With ca. 200 morphologically variable species placed in 20 putative genera within the tribe Selineae of subfamily Apioideae, the Perennial Endemic North American (PENA) clade of Apiaceae forms the second‐largest plant radiation entirely endemic to North America, yet, elucidating evolutionary relationships for this intractable plant lineage has been challenging. The objectives of this study are to elucidate the monophyly of the PENA clade and assess phylogenetic relationships to other clades in Selineae, contributing to a refined understanding of relationships. By analyzing a robust sample set, including ingroup and outgroup taxa, we employ high‐throughput sequencing technologies to capture a wide array of nuclear DNA sequences using the Angiosperms353 baits. Our bioinformatics pipeline, incorporating both HybPiper and HybPhaser workflows, facilitated the recovery and analysis of targeted sequences, ensuring high‐quality data for maximum likelihood and multispecies pseudo‐coalescent phylogenetic reconstructions. Our phylogenetic analyses do not recover a monophyletic PENA that includes all genera presumed to be part of this clade. Our results prompted the realignment of genera to include in the PENA clade. Genera that occur primarily in eastern North America are moved out of PENA. We also resolve, for the first time, the placement of the genus Eurytaenia within Apiaceae. This study contributes to a deeper understanding of the phylogenetic relationships within a taxonomically complex group of western North American Apiaceae, paving the way for broader insights into plant diversity and evolution in this botanically complex region.

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods^1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome^3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins^5–7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes⁸. This 15-fold increase in genus-level sampling relative to comparable nuclear studies⁹ provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.