Phylogenomic and ecological systematics of Melocactus (Cactaceae)

Melocactus (L.) Link & Otto (Cactaceae) is a widely distributed genus in the Neotropical region and has fascinated the botanical community since the 15th century due to its unique appearance. Even though this genus has been studied for centuries, its diversification, phylogenetic relationships, and species delimitation have not been evaluated using comprehensive taxon sampling and genetic data. Here, we inferred maximum likelihood and coalescent phylogenies using the Cactaceae591 genomic dataset and investigated potential environmental variables associated with Melocactus diversification. Ancestral character reconstructions were performed using edaphic and climatic data. A well-resolved Melocactus phylogeny was estimated, allowing the redefinition of informal infrageneric groups and the taxonomic rearrangement of some taxa. The ancestral character reconstructions suggest that the observed species relationships and distribution patterns in Melocactus result from the interplay of climatic and edaphic factors, highlighting a complex evolutionary history for the genus.

Methods
Alignments provided here are derived from the following methods: DNA was obtained from cactus root tissue using a CTAB 3% extraction protocol, and genomic data were obtained through a target sequencing capture method using the Cactaceae591 probe set. Raw reads were processed using the fastp v.0.23.3, and loci assembly was carried out using the Hybpiper pipeline. After, the data were processed using MAFFT v.7.520, TrimAL v.1.4, and spruceup. Parameters and detailed information are described in the manuscript.