Faecal n-alkanes differ significantly between two lemur species reflecting differences in consumed diet

• The n -alkane composition of lemur faeces differs between two lemur species. • Diet patterns, not gut microbiome composition, explains faecal n -alkane patterns. • Diets inform on species ecology, ecological niche and individual health. • Applications in the wild could inform on feeding ecology and niche partitioning. The diet of an animal reflects its species’ ecology and local food availability and is often a key metric for monitoring the health and welfare of endangered species. However, determining diets across individuals and through space and time, is an inherent challenge within ecology, being expensive and time-intensive to accomplish with observations. Faeces offer the opportunity for non-invasive sample collection and can provide a snapshot of the ingested diet of the producer. In modern ecology, faecal samples have been a prime target for genetic analyses of diet and the gut microbiome. Here, however, we explore whether high molecular weight (HMW) n -alkane biomarkers extracted from faeces can provide useful information about diet. HMW n- alkanes are commonly employed in palaeoecological reconstructions. Combining faecal HMW n -alkane analyses with gut microbiome composition and detailed foraging data applied to two species of lemur in captivity with access to naturalized forest enclosures, we show that recovered HMW n -alkanes are completely dietary in origin and not correlated to the gut microbiome. Signatures are significantly different between our two focal lemur species and seasons, reflecting differences in ingested diet. It is possible to infer changes in the relative contributions of major plant parts, particularly leaves and fruits, based on the faecal HMW n -alkane concentrations. Whereas n -alkane signatures alone are perhaps ill-suited to pinpoint plant species in animals with complex herbivorous diets, when integrated with other complementary methodologies can provide a more comprehensive dietary reconstruction. HMW n -alkanes are simple to identify and measure; only requiring commonly available and relatively affordable analytical chemistry instruments (e.g. GC-FID). Beyond discussing downstream uses of our methodology to captive and wild lemurs, other primates and herbivorous and omnivorous animals globally, our pilot study hints at the promise of the organic geochemist’s toolkit applied to dietary ecology.