DOI: 10.5061/dryad.bzkh189gf
title: Data from: Plastid phylogenomic analysis of Podostemaceae with an emphasis on Neotropical podostemoideae

description: Podostemaceae are a clade of aquatic flowering plants that form important
 components of tropical river ecosystems. Species in the family exhibit
 highly derived growth forms and high vegetative phenotypic plasticity,
 both of which contribute to taxonomic confusion. The backbone phylogeny of
 the family remains poorly resolved, many species remain to be included in
 a molecular phylogenetic analysis, and the monophyly of many taxa remains
 to be tested. To address these issues, we assembled sequence data for 73
 protein-coding plastid genes from 132 samples representing 68 species
 (~23% of described species) that span the breadth of most major taxonomic,
 morphological, and biogeographic groups of Podostemaceae. With these data,
 we conducted the first plastid phylogenomic analysis of the family with
 broad taxon sampling. These analyses resolved most nodes with high
 support, including relationships not recovered in previous analyses. No
 evidence of widespread, well-supported conflict among individual plastid
 genes and the concatenated phylogeny was observed. We present new evidence
 that four genera (Apinagia, Marathrum, Oserya, and Podostemum), as well as
 four species, are not monophyletic. In particular, we show that Podostemum
 flagelliforme should not be included in Podostemum and is better
 recognized as Devillea flagelliformis, and that Marathrum capillaceum is
 embedded within Lophogyne s.l. and should be recognized as Lophogyne
 capillacea. We also place a previously unsampled and undescribed species
 that likely represents a new genus. In contrast to previous studies, the
 neotropical genera Diamantina, Ceratolacis, Cipoia, and Podostemum are
 resolved as successive sister groups to a clade of all paleotropical
 Podostemoideae taxa sampled, suggesting a single dispersal event from the
 neotropics to the paleotropics in the history of the subfamily. These
 results provide a strong basis for improving the classification of
 Podostemaceae and a framework for future phylogenomic studies of the clade
 employing data from the nuclear genome.
description: # Data from: Plastid Phylogenomic Analysis of Podostemaceae with an
 Emphasis on Neotropical Podostemoideae
 [https://doi.org/10.5061/dryad.bzkh189gf](https://doi.org/10.5061/dryad.bzkh189gf) This Dryad submission contains five (5) files: 1) Concatenated nucleotide alignment, 2) tree file with bootstrap values, 3) HybPiper target sequences, 4) concatenated alignment partition file by gene, and 5) concatenated alignment model and partition file. Files used or output by HybPiper (target file) and IQ-TREE analyses (concatenated alignment, partition and model files, tree file) included. Each file is explained in further detail below. GenBank numbers for sequences used in these analyses are listed in Appendix 1 of the main publication and are available on GenBank. ## Description of the data and file structure Filename: HybPiper_Targets_nt.fasta Description: Target file used in HybPiper analyses to generate assemblies from trimmed reads. Sequence names include the taxon name and the gene region. References containing GenBank numbers for target sequences are listed in the Methods sections of the publication. Filename: allGenes.phy Description: concatenated nucleotide alignment (trimmed of codons that were missing data in &gt; 40% of the samples using pxclsq in Phyx as stated in Methods). Aligned (trimmed) and concatenated chloroplast gene regions from HybPiper analyses. This alignment was used along with the allGenesConcat.best_scheme.nex file to create the phylogeny in allGenes.Treefile_wBS.tre. Taxon names are followed by voucher collection numbers as noted in the main publication and match names used in figures.   Filename: Partitions.byGene.txt Description: partition file by gene for concatenated alignment (allGenes.phy). This file can be used to separate the concatenated alignment into individual alignments of each gene. Each gene name and its position in the concatenated alignment is listed. Filename: allGenesConcat.best_scheme.nex Description: best models and partition file for concatenated alignment (allGenes.phy) as output by IQ-TREE. Genes included in each partition, along with their positions in the concatenated alignment, are listed along with the appropriate model for that partition (e.g., GTR+F+I+G4). Filename: allGenes.Treefile_wBS.tre Description: Tree file with bootstrap values estimated with IQ-TREE using allGenes.phy and  allGenesConcat.best_scheme.nex for tree shown in main text (Figs. 1 and 2a,b)