Dataset Information

Human auditory ossicles as an alternative optimal source of ancient DNA.

ABSTRACT: DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.

SUBMITTER: Sirak K

PROVIDER: S-EPMC7111520 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Human auditory ossicles as an alternative optimal source of ancient DNA.

Sirak Kendra K Fernandes Daniel D Cheronet Olivia O Harney Eadaoin E Mah Matthew M Mallick Swapan S Rohland Nadin N Adamski Nicole N Broomandkhoshbacht Nasreen N Callan Kimberly K Candilio Francesca F Lawson Ann Marie AM Mandl Kirsten K Oppenheimer Jonas J Stewardson Kristin K Zalzala Fatma F Anders Alexandra A Bartík Juraj J Coppa Alfredo A Dashtseveg Tumen T Évinger Sándor S Farkaš Zdeněk Z Hajdu Tamás T Bayarsaikhan Jamsranjav J McIntyre Lauren L Moiseyev Vyacheslav V Okumura Mercedes M Pap Ildikó I Pietrusewsky Michael M Raczky Pál P Šefčáková Alena A Soficaru Andrei A Szeniczey Tamás T Szőke Béla Miklós BM Van Gerven Dennis D Vasilyev Sergey S Bell Lynne L Reich David D Pinhasi Ron R

Genome research 20200225 3

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in develo ...[more]

PMID: 32098773

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Project description:Measurements of auditory ossicles displacement are commonly carried out by means of laser-Doppler vibrometry (LDV), which is considered to be a gold standard. The limitation of the LDV method, especially for in vivo measurements, is the necessity to expose an object in a straight line to a laser beam operating from a distance. An alternative to this approach is the use of a handheld laser-fiber vibrometry probe (HLFVP) with a curved tip. We evaluate the feasibility of an HLFVP with a curved tip for measuring sound-induced displacement of the auditory ossicles. A handheld vibrometer probe guiding the laser beam with a fiber-optic cable was used for displacement measurements of the incus body and the posterior crus of the stapes. Tonal stimuli at frequencies of 0.5, 1, 2, and 4 kHz were presented by means of an insert earphone positioned in the outer ear canal. The probe was fixed at the measurement site using a tripod or hand-held by one of the two surgeons. The measurements were carried out on six fresh temporal bones. Multivariate analysis of variance showed statistically significant differences for stimulus frequency (F3,143 = 29.37, p < 0.001, and η2 = 0.35), bone (F5,143 = 4.61, p = 0.001, and η2 = 0.01), and measurement site (F1,143 = 4.74, p = 0.03, and η2 = 0.02) in the absence of statistically significant differences for the probe fixation method (F2,143 = 0.15, p = 0.862, and η2 = 0.001). Standard deviations of the means were 6.9, 2.6, 1.9, and 0.6 nm / Pa for frequency, bone, site, and fixation, respectively. Ear transfer functions were found to be consistent with literature data. The feasibility of applying HLFVP to measure the displacement of auditory ossicles has been confirmed. HLFVP offers the possibility of carrying out measurements at various angles; however, this needs to be standardized taking into account anatomical limitations and surgical convenience.

Project description: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.

Dataset Information

Human auditory ossicles as an alternative optimal source of ancient DNA.

Publications

Human auditory ossicles as an alternative optimal source of ancient DNA.

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