Human auditory ossicles as an alternative optimal source of ancient DNA

Sirak, Kendra; Fernandes, Daniel; Cheronet, Olivia; Harney, Éadaoin; Mah, Matthew; Mallick, Swapan; Rohland, Nadin; Adamski, Nicole; Broomandkhoshbacht, Nasreen; Callan, Kimberly; Candilio, Francesca; Lawson, Ann Marie; Mandl, Kirsten; Oppenheimer, Jonas; Stewardson, Kristin; Zalzala, Fatma; Anders, Alexandra; Bartík, Juraj; Coppa, Alfredo; Tumen, Dashtseveg; Évinger, Sándor; Farkaš, Zdeněk; Hajdu, Tamás; Bayarsaikhan, Jamsranjav; McIntyre, Lauren; Moiseyev, Vyacheslav; Okumura, Mercedes; Pap, Ildikó; Pietrusewsky, Michael; Raczky, Pál; Šefčáková, Alena; Soficaru, Andrei; Szeniczey, Tamás; B, Szöke; Gerven, Dennis Van; Vasilyev, Sergey; Bell, Lynne; Reich, David; Pinhasi, Ron

doi:10.1101/gr.260141.119

Cited by 46 publications

(23 citation statements)

References 71 publications

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“…We generated powder from the skeletal remains of all individuals excavated from sites throughout the Caribbean (see Supplementary Information section 2 for archaeological site information and Figures S1 - S11 for maps showing the location of the islands and/or sites studied). Powder was produced from a cochlea 38 , 39 , tooth, phalanx, or ossicle 40 from each individual in a clean room facility at Harvard Medical School (Boston, USA), University College Dublin (Dublin, Ireland), or the University of Vienna (Vienna, Austria); see Supplementary Data 2 for the skeletal element used for each individual and location of powder preparation.…”

Section: Methodsmentioning

confidence: 99%

A genetic history of the pre-contact Caribbean

Fernandes

Sirak

Ringbauer

et al. 2020

Nature

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Humans settled the Caribbean ~6,000 years ago, with ceramic use and intensified agriculture marking a shift from the Archaic to the Ceramic Age ~2,500 years ago 1 – 3 . We report genome-wide data from 174 individuals from The Bahamas, Hispaniola, Puerto Rico, Curaçao, and Venezuela co-analyzed with published data. Archaic Age Caribbean people derive from a deeply divergent population closest to Central and northern South Americans; contrary to previous work 4 , we find no support for ancestry contributed by a population related to North Americans. Archaic lineages were >98% replaced by a genetically homogeneous ceramic-using population related to Arawak-speakers from northeast South America who moved through the Lesser Antilles and into the Greater Antilles at least 1,700 years ago, introducing ancestry that is still present. Ancient Caribbean people avoided close kin unions despite limited mate pools reflecting small effective population sizes which we estimate to be a minimum of Ne=500–1500 and a maximum of Ne=1530–8150 on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the analyzed individuals lived. Census sizes are unlikely to be more than ten-fold larger than effective population sizes, so previous estimates of hundreds of thousands of people are too large 5 – 6 . Confirming a small, interconnected Ceramic Age population 7 , we detect 19 pairs of cross-island cousins, close relatives ~75 kilometers apart in Hispaniola, and low genetic differentiation across islands. Genetic continuity across transitions in pottery styles reveals that cultural changes during the Ceramic Age were not driven by migration of genetically-differentiated groups from the mainland but instead reflected interactions within an interconnected Caribbean world 1 , 8 .

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Section: Methodsmentioning

confidence: 99%

A genetic history of the pre-contact Caribbean

Fernandes

Sirak

Ringbauer

et al. 2020

Nature

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“…It has often been assumed that this better preservation is somehow related to the unusually high density of the petrous bone [ 8 ]. Other hypotheses for better DNA preservation are the presence of a large number of mineralized osteocytes may facilitate the preservation of DNA in fossil bones [ 15 ], that the petrous bone is essentially not remodeled [ 16 ], or bones that are most likely to preserve DNA are those with the highest amounts of endogenous DNA in vivo, namely bones with the highest concentrations of osteocytes [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

“…Bulk staining shows that lacunae and canaliculi seal off the apoptotic DNA contents which may be another explanation for better preservation of DNA [ 28 ]. Here we address the hypothesis that one possible reason that DNA is relatively well preserved in fossil petrous bone is because the fresh petrous bone contains significantly more DNA than other bones [ 15 ]. Andranowski measured DNA yields from different bone tissues (excluding the petrous bone) and assumed a correlation between the number of osteocyte lacuna numbers and DNA yields.…”

Section: Introductionmentioning

confidence: 99%

The petrous bone contains high concentrations of osteocytes: One possible reason why ancient DNA is better preserved in this bone

Ibrahim

Brumfeld²,

Addadi³

et al. 2022

PLoS ONE

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The characterization of ancient DNA in fossil bones is providing invaluable information on the genetics of past human and other animal populations. These studies have been aided enormously by the discovery that ancient DNA is relatively well preserved in the petrous bone compared to most other bones. The reasons for this better preservation are however not well understood. Here we examine the hypothesis that one reason for better DNA preservation in the petrous bone is that fresh petrous bone contains more DNA than other bones. We therefore determined the concentrations of osteocyte cells occluded inside lacunae within the petrous bone and compared these concentrations to other bones from the domestic pig using high resolution microCT. We show that the concentrations of osteocyte lacunae in the inner layer of the pig petrous bone adjacent to the otic chamber are about three times higher (around 95,000 lacunae per mm3) than in the mastoid of the temporal bone (around 28,000 lacunae per mm3), as well as the cortical bone of the femur (around 27,000 lacunae per mm3). The sizes and shapes of the lacuna in the inner layer of the petrous bone are similar to those in the femur. We also show that the pig petrous bone lacunae do contain osteocytes using a histological stain for DNA. We therefore confirm and significantly expand upon previous observations of osteocytic lacuna concentrations in the petrous bone, supporting the notion that one possible reason for better preservation of ancient DNA in the petrous bone is that this bone initially contains at least three times more DNA than other bones. Thus during diagenesis more DNA is likely to be preserved in the petrous bone compared to other bones.

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“…Among the methodological innovations that have made possible to overcome these difficulties there is the identification of the best skeletal elements, of which in primis petrous bones ( Edson et al, 2009 ; Gamba et al, 2014 ; Pinhasi et al, 2015 ). Even though, this skeletal element can lead to endogenous DNA yields that are up to 50–100-fold higher than those obtained from other bones, recent studies demonstrated that other samples ( in situ molars, thoracic vertebrae, talus, and distal phalanx) can yield adequate DNA for most applications in human palaeogenetics ( Higgins et al, 2013 ; Hansen et al, 2017 ; Parker et al, 2020 ), especially ear ossicles ( Sirak et al, 2020 ). Important methodological improvements also regarded the development of increasingly efficient extraction protocols and genotyping kits.…”

Section: Discussionmentioning

confidence: 99%

Twenty-Seven Y-Chromosome Short Tandem Repeats Analysis of Italian Mummies of the 16th and 18th Centuries: An Interdisciplinary Research

et al. 2021

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Roccapelago (MO) is a small village located in the Northern Central Apennines, with a population of 31 inhabitants (2014). In 2010, more than 400 individuals dated between the end of the 16th and the 18th century, many of which partially mummified, were discovered in the crypt of the church. This small village, because of its geographical location and surrounding environment, seems to possess the characteristics of a genetic isolate, useful for population genetics and genealogical analyses. Thus, a diachronic study of DNA aimed at investigating the structure and dynamics of the population of Roccapelago over the about 4 centuries, was conducted by analyzing ancient and modern inhabitants of the village. The 14 modern samples were selected by considering both the founder surnames of the village, identified thanks to the study of parish registers, and the grandparent’s criterion. From 25 ancient mummies, morphologically assigned to male individuals, the petrous bone, that harbors high DNA amounts, was selected for the DNA extraction. The quantification and qualitative assessment of total human male DNA were evaluated by a real-time PCR assay using the Quantifiler Trio DNA Quantification Kit and multiplex PCR of 27 Y-chromosome short tandem repeat (Y-STR) markers included in the Yfiler Plus PCR Amplification Kit, with seven rapidly mutating Y-STR loci for improving discrimination of male lineages, was performed to genotype the samples. Y-STRs were analyzed according to the criteria of ancient DNA (aDNA) analysis to ensure that authentic DNA typing results were obtained from these ancient samples. The molecular analysis showed the usefulness of the Y chromosome to identify historically relevant remains and discover patterns of relatedness in communities moving from anthropology to genetic genealogy and forensics.

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Human auditory ossicles as an alternative optimal source of ancient DNA

Cited by 46 publications

References 71 publications

A genetic history of the pre-contact Caribbean

A genetic history of the pre-contact Caribbean

The petrous bone contains high concentrations of osteocytes: One possible reason why ancient DNA is better preserved in this bone

Twenty-Seven Y-Chromosome Short Tandem Repeats Analysis of Italian Mummies of the 16th and 18th Centuries: An Interdisciplinary Research

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