| 1. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 2. |
- Leebens-Mack, James H., et al.
(författare)
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One thousand plant transcriptomes and the phylogenomics of green plants
- 2019
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
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Tidskriftsartikel (refereegranskat)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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| 3. |
- Savolainen, Vincent, et al.
(författare)
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Phylogeny of the eudicots : a nearly complete familial analysis based on rbcL gene sequences
- 2000
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Ingår i: Kew bulletin. - 0075-5974 .- 1874-933X. ; 55:2, s. 257-309
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Tidskriftsartikel (refereegranskat)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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| 4. |
- Xiang, Chun‐Lei, et al.
(författare)
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Revisiting the phylogeny of Dipsacales: New insights from phylogenomic analyses of complete plastomic sequences
- 2020
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Ingår i: Journal of Systematics and Evolution. - : Wiley. - 1674-4918 .- 1759-6831. ; 58:2, s. 103-117
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic relationships in Dipsacales have long been a major challenge. Although considerable progress has been made during the past two decades, questions remain; the uncertain systematic positions of Heptacodium, Triplostegia, and Zabelia, in particular, impede our understanding of Dipsacales evolution. Here we use 75 complete plastomic sequences to reconstruct the phylogeny of Dipsacales, of which 28 were newly generated. Two primary clades were recovered that form the phylogenetic backbone of Dipsacales. Seven of the primary clades correspond to the recognized families Adoxaceae, Caprifoliaceae s. str., Diervillaceae, Dipsacaceae, Linnaeaceae, Morinaceae, and Valerianaceae, and one corresponds to Zabelia, which was found to be the closest relative of Morinaceae in all analyses. Additionally, our results, with greatly increased confidence in most branches, show that Heptacodium and Triplostegia are members of Caprifoliaceae s. str. and Dipsacaceae, respectively. The results of our study indicate that the complete plastomic sequences provide a fully‐resolved and well‐supported representation of the phylogenetic relationships within Dipsacales.
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| 5. |
- Blaxter, Mark, et al.
(författare)
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Why sequence all eukaryotes?
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 119:4
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.
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| 6. |
- Lawniczak, Mara K. N., et al.
(författare)
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Standards recommendations for the Earth BioGenome Project
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 119:4
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Tidskriftsartikel (refereegranskat)abstract
- A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
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| 7. |
- Lewin, Harris A., et al.
(författare)
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The Earth BioGenome Project 2020 : Starting the clock
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 119:4
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 8. |
- Smedmark, Jenny E. E., 1972-
(författare)
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The evolutionary history of Geum (Rosaceae, Colurieae) : a study of ancient allopolyploid speciation
- 2004
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Allopolyploid speciation plays an important role in flowering plant evolution. Its contribution to diversity has been suggested to be significant in Geum. In this thesis the evolutionary history of Geum and its closest relatives was investigated by phylogenetic analysis of sequence data from the trnL-trnF region of the chloroplast, the ITS region of nuclear ribosomal DNA, and the nuclear low-copy gene GBSSI. The data were analysed using parsimony, Bayesian inference, and maximum likelihood. The phylogenies were used to test hypotheses about allopolyploid speciation, to investigate the evolution of some fruit characters and the implications for the taxonomy of the group. The GBSSI phylogenies indicated that allopolyploid speciation has occurred in the history of Geum. However, earlier hypotheses based on cytogenetic data about the allopolyploid ancestry of certain species were rejected. One tetraploid species and a morphologically diverse group of hexaploids, likely also including species with higher ploidy levels, were suggested to be of allopolyploid origin. A hypothesis of reticulate organismal relationships, including two instances where new lineages have been formed by allopolyploidy, was proposed based on the gene trees. A molecular dating analysis indicated that these reticulations occurred several million years ago. None of the previously suggested circumscriptions of Geum, Acomastylis, or Sieversia sensu lato were found to be monophyletic. Nested within Geum sensu lato were Waldsteinia, Coluria, and Taihangia and therefore Geum was recircumscribed to include these taxa. Colurieae, the former Dryadeae (in part), was recircumscribed and given a phylogenetic definition. According to this classification, Colurieae includes Fallugia, Sieversia sensu stricto, and Geum. Morphological evolution within the putative allopolyploid group appears to be homoplasious. Initial optimisation of the presence of a "joint", an abscission layer where the style, or part of it, is shed at maturity, on the gene trees indicated that it evolved four times from persistent, elongating styles. However, scanning electron microscopy showed that the development of the various types of fruits with jointed styles is similar, indicating that the joint and the deciduous segment of the style, of different lineages are homologous. The joint was thus hypothesised to have originated in the ancestral lineage of Waldsteinia and Coluria and to have been passed on via hybridisation to the polyploids. It is, however, only expressed in some lineages among the polyploids.
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| 9. |
- Struwe, Lena, 1967-
(författare)
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Morphological and Molecular Phylogenetic Studies in Neotropical Gentianaceae
- 1999
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The Gentianaceae of the Neotropics are a diverse taxonomic group representing several evolutionary lineages. The phylogenetic relationships of neotropical gentians are discussed based on cladistic analyses of morphological, trnL intron, and ITS 1 sequence data. Support for specific morphological and anatomical character evolutionary and biogeographic hypotheses are evaluated, with an emphasis on taxa from the Guayana Shield.Saccifolium, the only member of the family Saccifoliaceae, was found to be closely related to Gentiana and associated temperate-alpine genera. The boreotropics hypothesis is suggested as an explanation for the isolated occurrence of Saccifolium on the tepui complex Sierra de la Neblina (Brazilian-Venezuelan border), far from possible close relatives in eastern North America. Saccifolium is now considered a member of Gentianaceae due to this result.The majority of neotropical gentians belong to the Helia clade, a monophyletic, natural group restricted to the Neotropics. The Helia clade shows great morphological variation and occur in a diversity of habitats and geographic areas. Secondary woodiness appears to have evolved independently in this clade and in the Potalia clade, with perennial herbs being ancestral. Floral characters are also discussed from a phylogenetic perspective. The Helia clade has a high rate of white-sand and tepui endemic species including some that have been recently described. Several white-sand species are suggested to be relicts of basal evolutionary lineages in the tribe. The Pantepui and Quaternary forest refugium theory is discussed, and preliminary data suggest several independent origins of highland taxa from lowland lineages.The genus Potalia is most closely related to the African and Malagasy genus Anthocleista and it is suggested that the boreotropics hypothesis also explains their distribution. The first monograph of Potalia is presented. Potalia amara, the type species, is restricted to French Guiana and Amapá, Brazil. Three additional species are restricted to white-sand areas in lowlands of Amazonia and the Guayana Shield, and two species are restricted to Chocó, Colombia, and Panama and Costa Rica, respectively. Potalia resinifera is the most widespread species occurring over most of the Amazon basin, Andean foothills, and the Chocó. A morphological cladistic analysis of Potalia is presented, and this supports the proposed theory of white-sand taxa being representatives of basal, relictual lineages in neotropical plant groups (as in the Helia clade).<>P A cladistic analysis of the mycotrophic genus Voyria based on morphology and anatomy resulted in two large, monophyletic lineages, identified as two new subgenera. Ancestral distributions of Voyria and Potalia on the Guayana Shield are supported by morphological cladistic studies.
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