Genome skimming provides new insight into the relationships in Ludwigia section Macrocarpon , a polyploid complex

Premise of the Study Interpreting relationships within groups containing polyploids, which are frequent in angiosperms, can be greatly assisted by genomic techniques. In this study, we used a genome‐skimming approach to investigate the evolutionary relationships and origins of polyploids in the monophyletic group, Ludwigia section Macrocarpon (Onagraceae), which includes diploid, tetraploid, and hexaploid taxa. Methods We sampled all known taxa and ploidy levels in the section and conducted shotgun sequencing. We assembled plastomes, mitochondrial sequences, and completed nuclear ribosomal regions, reconstructed phylogenies, and conducted comparative genomic analyses for plastomes to gain insights into the relationships among studied taxa. Key Results Within the section, results showed that the South American diploid taxa L. bonariensis and L. lagunae were closely related. We reported the first chromosome count (2 n = 4× = 32) for L. neograndiflora , which is closely related to the two South American diploid taxa, although its exact origin remains unclear. The samples of the widespread, polyploid taxon L. octovalvis do not form a monophyletic group. Both tetraploid and hexaploid L. octovalvis lineages have originated more than once. At least one tetraploid in the L. octovalvis lineage may have been involved in the origins of hexaploids. One or more extinct/unsampled intermediate tetraploids in the L. octovalvis lineages had also likely been involved in the origins of hexaploids. Conclusions Genome skimming provided important insights into the complex evolutionary relationships within sect. Macrocarpon , but additional sampling and data from single‐copy nuclear regions are necessary to further elucidate the origins of the polyploids in this section.