Dataset DOI: 10.5061/dryad.ht76hdrxf

Description of the data and file structure

This dataset contains sequence data, phylogenetic trees, specimen metadata, and figure source files used to generate analyses and figures in:

Crouch et al. (2026), Proceedings of the National Academy of Sciences.

The dataset supports multilocus phylogenetic reconstruction of powdery mildews infecting Fragaria (strawberry) and Rubus (raspberry), including historical herbarium specimens and contemporary collections. Data include individual locus FASTA files, Single Locus Bayesian phylogenetic trees, geographic distribution mapping, and specimen-level metadata.

All nucleotide sequences are deposited in GenBank and are provided here as FASTA files to facilitate reuse.

Files and variables

Files Included

1. Sequence Data (FASTA format)

These files contain aligned or curated nucleotide sequences used in phylogenetic analyses. All files can be opened in any software capable of reading .fasta format (e.g., MEGA, Geneious, etc.).

• ITS_28S_genbank.fasta
• IGS_genbank.fasta
• GAP_genbank.fasta
• RPB2_genbank.fasta
• TUB_genbank.fasta

Each FASTA header includes voucher numbers.

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2. Phylogenetic Trees

Figure Files (PDF format)

• ITS_28S_tree_rough.pdf
• RPB2_tree_rough.pdf
• TUB_tree_rough.pdf
• GAP_tree_rough.pdf
• IGS_tree_rough.pdf
• Concatenated_tree_rough.pdf

Corresponding MCC tree files

• ITS_MCC_Rough.tree
• RPB2_MCC_Rough.tree
• TUB_MCC_Rough.tree
• GAP_MCC_Rough.tree
• IGS_MCC_Rough.tree
• Concatenated_MCC_Rough.tree

Bayesian phylogenies inferred in BEAST v1.10.4 using:

• Yule tree prior
• Strict molecular clock
• Single MCMC chain of 10^7 generations
• 25% burn-in
• Posterior probabilities calculated from remaining sampled trees
• Maximum clade credibility trees generated in TreeAnnotator v1.10.4
• Visualization in FigTree v1.3.1

Tree files correspond to individual loci except Concatenated_tree_rough.pdf. This file used only specimens with multiple regions sequenced and was used to determine the outgroup for the tree published in Crouch et al. 2026 (PNAS). Podosphaera mors-uvae was selected as an outgroup taxon as it is closely related to powdery mildew infecting raspberries and strawberries but in a supported clade basal to the highly supported strawberry/raspberry clade. 

Posterior support values are displayed at nodes. The PDF Tree files were generated from the MCC tree files which were visualized in FigTree v1.4.4

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3. Geographic Distribution Map

• Worldmap.pdf

This figure visualizes global sampling locations and lineage assignments. Species represented include:

• Podosphaera fragariae
• Podosphaera shepherdiae
• Podosphaera ruborum (including formae)
• Podosphaera rubi-spectabilis

Symbols and colors correspond to species-level assignments. The worldmap was generated in T-BAS from the locality data. T-BAS — Tree-Based Alignment Selector Toolkit

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4. Metadata Files (Excel format)

• Metadata_for_All_Specimens_Analyzed.xlsx

• Metadata_for_Specimens_Sequenced_for_the_Current_Study.xlsx

These files include:

• Specimen ID
• Host species
• Geographic origin
• Voucher/herbarium information
• Collection date
• GenBank accession numbers
• Lineage assignment

These metadata files link directly to FASTA sequence identifiers and tree tip labels.

Empty cells=information not available

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Dates of Data Collection

Specimens span early 1900s herbarium collections through contemporary collections.

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Spatial Scope

Global sampling including:

• North America
• Europe
• Asia
• South America

Precise localities are available in metadata files. Coordinates are included where available from specimen labels or herbarium records.

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Methods Summary

Detailed laboratory and analytical methods are provided in the Supporting Information of Crouch et al. (2026, PNAS).

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Code/software

Bayesian phylogenies inferred in BEAST v1.10.4

TreeAnnotator v1.10.4

FigTree v1.3.1

All sequence files can be opened in any software capable of reading .fasta format (e.g., MEGA, Geneious, etc.).

Access information

Other publicly accessible locations of the data:

• GenBank; T-BAS (https://guide-tbas.cifr.ncsu.edu/tbas)

Data was derived from the following sources:

• GenBank and Current Study