Summary Small island populations, particularly those of large vertebrates, are vulnerable to extinction due to environmental stochasticity and genetic drift. Here, we combined analyses of 113 newly generated ∼10x genomes of anoa ( Bubalus spp.) and babirusa ( Babyrousa spp.) with habitat suitability models to assess the evolutionary trajectories of small and large island populations within the Wallacea archipelago in Indonesia. Our analyses show that, compared to closely related species, populations on the largest island of Sulawesi exhibit low levels of heterozygosity, high levels of inbreeding, and a high proportion of deleterious alleles. In contrast, although populations on smaller islands such as Buton and Togean exhibit lower heterozygosity and higher inbreeding than in larger islands, they also possess fewer deleterious mutations. Analyses of site frequency spectra analyses indicate this likely the result of stronger, long-term purging acting in population from smaller islands. Combined with species distribution models, our results show that populations on small islands have persisted over a long time frame in high quality habitat while populations in the larger island have recently suffered from low habitat quality as a result of heavy exploitation of natural resources. In the case of anoa and babirusa, preservation of small island populations should focus more on improving habitat quality in small islands and avoid translocating individuals from the larger island. In the face of ongoing land-use change on the Sulawesi mainland, we suggest that offshore islands are increasingly crucial for the long-term survival of Wallacea’s iconic and indigenous mammals.

The importance of small island populations for the long term survival of endangered large-bodied insular mammals