A multi-locus plastid phylogeny of the Aulonemia clade (Poaceae: Bambusoideae: Bambuseae: Arthrostylidiinae) reveals three new genera of bamboo

Arthrostylidiinae (Poaceae: Bambusoideae), a subtribe of Neotropical woody bamboos with diverse morphology, comprises 200 species classified in 16 genera. Previous studies supported monophyly of the subtribe and recovered four major internal clades, however, some genera were found to be polyphyletic while others, like Aulonemia and Colanthelia, were either undersampled or not included. Aulonemia and Colanthelia are complex both in their taxonomy and morphology, and exhibit overlapping morphological characters. Prior morphological and molecular analyses suggested they share a close relationship, with Colanthelia emerging as monophyletic and either nested within Aulonemia or sister to it, but these studies sampled relatively few species of each genus. The aims of this study were to increase taxon sampling to test the monophyly of Aulonemia and Colanthelia, to investigate the relationships within the Aulonemia + Colanthelia clade, and to revise their classification as appropriate towards a..., , , # Alignment files containing DNA sequence data of Aulonemia bamboos and allies

[https://doi.org/10.5061/dryad.stqjq2c9t](https://doi.org/10.5061/dryad.stqjq2c9t)

DNA sequence alignment files and scripts used for inference of a plastid phylogeny of the neotropical woody bamboos.

## Description of the data and file structure

Nexus file containing DNA sequence alignments. File include character sets for plastid loci: rpL16-trnQ, trnC-rpoB, trnD-trnT, rpL16, ndhF, rpS16, and trnT-trnL.

## Code/Software

### SangerContigPipeline.py

a Python v.3 script to automate alignment of raw Sanger-sequenced contigs extracted from ab1 electropherogram files. Contigs with matching accession names but differing in the last character (‘F’ for forward or ‘R’ for reverse) are sequentially aligned and the total base pair difference is calculated. The positioning that minimizes this difference is taken to be the optimal alignment. Two arguments control the relative position for the initial alignment (per...