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.
Highlights
From the late Cretaceous origins of Poaceae Barnhart, to modern day agriculture, the grass family is well known for the impacts it has had in both conquering diverse landscapes and its economic significance as biofuel or food sources for wide varieties of animal species, including humans (Bouchenak-Khelladi et al, 2010; Orton et al, 2017, 2019)
The goal of our work is to explore how plastome level data in large-scale studies will provide added resolution to reticulate phylogenomic relationships in groups plagued by complex phylogenomic histories, determine how alignment gaps impact phylogenetic reconstruction, and in particular, how they impact topology
The results indicated that best practices in grass phylogenomics include utilizing complete plastome data while excluding ambiguously aligned regions by stripping alignment matrices
Summary
From the late Cretaceous origins of Poaceae Barnhart, to modern day agriculture, the grass family is well known for the impacts it has had in both conquering diverse landscapes and its economic significance as biofuel or food sources for wide varieties of animal species, including humans (Bouchenak-Khelladi et al, 2010; Orton et al, 2017, 2019). Two large clades are recognized (Kellogg, 2015; Soreng et al, 2015, 2017; Saarela et al, 2017): the BOP (Bambusoideae, Oryzoideae, and Pooideae) clade, and the PACMAD (Panicoideae, Aristidoideae, Chloridoideae, Micrair oideae, Arundinoideae, Danthonioideae) clade. The PACMAD is comprised of both C3 and C4 photosynthetic species with cosmopolitan distributions and greatly varying habitats (Cotton et al, 2015; Gallaher et al, 2019). While relationships of these clades have been extensively studied, many of these studies utilized single or multiloci data. Previous studies have incorporated morphological data to provide an additional avenue of exploration with regard to relationships among and within these clades (Kellogg, 2015; Saarela et al, 2015; Soreng et al, 2015, 2017)
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