A Phylogenomic Investigation of Species Diversity, Morphology, and Biogeography in <i>Neptunia</i> (Fabaceae: Caesalpinioideae: Mimoseae)

Abstract— Neptunia (Fabaceae) is a pantropical genus of 22 species and is the sole genus of Mimoseae with fully aquatic species, N. oleracea and N. plena . The aquatic species are pantropically distributed, while the 20 terrestrial species are confined within continents separated by oceanic barriers. Due to species having broad distributions, polyploidy, and cryptic morphology, Neptunia species delimitations remain uncertain and have not been comprehensively sampled in previous phylogenetic studies. To that end, we tested species delimitations in Neptunia by sampling multiple accessions of all species and infraspecific taxa and determined relationships through phylogenomics, identified the ancestral states of habitat and taxonomically defining characters, and estimated the historical biogeography of the group to determine the hypothetical ancestral area. A target-capture approach was applied with the Angiosperms353 bait-set to sequence 353 orthologous nuclear loci for phylogenetic inference of 94 ingroup and 11 outgroup individuals. Time calibrations and comparative methods were employed to reconstruct the chronogram and estimate ancestral states. Analyses of the filtered nuclear loci recovered a monophyletic Neptunia and provided insight into species delimitations in closely related diploid and polyploid species. We recognize N. windleriana and N. heliophila as synonyms based on phylogenetic reconstructions and morphology, reducing the number of species to 20. A newly described species, N. proxima , was polyphyletic. Single-seeded Neptunia species formed a clade, but other taxonomically important traits lacked phylogenetic signal. The aquatic N. oleracea was sister to the clade of the aquatic N. plena and the terrestrial species from the Americas, and ancestral character estimation analyses inferred two separate transitions into aquatic habitats. This transition into aquatic environments and being polyploid likely promoted the widespread distributions of the two aquatic Neptunia species. The early diversification of Neptunia was widespread in Asia, North America, or South America, and a rapid radiation occurred in Australia. Our results support recent taxonomic circumscriptions and provide the first fully sampled and well-resolved molecular phylogeny of Neptunia .