DOI: 10.5061/dryad.4n28n
title: Data from: Species tree estimation of diploid Helianthus (Asteraceae) using target enrichment

description: Premise of the study: The sunflower genus Helianthus has long been
 recognized as economically significant, containing species of agricultural
 and horticultural importance. Additionally, this genus displays a large
 range of phenotypic and genetic variation, making Helianthus a useful
 system for studying evolutionary and ecological processes. Here we present
 the most robust Helianthus phylogeny to date, laying the foundation for
 future studies of this genus. Methods: We used a target enrichment
 approach across 37 diploid Helianthus species/subspecies with a total of
 103 accessions. This technique garnered 170 genes used for both coalescent
 and concatenation analyses. The resulting phylogeny was additionally used
 to examine the evolution of life history and growth form across the genus.
 Key results: Coalescent and concatenation approaches were largely
 congruent, resolving a large annual clade and two large perennial clades.
 However, several relationships deeper within the phylogeny were more
 weakly supported and incongruent among analyses including the placement of
 H. agrestis, H. cusickii, H. gracilentus, H. mollis, and H. occidentalis.
 Conclusions: The current phylogeny supports three major clades including a
 large annual clade, a southeastern perennial clade, and another clade of
 primarily large-statured perennials. Relationships among taxa are more
 consistent with early phylogenies of the genus using morphological and
 crossing data than recent efforts using single genes, which highlight the
 difficulties of phylogenetic estimation in genera known for reticulate
 evolution. Additionally, conflict and low support at the base of the
 perennial clades may suggest a rapid radiation and/or ancient
 introgression within the genus.
description: Helianthus
 chloroplastThis file contains the
 aligned 96789bp chloroplast sequences from 103 accessions across 37
 diploid Helianthus species/subspecies and the outgroup Phoebanthus
 tenuifolius.Helianthus_chloroplast.fastaChloroplast_treeThe cholorplast tree in newick format containing 103 accessions.Helianthus_Species_branchlengthsThis is the file that contains the branch lengths as estimated with RAxML and using the MP-EST topology for the diploid Helianthus species.Helianthus_population_branchlengthsThis file contains the population level tree with branch lengths estimated by RAxML with the fixed MP-EST topology for the diploid Helianthus species.MPEST_SpeciestreeThe MP-EST species tree in newick format for 103 accessions estimated from 170 genes.MPEST_populationThe MP-EST population level tree estimated using 170 genes across 103 accessions.Accession_treeMP-EST accession tree estimated from 170 genes and 103 accessionsConcatenation_treeConcatenation tree estimated from RAxML (106,862bp) across 103 accessions of diploid Helianthus.Helianthus_concatenated_nDNAThis file contains the aligned 106862bp concatenated nDNA sequences from 103 accessions across 37 diploid Helianthus species/subspecies and the outgroup Phoebanthus tenuifolius.Helianthus_concated_nDNA.fastaHelianthus_fasta_filesThis is the zip folder containing the fasta files for 170 genes across 103 diploid Helianthus species. The fasta files have been aligned and trimmed with gblocks.Helianthus_fasta.zipbootstrap_genetreesThe zip file contains all the bootstrap gene files. There are 170 files (one for each gene) with 500 bootstrapped gene trees within each file. These were all estimated from RAxML and used in MP-EST to estimate the species tree.