Compacted hair in broken teeth reveal dietary prey of historic lions

The synergistic advancement of molecular and computational technologies has pushed genomics into a new era. Nuclear genome data for phylogenomic analyses can now be sequenced from minuscule quantities of DNA and from specimens that are more than a million years old. DNA analysis from hair is a well-established approach widely used in forensic science and wildlife conservation. Hair samples are largely resistant to contamination by exogenous DNA sources or can be effectively decontaminated, and can be used to identify the mammalian species from which the hair was shed. We aimed to use ancient DNA and bioinformatic methodologies optimized for degraded DNA to systematically identify dietary prey species from hair compacted in the teeth of two Tsavo lions that lived during the 1890s in Kenya. Analysis of hair DNA identified giraffe, human, oryx, waterbuck, wildebeest and zebra as prey, and also identified hair that originated from lion. DNA preservation allowed for analyses of complete mitogenome profiles of zebra, giraffe, and lion. Giraffe mitogenomes are phylogeographically partitioned, and we found that the lions ate at least two individuals that belong to a subspecies of Masai giraffe (Giraffa tippelskirchi tippelskirchi) typically found in southeast Kenya. The lion mitogenome from a hair sample was identical to the Tsavo lion endogenous mitogenome, and most closely matched other East African lions from Kenya and Tanzania. The protocol and approach reported here enable a better understanding of the hunting behaviors, diets, and ecology of historical individuals, populations, and species and holds promise for elucidating these characteristics in extinct populations and species.