In the face of the sixth mass extinction on Earth, with the flowering plant family Cactaceae assessed as the fifth most endangered plant or animal family by the International Union for the Conservation of Nature (IUCN), it is imperative that all available tools be used to understand the biodiversity, habitat suitability, climate change impacts and population viability of cacti. Within the Cactaceae, Mammillaria Haw and the closely related genus Cochemiea (K. Brandegee) Walton of Baja California, Mexico, are species-rich, with 46 regionally endemic taxa, 12 of which have been assessed as threatened or endangered by the IUCN. This study clarifies the evolutionary relationships in the Mammilloid clade, a complex and species-rich clade in tribe Cacteae, and generic circumscription of the genera Mammillaria Haw. and Cochemiea (K. Brandegee) Walton, estimates divergence times, diversification rates and ancestral ranges and explores habitat suitability and the risk of extinction of a representative species within these genera. The r species, Cochemiea halei (K. Brandegee) Walton, a narrowly distributed island endemic, is assessed using species distribution modeling (SDM) and population viability analysis (PVA). SDM in this study includes projections to two climate change scenarios over the next century, using four representative particle concentration pathways, and the PVA uses habitat-specific deterministic and stochastic models. The results of molecular phylogenetic analyses of the Mammilloid cladde restore the genus Mammillaria to monophyly via new combinations in the genus Cochemiea. The taxa in this study are shown to be of recent origin resulting from rapid diversification and radiation. Geological and climatic forces at multiple scales appear to be responsible for the high degree of biodiversity and endemism of these cacti. SDM shows that C. halei is likely to be stranded in its fragmented island habitat, has a facultative adaptation to ultramafic soils, and faces a 21%–53% contraction of its range on the islands under climate change scenarios. PVA suggests that C. halei is at increased risk of extinction in response to slight decreases in fecundity and persistence. In general, the perspectives in this dissertation fill several gaps in our prior knowledge of the evolution, biogeography, and conservation pressures of an important, species-rich group of cacti, occurring in a region of high biodiversity and endemism.

The family Cactaceae is extremely diverse and has a near global distribution yet very little has been described regarding the community of viruses that infect or are associated with cacti. This research characterizes the diversity of viruses associated with Cactaceae plants and their evolutionary aspects. Five viruses belonging to the economically relevant plant virus family Geminiviridae were identified, initially, two novel divergent geminiviruses named Opuntia virus 1 (OpV1) and Opuntia virus 2 (OpV2) and Opuntia becurtovirus, a new strain within the genus Becurtovirus. These three viruses were also found in co-infection. In addition, two known geminiviruses, the squash leaf curl virus (SLCV) and watermelon chlorotic stunt virus (WCSV) were identified infecting Cactaceae plants and other non-cactus plants in the USA and Mexico. Both SLCV and WCSV are known to cause severe disease in cultivated Cucurbitaceae plants in the USA and Middle East, respectively. This study shows that WCSV was introduced in the America two times, and it is the first identification of this virus in the USA, demonstrating is likely more widespread in North America. These findings along with the Opuntia becurtovirus are probable events of spill-over in agro-ecological interfaces. A novel circular DNA possibly bipartite plant-infecting virus that encodes protein similar to those of geminiviruses was also identified in an Opuntia discolor plant in Brazil, named utkilio virus, but it is evolutionary distinct likely belonging to a new taxon. Viruses belonging to the ssDNA viral family Genomoviridae are also described and those thus far been associated with fungi hosts, so it is likely the ones identified in plants are associated with their phytobiome. Overall, the results of this project provide a molecular and biological characterization of novel geminiviruses and genomoviruses associated with cacti as well as demonstrate the impact of agro-ecological interfaces in the spread of viruses from or to native plants. It also highlights the importance of viral metagenomics studies in exploring virus diversity and evolution given then amount of virus diversity identified. This is important for conservation and management of cacti in a global scale, including the relevance of controlled movement of plants within countries.