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Ancient DNA Screening of Rhinoceros Species at Denisova Cave
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Resumo(s)
The Rhinocerotidae family is among some of the most impressive megafauna of the Cenozoic. During the Pleistocene, rhinoceroses were widely distributed across Eurasia, with most species becoming extinct during the Late Pleistocene, 129 – 11.7 thousand years ago (ka). Research into the population dynamics of rhinoceroses and their responses to climatedriven environmental changes has primarily focused on the woolly rhinoceros (Coleodonta antiquitatis) and the period immediately preceding their extinction. While the Late Pleistocene has been extensively studied, the Middle Pleistocene (774 – 129 ka) remains poorly sampled. Mass spectrometry analysis of bone fragments found at Denisova Cave has revealed a vast archive of rhinoceros remains, deposited across stratigraphic layers spanning climatic transitions from the Middle to Late Pleistocene. In this project, we screened these rhinoceros bone fragments for ancient DNA (aDNA). Through the processing and analysis of genomic data, we taxonomically identified bone fragments from 12 woolly rhinoceros and one Merck’s rhinoceros (Stephanorhinus kirchbergensis). From this data, seven high coverage woolly rhinoceros mitogenomes from the late Middle Pleistocene were reconstructed and used to broaden the temporal and geographical reach of the species’ phylogeny. We found evidence that woolly rhinoceroses were present in the Altai region continually throughout marine-oxygen isotope stages (MIS) 5 and 6. Multiple maternal lineages co-existed in the region, highlighting a wide dispersal and connectivity between the populations of woolly rhinoceros across Eurasia, as well as the role of Altai as a point of contact between them. This study also investigated the presence of by-catch DNA in Rhinocerontidae and bovid bone fragments, exploring its applications and biological implications. Two hyena (Crocuta crocuta) mitogenomes were generated, belonging to haplogroup A1, which is prevalent in Europe. Together with the previous results, our research contributes to the study and interpretation of faunal assemblages from southern Siberia.
Descrição
Tese de mestrado, Biologia Molecular e Genética, 2025, Universidade de Lisboa, Faculdade de Ciências
Palavras-chave
ancient DNA paleogenetics mitochondrial phylogeny woolly rhinoceros Merck’s rhinoceros