Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1)

Abstract

Circumscriptions of and relationships among many genera and suprageneric taxa of the diverse grass tribe Poeae remain controversial. In an attempt to clarify these, we conducted phylogenetic analyses of >2400 new DNA sequences from two nuclear ribosomal regions (ITS, including internal transcribed spacers 1 and 2 and the 5.8S gene, and the 3’-end of the external transcribed spacer (ETS)) and five plastid regions (matK, trnL–trnF, atpF–atpH, psbK–psbI, psbA–rps19–trnH), and of more than 1000 new and previously published ITS sequences, focused particularly on Poeae chloroplast group 1 and including broad and increased species sampling compared to previous studies. Deep branches in the combined plastid and combined ITS+ETS trees are generally well resolved, the trees are congruent in most aspects, branch support across the trees is stronger than in trees based on only ITS and fewer plastid regions, and there is evidence of conflict between data partitions in some taxa. In plastid trees, a strongly supported clade corresponds to Poeae chloroplast group 1 and includes Agrostidinae p.p., Anthoxanthinae, Aveninae s.str., Brizinae, Koeleriinae (sometimes included in Aveninae s.l.), Phalaridinae and Torreyochloinae. In the ITS+ETS tree, a supported clade includes these same tribes as well as Sesleriinae and Scolochloinae. Aveninae s.str. and Sesleriinae are sister taxa and form a clade with Koeleriinae in the ITS+ETS tree whereas Aveninae s.str. and Koeleriinae form a clade and Sesleriinae is part of Poeae chloroplast group 2 in the plastid tree. All species of Trisetum are part of Koeleriinae, but the genus is polyphyletic. Koeleriinae is divided into two major subclades: one comprises Avellinia, Gaudinia, Koeleria, Rostraria, Trisetaria and Trisetum subg. Trisetum, and the other Calamagrostis/Deyeuxia p.p. (multiple species from Mexico to South America), Peyritschia, Leptophyllochloa, Sphenopholis, Trisetopsis and Trisetum subg. Deschampsioidea. Graphephorum, Trisetum cernuum, T. irazuense and T. macbridei fall in different clades of Koeleriinae in plastid vs. nuclear ribosomal trees, and are likely of hybrid origin. ITS and matK trees identify a third lineage of Koeleriinae corresponding to Trisetum subsect. Sibirica, and affinities of Lagurus ovatus with respect to Aveninae s.str. and Koeleriinae are incongruent in nuclear ribosomal and plastid trees, supporting recognition of Lagurus in its own subtribe. A large clade comprises taxa of Agrostidinae, Brizinae and Calothecinae, but neither Agrostidinae nor Calothecinae are monophyletic as currently circumscribed and affinities of Brizinae differ in plastid and nuclear ribosomal trees. Within this clade, one newly identified lineage comprises Calamagrostis coarctata, Dichelachne, Echinopogon (Agrostidinae p.p.) and Relchela (Calothecinae p.p.), and another comprises Chascolytrum (Calothecinae p.p.) and Deyeuxia effusa (Agrostidinae p.p.). Within Agrostidinae p.p., the type species of Deyeuxia and Calamagrostis s.str. are closely related, supporting classification of Dey...

Genetic diversity and taxonomic issues inGastridiumP.Beauv (Poaceae) inferred from plastid and nuclear DNA sequence analysis

“…Coss. & Durieu] appears as the most closely related to Gastridium (Clayton & Renvoize, 1986; Quintanar et al, 2007; Saarela & Graham, 2010), although their precise affinities, and relation with the other genera are unclear (Saarela et al, 2017).…”

“…In the light of this, the monophyly of Poaceae was first assessed with combined morphological and molecular analysis (Barker et al, 2001; Catalán et al, 1997), and later defined in an extensive phylogenetic framework (Bouchenak-Khelladi et al, 2008; Grass Phylogeny Working Group II, 2012; Saarela et al, 2018, Soreng et al, 2017). Nevertheless, despite many studies within Pooideae (e.g., Catalán et al, 2004; Hochbach et al, 2015; Persson & Rydin 2016; Quintanar et al, 2007; Schneider et al, 2012), diversity and evolutionary patterns in Agrostidinae remain poorly understood (Saarela et al, 2017). The wide application of plastid DNA sequences in species delimitation and phylogenetic analyses is due to some relevant operational features (availability of universal primers, large amounts of sequences in public databases usable for comparison), coupled with uniparental non-recombinant inheritance and mutation rates generally suitable for intrageneric inferences (Olmstead & Palmer, 1994; Saarela et al, 2017; Shaw et al, 2005; Soreng et al, 2015a).…”

“…Nevertheless, despite many studies within Pooideae (e.g., Catalán et al, 2004; Hochbach et al, 2015; Persson & Rydin 2016; Quintanar et al, 2007; Schneider et al, 2012), diversity and evolutionary patterns in Agrostidinae remain poorly understood (Saarela et al, 2017). The wide application of plastid DNA sequences in species delimitation and phylogenetic analyses is due to some relevant operational features (availability of universal primers, large amounts of sequences in public databases usable for comparison), coupled with uniparental non-recombinant inheritance and mutation rates generally suitable for intrageneric inferences (Olmstead & Palmer, 1994; Saarela et al, 2017; Shaw et al, 2005; Soreng et al, 2015a). In turn, the higher mutation rate of the nuclear ribosomal internal transcribed spacer (ITS) region has made this marker the most commonly used for taxonomic and phylogenetic resolution below the genus level (Baldwin et al, 1995).…”

“…Extensive phylogenetic/diversity studies at the intrageneric/intraspecific level have been performed on a few genera within the Agrostidinae subtribe (Amundsen & Warnke, 2012; Saarela et al, 2017). Other works on higher-level phylogenies (cf.…”

“…Other works on higher-level phylogenies (cf. Persson & Rydin, 2016; Quintanar et al, 2007; Saarela et al, 2017; Saarela et al, 2018) generally limited intrageneric sampling of Gastridium to one or two individuals of the major species ( G. ventricosum and G. phleoides ), preventing any inference on the genetic diversity of the genus and any attempt to identify evolutionary lineages. In this study, we performed a combined analysis of three markers from two independent genomic sources (nuclear: ITS; plastid: trnL-F, trnH-psbA) on an extensive Gastridium sample set to examine diversity patterns among the different taxa and clarify their systematic relationships.…”