Targeted sequencing of the C4 Cyperus Clade (Cyperaceae)

In several groups of angiosperms and at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing taxon and data sampling. The large amount of genomic data now available for phylogenetics, especially targeted sequencing data, provide new means to resolve rapid radiations. Evolutionary relationships in Cyperaceae have mainly been studied using Sanger sequencing leaving relationships in some genera unresolved. Relationships between C4 taxa are poorly-understood, hampered by an apparent faster rate of diversification leading to limited topological resolution and support in phylogenies published to date. A difficult clade to resolve is the C4 Cyperus Clade of the giant genus Cyperus. Previous studies based on a limited set of plastid and nuclear markers were able to resolve relationships between Cyperus species using C3 photosynthesis, but not between C4 Cyperus Clade taxa. We test the ability of two target enrichment probe kits to resolve relationships in C4 Cyperus Clade, i.e., the universal Angiosperms-353 kit and a Cyperaceae-specific kit. Sequences of the targeted low-copy nuclear genes were recovered from data generated with both probe kits. Overlap in data retrieved was investigated. The power to resolve low-level relationships was tested using summary and total evidence approaches to estimate phylogenetic relationships. High resolution and support are obtained using both approaches, but high levels of missing data impact the latter negatively. The phylogenetic reconstructions show similarities with Sanger sequencing results in, e.g., Cyperus cuspidatus being retrieved as sister to the rest of the C4 Cyperus Clade. Additionally, targeted sequencing provides new insights in the evolution of morphology in the C4 Cyperus Clade, e.g., the former segregate genus Alinula is polyphyletic. An unexpected result is that the Cyperus margaritaceus-Cyperus niveus complex forms a clade separate from and sister to the core C4 Cyperus Clade. Our results have implications for selecting universal vs. specific target sequencing kits—with our results not indicating that the data generated with a family-specific kit have more power than those obtained with the universal Angiosperms-353 kit—, how data generated with different probe kits can be merged for downstream analyses, and the capability of targeted sequencing data to resolve rapid radiations.