The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae.

The reconstruction of relationships within recently radiated groups is a challenging task even using massive sequencing data. The performance of restriction site-associated DNA sequencing (RAD-seq) to this end is promising but still is not defined the appropriate scale at which it remains efficient. Here, we assessed the performance of RAD-Seq to infer a species-level phylogeny in the rapid radiation of genus Cereus (Cactaceae), implementing distinct datasets and analyses to examine how the amount of genomic data affects resolution in this group. The sampling strategy includes representatives of Cereus, their closely allied genera Cipocereus and Praecereus, as well as outgroups. After library preparation and sequencing, three scenarios of permissiveness to missing data were carried out in iPyRAD, assembling datasets with 30% (333 loci), 45% (1440 loci) and 70% (6141 loci) of missing data. For each dataset, Maximum Likelihood trees were generated using two supermatrices: only SNPs and SNPs plus invariant sites. Accuracy and resolution were highest when using the largest dataset with 70% of missing data. Coalescent trees estimated using SVDQuartets and ASTRAL agrees with the main clades obtained by the concatenated approach. Overall, we present a phylogeny with an unprecedented resolution for the genus Cereus, which was resolved as a monophyletic group composed of four main clades with high support in their internal relationships. This confirms the power of RAD loci to resolve phylogenies. Further, our findings contribute to the debate on the impacts of missing data for phylogenetic analysis using RAD loci.