https://bioone.org/journals/harvard-papers-in-botany/volume-13/issue-2/1043-4534-13.2.299/Flora-of-China/10.3100/1043-4534-13.2.299.pdf

Flora of China

The utility of DNA barcoding for identifying representative specimens of the circumpolar tree genus Fraxinus (56 species) was investigated. We examined the genetic variability of several loci suggested in chloroplast DNA barcode protocols such as matK, rpoB, rpoC1 and trnH-psbA in a large worldwide sample of Fraxinus species. The chloroplast intergenic spacer rpl32-trnL was further assessed in search for a potentially variable and useful locus. The results of the study suggest that the proposed cpDNA loci, alone or in combination, cannot fully discriminate among species because of the generally low rates of substitution in the chloroplast genome of Fraxinus. The intergenic spacer trnH-psbA was the best performing locus, but genetic distance-based discrimination was moderately successful and only resulted in the separation of the samples at the subgenus level. Use of the BLAST approach was better than the neighbor-joining tree reconstruction method with pairwise Kimura's two-parameter rates of substitution, but allowed for the correct identification of only less than half of the species sampled. Such rates are substantially lower than the success rate required for a standardised barcoding approach. Consequently, the current cpDNA barcodes are inadequate to fully discriminate Fraxinus species. Given that a low rate of substitution is common among the plastid genomes of trees, the use of the plant cpDNA “universal” barcode may not be suitable for the safe identification of tree species below a generic or sectional level. Supplementary barcoding loci of the nuclear genome and alternative solutions are proposed and discussed.

/pdf/deciduous-trees-and-the-application-of-universal-dna-24af1y9y12.pdf

Deciduous Trees and the Application of Universal DNA Barcodes: A Case Study on the Circumpolar Fraxinus

DNA barcoding aims to develop an efficient tool for species identification based on short and standardized DNA sequences. In this study, the DNA barcode paradigm was tested among the genera of the tribe Sisyrinchieae (Iridoideae). Sisyrinchium, with more than 77% of the species richness in the tribe, is a taxonomically complex genus. A total of 185 samples belonging to 98 species of Sisyrinchium, Olsynium, Orthrosanthus and Solenomelus were tested using matK, trnH-psbA and internal transcribed spacer (ITS). Candidate DNA barcodes were analysed either as single markers or in combination. Detection of a barcoding gap, similarity-based methods and tree-based analyses were used to assess the discrimination efficiency of DNA barcodes. The levels of species identification obtained from plastid barcodes were low and ranged from 17.35% to 20.41% for matK and 5.11% to 7.14% for trnH-psbA. The ITS provided better results with 30.61-38.78% of species identified. The analyses of the combined data sets did not result in a significant improvement in the discrimination rate. Among the tree-based methods, the best taxonomic resolution was obtained with Bayesian inference, particularly when the three data sets were combined. The study illustrates the difficulties for DNA barcoding to identify species in evolutionary complex lineages. Plastid markers are not recommended for barcoding Sisyrinchium due to the low discrimination power observed. ITS gave better results and may be used as a starting point for species identification.

Species discrimination in Sisyrinchium (Iridaceae): assessment of DNA barcodes in a taxonomically challenging genus.

The recent uplift of the tropical Andes (since the late Pliocene or early Pleistocene) provided extensive ecological opportunity for evolutionary radiations. We test for phylogenetic and morphological evidence of adaptive radiation and convergent evolution to novel habitats (exposed, high-altitude paramo habitats) in the Andean fern genera Jamesonia and Eriosorus. We construct time-calibrated phylogenies for the Jamesonia-Eriosorus clade. We then use recent phylogenetic comparative methods to test for evolutionary transitions among habitats, associations between habitat and leaf morphology, and ecologically driven variation in the rate of morphological evolution. Paramo species (Jamesonia) display morphological adaptations consistent with convergent evolution in response to the demands of a highly exposed environment but these adaptations are associated with microhabitat use rather than the paramo per se. Species that are associated with exposed microhabitats (including Jamesonia and Eriorsorus) are characterized by many but short pinnae per frond whereas species occupying sheltered microhabitats (primarily Eriosorus) have few but long pinnae per frond. Pinnae length declines more rapidly with altitude in sheltered species. Rates of speciation are significantly higher among paramo than non-paramo lineages supporting the hypothesis of adaptation and divergence in the unique Paramo biodiversity hotspot.

/pdf/adaptation-and-convergent-evolution-within-the-jamesonia-5faellpxlu.pdf

Adaptation and convergent evolution within the Jamesonia-Eriosorus complex in high-elevation biodiverse Andean hotspots.

Classification of Angelica and its allies is complex and controversial, with previous phylogenetic studies restricted to examina- tion of small numbers of taxa using only nrDNA ITS sequences In this study, phylogenetic analyses of nrDNA ITS and ETS sequences, cpDNA sequences (rps16 intron, rps16-trnK, rpl32-trnL, and trnL-trnT), and morphological data, supplemented by observations of fruit anatomy and micromorphology, were used to ascertain evolutionary relationships and confirm generic boundaries within Angelica sl (including Angelica, Archangelica, Coelopleurum, Czernaevia, and Ostericum), with emphasis on its East Asian members Most species of Angelica sl fall into two major, disparate clades, the Ostericum clade and the Angelica group, with the latter comprising five major lineages that are distinguished both molecularly and morphologically: Angelica ss (including Czernaevia), Archangelica, Coelopleurum, Glehnia, and a newly identified Littoral Angelica clade A North American Angelica clade was also distinguished in the ITS trees Taxonomic realignments will be required, as many species of Angelica fall outside of Angelica ss and four species of Angelica occur outside of the Angelica group (A hirsutiflora, A oncosepala, A paeoniifolia, and A sinensis) The Angelica ss clade contains predominantly East Asian species and comprises five major lineages, two of which represent plants exclusively from the eastern Himalayas; each of these five lineages can also be defined morphologi- cally The results obtained are significantly different from traditional treatments of Angelica sl and provide new insights into the phylogeny and classification of the group

New Insights into the Phylogeny of Angelica and its Allies (Apiaceae) with Emphasis on East Asian Species, Inferred from nrDNA, cpDNA, and Morphological Evidence

https://www.life.illinois.edu/downie/LogachevaMPE.pdf

Jenny M. Stratton

Papers

A comparison of nrDNA ITS and ETS loci for phylogenetic inference in the Umbelliferae: an example from tribe Tordylieae.