Urbanization usually decreases biodiversity, but select species can tolerate or thrive in human-modified environments. Broad environmental tolerance typically characterizes species that persist in urban habitats. Heterogeneous environmental conditions used by urban-adapted species could influence the specialization that is adaptive for their parasites. Parasites subjected to diverse environments may experience selective pressures favoring host generalism, which could promote host-switching in parasites of urban-tolerant hosts. We test the hypothesis that a host species’ tolerance of urban habitats corresponds with decreased cophylogenetic congruence with their parasites using avian haemosporidians (genera Plasmodium and Haemoproteus). Bird species vary in their response to urbanization, ranging from exclusion to achieving high densities. Avian haemosporidia are diverse intra-erythrocytic parasites with specificity ranging from specialists with strong co-evolutionary relationships with their hosts to generalists more prone to host-switching. Employing a global database of associations between haemosporidian lineages and avian host species, we use the Procrustean Approach to Cophylogeny and phylogenetic generalized linear mixed models to test if host–parasite links associated with urban-adapted bird species have lower contributions to overall cophylogenetic congruence. Our results show that the integration between urban tolerance and migratory strategy affect co-evolutionary relationships between hosts and parasites. Specifically, fully migratory bird species known to occur in disturbed habitats on average have co-evolutionary histories with their haemosporidian parasites that are more strongly characterized by host-switching. Understanding the ecological drivers of host-switching is key to predicting and managing parasite spread mediated by cross-species transmission, especially as an urbanizing world promotes higher abundances of urban-adapted species.

Host-associated microbiota can be affected by factors related to environmental change, such as urbanization and invasive species. For example, urban areas often affect food availability for animals, which can change their gut microbiota. Invasive parasites can also influence microbiota through either competition or indirectly through a change in the host immune response. These interacting factors can have complex effects on host fitness, but few studies have disentangled the relationship between urbanization and parasitism on an organism’s gut microbial composition. To address this gap in knowledge, we investigated the effects of urbanization and parasitism by the invasive avian vampire fly (Philornis downsi) on the gut microbiota of nestling small ground finches (Geospiza fuliginosa) on San Cristóbal Island, Galápagos. We conducted a factorial study in which we experimentally manipulated parasite presence in an urban and non-urban area. Feces were then collected when nestlings to characterize the gut microbiota (i.e., alpha and beta diversity, community composition). Although we did not find an interactive effect of urbanization and parasitism on the microbiota, we did find main effects of each variable. Urban and parasitized nestlings had lower bacterial diversity and differences in relative abundance of bacterial phyla and genera compared to non-urban non-parasitized nestlings, respectively. Overall, this study advances our understanding of the complex effects of anthropogenic stressors on the gut microbiota of birds.