Ten petrous bones were selected from archaeological specimens, representing a wide range of geographical locations and climatic contexts (Table 1, for repository information see S1 File). The specimens were selected from Central Europe, Central Asia, Southeast Asia, the Levant, Anatolia, and North Africa. The specimens are from Holocene archaeological contexts dated to between 10,000–1,800 calibrated years before present (cal. BP). The samples from Nubia, Jordan and Turkmenistan are from hot and arid regions. The sample from Turkey is from the Eastern Mediterranean (northwestern Turkey); the samples from Hungary and Serbia are from the Carpathian Basin/Southeast Europe, while the two samples from Cambodia and Vietnam are from tropical/subtropical Southeast Asia. We also included a metatarsal bone for one Neolithic individual from Hungary (Polgár Ferenci hát, PF280-443) as a control to confirm the differences between petrous and non-petrous reported in the previous study .and:
It has recently been demonstrated  that petrous bone samples yield exceptionally high percentages of endogenous ancient DNA. Here we have shown that both the total amount of endogenous DNA that can be recovered as well as the percentage of all reads that represents endogenous DNA vary substantially for different parts of the petrous bone. Our results have several implications for aDNA studies. The results support the hypothesis that dense bone parts are especially suitable for ancient DNA research, with the densest part of the petrous bone, that which composes the otic capsule, providing the best results. For our samples the yields obtained for this part (part C) exceed those obtained for part B (i.e. dense bone part of the petrous outside the otic capsule) by up to 65-fold and those from part A by up to 177-fold. It is therefore apparent that while high endogenous yields can be obtained from part B, and hence from any dense part in the petrous, optimal yields should be obtained from bone sample taken directly from the otic capsule.and:
Finally, our results show that endogenous yields from the five samples which originated from hot (either arid or humid) regions were always lower than 1% including extractions from part C of the petrous bone. However, deamination patterns suggest for two (Ain Ghazal and Vat Komnou) of the three samples for which we obtained sufficient numbers of reads that the obtained sequences are likely endogenous to the bones (S3 Fig). In contrast, the deamination pattern for the third sample, Man Bac, suggests that the human reads obtained are more likely to represent contamination than endogenous ancient DNA. These results suggest that it may be possible to obtain endogenous DNA from part C also for samples with relatively low amounts of endogenous DNA from hot environments, although extreme caution will be necessary in the interpretation of the results obtained from such samples.
PLoS ONE 10(6): e0129102. doi:10.1371/journal.pone.0129102
Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone
Ron Pinhasi et al.
The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (~ 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,000-1,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses.