Palaeoproteomic analysis of Pleistocene cave hyenas from east Asia

Huiyun Rao,Chi Zhang,Yimin Yang,Qingfeng Shao,Michael V Westbury,Jinyi Liu

doi:10.1038/s41598-020-73542-x

Abstract

The spotted hyena (Crocuta crocuta) is the only extant species of the genus Crocuta, which once occupied a much wider range during the Pliocene and Pleistocene. However, its origin and evolutionary history is somewhat contentious due to discordances between morphological, nuclear, and mitochondrial data. Due to the limited molecular data from east Asian Crocuta, also known as cave hyena, and the difficulty of extracting ancient DNA from this area, here we present proteomic analysis of cave hyenas from three locations in northern China. This marks the first proteomic data generated from cave hyenas, adding new molecular data to the east Asian populations. Phylogenetic analysis based on these protein sequences reveals two different groups of cave hyenas in east Asia, one of which could not be distinguished from modern spotted hyenas from northern Africa, tentatively the result of previously suggested gene flow between these lineages. With developments of instrumentation and analytical methods, proteomics holds promising potential for molecular phylogenetic reconstructions of ancient fauna previously thought to be unreachable using ancient DNA.

Highlights

The spotted hyena (Crocuta crocuta) is the only extant species of the genus Crocuta, which once occupied a much wider range during the Pliocene and Pleistocene
Spotted hyenas are currently restricted to sub-Saharan Africa, this genus once inhabited almost the entire Eurasian continent during the Pliocene and Pleistocene, and comprised a variety of species, such as Crocuta dietrichi, C. eturono, C. honanensis, and the so-called Eurasian cave hyenas[1,2,6]
Western Eurasian cave hyenas are divided into two groups with one group intermingled with northern African spotted hyenas, while east Asian cave hyenas form a basal diverging lineage[10,11,12]

Summary

Introduction

The spotted hyena (Crocuta crocuta) is the only extant species of the genus Crocuta, which once occupied a much wider range during the Pliocene and Pleistocene. Due to the limited molecular data from east Asian Crocuta, known as cave hyena, and the difficulty of extracting ancient DNA from this area, here we present proteomic analysis of cave hyenas from three locations in northern China. As to the origin and evolutionary history of spotted hyena fossils, Rohland et al.[10] suggested three separate dispersal events out of Africa to Eurasia between 3.5 and 0.35 Ma, while Sheng et al.[11] proposed an Eurasian origin at a far more recent evolutionary timescale (430–163 kya) These mitochondrial findings were later debunked by Westbury et al.[12] who investigated the relationships between African spotted hyenas and Eurasian cave hyenas using ancient nuclear genomes. The obscure evolutionary history of Asian populations could be caused by the limited number

Methods

Results

Conclusion