23Mitochondrial DNA variants associated with diseases are widely studied in contemporary 24 populations, but their prevalence has not yet been investigated in ancient populations. The publicly 25 available AmtDB database contains 1443 ancient mtDNA Eurasian genomes from different 26 periods. The objective of this study was to use this data to establish the presence of pathogenic 27 mtDNA variants putatively associated with mitochondrial diseases in ancient populations. The 28 clinical significance, pathogenicity prediction and contemporary frequency of mtDNA variants 29 were determined using online platforms. The analyzed ancient mtDNAs contain six variants 30 designated as being "confirmed pathogenic" in modern patients. The oldest of these, m.7510T>C 31 in the MT-TS1 gene, was found in a sample from the Neolithic period dated 5800-5400 BCE. All 32 six have well established clinical association, and their pathogenic effect is corroborated by very 33 low population frequencies in contemporary populations. In addition, ten variants designated as 34 possibly or likely pathogenic were detected. The oldest of these were two variants in the MT-TD 35 gene, m.7543A>G and m.7554G>A, from Neolithic samples dated 8205-7700 BCE. A novel 36 mutation in contemporary populations, m.4440G>A in the MT-TM gene, is established in 12 ancient 37 mtDNA samples from different periods ranging from 2800 BCE to 920 CE. The pathogenic effect 38 of these possibly/likely pathogenic mutations is not yet well established, and further research is 39 warranted. All detected mutations putatively associated with mitochondrial disease in ancient 40 mtDNA samples are in tRNA coding genes. Most of these mutations are in a mt-tRNA type (Model 41 2) that is characterized by loss of D-loop/T-loop interaction. Seven mutations are located in CS-42 Anticodon stem, 4 are located in AS-Acceptor stem, 2 in TS-TΨC stem, and single mutations are 43 found in DL-Dihydrouridine Loop, CL-Anticodon Loop and DS-Dihydrouridine stem. Exposing 44 pathogenic variants in ancient human populations expands our understanding of their origin. 65 severity of the clinical and biochemical phenotype caused by pathogenic mtDNA mutations has 66however been found to be roughly proportionate to the percent mutant heteroplasmy (10, 11).
67Nucleotide polymorphisms accumulate in mtDNA during human evolution forming mitochondrial 68 haplogroups, and these also might alter the penetrance of mitochondrial diseases (12). Specific 69 subclades of haplogroup J, for example, have been shown to affect the penetrance and 70 pathogenicity of Leber's hereditary optic neuropathy (13). Certain mtDNA mutations and 71 haplogroups are also predictors of both lifespan and risk of various age-associated disease, 72 including degenerative diseases, cancer, diabetes, heart failure, sarcopenia and Parkinson's disease 73 (14). 74 We had previously performed whole-genome sequencing on 25 Thracian mtDNA samples dated 75 3000-2000 BCE, and 608 mtDNA variants were detected (15). Only one of these, however, 7...