Phylogenetics of Panicoideae (Poaceae) based on chloroplast and nuclear DNA sequences

Abstract

Phylogenetic relationships among major subfamilies in Poaceae and among major tribes within Panicoideae were evaluated using parsimony and Bayesian analyses of chloroplast trnL-F and atpβ-rbcL DNA sequences and a nuclear ribosomal DNA sequence, ITS1-ITS2. The PanicoideaeAristidoideae-Chloridoideae-Micrairoideae-Arundinoideae-Danthonioideae (PACMAD) clade was well resolved. A close relationship between Aristidoideae and Chloridoideae was found. The monophyly of Micrairoideae was resolved but the relationships of three tribes (Eriachneae, Isachneae, Micraireae) within Micrairoideae were unclear, only Eriachne and Isachne were monophyletic. Panicoideae sensu stricto were supported as monophyletic and sister to a clade of Danthoniopsis and Tristachya. Within Panicoideae, only a clade of Andropogoneae + Arundinella + Garnotia was supported. None of the analyses supported the monophyletic status of Paniceae. Within Paniceae, the bristle clade (excluding Cenchrus) + Alexfloydia, and the forest shade clade sensu Giussani et al. (2001), were found, but their circumscription remains ambiguous. A sister relationship between the endemic and rare Australian grasses Homopholis and Walwhalleya was also resolved. Arundinelleae were found to be polyphyletic. This study supported the separation of Arundinella and Garnotia from the remaining Arundinelleae and the inclusion of both genera in their own subtribes (Arundinellinae Honda sensu stricto and Garnotiinae Pilger) within the Andropogoneae. Arundinelleae should be abandoned as a taxonomic tribe within the Centothecoid + Panicoid clade. Within Andropogoneae, five out of a total of 11 subtribes (Chionachninae, Coicinae, Dimeriinae, Germainiinae, and Tripsacinae) were monophyletic. This was the first time that Dimeriinae and Germainiinae have been included in a molecular study. † Deceased November 26 2009. Telopea 13(1-2): 2011Teerawatananon, Jacobs and Hodkinson

Phylogenomics of Andropogoneae (Panicoideae: Poaceae) of Mainland Southeast Asia

“…Aligned regions were concatenated into whole plastomes using the script concat_plastomes.pl (https:// github.com/mrmckain/Chloroplast-Phylogenomics-Utilities). Arundinelleae, represented here by Garnotia Brongn., was selected as the outgroup for the ML reconstruction and BI, based on previous morphological and molecular data (Clayton and Renvoize 1986;Kellogg 2000;Teerawatananon et al 2011;Soreng et al 2015;Veldkamp et al 2015). ML analysis was performed on the concatenated sequences under the General Time Reversible (GTR) model with the proportion of invariant sites and a gammashaped distribution of rates across sites (GTR 1 G 1 I) in RAxML v8.2.4 (Stamatakis 2006) with 1,000 bootstraps.…”

“…The Core Andropogoneae-The core Andropogoneae has been widely accepted and retrieved in all phylogenetic studies to date, including analyses of nuclear genes such as PHYB (Mathews et al 2002), GBSSI (Mason-Gamer et al 1998;Mathews et al 2002), single-copy genes (Estep et al 2014;Welker et al 2015Welker et al , 2016, and ITS (Skendzic et al 2007), chloroplast genes such as ndhF (Giussani et al 2001;Mathews et al 2002) and trnL-F (Teerawatananon et al 2011), and combined data. Two clades are clearly found: 1) the group of Cymbopogon, Dichanthium, Heteropogon, and Themeda and 2) the group of Andropogon, Hyparrhenia, and Schizachyrium.…”

“…Hubb., and Pseudosorghum A. Camus (Clayton and Renvoize 1986;Buitenhuis and Veldkamp 2001;Neamsuvan et al 2009; Teerawatananon et al 2014). Few phylogenetic and evolutionary studies have included these genera (but see Skendzic et al 2007;Teerawatananon et al 2011;Soreng et al 2015). Consequently, additional data for these particular genera could help illuminate their evolutionary relationships, divergence pattern, and character evolution relative to other Andropogoneae species.…”

“…Considering the Andropogoneae as a whole, two of the largest genera of the core are Andropogon and Schizachyrium, which together form a clade (Giussani et al 2001;Mathews et al 2002;Skendzic et al 2007;Teerawatananon et al 2011;Estep et al 2014). These are major grasses for forage and ecosystems and have been used as representatives for many studies in ecology, taxonomy, and phylogenetics.…”

“…Depending on the taxon sample and marker used, Andropogon and Schizachyrium have appeared as polyphyletic or paraphyletic. No study has sampled the genera in any depth in any part of their range (Mathews et al 2002;Skendzic et al 2007;Teerawatananon et al 2011).…”