Hundreds of nuclear loci resolve an ancient rapid radiation in Apocynaceae

Ancient rapid radiations have impeded the resolution of several nodes in the Apocynaceae phylogeny that are key to reconstructing phenotypic evolution and biogeographic history in the family. Chloroplast-based Apocynaceae phylogenetic analyses and produced resolved topologies of the presumed rapid radiations in the rauvolfioid and apocynoid grades; however, these phylogenies have likely been affected by long branch attraction. The first nuclear phylogenomic analysis of Apocynaceae, based on the Angiosperm353 probe set, supported several nodes that were incongruent with the plastome topology, implicating lineage sorting and/or introgression. Furthermore, these data did not support the positions of several key taxa, including the tribe Rhabdadenieae and subfamily Periplocoideae in the APSA clade. Here, taxonomic sampling was expanded (175 species, 5-fold larger), with a focus on APSA clade lineages, and nuclear gene sequencing (837 genes, 2-fold larger) using a family-specific probe set was obtained and used to construct coalescent and concatenated species trees. After accounting for long branch attraction, both concatenated and coalescent trees reconstructed the same APSA clade topology. After the successive divergence of Wrightieae, Nerieae, and Malouetieae are two sister clades: 1) a New World and Asian clade and 2) an Old World clade. In the New World and Asian clade, Rhabdadenieae is fully supported as sister to Apocyneae and MOE (Mesechiteae, Odontadenieae, Echiteae). In the Old World clade, Periplocoideae diverges first, followed by Baisseeae, then Secamonoideae and Asclepiadoideae. Increased taxon and sequence sampling resolved the APSA clade topology with strong support, suggesting a similar strategy may be successful in other parts of Apocynaceae phylogeny.