Biology subjects

Bullock, M. R.

Publications and source records attributed to Bullock, M. R..

3 recordsLinked to original sources

bioRxiv2026

Reticulate History of Southern South American Wild Potatoes: Recurrent Hybridization, Cytonuclear Discordance, and Phylogenetic Placement of Solanum malmeanum

Hybridization is a powerful process in plant evolution generating reticulate patterns of speciation, introgression, and chloroplast capture. In the Petota clade of Solanum, which spans cultivated and wild potatoes, these processes cause much of the taxonomic complexity of the group. We examined the evolutionary history of the Commersoniana group (Solanum commersonii and S. malmeanum) relative to S. chacoense (Tuberosa Group) using an integrative framework of phylogenomics and morphology. With target-capture sequencing (Angiosperms353) of nuclear and plastid loci recovered from herbarium specimens, together with data mining we built nuclear and plastome phylogenies and ran symmetry tests, gene concordance analyses, and coalescent simulations to weigh incomplete lineage sorting against chloroplast capture. The data reveal cytonuclear discordance and events consistent with chloroplast capture from S. chacoense into Commersoniana lineages supported by both empirical and simulated results. Phylogenetic networks confirm repeated historical and recent reticulation, especially involving S. malmeanum. Non-metric Multidimensional Scaling (NMDS) of morphological traits did not recover clear species boundaries but was consistent with a hybrid origin for the group. These results indicate that recurrent hybridization and event consistent with chloroplast capture are strongly influencing evolution in the examined wild potatoes, complicating classical taxonomy and informing conservation and breeding. They also underscore the value of combining genomic and phenotypic data to resolve species boundaries in plant groups with tangled hybrid histories.

evolutionary biology↗

bioRxiv2026

SPrOUT: A computational and targeted sequencing approach for mixed plant DNA identification with Angiosperms353

PremiseThe identification of plant species from mixed samples is crucial in various fields, including ecological surveys, conservation efforts, and food and dietary supplement safety. Traditional methods face potential challenges due to the high costs of DNA sequencing, inefficiencies in computational workflows, and incomplete sequence databases. Methods and ResultsThis study introduces a novel approach using the Angiosperms353 target sequencing kit for efficient taxonomic identification of angiosperm DNA in mixed samples. Our method assembles short pair-end reads for each mixed sample. Using gene sets of Angiosperms353 from 871 species, we apply phylogenetic inference to categorize the variance in phylogenetic distance across genes to identify the presence of taxa in mixed plant samples. The pipeline reaches 98.1 to 99.6% accuracy, 92.9 to 100% precision for identifying unknown taxa in in-silico mixes, and 90.7% accuracy and 98.0% precision for mock supplement mixtures. We explored the parameter cutoffs of the pipeline to offer an empirical range for different applications. ConclusionsThe Angiosperms353 and HybPiper assembly proved effective in sorting mixed plant DNA samples. Our method offers a framework for scientific and practical applications in plant species identification in both single and mixed samples.

bioinformatics↗

bioRxiv2025

Fun-Sized Library Prep: Miniaturization is a valid method for per-sample cost reduction in targeted sequencing of angiosperm DNA

PremiseGenomic analysis of population structure is important to the conservation of plant species of concern. A limitation of using genetic information in conservation is the cost of obtaining large datasets. Targeted sequencing and low-volume robotic liquid handlers can reduce library preparation reaction volumes and costs. MethodsWe used targeted sequencing via Angiosperms353 to obtain data for 768 samples, 18 of which were identical, at 0.5X and 0.1X reaction volumes. We calculated quality and quantity control statistics to compare the effects of tissue age and library reaction volume on sequencing results for on-target nuclear and off-target plastid genes. ResultsLibrary miniaturization to 0.1X reduces costs and generally performs comparably to 0.5X libraries. In the full dataset, Tenth-Volume Only libraries showed smaller insert sizes and fewer genes with mapped sequences, but no reduction in mapped reads. In the Overlap Set, 0.1X had equal or improved performance with no significant decrease in sequencing efficiency. Differences by tissue type likely reflected sampling variation. ConclusionsMiniaturization to 0.1X substantially reduces per-sample costs while maintaining comparable sequencing quality across fresh and herbarium angiosperm DNA. Overall, miniaturization provides a reliable, cost-effective approach for targeted sequencing, increasing the feasibility of using herbarium collections and enabling broader access to population-level genomic studies.

plant biology↗