Candidate Denisovan fossils identified through gene regulatory phenotyping

Denisovans are an extinct group of humans whose morphology is mostly unknown. The scarcity of verified Denisovan fossils makes it challenging to study their anatomy, and how well they were adapted to their environment. We previously developed a genetic phenotyping approach to gain insight into Denisovan anatomy by detecting gene regulatory changes that likely altered Denisovan skeletal morphology. Here, we scan the Middle Pleistocene fossil record for crania matching the predicted Denisovan morphology and might therefore be related to Denisovans. We developed quantitative measures to assess both the proportion and extent of matches. These analyses revealed that the East Asian specimens of Harbin and Dali show an exceptionally high concordance with the Denisovan profile, surpassing all other examined Middle Pleistocene hominin specimens, including Neanderthals. Specifically, 15 out of 18 of Dali’s features and 16 out of 18 of Harbin’s matched Denisovan predictions. These findings are robust to overall skull size and to correlations between phenotypes. We also found that Kabwe 1 shows a strong affinity to the Denisovan–Neanderthal clade and might be placed near its root. Our results show that gene regulatory phenotyping may assist in classifying poorly understood specimens.