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 - TY - JOUR A1 - González-Fortes, Gloria M. A1 - Kolbe, Ben A1 - Fernandes, Daniel A1 - Meleg, Ioana N. A1 - Garcia-Vazquez, Ana A1 - Pinto-Llona, Ana C. A1 - Constantin, Silviu A1 - de Torres, Trino J. A1 - Ortiz, Jose E. A1 - Frischauf, Christine A1 - Rabeder, Gernot A1 - Hofreiter, Michael A1 - Barlow, Axel T1 - Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears JF - Molecular ecology N2 - Ancient DNA studies have revolutionized the study of extinct species and populations, providing insights on phylogeny, phylogeography, admixture and demographic history. However, inferences on behaviour and sociality have been far less frequent. Here, we investigate the complete mitochondrial genomes of extinct Late Pleistocene cave bears and middle Holocene brown bears that each inhabited multiple geographically proximate caves in northern Spain. In cave bears, we find that, although most caves were occupied simultaneously, each cave almost exclusively contains a unique lineage of closely related haplotypes. This remarkable pattern suggests extreme fidelity to their birth site in cave bears, best described as homing behaviour, and that cave bears formed stable maternal social groups at least for hibernation. In contrast, brown bears do not show any strong association of mitochondrial lineage and cave, suggesting that these two closely related species differed in aspects of their behaviour and sociality. This difference is likely to have contributed to cave bear extinction, which occurred at a time in which competition for caves between bears and humans was likely intense and the ability to rapidly colonize new hibernation sites would have been crucial for the survival of a species so dependent on caves for hibernation as cave bears. Our study demonstrates the potential of ancient DNA to uncover patterns of behaviour and sociality in ancient species and populations, even those that went extinct many tens of thousands of years ago. KW - ancient DNA KW - extinction KW - homing KW - sociality KW - Ursus arctos KW - Ursus spelaeus Y1 - 2016 U6 - https://doi.org/10.1111/mec.13800 SN - 0962-1083 SN - 1365-294X VL - 25 SP - 4907 EP - 4918 PB - Wiley-Blackwell CY - Hoboken ER -