There is a fundamental gap in our understanding of genetic adaptations that facilitate and enable host shifts in malaria parasites. Specifically, it is unclear how transitions occur between vertebrate hosts and how malaria parasites adapt in what are in some cases major host shifts. This project will specifically determine how genes in critical metabolic pathways have adapted to different hosts across the evolutionary tree of malaria parasites. The long-term goal of the research presented in this proposal is to identify key adaptations of malaria parasites to their hosts in order to understand mechanisms of host switches in malaria parasites. The objective of this application is to develop a set of genetic tools to study malaria parasite adaptations by identifying genes under selection between different genera of malaria parasites, with an initial focus on metabolic pathways, for which there is evidence of selection between parasite genera. These tools can be used as molecular markers for improving our understanding of potentially emergent malaria pathogens. The central hypothesis is that adaptations in metabolic pathways differentiate the genera of malaria parasites. This hypothesis has been formulated from preliminary data generated in the applicant's laboratory. The rationale for this work is that it wil become possible to identify key genes that may be involved in host shifts, providing not only an evolutionary explanation for diversification in malaria parasites, but also a practical understanding of the mechanisms of malaria parasite emergence in novel hosts. Guided by compelling prior studies and preliminary data, the central hypothesis will be addressed by pursuing two specific aims: 1) identify genes with a signature of selection be- tween malaria parasite groups; and 2) characterize patterns of selection in malaria parasite genes related to host shifts. The first aim will be accomplished with established techniques including: targeted PCR/DNA sequencing of components of important metabolic pathways, and genome sequencing of samples from each parasite genus. The applicant has established the feasibility of these techniques, as well as put together a team of malaria parasite experts with next-generation sequencing and bioinformatics skills. The second aim requires detailed analyses of the data generated in the first aim using approaches of identifying rates of non- synonymous and synonymous substitutions within and between genera of parasites in a phylogenetic (evolutionary) context. When this research is complete, candidate genes will be characterized by patterns of selection and adaptive, amino acid residues will be identified in malaria parasites. This study is innovative because it represents the first taxonomically comprehensive inventory of genes that may explain how malaria parasites adapt to novel hosts, and is particularly timely because many recent studies have shown host shifts between humans and apes and between birds and bats. The proposed research is significant because it represents the first step to identifying adaptations in malaria parasites to their hosts, with the expectation that this knowledge will lead to a deeper understanding of how parasites emerge in novel hosts.