DOI: 10.5061/dryad.cc2fqz68x
title: A first complete phylogenomic hypothesis for diploid blueberries (Vaccinium section Cyanococcus)

description: The premise of the study: The true blueberries, (Vaccinium sect.
 Cyanococcus; Ericaceae), endemic to North America, have been intensively
 studied for over a century. However, with species estimates ranging from 9
 to 24 and much confusion regarding species boundaries, this ecologically
 and economically valuable group remains inadequately understood at a basic
 evolutionary and taxonomic level. As a first step toward understanding the
 evolutionary history and taxonomy of this species complex, we present the
 first phylogenomic hypothesis of the known diploid blueberries. Methods:
 We used flow cytometry to verify the ploidy of putative diploid taxa and a
 target-enrichment approach to obtain a genomic dataset for phylogenetic
 analyses. Results: Despite evidence of gene flow, we found that a primary
 phylogenetic signal is present. Monophyly for all morphospecies was
 recovered, with two notable exceptions: one sample of V. boreale was
 consistently nested in the V. myrtilloides clade, and V. caesariense was
 nested in the V. fuscatum clade. One diploid taxon, Vaccinium pallidum, is
 implicated as having a homoploid hybrid origin. Conclusions: This
 foundational study represents the first attempt to elucidate evolutionary
 relationships of the true blueberries of North America with a phylogenomic
 approach and sets the stage for multiple avenues of future study such as a
 taxonomic revision of the group, the verification of a homoploid hybrid
 taxon, and the study of polyploid lineages within the context of a diploid
 phylogeny.
description: # A first complete phylogenomic hypothesis for diploid blueberries
 (Vaccinium section Cyanococcus)
 [https://doi.org/10.5061/dryad.cc2fqz68x](https://doi.org/10.5061/dryad.cc2fqz68x) Publication: [https://doi.org/10.1002/ajb2.16065](https://doi.org/10.1002/ajb2.16065) The Angiosperms353 v1 target capture kit (Johnson et al., 2019) was used for targeted enrichment of each sample. Raw sequences were filtered and processed with the Trim Galore wrapper script (v.0.6.5) was used to trim adapters and low-quality reads based on a given Phred quality score cutoff (-q 20). Consensus read assembly for target loci was performed with the default settings in HybPiper v1.3.1 (Johnson et al., 2016). Supercontig sequences were assembled with the intronerate.py script available as a part of HybPiper. Allele and IUPAC datasets were constructed using PATÉ (https://github.com/gtiley/Phasing; Tiley et al. 2021) and aligned with fsa. The alignments were then filtered to include only columns with &lt;50% missing data. ## Description of the data and file structure **"individual\_alignments\_\_XXX.zip"** Individual IUPAC gene alignments and individual allele alignments. Allele alignments include two sequences for diploid samples. These will be identical sequences in the case of a homozygous gene. **"concat\_2x\_IUPAC\_fsa\_rm\_paralogs\_50missing.fa"** The concatenated IUPAC alignment and corresponding partition file (concat\_2x\_IUPAC\_fsa\_rm\_paralogs\_50missing.partitions.txt). **"00\_genetrees\_XXX.tre"** Individual gene trees resulting from IQTREE analysis of individual gene alignments.