Phylogenomics, domestication history, and conservation insights for a neglected and underutilized crop: Sechium edule ssp. edule (Cucurbitaceae) and its wild relatives

Understanding evolutionary relationships in domesticated crops and their wild relatives is often challenging because of their recent divergence, and still ongoing interspecific gene flow. These processes blur species boundaries and complicate phylogenetic reconstruction. The genus Sechium (Cucurbitaceae), which includes the cultivated chayote ( S. edule ssp. edule ), a Neglected and Underutilized Species (NUS), and its related wild taxa, represents one of such cases. Using genome-wide Single Nucleotide Polymorphisms (SNPs) analyzed under a population genomics framework, we explored the species barriers of Sechium and reconstructed its phylogeny using multispecies coalescent models. Our results clarify taxonomic boundaries within the genus, confirming S. edule ssp. sylvestre as the closest wild relative of the cultivated chayote, and supporting species-level distinction among wild taxa. Divergence within Sechium mostly occurred during the Pleistocene, and our data point to the “Oaxaca” biogeographic province, in southern Mexico, including parts of the states of Oaxaca, Puebla and Veracruz, as the most likely center of chayote domestication. Several metrics revealed low genetic diversity and small contemporary effective population sizes ( N e ) in wild taxa, highlighting their vulnerability under ongoing tropical cloud forest loss. These findings emphasize the urgent need to integrate wild Sechium species into national and international conservation frameworks. More broadly, this study demonstrates how combining phylogenomics and conservation genomics can help resolve taxonomic uncertainty, trace domestication processes, and guide the preservation of Crop Wild Relatives (CWR); particularly those associated with NUS that remain vital for future food security and agroecosystem resilience.