Candidate Denisovan fossils identified through gene regulatory phenotyping

Abstract

Denisovans are an extinct group of humans whose morphology is mostly unknown. The scarcity of verified Denisovan fossils makes it challenging to study how they differed in their anatomy, and how well they were adapted to their environment. To gain insight into their evolutionary history, we used a genetic phenotyping approach, where predicted Denisovan anatomy was inferred by detecting gene regulatory changes that likely altered Denisovan skeletal morphology. We then scanned Middle Pleistocene skulls for unclassified specimens that match our Denisovan profile and thus might have been related to Denisovans. We found that the Harbin, Dali, and Kabwe specimens show a particularly good match to the predicted Denisovan profile. We conclude that our genetic phenotyping approach could help classify unidentified specimens, and that Harbin, Dali, and Kabwe likely belonged to individuals closely linked to the Denisovan lineage.