DOI: 10.5061/dryad.ksn02v7cr
title: Data from: A global blueberry phylogeny: Evolution, diversification, and biogeography of the tribe Vaccinieae (Ericaceae)

description: Vaccinieae is a morphologically diverse and species-rich (~1440 species)
 tribe in Ericaceae, itself a clade of ~4600 species. Although the majority
 of diversity is tropical, Vaccinieae are best known for temperate crops
 (i.e., blueberries, cranberries, huckleberries, lingonberries) in
 Vaccinium. Vaccinium itself (~500 species) has been previously suggested
 as highly polyphyletic, and taxonomic boundaries among many of the other
 genera in the tribe remain uncertain. We assessed the evolutionary history
 of Vaccinieae with phylogenomic analyses based on a target-enrichment
 dataset containing 353 low-copy nuclear gene regions and over 200 taxa
 representing 30 of the 34 genera in the tribe, and 25 of the 29 sections
 of Vaccinium. A plastome dataset for a subset of these taxa was
 additionally constructed. We conducted time-calibrated biogeographic
 analyses and diversification analyses to explore the area of origin and
 global dispersal history of the tribe. The analysis recovered a temperate
 North American origin for Vaccinieae approximately 30 million years ago.
 Tropical diversity of Vaccinieae was inferred to result from multiple,
 independent movements into the tropics from north-temperate ancestors.
 Diversification rate increases corresponded to radiation into the Andes
 and SE Asia. The pseudo-10-locular ovary evolved once in the tribe from
 the five-locular state, coinciding with the diversification of a major
 clade that includes most Asian Vaccinium and the group from which
 commercial blueberries are derived (V. sect. Cyanococcus). A
 reconstruction from available chromosome counts suggests that a major
 polyploid event predated the evolution of nearly half the diversity of
 Vaccinieae. The extent of polyphyly in Vaccinium documented here supports
 the need for a generic reclassification of the tribe.
description: DNA sequence data were derived from three sources. The DNA of
 most samples was extracted from herbarium specimens with the SLIMS method,
 a system connecting sampling and wet lab methodology (Folk et al., 2021).
 Specimens were sampled from the following herbaria (acronyms as in Thiers,
 updated continuously): FLAS, K, MICH, MO, and NY. Some DNAs (those from
 PWF) were from silica gel-dried leaf material. The DNA of these samples
 was extracted with DNeasy®. We quantified DNA amounts of these samples
 using a Qubit 2.0 fluorometer (Invitrogen, Carlsbad, California, USA) with
 the Qubit dsDNA Broad Range Assay Kit as per manufacturer recommendations.
 Finally, some sequence data were downloaded from the Kew DNA
 Bank. Library preparation and target capture were
 performed at Rapid Genomics (Gainesville, FL, USA) with the Angiosperms353
 v1 target capture kit (Johnson et al., 2019) to obtain 353 putatively
 single-copy nuclear loci from each sample. DNA sequencing was conducted on
 Illumina sequencing machines (Illumina, San Diego, California, USA)
 predominantly with 2x150-base pair (bp) chemistry, or occasionally
 2x250-bp. Additionally, a plastome dataset was assembled from
 genome-skimming reads from non-enriched libraries. For
 the nuclear loci, raw sequence data were filtered and adapters removed
 with Cutadapt v2.6 (Martin, 2011) and FastQC v.0.11.9 (Andrews, 2010),
 with a phred quality score cutoff of 20 (-q 20). Reads were assembled with
 HybPiper v1.3.1 (Johnson et al., 2016) under default settings. In addition
 to the standard Angiosperms353 targets, we included available Ericales
 sequences in the target reference file using the mega353 approach (McLay
 et al., 2021). Resulting supercontig sequences (introns and exons) were
 used for subsequent analyses. Putative paralogs were flagged with the
 <em>paralog_investigator.py</em> script in HybPiper. All
 flagged loci were removed from the dataset. For the
 plastome dataset, we constructed a target file from available Ericales
 sequences for 79 protein-coding plastid loci as reference. HybPiper was
 run as above to extract and assemble the dataset.
 Individual gene alignments (371 initial samples), a concatenated
 alignment for the nuclear data, and a concatenated single alignment for
 the plastome data were constructed with MAFFT v7.245 (Katoh et al., 2013).
 To reduce potential issues with missing data and poorly aligned regions,
 we removed columns from the individual gene alignments containing &gt;
 50% missing data and samples containing &gt; 90% missing data in the
 concatenated datasets. These quality filtering steps resulted in a final
 nuclear dataset of 260 samples and 122 samples in the plastome dataset
 (Supplementary Table S2).
description: # A global blueberry phylogeny: Evolution, diversification, and
 biogeography of the tribe Vaccinieae (Ericaceae)
 [https://doi.org/10.5061/dryad.ksn02v7cr](https://doi.org/10.5061/dryad.ksn02v7cr) ## Description of the data and file structure These are alignment files (.fasta) of sequences that have already been through a filtering process (see methods), that we used to generate the main topologies in our study with IQtree. This submission includes (1) the nuclear dataset of 262 samples of 353 nuclear loci, and (2) the other is 78 of the plastome for 122 species.  ## Sharing/Access information The data, novel scripts, and output files that support the findings of this study are openly available in supplementary materials to the related article. Raw sequence reads are available from NCBI PRNA839108, PRJEB49299, and PRJEB51566.