Simultaneous Inference of Flora‐Wide Nuclear and Plastid Phylogenies Using Angiosperms353 Sequence Capture Data

ABSTRACT Accurate knowledge of phylogenetic relationships and divergence time among plant species composing a regional flora is crucial for understanding the origin of the biodiversity patterns we observe today. Despite advances in phylogenomics, resources available for reconstructing regional phylogenies are still largely incomplete and poorly resolved at the species level. We developed a workflow to assemble a phylogenetic dataset for a regional flora using Angiosperms353 target‐enrichment and high‐throughput genome sequencing. We sampled tissues from freshly collected plants and herbarium specimens representing the angiosperm diversity of the Geneva canton in Switzerland (1098 species). We used ORTHOSKIM to recover targeted nuclear genes and plastid loci from off‐target reads, estimated relationships and time divergence using IQTREE, weighted‐ASTRAL and treePL, and compared the results obtained from nuclear and plastid genes. We recovered a mean of 289 nuclear and 54 plastid genes for 1316 taxa, representing 92% of the species native to the Geneva canton. We demonstrate that nuclear genes provide increased resolution and phylogenetic support, but similar divergence time estimates compared to plastomes. Our workflow based on Angiosperms353 data provides a phylogenetic framework for an entire regional flora that is consistent with current systematic knowledge and more resolved and complete at the infrageneric level than trees obtained from phylogenetic resources available for angiosperms. This type of genomic data opens perspectives for fine‐scale biodiversity and conservation research that integrates evolutionary history.