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- De Lima Ferreira, Paola, et al.
(author)
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Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses
- 2022
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In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903. ; 169
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Journal article (peer-reviewed)abstract
- Target sequence capture has emerged as a powerful method to sequence hundreds or thousands of genomic regions in a cost- and time-efficient approach. In most cases, however, targeted regions lack full sequence information for certain samples, due to taxonomic, laboratory, or stochastic factors. Loci lacking molecular data for a large number of samples are commonly excluded from downstream analyses, even though they may still contain valuable information. On the other hand, including data-poor loci may bias phylogenetic analyses. Here we use a target sequence capture dataset of an ecologically and taxonomically diverse group of spiny sunflowers (Asteraceae, or Compositae: Barnadesioideae) to test how the inclusion or exclusion of such data-poor loci affects phylogenetic inference. We investigate the sensitivity of concatenation and coalescent approaches to missing data with matrices of varying taxonomic completeness by filtering loci with different proportions of missing samples prior to data analysis. We find that missing data affect both the topology and branch support of the resulting phylogenies. The matrix containing all loci yielded the overall highest node support values, independently of the amount of missing nucleotides. These results provide empirical support to earlier suggestions based on single genes and data simulations that taxa with high amounts of missing data should not be readily dismissed as they can provide essential information for phylogenomic reconstruction. © 2022 The Authors
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| 2. |
- De Lima Ferreira, Paola, et al.
(author)
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Touch me carefully: a step towards understanding morphological diversity in the South American spiny sunflowers (Compositae, Barnadesioideae)
- 2021
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In: Phytotaxa. - : Magnolia Press. - 1179-3155 .- 1179-3163. ; 518:2, s. 109-142
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Journal article (peer-reviewed)abstract
- The subfamily Barnadesioideae (Compositae) is endemic to South America, comprising 10 genera and 80 species of mostly spiny herbs, subshrubs, shrubs, trees, or woody vines distributed from Venezuela to Argentina. Three genera, Dasyphyllum (27 species), Chuquiraga (22 spp.) and Barnadesia (19 spp.) contain 85% of the species, while the other seven genera (Archidasyphyllum, Arnaldoa, Doniophyton, Duseniella, Fulcaldea, Huarpea, and Schlechtendalia) are represented by up to three species each. Most species are found in xeric areas in the Andean and Patagonian regions-as in the Paramos, Puna and Patagonian steppe vegetation-with a secondary center of diversity in eastern South America. Previous phylogenetic hypotheses have clarified the relationships within the subfamily, showing that there are many non-monophyletic groups in different taxonomic ranks. As a result, taxonomic changes have been proposed over recent decades in order to reflect classifications comprising only monophyletic groups. In the present study, we provide a generic synopsis of the subfamily Barnadesioideae based on the most recent generic circumscriptions, including a key, expanded morphological descriptions, information on geographical distribution and habitat, photographs and taxonomic notes for all genera.
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| 3. |
- Groppo, Milton, et al.
(author)
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Placement of Kuhlmanniodendron Fiaschi & Groppo in Lindackerieae (Achariaceae, Malpighiales) confirmed by analyses of rbcL sequences, with notes on pollen morphology and wood anatomy
- 2010
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In: PLANT SYSTEMATICS AND EVOLUTION. - : Springer Science and Business Media LLC. - 0378-2697 .- 1615-6110. ; 286:1-2, s. 27-37
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Journal article (peer-reviewed)abstract
- The phylogenetic placement of Kuhlmanniodendron Fiaschi & Groppo (Achariaceae) within Malpighiales was investigated with rbcL sequence data. This genus was recently created to accommodate Carpotroche apterocarpa Kuhlm., a poorly known species from the rainforests of Espirito Santo, Brazil. One rbcL sequence was obtained from Kuhlmanniodendron and analyzed with 73 additional sequences from Malpighiales, and 8 from two closer orders, Oxalidales and Celastrales, all of which were available at Genbank. Phylogenetic analyses were carried out with maximum parsimony and Bayesian inference; bootstrap analyses were used in maximum parsimony to evaluate branch support. The results confirmed the placement of Kuhlmanniodendron together with Camptostylus, Lindackeria, Xylotheca, and Caloncoba in a strongly supported clade (posterior probability = 0.99) that corresponds with the tribe Lindackerieae of Achariaceae (Malpighiales). Kuhlmanniodendron also does not appear to be closely related to Oncoba (Salicaceae), an African genus with similar floral and fruit morphology that has been traditionally placed among cyanogenic Flacourtiaceae (now Achariaceae). A picrosodic paper test was performed in herbarium dry leaves, and the presence of cyanogenic glycosides, a class of compounds usually found in Achariaceae, was detected. Pollen morphology and wood anatomy of Kuhlmanniodendron were also investigated, but both pollen (3-colporate and microreticulate) and wood, with solitary to multiple vessels, scalariform perforation plates and other features, do not seem to be useful to distinguish this genus from other members of the Achariaceae and are rather common among the eudicotyledons as a whole. However, perforated ray cells with scalariform plates, an uncommon wood character, present in Kuhlmanniodendron are similar to those found in Kiggelaria africana (Pangieae, Achariaceae), but the occurrence of such cells is not mapped among the angiosperms, and it is not clear how homoplastic this character could be.
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