Phylogenomics reveals the reticulate evolution and biogeographic history of New World cypresses, Hesperocyparis (Cupressaceae)

Abstract Deciphering the evolutionary history of lineages shaped by rapid radiation, hybridization and incomplete lineage sorting (ILS) remains a major challenge in phylogenetics. Previous studies of Hesperocyparis (Cupressaceae) relied on limited markers and yielded inconsistent results. Here, we applied target enrichment sequencing across multiple individuals per species to generate comprehensive genomic datasets, including 2628 nuclear single‐copy genes and nearly complete plastid genomes. We reconstructed robust phylogenies, assessed gene flow and reticulation and inferred the spatiotemporal and ecological niche evolution of Hesperocyparis . Our analyses resolved the genus into three clades—Macrocarpa, Arizonica and the basal H. bakeri —and strongly supported its monophyly within the HCX clade ( Hesperocyparis , Callitropsis , Xanthocyparis ). However, significant cytonuclear discordance was observed, reflecting the influence of ancient hybridization and ILS. Molecular dating placed the origin of Hesperocyparis in the late Eocene (~39.2 Ma), with most diversification occurring during the Oligocene and Miocene. Ancestral range and state reconstructions support a northwestern North American origin, followed by complex southward and eastward dispersal patterns likely driven by climatic shifts towards increased aridity. This study highlights the utility of genome‐scale data in resolving complex evolutionary relationships and underscores hybridization, climate‐driven dispersal and ecological adaptation as key drivers of diversification in Hesperocyparis .