Distribution Patterns of Postmortem Damage in Human Mitochondrial DNA

Abstract

The distribution of postmortem damage in mitochondrial DNA retrieved from 37 ancient human DNA samples was analyzed by cloning and was compared with a selection of published animal data. A relative rate of damage (rho(v)) was calculated for nucleotide positions within the human hypervariable region 1 (HVR1) and cytochrome oxidase subunit III genes. A comparison of damaged sites within and between the regions reveals that damage hotspots exist and that, in the HVR1, these correlate with sites known to have high in vivo mutation rates. Conversely, HVR1 subregions with known structural function, such as MT5, have lower in vivo mutation rates and lower postmortem-damage rates. The postmortem data also identify a possible functional subregion of the HVR1, termed "low-diversity 1," through the lack of sequence damage. The amount of postmortem damage observed in mitochondrial coding regions was significantly lower than in the HVR1, and, although hotspots were noted, these did not correlate with codon position. Finally, a simple method for the identification of incorrect archaeological haplogroup designations is introduced, on the basis of the observed spectrum of postmortem damage.

Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data

“…Next, the samples were rinsed with DNase/RNase‐free distilled water once again and allowed to air‐dry under irradiation in a UV crosslinker for 90 min, during which time they were turned over twice. The samples were then encased in Exafine silicone rubber (GC, Tokyo, Japan) following the protocol described by Gilbert et al (2003). After approximately 5 min, or once the rubber was hard, the tip of the root of the tooth sample was removed with a horizontal cut and then powdered using a mill (Multi‐beads Shocker ® ; Yasui Kikai, Osaka, Japan).…”

Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims

“…(iii) Fifty-three teeth (5AN/2RM/2SP/44CP) were encased in silicone rubber ('silicone') prior to the removal of dentine with a dental drill as reported in Gilbert et al (2003b) (Fig. 1).…”

Mitochondrial haplogroup C in ancient mitochondrial DNA from Ukraine extends the presence of East Eurasian genetic lineages in Neolithic Central and Eastern Europe

“…Most clones displayed amplification-replica-specific random non-repeatable nucleotide misincorporations occurring at non-phylogenetically relevant positions, which is consistent with the expected post-mortem nucleotide damage. 7,8 Two specimens were designated as members of haplogroup H, two were members of the U clade and three shared the 16223-16298-16327 HVS1 sequence motif characteristic of the root sequence of haplogroup C. 9,10 Specimen Ya34 carried a transition at 16357, characteristic of the C4a2 subbranch of the C clade. 10 While the majority of mtDNA lineages found in the Neolithic remains from the NPR can be ascribed to the haplogroups of West Eurasian origin and are in agreement with those previously reported for prehistoric haplogroups in West Eurasia, [11][12][13][14][15][16][17][18] our finding of East Eurasian lineages is uncommon in ancient European remains and has only been observed in the neighboring populations of the Carpathian Mountains.…”