Reassessing genetic relationships of Homo heidelbergensis among primates based on mitochondrial and nuclear DNA

Abstract

Abstract Mitochondrial and nuclear DNA isolated from the fossils of Homo heidelbergensis are a real godsend. Morphological assessments of a given fossil can be highly subjective, sometimes having to transfer species from Homo to Australopithecus. However, sequencing data makes the accurate genetic reassessment of this fossil among primates possible. The mtDNA for 36 primates including Neanderthal, Denisovan, and Homo heidelbergensis were downloaded from NCBI and aligned and visualized in a heat map. Homo heidelbergensis appears to be a member of the human clade, separating sharply from all other primates. Comparisons between 21 modern humans, three archaic humans, and three Pan sequences show that archaic humans fit within the variation of modern humans, meaning that together with Neanderthal and Denisovans, Homo heidelbergensis is also part of the human clade. Reads from nine Homo heidelbergensis SRAs were downloaded from BioProject PRJEB10957 and ten for an archaic human from PRJEB22592. These reads were mapped to the hg38, the Neanderthal, and the panTro6 genomes, and variants were called using the samtools pipeline. The same proportion of reads mapped to hg38 as did from the archaic human genome, and more than to panTro6. Furthermore, the variant density was also the same between Homo heidelbergensis and archaic human, when mapping to hg38. BLASTing read sequences against hg38 and panTro6 gave similar results. Finally, the proportion of C > T/G > A point mutations in Homo heidelbergensis (40.1%) was statistically significantly greater than in modern human (33.2%). This indicates that 6.9% of these mutations stem from deamination. Homo heidelbergensis genetically behaves very much like archaic human, and thus can be considered to be human, just like Neanderthal and Denisovan. It would be of tremendous value if either mtDNA and/or nuclear DNA could be found in the fossils of other hominids so as to make a more precise assessment of human phylogenetics possible.