Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird

The highlands of Mesoamerica harbour some of the highest biodiversity in the world, especially in cloud forests, but the landscape drivers of this diversification are not well known. Taxonomy in this region has been challenging owing to a lack of consensus about how to test species limits. We apply integrative taxonomy to an emblematic species of the Mesoamerican cloud forests, the unicolored jay (Aphelocoma unicolor). We assess divergence along three complementary axes (genetics, phenotype and ecological niche), finding evidence for differentiation among five lineages, currently described as subspecies, in isolated forest patches. DNA suggests that these lineages have long histories of divergence. Multivariate analysis of phenotype, along with an objective method for detecting phenotypic clusters, suggest that at least four of the five lineages are diagnosable. There was also a pattern of increasing ecological divergence through time. The divergence observed among lineages is comparable to other species-level divergences in the genus, arguing for elevation of at least two, and as many as four, lineages within A. unicolor to species rank. According to our time tree, cloud forest patches became isolated starting in the Pliocene and continuing into the Pleistocene, suggesting glacial cycles as the main drivers of speciation.