A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions

PeerJ

article

Jeffery M. Saarela¹  Sean V. Burke²  William P. Wysocki³  Matthew D. Barrett⁴  Lynn G. Clark⁶  Joseph M. Craine⁷  Paul M. Peterson⁸  Robert J. Soreng⁸  Maria S. Vorontsova⁹  Melvin R. Duvall² 

[1] Beaty Centre for Species Discovery and Botany Section;Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University;Center for Data Intensive Sciences, University of Chicago;Botanic Gardens and Parks Authority;School of Biological Sciences, The University of Western Australia;Department of Ecology, Evolution and Organismal Biology, Iowa State University;Jonah Ventures;Department of Botany, National Museum of Natural History, Smithsonian Institution;Comparative Plant & Fungal Biology, Royal Botanic Gardens

关键词: Grasses;    Phylogenomics;    Plastome;    Classification;    Systematics;    Incongruence;    Positive selection;    Purifying selection;    Aristidoideae;    Panicoideae;   

DOI  :  10.7717/peerj.4299

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity.

【 授权许可】

CC BY