Host–parasite associations provide a benchmark for investigating evolutionary arms races and antagonistic coevolution. However, potential ecological mechanisms underlying such associations are difficult to unravel. In particular, local adaptations of hosts and/or parasites may hamper reliable inferences of host–parasite relationships and the specialist–generalist definitions of parasite lineages, making it problematic to understand such relationships on a global scale. Phylogenetic methods were used to investigate co-phylogenetic patterns between vector-borne parasites of the genus Haemoproteus and their passeriform hosts, to infer the ecological interactions of parasites and hosts that may have driven the evolution of both groups in a local geographic domain. As several Haemoproteus lineages were only detected once, and given the occurrence of a single extreme generalist, the effect of removing individual lineages on the co-phylogeny pattern was tested. When all lineages were included, and when all singly detected lineages were removed, there was no convincing evidence for host–parasite co-phylogeny. However, when only the generalist lineage was removed, strong support for co-phylogeny was indicated, and ecological interactions could be successfully inferred. This study exemplifies the importance of identifying locally abundant lineages when sampling host–parasite systems, to provide reliable insights into the precise mechanisms underlying host–parasite interactions.

Unlike most bird species, individual kingfisher species (Aves: Alcedinidae) are typically parasitized by only a single genus of louse (Alcedoffula, Alcedoecus, or Emersoniella). These louse genera are typically specific to a particular kingfisher subfamily. Specifically, Alcedoecus and Emersoniella parasitize Halcyoninae, whereas Alcedoffula parasitizes Alcedininae and Cerylinae. Although Emersoniella is geographically restricted to the Indo-Pacific region, Alcedoecus and Alcedoffula are geographically widespread. We used DNA sequences from two genes, the mitochondrial COI and nuclear EF-1α genes, to infer phylogenies for the two geographically widespread genera of kingfisher lice, Alcedoffula and Alcedoecus. These phylogenies included 47 kingfisher lice sampled from 11 of the 19 currently recognized genera of kingfishers. We compared louse phylogenies to host phylogenies to reconstruct their cophylogenetic history. Two distinct clades occur within Alcedoffula, one that infests Alcedininae and a second that infests Cerylinae. All species of Alcedoecus were found only on host species of the subfamily Halcyoninae. Cophylogenetic analysis indicated that Alcedoecus, as well as the clade of Alcedoffula occurring on Alcedininae, do not show evidence of cospeciation. In contrast, the clade of Alcedoffula occurring on Cerylinae showed strong evidence of cospeciation.

The sequences of four mitochondrial genes were determined for Demodex mites isolated from two distantly related species within the family Cervidae, and identified morphologically as belonging to the species Demodex kutzeri. The sequences were used to test the hypothesis that Demodex are strictly host-specific, and hence cospeciate with their hosts: (1) The estimated divergence time between mites found on elk vs humans agreed closely with a previous estimate of the time that these host species last shared a common ancestor, suggesting cospeciation of mites and hosts, at least over long evolutionary timescales. (2) The extremely low levels of sequence divergence between the mites found on elk vs mule deer hosts indicated that these mites belong to the same species, which suggests that Demodex are able to move across host species boundaries over shorter timescales. Together, the results are consistent with the model that Demodex mites are not strict host-specialists, but instead lose the ability to move between host lineages gradually.

The coevolutionary relationships between avian malaria parasites and their hosts influence the host specificity, geographical distribution and pathogenicity of these parasites. However, to understand fine scale coevolutionary host–parasite relationships, robust and widespread sampling from closely related hosts is needed. We thus sought to explore the coevolutionary history of avian Plasmodium and the widespread African sunbirds, family Nectariniidae. These birds are distributed throughout Africa and occupy a variety of habitats. Considering the role that habitat plays in influencing host-specificity and the role that host-specificity plays in coevolutionary relationships, African sunbirds provide an exceptional model system to study the processes that govern the distribution and diversity of avian malaria. Here we evaluated the coevolutionary histories using a multi-gene phylogeny for Nectariniidae and avian Plasmodium found in Nectariniidae. We then assessed the host–parasite biogeography and the structuring of parasite assemblages. We recovered Plasmodium lineages concurrently in East, West, South and Island regions of Africa. However, several Plasmodium lineages were recovered exclusively within one respective region, despite being found in widely distributed hosts. In addition, we inferred the biogeographic history of these parasites and provide evidence supporting a model of biotic diversification in avian Plasmodium of African sunbirds.

Even the most generalist parasites usually occur in only a subset of potential host species, a tendency which reflects overriding environmental constraints on their distributions in nature. The periodic shifting of these limitations represented by host-switches may have been an important process in the evolution of many host-parasite assemblages. To study such events, however, it must first be established where and when they have occurred. Past host-switches within a group of parasites are usually inferred from a comparison of the parasite phylogeny with that of the hosts. Congruence between the phylogenies is often attributed to a history of association by descent with cospeciation, and incongruence to host-switching or extinction in ‘duplicated’ parasite lineages (which diverged without a corresponding branching of the host tree). The inference of host-switching from incongrucnt patterns is discussed. Difficulties arise because incongruence can frequently be explained by different combinations of biologically distinct events whose relative probabilities are uncertain. Also, the models of host parasite relationships implicit in historical reconstructions may often not allow for plausible sources of incongruence other than host-switching or duplication/extinction, or for the possibility that colonization could, in some circumstances, be disguised by ‘false’ congruence.