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Metagenomic and genomic data associated with the tooth-cavity hair and endogenous DNA of the Tsavo lions

de Flamingh, Alida1; Gnoske, Thomas2; Kerbis Peterhans, Julian2; Simeonovski, Velizar2; Gitahi, Nduhiu3; Mwebi, Ogeto4; Agwanda, Bernard4; Catchen, Julian1; Roca, Alfred1; Malhi, Ripan1

Research facility: University of Illinois Urbana-Champaign
Published Jun 30, 2025 on Dryad. https://doi.org/10.5061/dryad.2fqz612zb

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Abstract

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 (Essel et al., 2023) and from specimens that are more than a million years old (van der Valk et al., 2021). DNA analysis from hair is a well-established approach (Higuchi et al., 1988) widely used in forensic science (Bisbing, 2020) and wildlife conservation (Phoebus et al., 2020). Hair samples are largely resistant to contamination by exogenous DNA sources or can be effectively decontaminated (Gilbert et al., 2006), and can be used to identify the mammalian species from which the hair was shed (Singh et al., 2020; Meiklejohn et al., 2021). We aimed to use ancient DNA and bioinformatic methodologies (Figure 1; STAR methods) 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 for background on the Tsavo lion specimens and hair samples; and Patterson, 1907; Kerbis Peterhans and Gnoske, 2001 for general 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. 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.