Abstract The ecological niche of species is often studied from two different perspectives. Environmental niche modelling (ENM) infers a species’ current niche from contemporary occurrence records, while phylogenetic comparative methods (PCM) infer the history of niche evolution. Although these two areas of research are conceptually linked, they are analysed independently, within separate analytical frameworks. Here we provide a new method, NEMo (Niche Evolution Model), for simultaneous inference of niche evolution and estimation of contemporary niches of species. NEMo explicitly models three fundamental processes of niche evolution – adaptation, speciation, and dispersal – applying a reversible jump algorithm to infer occurrences of these processes on a phylogeny. The model permits ENMs to account for the role of history in shaping current species distributions, and offers more realistic models of evolution in PCMs. Simulations show that NEMo has high accuracy for estimating the ecological niche of species, and reasonable power to identify the occurrences of the three processes on phylogeny. When applied to a real case study (the Australian plant genus Acacia ), the method is more effective at predicting a key environmental niche axis (salt tolerance) than using ENM alone, and it infers temporal patterns in the evolution of drought tolerance in response to aridification that are consistent with prior expectations NEMo makes it possible to combine many types of data to study niche evolution and estimate species niches, not only species distributions and phylogeny, but also paleoclimate, species tolerance range, and fossil records.

Tracking niche change through time: simultaneous inference of ecological niche evolution and estimation of contemporary niches