| 1. |
- Zuntini, Alexandre R., et al.
(författare)
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Phylogenomics and the rise of the angiosperms
- 2024
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Ingår i: NATURE. - 0028-0836 .- 1476-4687. ; 629, s. 843-850
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Tidskriftsartikel (refereegranskat)abstract
- Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods(1,2). A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome(3,4). Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins(5-7). However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes(8). This 15-fold increase in genus-level sampling relative to comparable nuclear studies(9) provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.
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| 2. |
- Hernández-Ledesma, P., et al.
(författare)
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A taxonomic backbone for the global synthesis of species diversity in the angiosperm order Caryophyllales
- 2015
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Ingår i: Willdenowia. - : Botanic Garden and Botanical Museum Berlin, Freie Universitaet Berlin. - 0511-9618 .- 1868-6397. ; 45:3, s. 281-383
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Tidskriftsartikel (refereegranskat)abstract
- The Caryophyllales constitute a major lineage of flowering plants with approximately 12500 species in 39 families. A taxonomic backbone at the genus level is provided that reflects the current state of knowledge and accepts 749 genera for the order. A detailed review of the literature of the past two decades shows that enormous progress has been made in understanding overall phylogenetic relationships in Caryophyllales. The process of re-circumscribing families in order to be monophyletic appears to be largely complete and has led to the recognition of eight new families (Anacampserotaceae, Kewaceae, Limeaceae, Lophiocarpaceae, Macarthuriaceae, Microteaceae, Montiaceae and Talinaceae), while the phylogenetic evaluation of generic concepts is still well underway. As a result of this, the number of genera has increased by more than ten percent in comparison to the last complete treatments in the Families and genera of vascular plants” series. A checklist with all currently accepted genus names in Caryophyllales, as well as nomenclatural references, type names and synonymy is presented. Notes indicate how extensively the respective genera have been studied in a phylogenetic context. The most diverse families at the generic level are Cactaceae and Aizoaceae, but 28 families comprise only one to six genera. This synopsis represents a first step towards the aim of creating a global synthesis of the species diversity in the angiosperm order Caryophyllales integrating the work of numerous specialists around the world.
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| 3. |
- Jafari, Farzaneh, et al.
(författare)
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A new taxonomic backbone for the infrageneric classification of the species-rich genus Silene(Caryophyllaceae)
- 2020
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Ingår i: Taxon. - : Wiley. - 0040-0262 .- 1996-8175. ; 69:2, s. 337-368
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Tidskriftsartikel (refereegranskat)abstract
- The systematization of species in plant taxonomy based on the phylogenetic relationships among them are of utmost importance and also very challenging in large genera. In those, phylogenetic results often may suggest substantially different relationships than previous classifications, and call for large-scale taxonomic revisions. Delimitation of the genusSilenehas been and is still somewhat controversial, and recent molecular phylogenetic studies have settled several monophyletic groups that differ substantially from previous taxonomies. The infrageneric taxonomy ofSilenes.str. has not been updated as a whole taking the phylogenetic information into account. In this study, we review previous phylogenetic results based on multiple loci, and conducted comprehensive gene tree analyses based on the nrDNA ITS and cpDNArps16regions for 1586 and 944 samples representing 415 and 397 species, respectively, includingSileneand its allies, as well as a species tree analysis including 262 samples representing 243 species. We sampled representatives from all 44 sections recognized in the most recent global revision of the genus. The results support the recognition of three subgenera, i.e.,S.subg.Behenantha,S.subg.LychnisandS. subg.Silene, which is partly in agreement with previous molecular phylogenetic findings and contradicts all previous traditional classifications.Silenesect.Atocion, with a few annual species showing a narrow distribution range in the eastern Mediterranean, is treated as incertae sedis because of its uncertain phylogenetic position, possibly due to exceptionally high substitution rates.Silenesubg.Lychnis, weakly supported as sister to the other subgenera, splits into three main clades and includes four sections.Silenesubg.Behenantha, which forms a possible sister group in relation toS.subg.Silene, is poorly resolved basally and includes a large number of mostly small clades recognized as 18 sections. InS.subg.Silene, 11 sections are recognized, among which four are broadly circumscribed:S.sect.Auriculatae,S.sect.Sclerocalycinae,S.sect.SileneandS.sect.Siphonomorpha.Silenesect.AcutifoliaeandS.sect.Portensesare described here as new taxa, whereas new status or new combinations are proposed forS.sect.Anotites,S.sect.Muscipula,S.sect.Petrocoma,S.sect.Pulvinatae,S.sect.SclerophyllaeandS.sect.Uebelinia. Five new combinations and two new names are proposed for taxa inSileneformerly assigned toLychnisandUebelinia. The correct infrageneric nomenclature compatible with the new infrageneric system is provided along with synonymy and type citations. Shortcomings of this study, such as the lack of a morphological diagnostic key and sparse sampling of some large sections, are listed and discussed.
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| 4. |
- Pirani, A., et al.
(författare)
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Phylogeny ofAcanthophyllums.l. revisited: An update on generic concept and sectional classification
- 2020
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Ingår i: Taxon. - : Wiley. - 0040-0262 .- 1996-8175. ; 69:3, s. 500-514
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Tidskriftsartikel (refereegranskat)abstract
- The generic boundary of the broadly definedAcanthophyllums.l., the third-largest genus of the tribe Caryophylleae (Caryophyllaceae), has been a subject of taxonomic confusion.Acanthophyllums.l. now includes five minor genera previously recognized as independent. Among these small genera, the inclusion ofAllochrusa,Ochotonophila, andScleranthopsiswithinAcanthophyllums.l. was confirmed by previous molecular studies, while the positions ofDiaphanopteraandKuhitangiaremained uncertain. We have performed an updated molecular study ofAcanthophyllums.l. including an increased sampling of the genera and sections assigned to this group, using intron sequences of the chloroplast generps16and nuclear ribosomal internal transcribed spacer (ITS) sequences.Cyathophylla,Heterochroa, andSaponariawere chosen as outgroups for performing phylogenetic analyses using maximum likelihood and Bayesian methods. The present results suggest that, in addition to the genera mentioned above, bothDiaphanopteraandKuhitangiashould also be synonymized withinAcanthophyllum. SectionsDiaphanoptera,KuhitangiaandPseudomacrostegiaare introduced as new infrageneric taxa withinAcanthophyllum.Our results also indicate that some annual species ofSaponariaare closely related toAcanthophyllum.
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