Theoretical investigation of host defense strategy evolution and phylogenomic analyses of apicomplexan parasites

Abstract

This dissertation consists of theoretical and phylogenomic approaches to study the evolution of hosts and parasites. The first chapter describes two mathematical models that investigate the evolution of resource allocation strategy in hosts. We found that in a population of hosts that are faced with a potentially costly infection, the evolutionarily stable strategy (ESS) at the host population level is a balanced investment between reproduction and immunity that maintains parasites, even if the host has the capacity to eliminate parasites. Furthermore, hosts exhibiting the ESS can invade any other population through parasite-mediated competition, using the parasites as biological weapons. At the metapopulation level, the dominant strategy is sometimes different from the population-level ESS, depending on the ratio of local extinction rate to colonization rate. This study could help to explain the ubiquity of parasites, and could serve as a framework for investigating parasite-mediated ecological invasions. The second chapter describes a novel high-throughput method that utilizes genomics data for phylogenetic inference. Results from two exemplar data sets, Vertebrata and Apicomplexa, demonstrate that the identity of phylogenetically informative genes are specific to each taxonomic group, even for phylogenies of similar time scale. The apicomplexans exhibit a high level of incongruence among gene trees, indicating that a relatively large number of genes are necessary for inferring the species tree. Nonetheless, the availability of genomics data permits the inference of a robust molecular phylogeny that is consistent with our prior knowledge of apicomplexan evolution based on morphology and development. Using the phylogeny as the foundation, the third chapter is focused on the characterization of lineage-specific (LS) genes in two major apicomplexan lineages, Plasmodium and Theileria. Consistent with previous studies in animals and bacteria, LS genes have a higher level of sequence divergence in both parasites. The result that many genus- or species-specific genes are putative surface antigens indicates that LS genes could be important in parasite adaptation. The contrasting properties regarding GC content and chromosomal location between LS genes in the two focal genera suggest that closely related parasite lineages can differ in the mechanisms of generating LS genes and their subsequent evolutionary fates.