The evolutionary relationships among the apicomplexan blood pathogens known as the malaria parasites (order Haemosporida), some of which infect nearly 200 million humans each year, has remained a vexing phylogenetic problem due to limitations in taxon sampling, character sampling and the extreme nucleotide base composition biases that are characteristic of this clade. Previous phylogenetic work on the malaria parasites has often lacked sufficient representation of the broad taxonomic diversity within the Haemosporida or the multi-locus sequence data needed to resolve deep evolutionary relationships, rendering our understanding of haemosporidian life-history evolution and the origin of the human malaria parasites incomplete. Here we present the most comprehensive phylogenetic analysis of the malaria parasites conducted to date, using samples from a broad diversity of vertebrate hosts that includes numerous enigmatic and poorly known haemosporidian lineages in addition to genome-wide multi-locus sequence data. We find that if base composition differences were corrected for during phylogenetic analysis, we recovered a well-supported topology indicating that the evolutionary history of the malaria parasites was characterized by a complex series of transitions in life-history strategies and host usage. Notably we find that Plasmodium , the malaria parasite genus that includes the species of human medical concern, is polyphyletic with the life-history traits characteristic of this genus having evolved in a dynamic manner across the phylogeny. We find support for multiple instances of gain and loss of asexual proliferation in host blood cells and production of haemozoin pigment, two traits that have been used for taxonomic classification as well as considered to be important factors for parasite virulence and used as drug targets. Lastly, our analysis illustrates the need for a widespread reassessment of malaria parasite taxonomy.

Significance: Understanding the evolution of malaria parasites and their phylogenetic context is key to understanding this important human disease. We report an unexpected high diversity of malaria parasite genera in bats from West African forest ecosystems. Two lineages are closely related toPlasmodiumparasites from rodents, which are common laboratory model systems, and the results are consistent with switches between these hosts over their evolutionary history. Bats are considered important reservoir hosts for many pathogens, particularly viruses, and have unusually high immunological tolerances. The abundant malaria parasite infections are consistent with this exceptional immunology and suggest that in bats the parasites repeatedly evolved life cycles away from disease-causing replication in red blood cells to less pathogenic propagation in liver tissue.

Parasitic protozoan parasites have evolved many co-evolutionary paths towards stable transmission to their host population. Plasmodium spp., the causative agents of malaria, and related haemosporidian parasites are dipteran-borne eukaryotic pathogens that actively invade and use vertebrate erythrocytes for gametogenesis and asexual development, often resulting in substantial morbidity and mortality of the infected hosts. Here, we present results of a survey of insectivorous bats from tropical Africa, including new isolates of species of the haemosporidian genus Nycteria. A hallmark of these parasites is their capacity to infect bat species of distinct families of the two evolutionary distant chiropteran suborders. We did detect Nycteria parasites in both rhinolophid and nycterid bat hosts in geographically separate areas of Sub-Saharan Africa, however our molecular phylogenetic analyses support the separation of the parasites into two distinct clades corresponding to their host genera, suggestive of ancient co-divergence and low levels of host switching. For one clade of these parasites, cytochrome b genes could not be amplified and cytochrome oxidase I sequences showed unusually high rates of evolution, suggesting that the mitochondrial genome of these parasites may have either been lost or substantially altered. This haemosporidian parasite-mammalian host system also highlights that sequential population expansion in the liver and gametocyte formation is a successful alternative to intermediate erythrocytic replication cycles.

Hepatocystis parasites are closely related to mammalian Plasmodium species, the causative agents of malaria. Despite the close phylogenetic relationship, Hepatocystis parasites lack the intermittent erythrocytic replication cycles, the signature and exclusive cause of malaria-related morbidity and mortality. Hepatocystis population expansion in the mammalian host is thought to be restricted to the pre-erythrocytic liver phase. Complete differentiation of first generation blood stages into sexual stages for subsequent vector transmission indicates alternative parasite/host co-evolution. In this study, we identified a region of exceptionally high prevalence of Hepatocystis infections in Old World fruit bats in South Sudan. Investigations over the course of five consecutive surveys revealed an average of 93 percent prevalence in four genera of African epauletted fruit bats. We observed a clear seasonal pattern and tolerance of high parasite loads in these bats. Phylogenetic analyses revealed several cryptic Hepatocystis parasite species and, in contrast to mammalian Plasmodium parasites, neither host specificity nor strong geographical patterns were evident. Together, our study provides evidence for Pan-African distribution and local high endemicity of a Hepatocystis species complex in Pteropodidae.