) from the worldwide distribution of a genus and including species encompassing the wide physiological and morphological diversity of the genus. Our results indicate that some remarkably complex features arose multiple times in parallel in Euploca, including attributes of its subsections under section Orthostachys, notably plants that, above ground, consist almost entirely of inflorescences. To elucidate in greater detail the distribution of C-4 species in Euploca and Heliotropium s.s., we made > 800 delta C-13 determinations, including some from the traditional genus Tournefortia. We greatly increase the number of proven C-4 species in Euploca, but found none outside Euploca. Of the tested Euploca spp., c. 28% are C-3 or intermediate in carbon fixation pathway. Our phylogenetic results indicate four parallel/convergent acquisitions of C-4 photosynthesis or fewer origins with subsequent loss in some species.
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| 4. |
- Frohlich, Michael W., et al.
(author)
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Ninety-three new combinations in Euploca for species of Heliotropium section Orthostachys (Boraginaceae sensu APG)
- 2020
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In: Phytotaxa. - : MAGNOLIA PRESS. - 1179-3155 .- 1179-3163. ; 434:1, s. 13-21
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Journal article (peer-reviewed)abstract
- Many new combinations are needed in Euploca, previously regarded as Heliotropium section Orthostachys, to correspond with results of our forthcoming, world-wide, molecular phylogenetic analysis. We also need these names for our many delta C-13 determinations that identify many Euploca species exhibiting C-4 photosynthesis and show that other Euploca species are not C-4. Here we make the many new combinations required to support these results.
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| 5. |
- Perez-Escobar, Oscar A., et al.
(author)
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The origin and speciation of orchids
- 2024
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In: NEW PHYTOLOGIST. - 0028-646X .- 1469-8137.
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Journal article (peer-reviewed)abstract
- Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation.
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| 6. |
- Savolainen, Vincent, et al.
(author)
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Phylogeny of the eudicots : a nearly complete familial analysis based on rbcL gene sequences
- 2000
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In: Kew bulletin. - 0075-5974 .- 1874-933X. ; 55:2, s. 257-309
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Journal article (peer-reviewed)abstract
- A phylogenetic analysis of 589 plastid rbcL gene sequences representing nearly all eudicot families (a total of 308 families; seven photosynthetic and four parasitic families are missing) was performed, and bootstrap re-sampling was used to assess support for clades. Based on these data, the ordinal classification of eudicots is revised following the previous classification of angiosperms by the Angiosperm Phylogeny Group (APG). Putative additional orders are discussed (e.g. Dilleniales, Escalloniales, Vitales), and several additional families are assigned to orders for future updates of the APG classification. The use of rbcL alone in such a large matrix was found to be practical in discovering and providing bootstrap support for most orders. Combination of these data with other matrices for the rest of the angiosperms should provide the framework for a complete phylogeny to be used in macro-evolutionary studies.
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| 7. |
- Balao, Francisco, et al.
(author)
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Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima
- 2017
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In: Molecular Ecology. - : Wiley. - 0962-1083. ; 26:14, s. 3649-3662
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Journal article (peer-reviewed)abstract
- The orchid family is the largest in the angiosperms, but little is known about the molecular basis of the significant variation they exhibit. We investigate here the transcriptomic divergence between two European terrestrial orchids, Dactylorhiza incarnata and Dactylorhiza fuchsii, and integrate these results in the context of their distinct ecologies that we also document. Clear signals of lineage-specific adaptive evolution of protein-coding sequences are identified, notably targeting elements of biotic defence, including both physical and chemical adaptations in the context of divergent pools of pathogens and herbivores. In turn, a substantial regulatory divergence between the two species appears linked to adaptation/acclimation to abiotic conditions. Several of the pathways affected by differential expression are also targeted by deviating post-transcriptional regulation via sRNAs. Finally, D. incarnata appears to suffer from insufficient sRNA control over the activity of RNA-dependent DNA polymerase, resulting in increased activity of class I transposable elements and, over time, in larger genome size than that of D. fuchsii. The extensive molecular divergence between the two species suggests significant genomic and transcriptomic shock in their hybrids and offers insights into the difficulty of coexistence at the homoploid level. Altogether, biological response to selection, accumulated during the history of these orchids, appears governed by their microenvironmental context, in which biotic and abiotic pressures act synergistically to shape transcriptome structure, expression and regulation.
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| 8. |
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| 9. |
- Brandrud, Marie K., et al.
(author)
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Phylogenomic relationships of diploids and the origins of allotetraploids in Dactylorhiza (Orchidaceae)
- 2020
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In: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 69:1, s. 91-109
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Journal article (peer-reviewed)abstract
- Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum likelihood methods, and then group 16 allotetraploids by maximum affiliation to their putative parental diploids, implementing a method based on genotype likelihoods. The direction of hybrid crosses is inferred for each allotetraploid using information from maternally inherited plastid RADseq loci. Starting from age estimates of parental taxa, the relative ages of these allotetraploid entities are inferred by quantifying their genetic similarity to the diploids and numbers of private alleles compared with sibling allotetraploids. Whereas northwestern Europe is dominated by young allotetraploids of postglacial origins, comparatively older allotetraploids are distributed further south, where climatic conditions remained relatively stable during the Pleistocene glaciations. Our bioinformatics approach should prove effective for the study of other naturally occurring, non-model, polyploid plant complexes.
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| 10. |
- Bremer, Kåre, et al.
(author)
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An ordinal classification for the families of flowering plants
- 1998
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In: ANNALS OF THE MISSOURI BOTANICAL GARDEN. - : MISSOURI BOTANICAL GARDEN. - 0026-6493. ; 85:4, s. 531-553
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Journal article (other academic/artistic)abstract
- Recent cladistic analyses are revealing the phylogeny of flowering plants in increasing detail, and there is support for the monophyly of many major groups above the family level. With many elements of the major branching sequence of phylogeny established
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