Towards a monophyletic classification of Cardueae: restoration of the genus Lophiolepis (= Cirsium p.p.) and new circumscription of Epitrachys

References

• Aceto S, Caputo P, Cozzolino S, Gaudio L, Moretti A. 1999. Phylogeny and evolution of Orchis and allied genera based on ITS DNA variation: morphological gaps and molecular continuity. Mol Phylogenet Evol. 13(1):67–76.
   PubMed Web of Science ®Google Scholar
• Ackerfield J, Susanna A, Funk V, Kelch D, Park DS, Thornhill AH, Yıldız B, Arabacı T, Dirmenci T. 2020. A prickly puzzle: Generic delimitations in the Carduus-Cirsium group (Compositae: Cardueae: Carduinae). Taxon. 69(4):715–738.
   Web of Science ®Google Scholar
• APG [The Angiosperm Phylogeny Group]. 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot J Linn Soc. 181:1–20.
   Web of Science ®Google Scholar
• Arevschatjan N. 1995. Cirsium Mill. In: Takhtajan A, editor, Flora Armenii, vol. 9. Erevan: Koeltz Scientific Books; p. 286–305.
   Google Scholar
• Avino M, Tortoriello G, Caputo P. 2009. A phylogenetic analysis of Dipsacaceae (Dipsacales) based on four DNA regions. Plant Syst Evol. 279(1–4):69–86.
   Web of Science ®Google Scholar
• Barres L, Sanmartín I, Anderson C-L, Susanna A, Buerki S, Galbany-Casals M, Vilatersana R. 2013. Why are thistles everywhere? Reconstructing the evolution and biogeographic history of tribe Cardueae (Compositae). Am J Bot. 100(5):867–882.
   PubMed Web of Science ®Google Scholar
• Bateman RM, Hollingsworth PM, Preston J, Yi-Bo L, Pridgeon AC, Chase MW. 2003. Molecular phylogenetics and evolution of Orchidinae and selected Habenariinae (Orchidaceae). Bot J Linn Soc. 142(1):1–40.
   Web of Science ®Google Scholar
• Besser VS. 1822. Emuneration plantarum. Vilnae: Josephi Zawadzki.
   Google Scholar
• Bieberstein FM. 1808. Flora Taurico-Caucasica exhibens stirpes phaenogamas. In Chersoneso Taurica et regionibus caucasicis sponte crescentes, vol. 2, Charkouiae: Typis Academicis.
   Google Scholar
• Blasi C, Biondi E, Izco J. 2011. 100 years of plant sociology: A celebration. Plant Biosystems. 145(sup1):1–3. doi:https://doi.org/10.1080/11263504.2011.602865.
   Google Scholar
• Bremer K. 1994. Asteraceae: Cladistics and Classification. Portland: Timber Press.
   Google Scholar
• Bureš P, Özcan M, Šmerda J, Michálková E, Horová L, Plačková K, Šmarda P, Elliott TL, Veselý P, Norouzi M, et al. 2022. Evolution of genome size and GC content in genus Cirsium and related Carduinae: rare descending dysploidy and polyploidy, limited environmental control, and strong phylogenetic signal. Preslia, in publ.
   Google Scholar
• Bureš P, Šmarda P, Rotreklová O, Oberreiter M, Burešová M, Konečný J, Knoll A, Fajmon K, Šmerda J. 2010. Pollen viability and natural hybridization of Central European species of Cirsium. Preslia. 82:391–422.
   Web of Science ®Google Scholar
• Bureš P, Šmerda J, Michálková E, Šmarda P, Knoll A, Vavrinec M. 2018. Cirsium greimleri – a new thistle species endemic to the Eastern Alps and Dinarids. Preslia. 90(2):105–134.
   Web of Science ®Google Scholar
• Bureš P, Wang YF, Horová L, Suda J. 2004. Genome size variation in Central European species of Cirsium (Compositae) and their natural hybrids. Ann Bot. 94(3):353–363.
   PubMed Web of Science ®Google Scholar
• Bureš P. 2004. Cirsium Mill. – thistle. In Slavík B., Štěpánková J., editors, Flora of the Czech Republic, vol. 7. Praha: Academia; p. 385–419.
   Google Scholar
• Candolle AP. 1838 [“1837”]. Prodromus Systematis Naturalis Regni Vegetabilis, vol. 6. Parisiis: Sumptibus Sociorum Treuttel et Würtz. https://doi.org/10.5962/bhl.title.286
   Google Scholar
• Capotorti G, Zavattero L, Anzellotti I, Burrascano S, Frondoni R, Marchetti M, Marignani M, Smiraglia D, Blasi C. 2012. Do National Parks play an active role in conserving the natural capital of Italy? Plant Biosyst. 146(2):258–265. doi:https://doi.org/10.1080/11263504.2012.695298.
   Web of Science ®Google Scholar
• Carucci F. 2011. Filogenesi molecolare del genere Cirsium Mill. sect. Eriolepis (Cass.) Dumort. Ph.D. diss. Naples: University of Naples “Federico II.”
   Google Scholar
• Cassini H. 1822. Lamyre, Lamyra. In: Cuvier F., editor, Dic sci nat. 25: p. 218–228. Paris and Strasbourg: F.G. Levrault and Le Normant.
   Google Scholar
• Cassini H. 1823. Lophiolèpe, Lophiolepis. In: Cuvier F., editor, Dict sci nat. 27: p. 180–192. Paris and Strasbourg: F.G. Levrault and Le Normant.
   Google Scholar
• Cassini H. 1826. Eriolepis. In: Cuvier F., editor, Dict sci nat. 41: p. 331–332. Paris and Strasbourg: F.G. Levrault and Le Normant.
   Google Scholar
• Chernomor O, von Haeseler A, Minh BQ. 2016. Terrace aware data structure for phylogenomic inference from supermatrices. Syst Biol. 65(6):997–1008.
   PubMed Web of Science ®Google Scholar
• CWG [Compositae Working Group]. 2022. Global compositae database. [accessed 2022 Jun 9]. http://www.compositae.org.
   Google Scholar
• Czerepanov SK. 1995. Vascular plants of Russia and adjacent States, 2nd ed. Cambridge: Cambridge University Press.
   Google Scholar
• Davis PH, Parris SB. 1975. Cirsium Mill. In Davis PH, ediror, Flora of Turkey and the East Aegean Islands, vol. 5. Edinburgh: Edinburgh University Press; p. 370–412.
   Google Scholar
• De Luca D, Del Guacchio E, Conti F, Iamonico D, Caputo P. 2022. Relationships within Mcneillia indicate a complex evolutionary history and reveal a new species of Minuartiella (Caryophyllaceae, Alsinoideae). Plants. 11(16):2118. doi:https://doi.org/10.3390/plants11162118.
   Google Scholar
• Del Guacchio E, Bernardo L, Caputo P, Carucci F, Domina G, Iamonico D. 2021. Nomenclatural Synopsis of Cirsium sect. Eriolepis (Asteraceae) in Italy. Plants. 10(2):223. doi:https://doi.org/10.3390/plants10020223.
   Google Scholar
• Del Guacchio E, Caputo P, Iamonico D. 2019. Typification of the name Cirsium lacaitae (Asteraceae). Phytotaxa. 423(4):273–276. doi:https://doi.org/10.11646/phytotaxa.423.4.6.
   Web of Science ®Google Scholar
• Del Guacchio E, Caputo P. 2020. Splitting Asperula (Rubiaceae): a proposal for consistency purposes within sections Cynanchicae, Thliphthisa and Hexaphylla. Plant Biosyst. 154(5):766–782.
   Google Scholar
• Del Guacchio E, Iamonico D. 2015. Typifications of the Linnaean names Carduus eriophorus, Carduus eriophorus var. spurius, and Cnicus ferox (Asteraceae). Phytotaxa. 238(2):196–200. doi:http://dx.doi.org/10.11646/phytotaxa.238.2.8.
   Web of Science ®Google Scholar
• Dirmenci T, Özcan T, Arabacı T, Çelenk S, İsmailova G, Yıldız B. 2019. Hybridization among three Cirsium (Asteraceae) species and important evidence for three new hybrids from Turkey. Turk J Bot. 43(3):366–385.
   Web of Science ®Google Scholar
• Ehrendorfer F, Barfuss MHJ, Manen J-F, Schneeweiss GM. 2018. Phylogeny, character evolution and spatiotemporal diversification of the species-rich and world-wide distributed tribe Rubieae (Rubiaceae). PLoS ONE. 13(12):e0207615.
   PubMed Web of Science ®Google Scholar
• Fischer FEL. 1808. Catalogue du jardin des plantes, de S. E. Monsieur Le Comte Aléxis de Razoumoffsky. Moskva: à Gorenki pres de Moscou.
   Google Scholar
• Flann C, Greuter W, Hind DJN. 2010. Cassini’s Compositae genera: A nomenclatural and taxonomic assessment. Taxon. 59(4):1206–1244.
   Web of Science ®Google Scholar
• Garcia-Jacas N, Garnatje T, Susanna A, Vilatersana R. 2002. Tribal and subtribal delimitation and phylogeny of the Cardueae (Asteraceae): a combined nuclear and chloroplast DNA analysis. Mol Phylogenet Evol. 22(1):51–64.
   PubMed Web of Science ®Google Scholar
• Greuter W. 2006+. Compositae (pro parte majore). In von Raab-Straube E, editors. Compositae. Euro + Med Plantbase – the information resource for Euro-Mediterranean plant diversity. [accessed 2022 Jun 9]. http://ww2.bgbm.org/EuroPlusMed/.
   Google Scholar
• Guerrero PC, Walter HE, Arroyo MTK, Peña CM, Tamburrino I, De Benedictis M, Larridon I. 2019. Molecular phylogeny of the large South American genus Eriosyce (Notocacteae, Cactaceae): Generic delimitation and proposed changes in infrageneric and species ranks. Taxon. 68(3):557–573.
   Web of Science ®Google Scholar
• Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59(3):307–321.
   PubMed Web of Science ®Google Scholar
• Häffner E, Hellwig FH. 1999. Phylogeny of the tribe Cardueae (Compositae) with emphasis on the subtribe Carduinae: an analysis based on ITS sequence data. Willdenowia. 29(1/2):27–39.
   Google Scholar
• Häffner E. 2000. On the phylogeny of the subtribe Carduinae (tribe Cardueae, Compositae). Englera. 21(21):3–208.
   Google Scholar
• Handel-mazzetti H. 1926. Plantae novae sinenses. Anz Österr Akad Wiss, Math-Naturwiss Kl. 63(8–12):95–112.
   Google Scholar
• Hassler M. 2022. World Plants. Synonymic checklist and distribution of the world flora. Version 13.0. [accessed 2022 Jun 8] www.worldplants.de.
   Google Scholar
• Herrando-Moraira S, Cardueae Radiations G, Calleja JA, Galbany-Casals M, Garcia-Jacas N, Liu JQ, López-Alvarado J, López-Pujol J, MandeL JR, Massó S, et al. 2019. Nuclear and plastid DNA phylogeny of tribe Cardueae (Compositae) with Hyb-Seq data: a new subtribal classification and a temporal diversification framework. Mol Phylogenet Evol. 137:313–332.
   PubMed Web of Science ®Google Scholar
• IPNI. 2022. onwards. The International Plant Names Index. [accessed 2022 Jun 9]. http://www.ipni.org.
   Google Scholar
• Jin W-T, Jin X-H, Schuiteman A, Li D-Z, Xiang X-G, Huang W-C, Li J-W, Huang L-Q. 2014. Molecular systematics of subtribe Orchidinae and Asian taxa of Habenariinae (Orchideae, Orchidaceae) based on plastid matK, rbcL and nuclear ITS. Mol Phylogenet Evol. 77:41–53.
   PubMed Web of Science ®Google Scholar
• Kadota Y. 2007. Species diversification of genus Cirsium (Asteraceae) in Japan. Korean J Pl Taxon. 37(4):335–349.
   Google Scholar
• Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 14(6):587–589.
   PubMed Web of Science ®Google Scholar
• Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30(14):3059–3066.
   PubMed Web of Science ®Google Scholar
• Keil DJ. 2006. Cirsium Miller. In: Flora of North America Editorial Committee, editors, Flora of North America North of Mexico, vol. 19. New York and Oxford: Oxford University Press; p. 95–164.
   Google Scholar
• Kelch D, Baldwin B. 2003. Phylogeny and ecological radiation of New World thistles (Cirsium, Cardueae-Compositae) based on ITS and ETS rDNA sequence data. Mol Ecol. 12(1):141–151.
   PubMed Web of Science ®Google Scholar
• Kharadze A, Gagnidze R. 2007. Cirsium Mill. In: Gagnidze R., editor, Flora Georgiae, 2nd ed., vol. 15. Tbilisi: Universal; p. 325–373.
   Google Scholar
• Kharadze A. 1963. Cirsium Mill. emend. Scop. In: Bobrov EG, Czerepanov SK, editors, Flora of the USSR, vol. 28. Mosqua [Moskow] and Leningrad [Saint Petersburg]: Editio Academiae Scientiarum URSS; p. 51–215.
   Google Scholar
• Kim JS, Kim JH. 2018. Updated molecular phylogenetic analysis, dating and biogeographical history of the lily family (Liliaceae: Liliales). Bot J Linn Soc. 187(4):579–593.
   Web of Science ®Google Scholar
• Koch K. 1851. Beitrage zu einer Flora des Orientes. Linnaea. 24:305–475.
   Google Scholar
• Köstekçi S, Arabacı T. 2011. Cypsela morphology of Cirsium sect. Cirsium (Asteraceae) taxa in Turkey. Biologia. 66:988–995.
   Web of Science ®Google Scholar
• Lanfear R, Calcott B, Ho SY, Guindon S. 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol. 29(6):1695–1701.
   PubMed Web of Science ®Google Scholar
• Lanfear R, Calcott B, Kainer D, Mayer C, Stamatakis A. 2014. Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evol Biol. 14:82.
   PubMed Web of Science ®Google Scholar
• Larridon I, Bauters K, Reynders M, Huygh W, Muthama Muasya A, Simpson DA, Goetghebeur P. 2013. Towards a new classification of the giant paraphyletic genus Cyperus (Cyperaceae): phylogenetic relationships and generic delimitation in C4 Cyperus. Bot J Linn Soc. 172(1):106–126.
   Web of Science ®Google Scholar
• Menitsky UL. 1996. Conspectus of the Caucasus species of the genus Cirsium (Asteraceae). Bot Zhurn. 81:92–105. (Also published as Menitsky UL. 2008. Cirsium Mill. In: Takhtajan A. editor, Caucasian Flora Conspectus, vol. 3(1). Saint-Petersburg et Moscow: KMK Scientific Press; pp. 261–276).
   Google Scholar
• Meusel H, Jäger EJ. editors. 1992. Vergleichende Chorologie der zentraleuropäischen Flora, vol. 3, Jena, Stuttgart and New York: Gustav Fischer.
   Google Scholar
• Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molec Biol Evol. 37(5):1530–1534.
   PubMed Web of Science ®Google Scholar
• Moench C. 1802. Supplementum ad methodum a staminum situ describendi. Marburgi Cattorum: In officina nova libraria academiae.
   Google Scholar
• Negaresh K, Khoshroo SMR. 2016. Nomenclatural notes on Cirsium lappaceum (Asteraceae, Cardueae) from Iran. Ann Bot Fennici. 53(5-6):405–409.
   Web of Science ®Google Scholar
• Nouroozi M, Sheidai M, Attar F, Noormohammadi Z. 2012. Pollen morphological studies on the genus Cirsium Mill. (Asteraceae) in Iran. J Jap Bot. 87:268–279.
   Google Scholar
• Nyárády EI. 1964. Cirsium Mill. In Săvŭlescu T., editor, Flora Reipublicae Popularis Romanicae, vol. 9. Bucharest: Editio Academiae Reipublicae Popularis Romanicae; p. 672–743.
   Google Scholar
• Nyman CF. 1879. Conspectus Florae Europaeae. Örebro: Typis Officinae Bohilinanae.
   Google Scholar
• Özcan M. 2017. Cypsela micromorphology and anatomy in Cirsium sect. Epitrachys (Asteraceae, Carduoideae) and its taxonomic implications. Nord J Bot. 35:653–668.
   Web of Science ®Google Scholar
• Petrak F. 1911. Cirsium Sommieri, eine neue Art aus Türkisch-Armenien. Repert Spec Nov Regni Veg. 9:166–169.
   Google Scholar
• Petrak F. 1912. Der Formenkreis Des Cirsium eriophorum (L.) Scop. in Europa. Biblioth Bot. 18(78):1–92.
   Google Scholar
• Petrak F. 1960. Über einige Arten und Bastarde der Gattung Cirsium. Mitt Thüring Bot Ges. 2:13–41.
   Google Scholar
• Petrak F. 1979. Cirsium Mill. In Rechinger KH, editor, Flora Iranica, vol. 139a. Graz: Akademische Druck- und Verlagsanstalt; p. 231–280.
   Google Scholar
• POWO. 2022. Plants of the World Online. Facilitated by the Royal Botanic Gardens, Kew. [accessed 2022 Jun 7]. http://www.plantsoftheworldonline.org/.
   Google Scholar
• Sánchez Del Pino I, Iamonico D. 2016. Jamesbondia, a new Subgenus of Alternanthera (Gomphrenoideae, Amaranthaceae) from Central America and the Caribbean Islands. Plant Biosyst. 150(2):190–200. doi:http://dx.doi.org/10.1080/11263504.2014.941034.
   Web of Science ®Google Scholar
• Schäferhoff B, Fleischmann A, Fischer E, Albach DC, Borsch T, Heubl G, Müller KF. 2010. Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences. BMC Evol Biol. 10:352.
   PubMed Web of Science ®Google Scholar
• Schübler G. 1836. Flora von Würtemberg: Mit 1 Charte der Umgebungen von Tübingen, vol. 1, Tubingen: C. F. Osiander.
   Google Scholar
• Sela I, Ashkenazy H, Katoh K, Pupko T. 2015. GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Res. 43(W1):W7–14.
   PubMed Web of Science ®Google Scholar
• Shih C. 1984. Notulae de Plantis Tribus Cynarearum Familiae Compositarum Sinicae (II). Acta Phytotax Sin. 22:386–396.
   Google Scholar
• Slotta TAB, Horvath DP, Foley ME. 2012. Phylogeny of Cirsium spp. in North America: host specificity does not follow phylogeny. Plants (Basel). 1(2):61–73.
   PubMedGoogle Scholar
• Spach E. 1841. Histoire Naturelle des végétaux. Phanérogames, vol. 10, Paris: Librarie Encyclopédique de Roret.
   Google Scholar
• Stafleu FA, Cowan RS. 1976. Taxonomic literature, 2nd ed, vol. 1 (A–G), Bohn and Utrecht: Scheltema and Holtema.
   Google Scholar
• Steudel ET. 1841. Nomenclator botanicus, 2nd ed., Stuttgartiae et Tubingae: Typis et sumptibus J. G. Cottae.
   Google Scholar
• Susanna A, Garcia-Jacas N, Hidalgo O, Vilatersana R, Garnatje T. 2006. The Cardueae (Compositae) revisited: insights from ITS, trnL-trnF, and matK nuclear and chloroplast DNA analysis. Ann Mo Bot Garden. 93(1):150–171.2.0.CO;2]
   Web of Science ®Google Scholar
• Susanna A, Garcia-Jacas N. 2009. Cardueae (Carduoideae). In: Funk VA, Susanna A, Stuessy TF, Bayer RJ, editors, Systematics, evolution, and biogeography of Compositae Vienna: IAPT; p. 293–313.
   Google Scholar
• Szlachetko DL, Górniak M, Kowalkowska AK, Kolanowska M, Jurczak-Kurek A, Archila Morales F. 2021. The natural history of the genus Cypripedium (Orchidaceae). Plant Biosyst. 155(4):772–796. doi:https://doi.org/10.1080/11263504.2020.1785963.
   Web of Science ®Google Scholar
• Talavera S, Valdés B. 1976. Revisión del género Cirsium (Compositae) en la Península Ibérica. Lagascalia. 5(2):127–223.
   Google Scholar
• Talavera S. 2015. Cirsium Mill. In Devesa JA., Quintanar A., García MÁ., editors, Flora Iberica, vol. 16(1). Madrid: Real Jardín Botánico Madrid (CSIC); p. 136–176.
   Google Scholar
• The Plant List. 2013. The Plant List. A working list of all plant species. [accessed 2022 Jun 7]. http://www.theplantlist.org/.
   Google Scholar
• Turland NJ, Wiersema JH, Barrie FR, Greuter W, Hawksworth DL, Herendeen PS, Knapp S, Kusber W-H, Li D-Z, Marhold K, et al. 2018. International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017. Regnum Veg. 159:1–254. doi:https://doi.org/10.12705/Code.2018.
   Google Scholar
• Vasconcelos TNC, Prenner G, Santos MF, Wingler A, Lucas EJ. 2017. Links between parallel evolution and systematic complexity in angiosperms—A case study of floral development in Myrcia s.l. (Myrtaceae). Perspect Plant. 24:11–24.
   Web of Science ®Google Scholar
• Villaseñor JL. 2016. Checklist of the native vascular plants of Mexico. Rev Mex Biodiver. 87(3):559–902.
   Web of Science ®Google Scholar
• Werner K. 1976. Cirsium Miller. In: Tutin TG, Heywood VH, Burges NA, Moore DM, Valentine DH, Walters SM, Webb DA, edirors. Flora Europaea, vol. 4. Cambridge: Cambridge University Press; p. 232–242.
   Google Scholar
• Winkworth RC, Bell CD, Donoghue MJ. 2008. Mitochondrial sequence data and Dipsacales phylogeny: mixed models, partitioned Bayesian analyses and model selection. Mol Phylogenet Evol. 46(3):830–843.
   PubMed Web of Science ®Google Scholar
• Yang L-E, Meng Y, Peng D-L, Nie Z-L, Sun H. 2018. Molecular phylogeny of Galium L. of the tribe Rubieae (Rubiaceae) – Emphasis on Chinese species and recognition of a new genus Pseudogalium. Mol Phylogenet Evol. 126:221–232.
   PubMed Web of Science ®Google Scholar
• Yıldız B, Arabacı T, Dirmencı T, Köstecki S. 2016. A taxonomic revision of the genus Cirsium Mill. sect. Cirsium (Asteraceae: Cardueae) in Turkey. Turk J Bot. 40:514–530.
   Web of Science ®Google Scholar
• Zhigila DA, Verboom GA, Muasya AM. 2020. An infrageneric classification of Thesium (Santalaceae) based on molecular phylogenetic data. Taxon. 69(1):100–123.
   Web of Science ®Google Scholar