Wild–urban gradient leads to ecological stratification in Singapore’s long-tailed macaques

Large-scale urbanization, with a mosaic of different disturbance levels, forces species to adapt in often unpredictable ways. To better understand such adaptations, we here use a multidimensional analysis of DNA from >350 fecal samples of long-tailed macaques (Macaca fascicularis) collected across a wild–urban gradient in highly urbanized Singapore, investigating their population structure, diet and microbiome. Macaques grouped into eight distinct matrilines, which exhibited specific habitat associations. Total plants in the diet were more diverse in wild than urban areas, with the total diversity of an important group of exotic fruiting plants decreasing markedly along the wild–urban gradient. Similarly, total bacterial diversity, including that of pathogens, showed steep declines from wild to urban habitat. Our analysis suggests that the wild–urban gradient produces different pathogenic and dietary environments and that kinship and learning may lead to adaptations to a diverse city landscape. These results open avenues for understanding animal adjustment to anthropogenic environments in general and specifically enable managers and city planners to take into account long-tailed macaques’ relationships, habitat-use patterns and dietary preferences to facilitate human–macaque coexistence. This study assessed the diet, gut bacteria and habitat preferences of long-tailed macaques in Singapore across a gradient of urbanization. Animal dietary diversity and gut bacterial diversity both declined with urbanization, while dietary plant diversity varied with urbanization according to ecological category. The macaque population exhibits eight female-line groups associated with specific habitats ranging in degree of urbanicity.