Compacted hair in broken teeth reveals dietary prey of historic lions

With recent advances, nuclear genome data for phylogenomic analyses can now be sequenced from minuscule quantities of DNA¹ and from specimens that are more than a million years old.² DNA analysis from hair is a well-established approach³ widely used in forensic science⁴ and wildlife conservation.⁵ Hair samples can be effectively decontaminated⁶ and can be used to identify the mammalian species from which the hair was shed.^7,8 We aimed to use advances 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 (see description of samples in the STAR Methods and Patterson⁹ and Kerbis Peterhans and Gnoske¹⁰ for background on the Tsavo "man-eaters"). 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. Our approach enables a better understanding of the hunting behaviors, diets, and ecology of historical individuals, populations, and species and holds promise for extinct populations and species.