ABSTRACT
In this study, we analyzed 313 plastid genomes (plastomes) of Poaceae with a focus on expanding our current knowledge of relationships among the subfamily Pooideae, which represented over half the dataset (164 representatives). In total, 47 plastomes were sequenced and assembled for this study. This is the largest study of its kind to include plastome-level data, to not only increase sampling at both the taxonomic and molecular levels with the aim of resolving complex and reticulate relationships, but also to analyze the effects of alignment gaps in large-scale analyses, as well as explore divergences in the subfamily with an expanded set of 14 accepted grass fossils for more accurate calibrations and dating. Incorporating broad systematic assessments of Pooideae taxa conducted by authors within the last five years, we produced a robust phylogenomic reconstruction for the subfamily, which included all but two supergeneric taxa (Calothecinae and Duthieeae). We further explored how including alignment gaps in plastome analyses oftentimes can produce incorrect or misinterpretations of complex or reticulate relationships among taxa of Pooideae. This presented itself as consistently changing relationships at specific nodes for different stripping thresholds (percentage-based removal of gaps per alignment column). Our summary recommendation for large-scale genomic plastome datasets is to strip alignment columns of all gaps to increase pairwise identity and reduce errant signal from poly A/T bias. To do this we used the "mask alignment" tool in Geneious software. Finally, we determined an overall divergence age for Pooideae of roughly 84.8 Mya, which is in line with, but slightly older than most recent estimates.
Subject(s)
Genome, Plant , Genome, Plastid , Phylogeny , Poaceae/classification , Bayes Theorem , Biological Evolution , GenomicsABSTRACT
The Checklist of the Vascular Plants of the Republic of Guinea (CVPRG) is a specimen-based, expert-validated knowledge product, which provides a concise synthesis and overview of current knowledge on 3901 vascular plant species documented from Guinea (Conakry), West Africa, including their accepted names and synonyms, as well as their distribution and status within Guinea (indigenous or introduced, endemic or not). The CVPRG is generated automatically from the Guinea Collections Database and the Guinea Names Backbone Database, both developed and maintained at the Royal Botanic Gardens, Kew, in collaboration with the staff of the National Herbarium of Guinea. A total of 3505 indigenous vascular plant species are reported of which 3328 are flowering plants (angiosperms); this represents a 26% increase in known indigenous angiosperms since the last floristic overview. Intended as a reference for scientists documenting the diversity and distribution of the Guinea flora, the CVPRG will also inform those seeking to safeguard the rich plant diversity of Guinea and the societal, ecological and economic benefits accruing from these biological resources.
Subject(s)
Magnoliopsida , Tracheophyta , Guinea , PlantsABSTRACT
Based on a molecular DNA phylogeny of three plastid (rpl32-trnK, rps16 intron, and rps16-trnK) and nuclear ITS regions investigating 32 species of Agrostidinae, we describe two new genera, Agrostula gen. nov. with a single species and Alpagrostis gen. nov. with four species; provide support for five species in a monophyletic Podagrostis; and include a small sample of 12 species of a monophyletic Agrostis s.s. (including the type and most species of Neoschischkinia), that separates into two clades corresponding to A. subg. Agrostis and A. subg. Vilfa. Agrostula differs from Agrostis in having leaf blades with pillars of sclerenchyma which are continuous between the adaxial and abaxial surface of the blades, dorsally rounded glumes with blunt to truncate and erose to denticulate apices, florets ½ the length of the glumes, lemmas equally wide as long, widest at (or near) apex, apices broadly truncate, irregularly 5 to 7 denticulate to erose, awnless, anthers longer than the lemmas, and rugose-papillose caryopses. Alpagrostis differs from Agrostis in having geniculate basally inserted awns and truncate lemma apices with lateral veins prolonged from the apex in (2)4 setae. The following eight new combinations are made: Agrostula truncatula, Agrostula truncatula subsp. durieui, Alpagrostis alpina, Alpagrostis alpina var. flavescens, Alpagrostis barceloi, Alpagrostis setacea, Alpagrostis setacea var. flava, and Alpagrostis schleicheri. In addition, we provide a key separating Agrostula and Alpagrostis from Agrostis s.s. and other genera previously considered as synonyms of Agrostis; lectotypify Agrostis alpina Scop., A. schleicheri Jord. & Verl., A. truncatula Parl., and A. truncatula var. durieui Henriq.; and neotypify A. setacea Curtis.
ResumenSobre la base de una filogenia molecular de ADN de tres regiones plastidiales (rpl32-trnK, rps16 intrón y rps16-trnK) e ITS nuclear de 32 especies de Agrostidinae, describimos dos nuevos géneros, Agrostula gen. nov. con una sola especie, y Alpagrostis gen. nov. con cuatro especies; mostramos el apoyo para las cinco especies dentro de Podagrostis monofilético; e incluimos una pequeña muestra de 12 especies de Agrostis s.s (que incluye el tipo y la mayoría de las especies de Neoschischkinia), este último dividido en dos subclados que corresponden a A. subg. Agrostis y A. subg. Vilfa. Agrostula se diferencia de otras especies de Agrostis por tener láminas foliares con haces de esclerénquima continuos entre las superficies adaxial y abaxial de los limbos, glumas de dorso redondeado y ápice embotado a truncado y eroso a denticulado, antecios de ½ de la longitud de las glumas, lemas tan anchas como largas, lo más ancho en o cerca del ápice, ápices anchamente truncados, irregularmente 5 a 7 denticulados o erosos, sin arista, anteras más largas que los lemas y cariopsis rugosa-papilosa. Alpagrostis se diferencia de otras especies de Agrostis por tener aristas geniculadas insertas basalmente y ápices de lema truncados con venas laterales que se prolongan en (2)4 arístulas apicales. Presentamos las siguientes ocho nuevas combinaciones: Agrostula truncatula, Agrostula truncatula subsp. durieui, Alpagrostis alpina, Alpagrostis alpina var. flavescens, Alpagrostis barceloi, Alpagrostis setacea, Alpagrostis setacea var. flava y Alpagrostis schleicheri. Además, proporcionamos una clave que separa Agrostula y Alpagrostis de Agrostis s.s. y otros géneros previamente considerados como sinónimos de Agrostis, lectotipificamos Agrostis alpina Scop., A. schleicheri Jord. & Verl., A. truncatula Parl. y A. truncatula var. durieui Henriq. y neotipificamos A. setacea Curtis.
ABSTRACT
New insights into evolutionary trends in the economically important oat tribe (Aveneae) are presented. Plastid trnT-F and nuclear ribosomal ITS sequences were used to reconstruct the phylogeny of the Aveneae-Poeae-Seslerieae complex (Pooideae, Poaceae) through Bayesian- and maximum parsimony-based analyses, separately and in combination. The plastid data identified a strongly supported core Aveneae lineage that separated from other former Aveneae and Poeae groups. Koeleriinae, Aveninae, and Agrostidinae emerged as the main groups of this core Aveneae, which also included other minor subgroups with uncertain relationships and a few former Poeae members. Several former Aveneae representatives were also placed in independent sublineages in Poeae. Seslerieae resolved as close allies of Poeae or Aveneae in the plastid and nuclear topologies, respectively. Because of the intermingling of some Aveneae and Seslerieae lineages in Poeae and vice versa, we propose to expand Poeae to include all the aforementioned lineages. This best reflects our current understanding of the phylogeny of these important temperate grasses and sheds light on their evolutionary history.