File Name: ribosomal its sequences and plant phylogenetic inference .zip
We identified eight putative ITS pseudogenes from four taxa with low predicted secondary structure stability and high substitution rates. Maximum likelihood ML and neighbor-joining NJ methods were used for phylogenetic reconstruction. In the former clade, most tetraploid taxa appear to be polyphyletic; sequences from individual plants did not correspond to recognized taxonomic units.
Agarwood is a type of wood that is used in traditional Thai medicines and has been applied in several recipes; in particular, this wood is considered as a costly resinous non-wood product. However, the morphological characteristics of the plant in the genus Aquilaria are quite similar, and so the authentication steps need a botanical expert for the purposes of identification and then also require an efficient tool for species-level discrimination. DNA barcoding is an approved molecular technique which uses a short sequence as a barcoding region specific for identified species.
Flowering times in Viburnum. Arnoldia PDF Donoghue, M. Growth patterns in woody plants with examples from the genus Viburnum. PDF Coombs, E. Donoghue, and R. Characters, computers, and cladograms: a review of the Berkeley cladistics workshop.
A botanical classification. Review of Dahlgren, R. The Monocotyledons. A Comparative Study. New York: Academic Press. Science PDF Mishler, B. Species concepts: a case for pluralism. A preliminary analysis of phylogenetic relationships in Viburnum Caprifoliaceae s. The phylogenetic relationships of Viburnum. In Advances in Cladistics, Volume 2, pp. Platnick and V.
Funk eds. New York: Columbia Univ. Caprifoliaceae of Japan. Review of Hara, H. Tokyo: Academia Sci. PDF Maddison, W. Donoghue, and D. Outgroup analysis and parsimony. The logic and limitations of the outgroup substitution approach to cladistic analysis.
Pollen diversity and exine evolution in Viburnum and the Caprifoliaceae sensu lato. Arnold Arb. A critique of the biological species concept and recommendations for a phylogenetic alternative. The Bryologist Miscellaneous cladistics.
Review of Duncan, T. Cladistics: Perspectives on the Reconstruction of Evolutionary History. Polarity assessment in phylogenetic systematics: a response to Meacham. Taxon PDF Doyle, J. Relationships of angiosperms and Gnetales: a numerical cladistic analysis.
Thomas and R. Spicer eds. London: Oxford Univ. Seed plant phylogeny and the origin of angiosperms: an experimental cladistic approach. Experiments and hypotheses in systematics. The importance of fossils in elucidating seed plant phylogeny and macroevolution. South African perspectives on species: an evaluation of the recognition concept. Review of Vrba, E. Species and Speciation. Pretoria: Transvaal Museum.
Cladistics The origin of angiosperms: a cladistic approach. Friis, W. Chaloner, and P. Crane eds. Cambridge: Cambridge Univ. Paraphyly, ancestors, and the goals of taxonomy: a botanical defense of cladism.
PDF de Queiroz, K. Phylogenetic systematics and the species problem. Phylogenetic analysis of angiosperms and the relationships of Hamamelidae. Crane and S. Blackmore eds. Oxford: Clarendon Press. Phylogenetic studies of seed plants and angiosperms based on morphological characters. In The Hierarchy of Life, pp. Fernholm, K.
Bremer, and H. Jornvall eds. Nobel Symposium Amsterdam: Elsevier Publ. Phylogenies and the analysis of evolutionary sequences, with examples from seed plants. Evolution PDF Crane, P. Donoghue, J. Doyle, and E. Angiosperm origins. Nature Doyle, J. Gauthier, A. Kluge, and T. The importance of fossils in phylogeny reconstruction. PDF Sanderson, M. Patterns of variation in levels of homoplasy. Phylogenetic systematics or Nelson's version of cladistics? Sociology, selection, and success: a critique of David Hull's analysis of science and systematics.
Phylogenetic systematics and species revisited. Why parsimony? Review of Sober, E. Reconstructing the Past: Parsimony, Evolution, and Interference.
Cambridge: M. Angiosperm monophyly. Trends Ecol. PDF Barrett, M. Donoghue, and E. Against consensus. The suitability of molecular and morphological evidence in reconstructing plant phylogeny. In Molecular Systematics in Plants, pp. Soltis, D. Soltis, and J. Doyle eds.
In this paper, we discuss the possibility of using a short nuclear DNA sequence as a barcode to identify a wide range of medicinal plant species. First, the PCR and sequencing success rates of ITS and ITS2 were evaluated based entirely on materials from dry medicinal product and herbarium voucher specimens, including some samples collected back to 90 years ago. Our results supported the hypothesis that ITS2 can be used as a minibarcode to effectively identify species in a wide variety of specimens and medicinal materials. DNA barcoding takes advantage of short standard sequences to discover and identify species [ 1 ]. An ideal DNA barcode should be short enough to be amplified from archival specimens using universal primers. The results of that study showed that minibarcodes can be isolated from different types of specimens, including museum samples, trace tissue samples with degraded DNA and other specimens, from which the acquisition of a full-length barcode CO1 is not feasible [ 2 ]. The amplification of DNA from herbarium specimens is also important for barcoding studies because it is often necessary to confirm the species identification of fresh specimens by comparing their sequences with those of older museum specimens [ 3 ].
Phylogenetic analyses were conducted to evaluate relationships of 7 taxa of Korean Carpesium including three outgroup Inula britannica L. Phylogenetic studies used maximum parsimony, neighbor-joining and maximum likelihood methods analysis. The total number of variable sites was for the entire sequences, and a parsimony informative sites of 64 are valid. As the result, Korean Carpesium were formed monophyletic group and C. The results show that C. These results suggest that the ITS data used in this study could be useful for the phylogenetic analysis of Korean Carpesium. Download PDF.
One of the most popular sequences for phylogenetic inference at the generic and infrageneric levels in plants is the internal transcribed spacer (ITS) region of.
Flowering times in Viburnum. Arnoldia PDF Donoghue, M. Growth patterns in woody plants with examples from the genus Viburnum.
Separate and combined analyses were performed. ITS-variation was extensive and, because of alignment ambiguities, some sites were excluded from the analyses. Several topologies from the rbc L analysis that conflicted with earlier classifications are corroborated by the ITS data: 1 Posoqueria should be excluded from Gardenieae. Incongruities found between the two data sets may be caused by density of taxon sampling, different evolutionary rates, phylogenetic sorting, homoplasy caused by functional constraints, or sampling of non-orthologous ITS types. This is a preview of subscription content, access via your institution.
Barcode of nuclear ribosomal internal transcribed spacer regions ITS as a useful tool to recognize a newly naturalized and potentially invasive weed, Chloris pilosa Schumach. Poaceae , in Taiwan. PDF Download Appendix. Akaike, H. A new look at the statistical model identification.
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