TY  - JOUR
A1  - Pinhasi, Ron
A1  - Fernandes, Daniel
A1  - Sirak, Kendra
A1  - Novak, Mario
A1  - Connell, Sarah
A1  - Alpaslan-Roodenberg, Songul
A1  - Gerritsen, Fokke
A1  - Moiseyev, Vyacheslav
A1  - Gromov, Andrey
A1  - Raczky, Pal
A1  - Anders, Alexandra
A1  - Pietrusewsky, Michael
A1  - Rollefson, Gary
A1  - Jovanovic, Marija
A1  - Trinhhoang, Hiep
A1  - Bar-Oz, Guy
A1  - Oxenham, Marc
A1  - Matsumura, Hirofumi
A1  - Hofreiter, Michael
T1  - Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone
JF  - PLoS one
N2  - 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 (similar to 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 10,0001,800 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.
Y1  - 2015
U6  - https://doi.org/10.1371/journal.pone.0129102
SN  - 1932-6203
VL  - 10
IS  - 6
PB  - PLoS
CY  - San Fransisco
ER  - 
TY  - GEN
A1  - Pinhasi, Ron
A1  - Fernandes, Daniel
A1  - Sirak, Kendra
A1  - Novak, Mario
A1  - Connell, Sarah
A1  - Alpaslan-Roodenberg, Songül
A1  - Gerritsen, Fokke
A1  - Moiseyev, Vyacheslav
A1  - Gromov, Andrey
A1  - Raczky, Pál
A1  - Anders, Alexandra
A1  - Pietrusewsky, Michael
A1  - Rollefson, Gary
A1  - Jovanovic, Marija
A1  - Trinhhoang, Hiep
A1  - Bar-Oz, Guy
A1  - Oxenham, Marc
A1  - Matsumura, Hirofumi
A1  - Hofreiter, Michael
T1  - Optimal ancient DNA yields from the inner ear part of the human petrous bone
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschafliche Reihe
N2  - 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 (similar to 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 10,0001,800 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 515 
KW  - genome sequence
KW  - extraction
KW  - patterns
KW  - survival
KW  - damage
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-409557
SN  - 1866-8372
IS  - 515
ER  -