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Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone.

Pinhasi R, Fernandes D, Sirak K, Novak M, Connell S, Alpaslan-Roodenberg S, Gerritsen F, Moiseyev V, Gromov A, Raczky P, Anders A, Pietrusewsky M, Rollefson G, Jovanovic M, Trinhhoang H, Bar-Oz G, Oxenham M, Matsumura H, Hofreiter M - PLoS ONE (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus

(A) Deamination patterns for each of the cases for bone parts A, B and C, before subsampling, (B) Deamination patterns for each of the cases for bone parts A, B and C, after subsampling.
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pone.0129102.g003: (A) Deamination patterns for each of the cases for bone parts A, B and C, before subsampling, (B) Deamination patterns for each of the cases for bone parts A, B and C, after subsampling.

Mentions: Of the five samples from hot regions with low numbers of reads mapping to the human genome, the one from Man Bac, Vietnam has a much higher percentage of endogenous yields in part C (0.7% vs. 0.03% for part A and 0.04% for part B). A similar pattern is evident in the case of Ain Ghazal with 0.97% endogenous yield for part C vs. 0.13% for part A and 0.11% for part B (Fig 2b). However, human DNA read numbers are too low to compare deamination patterns for the reads obtained from different parts of the samples from hot environments, except for part C from samples Man Bac, Ain Ghazal and Vat Komnou. For the latter two of these samples, the deamination patterns for reads from part C show > 30% deaminated cytosines at both ends of the DNA fragments, strongly suggestive that the majority of these sequence is ancient, and therefore authentic [19]. In contrast, the deamination pattern for the results obtained from part C of the sample Man Bac, 3800–3500 cal. BP, does not match what is generally expected for endogenous ancient DNA sequences, although it shows a slight elevation of deamination at either end of the reads (Fig 3a). Moreover, the human reads for part C from this sample are also substantially longer than the human reads from the other two parts, but also longer than the non-aligned (most likely microbial) reads obtained from this sample. Thus, the human sequencing reads in this case could well be the result of contamination, despite extremely low estimated modern contamination for part C (0.09%) (S2 File). The only other significant differences in read lengths between parts from individual samples were found for sample Vat Komnou (AB40 Cambodia). Here, reads from part A are substantially longer than reads from parts B and C. However, there are so few human reads from part A (33) that it is not possible to calculate deamination patterns for this part, as also shown by subsampling the reads from the other two parts down to 33 reads (Fig 3b). In contrast, using all mapping reads especially part C shows high deamination, with between 20 and 30% on both ends of the sequenced fragments.


Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone.

Pinhasi R, Fernandes D, Sirak K, Novak M, Connell S, Alpaslan-Roodenberg S, Gerritsen F, Moiseyev V, Gromov A, Raczky P, Anders A, Pietrusewsky M, Rollefson G, Jovanovic M, Trinhhoang H, Bar-Oz G, Oxenham M, Matsumura H, Hofreiter M - PLoS ONE (2015)

(A) Deamination patterns for each of the cases for bone parts A, B and C, before subsampling, (B) Deamination patterns for each of the cases for bone parts A, B and C, after subsampling.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4472748&req=5

pone.0129102.g003: (A) Deamination patterns for each of the cases for bone parts A, B and C, before subsampling, (B) Deamination patterns for each of the cases for bone parts A, B and C, after subsampling.
Mentions: Of the five samples from hot regions with low numbers of reads mapping to the human genome, the one from Man Bac, Vietnam has a much higher percentage of endogenous yields in part C (0.7% vs. 0.03% for part A and 0.04% for part B). A similar pattern is evident in the case of Ain Ghazal with 0.97% endogenous yield for part C vs. 0.13% for part A and 0.11% for part B (Fig 2b). However, human DNA read numbers are too low to compare deamination patterns for the reads obtained from different parts of the samples from hot environments, except for part C from samples Man Bac, Ain Ghazal and Vat Komnou. For the latter two of these samples, the deamination patterns for reads from part C show > 30% deaminated cytosines at both ends of the DNA fragments, strongly suggestive that the majority of these sequence is ancient, and therefore authentic [19]. In contrast, the deamination pattern for the results obtained from part C of the sample Man Bac, 3800–3500 cal. BP, does not match what is generally expected for endogenous ancient DNA sequences, although it shows a slight elevation of deamination at either end of the reads (Fig 3a). Moreover, the human reads for part C from this sample are also substantially longer than the human reads from the other two parts, but also longer than the non-aligned (most likely microbial) reads obtained from this sample. Thus, the human sequencing reads in this case could well be the result of contamination, despite extremely low estimated modern contamination for part C (0.09%) (S2 File). The only other significant differences in read lengths between parts from individual samples were found for sample Vat Komnou (AB40 Cambodia). Here, reads from part A are substantially longer than reads from parts B and C. However, there are so few human reads from part A (33) that it is not possible to calculate deamination patterns for this part, as also shown by subsampling the reads from the other two parts down to 33 reads (Fig 3b). In contrast, using all mapping reads especially part C shows high deamination, with between 20 and 30% on both ends of the sequenced fragments.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus