Malaria parasites (Plasmodium spp.) have plagued humans for millennia. Less well known are related parasites (Haemosporida), with diverse life cycles and dipteran vectors that infect other vertebrates. Understanding the evolution of parasite life histories, including switches between hosts and vectors, depends on knowledge of evolutionary relationships among parasite lineages. In particular, inferences concerning time of origin and trait evolution require correct placement of the root of the evolutionary tree. Phylogenetic reconstructions of the diversification of malaria parasites from DNA sequences have suffered from uncertainty concerning outgroup taxa, limited taxon sampling, and selection on genes used to assess relationships. As a result, inferred relationships among the Haemosporida have been unstable, and questions concerning evolutionary diversification and host switching remain unanswered. A recent phylogeny placed mammalian malaria parasites, as well as avian/reptilian Plasmodium, in a derived position relative to the avian parasite genera Leucocytozoon and Haemoproteus, implying that the ancestral forms lacked merogony in the blood and that their vectors were non-mosquito dipterans. Bayesian, outgroup-free phylogenetic reconstruction using relaxed molecular clocks with uncorrelated rates instead suggested that mammalian and avian/reptilian Plasmodium parasites, spread by mosquito vectors, are ancestral sister taxa, from which a variety of specialized parasite lineages with modified life histories have evolved.Bayes factors | parasite diversification | Plasmodiidae M alaria parasites [broadly Apicomplexa: Haemosporida (1, 2)] have been well sampled in primates and songbirds, but are poorly known in other vertebrate groups. Recent surveys of blood parasites in vertebrate wildlife populations, using PCR to screen hosts for infections and DNA sequencing to identify parasite lineages, have revealed a rich diversity of hemosporidian parasites (3-6), possibly comparable to the number of hosts surveyed (7,8). It is important to reevaluate our interpretation of hemosporidian evolution as we expand sampling, to provide insight into shifts among hosts and vectors-often implicated in emerging infectious diseases-and to interpret the evolution of malaria parasite life cycles. Because choice of outgroup taxa critically influences the reconstruction of evolutionary relationships (9), it is also important to reassess assumptions about ancestral relationships and the monophyly of taxa. Premolecular reconstructions based on morphology and life history traits presumed that a monophyletic clade of Plasmodium parasites exhibited the most derived traits [e.g., asexual reproduction (merogony) in the circulating blood of the vertebrate host, production of hemozoin pigment from the metabolism of hemoglobin] (10, 11); accordingly, Leucocytozoon, a parasite of birds that lacks these traits, was placed in a basal position (Fig. 1A). Such a position for Leucocytozoon was indeed suggested in early molecular analyses based on the ...