Endemic within endemics: the microbiota of the Galapagos Marine Iguanas

Abstract The ecological processes shaping host-associated microbial communities in geographically isolated ecosystems remain poorly understood—particularly the interplay between dispersal, selection, and microbial speciation. Here, we characterize the fecal microbiota of the Galápagos marine iguana (Amblyrhynchus cristatus), an iconic endemic vertebrate that depends on its microbiota to digest an algae-based diet. We analyzed fecal samples from 111 individuals across three remote colonies and found that fecal microbial composition is dominated by Clostridia, closely following a neutral dispersal model. Yet, ecological and phylogenetic analyses revealed novel, host-restricted Clostridia clades—spanning species to family level—that appear to have diversified within marine iguanas. These lineages are consistently retained across host populations through strong purifying selection, resulting in striking microbiota homogenization. Our findings demonstrate that endemic hosts can support microbially distinct lineages shaped by stochastic dispersal and parallel selection, advancing our understanding of microbial community assembly in obligate host–microbiota systems.