Phylogenetic relationships and taxonomic issues in Gastridium (Poaceae) inferred from plastid and nuclear DNA sequence analysis

References

• Álvarez I, Wendel JF. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Mol Phylogenet E. 29(3):417–434.
   PubMed Web of Science ®Google Scholar
• Amundsen K, Warnke S. 2012. Agrostis species relationships based on trnL-trnF and atpI-atpH intergenic spacer regions. HortScience. 47(1):18–24.
   Web of Science ®Google Scholar
• Avise JC, Ball RM. 1990. Principles of genealogical concordance in species concepts and biological taxonomy. Oxford Surv Evol Biol. 7:45–67.
   PubMed Web of Science ®Google Scholar
• Baldwin BG, Sanderson MJ, Porter JM, Wojciechowski MF, Campbell CS, Donoghue MJ. 1995. The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Ann Missouri Bot Gard. 82(2):247–277.
   Web of Science ®Google Scholar
• Barberá P, Soreng RJ, Peterson PM, Romaschenko K, Quintanar A, Aedo C. 2019. Molecular phylogenetic analysis resolves Trisetum (Poaceae: Pooideae: Koeleriinae) polyphyletic: evidence for a new genus, Sibirotrisetum and resurrection of Acrospelion. J Syst Evol. 0(0):1–10.
   Google Scholar
• Barker NP, Clark LG, Davis JI, Duvall MR, Guala GF, Hsiao C, Kellogg EA, Linder HP. 2001. Phylogeny and subfamilial classification of the grasses (Poaceae). Ann Missouri Bot Gard. 88(3):373–457.
   Web of Science ®Google Scholar
• Bartolucci F, Peruzzi L, Galasso G, Albano A, Alessandrini A, Ardenghi NMG, Astuti G, Bacchetta G, Ballelli S, Banfi E, et al. 2018. An updated checklist of the vascular flora native to Italy. Plant Biosyst. 152(2):179–303.
   Web of Science ®Google Scholar
• Blondel J, Aronson J, Bodiou J-Y, Boeuf G. 2010. The mediterranean region: biological diversity in space and time. 2nd ed. Oxford (UK): Oxford University Press.
   Google Scholar
• Bolòs O, Vigo J. 2001. Flora dels Països Catalans. Vol 4. Barcelona: Editorial Barcino.
   Google Scholar
• Bouchenak-Khelladi Y, Salamin N, Savolainen V, Forest F, van der Bank M, Chase MW, Hodkinson TR. 2008. Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling. Mol Phylogenet E. 47(2):488–505.
   PubMed Web of Science ®Google Scholar
• Brown AJ. 2015. A morphological search for Lachnagrostis among the South African Agrostis and Polypogon (Poaceae). Muelleria. 34:23–46.
   Google Scholar
• Bryant D, Moulton V. 2004. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol E. 21(2):255–265.
   PubMed Web of Science ®Google Scholar
• Catalán P, Kellogg EA, Olmstead R. 1997. Phylogeny of Poaceae subfamily Pooideae based on chloroplast ndhF gene sequences. Mol Phylogenet E. 8(2):150–166.
   PubMed Web of Science ®Google Scholar
• Catalán P, Torrecilla P, Rodrı́guez JÁL, Olmstead RG. 2004. Phylogeny of the festucoid grasses of subtribe Loliinae and allies.Poeae, Pooideae) inferred from ITS and trnL-F sequences. Mol Phylogenet Evol. 31(2):517–541.
   PubMed Web of Science ®Google Scholar
• Chiapella J. 2007. A molecular phylogenetic study of Deschampsia (Poaceae: Aveneae) inferred from nuclear ITS and plastid trnL sequence data: support for the recognition of Avenella and Vahlodea. Taxon. 56(1):55–64.
   Web of Science ®Google Scholar
• Clayton WD, Renvoize SA. 1986. Genera Graminum. Grasses of the world. Richmond, UK: Royal Botanical Gardens. Kew. Kew Bulletin. Additional Series, 23.
   Google Scholar
• Clayton WD, Vorontsova MS, Harman KT, Williamson H. 2006. GrassBase - The online world grass flora. [accessed 2019 Aug 2]. http://www.kew.org/data/grasses-db.html.
   Google Scholar
• Coleman AW. 2003. ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends Genet. 19(7):370–375.
   PubMed Web of Science ®Google Scholar
• De Leonardis W, Pavone P, Terrasi MC, Zizza A. 1983. Numeri cromosomici per la flora Italiana: 827. Inform Bot Ital. 13(1981):166–167.
   Google Scholar
• de Queiroz K. 1998. The general lineage concept of species, species criteria, and the process of speciation: A conceptual unification and terminological recommendations. In: Howard DJ, Berlocher SH, editors, Endless forms: species and speciation. New York (NY): Oxford University Press; p. 57–75.
   Google Scholar
• de Queiroz K. 2007. Species concepts and species delimitation. Syst Biol. 56(6):879–886.
   PubMed Web of Science ®Google Scholar
• de Queiroz K, Good DA. 1997. Phenetic clustering in biology: a critique. Q Rev Biol. 72(1):3–30.
   Web of Science ®Google Scholar
• Dimopoulos P, Raus T, Bergmeier E, Constantinidis T, Iatroú G, Kokkini S. 2013. Vascular plants of Greece: an annotated checklist. Englera. 31:1–372.
   Google Scholar
• Doğan M. 1985. Gastridium P. Beauv. In: Davis PH, editor. Flora of Turkey and the East Aegean Islands. Vol. 9. Edinburgh (UK): Edinburgh University Press; p. 358–360.
   Google Scholar
• Feinbrun-Dothan N. 1986. Flora Palestina. Vol. 4. Jerusalem (IL): Israel Acad Sciences and Humanities; p. 217–219.
   Google Scholar
• Funk DJ, Omland KE. 2003. Species-level monophyly and paraphyly: frequency, causes and consequences with insights from animal mitochondrial DNA. Annu Rev Ecol Evol Syst. 34(1):397–423.
   Google Scholar
• Gallaher TJ, Adams DC, Attigala L, Burke SV, Craine JM, Duvall MR, Klahs PC, Sherratt E, Wysocki WP, Clark LG. 2019. Leaf shape and size track habitat transitions across forest–grassland boundaries in the grass family (Poaceae). Evolution. 73(5):927–946.
   PubMed Web of Science ®Google Scholar
• Grass Phylogeny Working Group II. 2012. New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins. New Phytol. 193(2):304–312.
   PubMed Web of Science ®Google Scholar
• Hajibabaei M, Singer MAC, Hebert PDN, Hickey DA. 2007. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet. 23(4):167–172.
   PubMed Web of Science ®Google Scholar
• Harpke D, Peterson A. 2008. 5.8S motifs for the identification of pseudogenic ITS regions. Botany. 86(3):300–305.
   Google Scholar
• Hennig W. 1965. Phylogenetic systematics. Annu Rev Entomol. 10(1):97–116.
   Google Scholar
• Hochbach A, Schneider J, Röser M. 2015. A multi‐locus analysis of phylogenetic relationships within grass subfamily Pooideae (Poaceae) inferred from sequences of nuclear single copy gene regions compared with plastid DNA. Mol Phylogenet E. 87:14–27.
   PubMed Web of Science ®Google Scholar
• Hörandl E. 2006. Paraphyletic versus monophyletic taxa – evolutionary versus cladistic classifications. Taxon. 55(3):564–570.
   Web of Science ®Google Scholar
• Hunte AM, Orlovich DA, Lloyd KM, Lee WG, Murphy DJ. 2004. The generic position of Austrofestuca littoralis and the reinstatement of Hookerochloa and Festucella (Poaceae) based on evidence from nuclear (ITS) and chloroplast (trnL-trnF) DNA sequences. N Z J Bot. 42(2):253–262.
   Web of Science ®Google Scholar
• Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol Biol E. 23(2):254–267.
   PubMed Web of Science ®Google Scholar
• Jauzein P. 2003. Contribution à la connaissance du genre Gastridium Beauv. en France. Le Monde Des Plantes. 481:1–3.
   Google Scholar
• Kellogg EA. 2015. Flowering Plants. Monocots: Poaceae. VI. Subfamily Pooideae Benth. (1861). In: Kubitzki K, editor. The families and genera of vascular plants. Vol. 13. Cham: Springer; p. 199–265.
   Google Scholar
• Knowles LL, Carstens BC. 2007. Delimiting species without monophyletic gene trees. Syst Biol. 56(6):887–895.
   PubMed Web of Science ®Google Scholar
• Kress WJ. 2017. Plant DNA barcodes: applications today and in the future. J Syst Evol. 55(4):291–307.
   Web of Science ®Google Scholar
• Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. 2005. Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA. 102(23):8369–8374.
   PubMed Web of Science ®Google Scholar
• Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 33(7):1870–1874.
   PubMed Web of Science ®Google Scholar
• Kyriazopoulos AP, López-Francos A, Porqueddu C, Sklavou P, editors. 2016. Ecosystem services and socio-economic benefits of Mediterranean Grasslands. Options Méditerranéennes: Série A. Mediterranean seminars No. 114. Zaragoza: CIHEAM.
   Google Scholar
• Lambinon J, Deschâtres R. 1994. Le genre Gastridium (Poaceae) en Corse. Candollea. 49:607–612.
   Google Scholar
• López-Tirado J, Scoppola A. 2017. Gastridium lainzii (Romero García) Romero Zarco (Poaceae), novedad corológica para la provincia de Cádiz (España). Revista de la Sociedad Gaditana de Historia Natural. 11:55–56.
   Google Scholar
• Lovatt CM. 1981. The history, ecology, and status of Gastridium ventricosum (Gouan) Schinz and Thell. in the Avon Gorge. Bristol Watsonia. 13:287–298.
   Google Scholar
• Mace GM. 2004. The role of taxonomy in species conservation. Philos Trans R Soc Lond B Biol Sci. 359(1444):711–719.
   PubMed Web of Science ®Google Scholar
• Mallet J. 2007. Species, concepts of. In: Levin SA, editor. Encyclopedia of biodiversity. Oxford (UK): Elsevier; p. 427–440.
   Google Scholar
• Mason-Gamer RJ, Kellogg EA. 1996. Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Syst Biol. 45(4):524–545.
   Web of Science ®Google Scholar
• Minaya M, Díaz-Pérez A, Mason-Gamer R, Pimentel M, Catalán P. 2015. Evolution of the beta-amylase gene in the temperate grasses: Non-purifying selection, recombination, semiparalogy, homeology and phylogenetic signal. Mol Phylogenet E. 91(2015):8–85.
   Google Scholar
• Nieto Feliner GL, Rosselló JA. 2007. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol Phylogenet E. 44(2):911–919.
   PubMed Web of Science ®Google Scholar
• Olmstead RG, Palmer JD. 1994. Chloroplast DNA systematics: a review of methods and data analysis. Am J Bot. 81(9):1205–1224.
   Web of Science ®Google Scholar
• Orton LM, Burke SV, Duvall MR. 2019. Plastome phylogenomics and characterization of rare genomic changes as taxonomic markers in plastome groups 1 and 2 Poeae (Pooideae; Poaceae). PeerJ. 7:e6959.
   PubMed Web of Science ®Google Scholar
• Pang X, Liu C, Shi L, Liu R, Liang D, Li H, Cherny SS, Chen S. 2012. Utility of the trnH–psbA intergenic spacer region and its combinations as plant DNA barcodes: a meta-analysis. PLoS One. 7(11):e48833.
   PubMed Web of Science ®Google Scholar
• Pante E, Schoelinck C, Puillandre N. 2015. From integrative taxonomy to species description: one step beyond. Syst Biol. 64(1):152–160.
   PubMed Web of Science ®Google Scholar
• Pattengale ND, Masoud A, Bininda-Emonds ORP, Moret BME, Stamatakis A. 2009. How many bootstrap replicates are necessary? In: Batzoglou S, editor. RECOMB 2009. Berlin: Springer-Verlag; p. 184–200.
   Google Scholar
• Persson NL, Rydin C. 2016. Phylogenetic relationships of the ‘Briza complex’ to other members of the subfamily Pooideae (Poaceae). Plecevo. 149(2):216–227.
   Google Scholar
• Pignatti S. 1982. Flora d’Italia. Vol. 1. Bologna: Edagricole; p. 15–16.
   Google Scholar
• Pignatti S. 2017. Flora d’Italia. Vol. 1. Bologna: Edagricole-New Business Media; p. 617–618.
   Google Scholar
• Porqueddu C, Ates S, Louhaichi M, Kyriazopoulos AP, Moreno G, del Pozo A, Ovalle C, Ewing MA, Nichols P. 2016. Grasslands in ‘old world’ and ‘new world’ mediterranean‐climate zones: past trends, current status and future research priorities. Grass Forage Sci. 71(1):1–35.
   Web of Science ®Google Scholar
• Pyke P. 2008. Gastridium phleoides (Gramineae) en Cataluña. Collect Bot. 27:91–94.
   Google Scholar
• Quintanar A, Castroviejo BS, Catalán P. 2007. Phylogeny of the tribe Aveneae (Pooideae, Poaceae) inferred from plastid trnT‐F and nuclear ITS sequences. Am J Bot. 94(9):1554–1569.
   PubMed Web of Science ®Google Scholar
• Rice A, Glick L, Abadi S, Einhorn M, Kopelman NM, Salman-Minkov A, Mayzel J, Chay O, Mayrose I. 2015. The chromosome counts database (CCDB) – a community resource of plant chromosome numbers. New Phytol. 206(1):19–26.
   PubMed Web of Science ®Google Scholar
• Romero García AT. 1996. Un taxón nuevo del género Gastridium P. Beauv. (Gramineae) en Andalucía occidental (España). Anales Del Jardín Botánico de Madrid. 54:399–406.
   Google Scholar
• Romero García AT. 2017. Gastridium P. Beauv., versión 2b. In: Romero-Zarco C, editor. Gramina Iberica. Genera graminum in opus "Flora iberica" intendentes. [accessed 2019 Mar 21]. Available from: https://sites.google.com/site/graminaiberica.
   Google Scholar
• Romero Zarco C. 2013. Notas sobre gramíneas del N de Marruecos. Acta Botanica Malacitana. 38:224–227.
   Google Scholar
• Romero Zarco C. 2015. Las Gramíneas de la Península Ibérica e Islas Baleares. Claves ilustradas para la determinación de los géneros y catálogo preliminar de las especies. Monografías de Botánica Ibérica. 15.
   Google Scholar
• Rouhan G, Gaudeul M. 2014. Plant taxonomy: an historical perspective, current challenges and perspectives. In: Besse P, editor. Molecular plant taxonomy: methods and protocols. New York (NY). Humana Press; p. 1–37.
   Google Scholar
• Rozas J, Ferrer-Mata A, Sánchez-Del Barrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large datasets. Mol Biol E. 34(12):3299–3302.
   PubMed Web of Science ®Google Scholar
• Saarela JM, Bull RD, Paradis MJ, Ebata SN, Peterson PM, Soreng RJ, Paszko B. 2017. Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae: Pooideae: Poeae: Poeae chloroplast group 1). Phytokeys 87:1–139.
   Google Scholar
• Saarela JM, Burke SV, Wysocki WP, Barrett MD, Clark LG, Craine JM, Peterson P, Soreng RJ, Vorontsova MS, Duvall MR. 2018. A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions. PeerJ. 6:e4299.
   PubMed Web of Science ®Google Scholar
• Saarela JM, Graham SW. 2010. Inference of phylogenetic relationships among the subfamilies of grasses (Poaceae: Poales) using meso-scale exemplar-based sampling of the plastid genome. Botany. 88(1):65–84.
   Web of Science ®Google Scholar
• Schneider J, Winterfeld G, Röser M. 2012. Polyphyly of the grass tribe Hainardieae (Poaceae: Pooideae): identification of its different lineages based on molecular phylogenetics, including morphological and cytogenetic characteristics. Org Divers Evol. 12(2):113–132.
   Web of Science ®Google Scholar
• Scholz H. 1986. Bemerkungen zur Flora Griechenlands: Gastridium phleoides und G. ventricosum (Poaceae). Willdenowia. 16:65–68.
   Google Scholar
• Scoppola A, Cancellieri L. 2019. A comparative morphometric study of genus Gastridium P. Beauv. (Poaceae) and its implications for species delimitation. Nord J Bot. 37(9):e02377.
   Web of Science ®Google Scholar
• Shaw J, Lickey EB, Beck JT, Farmer SB, Liu W, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL. 2005. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot. 92(1):142–166.
   PubMed Web of Science ®Google Scholar
• Shaw J, Lickey EB, Schilling EE, Small RL. 2007. Comparison of the whole chroloplast genome sequences to choose noncoding regions for phylogenetic studies in Angiosperms: the tortoise and the hare III. Am J Bot. 94(3):275–288.
   PubMed Web of Science ®Google Scholar
• Simpson MG. 2010. Plant systematics. Burlington (VT): Elsevier-Academic Press.
   Google Scholar
• Soreng RJ, Gillespie LJ, Koba H, Boudko E, Bull RD. 2015b. Molecular and morphological evidence for a new grass genus, Dupontiopsis (Poaceae tribe Poeae subtribe Poinae s.l.), endemic to alpine Japan, and implications for the reticulate origin of Dupontia and Arctophila within Poinae s.l. J Syst Evol. 53(2):138–162.
   Web of Science ®Google Scholar
• Soreng RJ, Peterson PM, Romaschenko K, Davidse G, Teisher JK, Clark LG, Barberá P, Gillespie LJ, Zuloaga FO. 2017. A worldwide phylogenetic classification of the Poaceae (Gramineae) II. An update and comparison of two 2015 classifications. J Syst Evol. 55(4):259–290.
   Web of Science ®Google Scholar
• Soreng RJ, Peterson PM, Romaschenko K, Davidse G, Zuloaga FO, Judziewicz EJ, Filgueiras TS, Davis JI, Morrone O. 2015a. A worldwide phylogenetic classification of the Poaceae (Gramineae). J Syst Evol. 53(2):117–137.
   Web of Science ®Google Scholar
• Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post- analysis of large phylogenies. Bioinformatics. 30(9):1312–1313.
   PubMed Web of Science ®Google Scholar
• Taberlet P, Gielly L, Pautou G, Bouvet J. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol. 17(5):1105–1109.
   PubMed Web of Science ®Google Scholar
• Thiers B. 2018. Index Herbariorum: A global directory of public herbaria and associated staff. New York Botanical Garden’s Virtual Herbarium. [accessed 2019 Mar 21]. http:sweetgum.nybg.org.ih.
   Google Scholar
• Tison JM, De Foucault B. 2014. Flora Gallica. Flore de France. Mèze: Biotope ed; p. 248.
   Google Scholar
• Torrecilla P, Catalán P. 2002. Phylogeny of broad-leaved and fine-leaved Festuca lineages (Poaceae) based on nuclear ITS sequences. Syst Bot. 27(2):241–251.
   Web of Science ®Google Scholar
• Torrecilla P, López Rodríguez JA, Catalán P. 2004. Phylogenetic relationships of Vulpia and related genera (Poeae, Poaceae) based on analysis of ITS and trnL-F sequences. Ann Mo Bot Gard. 91:124–158.
   Web of Science ®Google Scholar
• Valdés B, Scholz H. 2009. (with contributions from Raab-Straube E, Parolly G). Poaceae (pro parte majore). Euro + Med PlantBase - the information resource for Euro-Mediterranean plant diversity. [accessed 2018 Dec 12]. http://ww2.bgbm.org/EuroPlusMed/.
   Google Scholar
• Wheeler QD, Raven PH, Wilson EO. 2004. Taxonomy: impediment or expedient? Science. 303(5656):285.
   PubMed Web of Science ®Google Scholar
• White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M, Gelfand D, Sninsky J, White T, editors. PCR protocols: a guide to methods and applications. San Diego (CA): Academic Press; p. 315–322.
   Google Scholar
• Whitlock BA, Hale AM, Groff PA. 2010. Intraspecific inversions pose a challenge for the trnH-psbA plant DNA barcode. PLoS One. 5(7):e11533.
   PubMed Web of Science ®Google Scholar
• Wiley EO, Siegel-Causey D, Brooks DR, Funk VA. 1991. The compleat cladist - a primer of phylogenetic procedures. Lawrence (KS): The University of Kansas. Museum of Natural History Special Publication No. 19.
   Google Scholar
• Zwickl DJ, Hillis DM. 2002. Increased taxon sampling greatly reduces phylogenetic error. Syst Biol. 51(4):588–598.
   PubMed Web of Science ®Google Scholar