title: Phylogenetic estimation and morphological evolution of Arundinarieae (Bambusoideae: Poaceae) based on plastome phylogenomic analysis.
abstract: We explored phylogenetic relationships among the twelve lineages of the temperate woody bamboo clade (tribe Arundinarieae) based on plastid genome (plastome) sequence data. A representative sample of 28 taxa was used and maximum parsimony, maximum likelihood and Bayesian inference analyses were conducted to estimate the Arundinarieae phylogeny. All the previously recognized clades of Arundinarieae were supported, with Ampelocalamus calcareus (Clade XI) as sister to the rest of the temperate woody bamboos. Well supported sister relationships between Bergbambos tessellata (Clade I) and Thamnocalamus spathiflorus (Clade VII) and between Kuruna (Clade XII) and Chimonocalmus (Clade III) were revealed by the current study. The plastome topology was tested by taxon removal experiments and alternative hypothesis testing and the results supported the current plastome phylogeny as robust. Neighbor-net analyses showed few phylogenetic signal conflicts, but suggested some potentially complex relationships among these taxa. Analyses of morphological character evolution of rhizomes and reproductive structures revealed that pachymorph rhizomes were most likely the ancestral state in Arundinarieae. In contrast leptomorph rhizomes either evolved once with reversions to the pachymorph condition or multiple times in Arundinarieae. Further, pseudospikelets evolved independently at least twice in the Arundinarieae, but the ancestral state is ambiguous.
authors.affiliation: Department of Ecology Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011-1020, United States. Electronic address: lakshmi@iastate.edu.
authors.forename: Lakshmi
authors.initials: L
authors.lastname: Attigala
authors.affiliation: Biological Sciences, Northern Illinois University, 1425 W Lincoln Hwy, DeKalb, IL 60115-2861, United States. Electronic address: wwysoc2@gmail.com.
authors.forename: William P
authors.initials: WP
authors.lastname: Wysocki
authors.affiliation: Biological Sciences, Northern Illinois University, 1425 W Lincoln Hwy, DeKalb, IL 60115-2861, United States. Electronic address: mel-duvall@niu.edu.
authors.forename: Melvin R
authors.initials: MR
authors.lastname: Duvall
authors.affiliation: Department of Ecology Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011-1020, United States. Electronic address: lgclark@iastate.edu.
authors.forename: Lynn G
authors.initials: LG
authors.lastname: Clark
mesh_terms: D001483:Base Sequence; D001499:Bayes Theorem; D054627:Genome, Plastid; D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D006109:Poaceae / Q000033:anatomy & histology* / Q000145:classification* / Q000235:genetics
keywords: Alternate hypothesis testing; Morphological character mapping; Plastomes; Pseudospikelets; Rhizomes; Taxon removal experiments