Survival and recovery of DNA from ancient teeth and bones

Adler, Christina; Haak, Wolfgang; Donlon, Denise; Cooper, Alan

doi:10.1016/j.jas.2010.11.010

Cited by 164 publications

(105 citation statements)

References 64 publications

(99 reference statements)

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“…Each sample was washed with full-strength Clorox bleach, followed by rinsing with DNA-free double-distilled H 2 O and ultraviolet irradiation of each facet for 30 min (Muñoz et al 2012a). Gloves, masks, hats, coats, and filter pipette tips were used in all experiments to avoid sample contamination in the laboratory (Adler et al 2011;Campos et al 2012;Muñoz et al 2012a).…”

Section: Samplesmentioning

confidence: 99%

Genetic Affiliation of Pre-Hispanic and Contemporary Mayas through Maternal Linage

Ochoa-Lugo¹,

Muñoz²,

Pérez-Ramírez³

et al. 2016

Human Biology

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Maya civilization developed in Mesoamerica and encompassed the Yucatan Peninsula, Guatemala, Belize, part of the Mexican states of Tabasco and Chiapas, and the western parts of Honduras and El Salvador. This civilization persisted approximately 3,000 years and was one of the most advanced of its time, possessing the only known full writing system at the time, as well as art, sophisticated architecture, and mathematical and astronomical systems. This civilization reached the apex of its power and influence during the Preclassic period, from 2000 BCE to 250 CE. Genetic variation in the pre-Hispanic Mayas from archaeological sites in the Mexican states of Yucatan, Chiapas, Quintana Roo, and Tabasco and their relationship with the contemporary communities in these regions have not been previously studied. Consequently, the principal aim of this study was to determine mitochondrial DNA (mtDNA) variation in the pre-Hispanic Maya population and to assess the relationship of these individuals with contemporary Mesoamerican Maya and populations from Asia, Beringia, and North, Central, and South America. Our results revealed interactions and gene flow between populations in the different archaeological sites assessed in this study. The mtDNA haplogroup frequency in the pre-Hispanic Maya population (60.53%, 34.21%, and 5.26% for haplogroups A, C, and D, respectively) was similar to that of most Mexican and Guatemalan Maya populations, with haplogroup A exhibiting the highest frequency. Haplogroup B most likely arrived independently and mixed with populations carrying haplogroups A and C based on its absence in the pre-Hispanic Mexican Maya populations and low frequencies in most Mexican and Guatemalan Maya populations, although this also may be due to drift. Maya and Ciboneys sharing haplotype H10 belonged to haplogroup C1 and haplotype H4 of haplogroup D, suggesting shared regional haplotypes. This may indicate a shared genetic ancestry, suggesting more regional interaction between populations in the circum-Caribbean region than previously demonstrated. Haplotype sharing between the pre-Hispanic Maya and the indigenous populations from Asia, the Aleutian Islands, and North, Maternal Lineage in Pre-Hispanic and Contemporary Mayas ■ 137Central, and South America provides evidence for gene flow from the ancestral Amerindian population of the pre-Hispanic Maya to Central and South America.

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Section: Samplesmentioning

confidence: 99%

Genetic Affiliation of Pre-Hispanic and Contemporary Mayas through Maternal Linage

Ochoa-Lugo¹,

Muñoz²,

Pérez-Ramírez³

et al. 2016

Human Biology

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“…In particular, it is possible to mention some different applications like DNA-based drugs, recombinant DNA for the creation of industrial microorganisms, DNA for biosensors development, DNA application in the environmental monitoring, and so on [1][2][3][4][5].…”

Section: Introductionmentioning

confidence: 99%

DNA coatings on cotton fabrics: Effect of molecular size and pH on flame retardancy

Bosco

Casale

Mollea

et al. 2015

Surface and Coatings Technology

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Deoxyribonucleic acid (DNA) has been mostly considered as a carrier of genetic information and gene expression. Recently, we have demonstrated that this biomacromolecule is very effective in providing cellulosic fabrics with flame retardant features, thanks to its intrinsic intumescent-like behaviour. Here, we have investigated the role played by different parameters on the overall flame retardant features: DNA molecular size, pH of the DNA aqueous solutions, and number of impregnations. For this purpose, herring DNA, at three different molecular sizes, low (100-200 base pairs, bp), medium (400-800 bp) and high (2000-10000 bp), has been selected as model biomacromolecule; its effect as fire protective coating on cotton fabrics has been assessed in terms of resistance to a flame application (through horizontal flame spread tests) and to an irradiative heat flux of 35kW/m 2 (by cone calorimetry). Furthermore, thermogravimetric analyses have been exploited for evaluating thermal and thermo-oxidative stability of the treated fabrics. *Manuscript Click here to view linked References 2The results clearly indicate that, despite a similar composition, the coatings containing low molecular size DNA exert a superior fire protection on the fabric substrate, as clearly indicated by horizontal flame spread and cone calorimetry tests. Multiple impregnation treatment turned out to be more performing than the single one, being equal the final add-on achieved. More specifically, the use of multiple impregnations at pH=4 and 8 allowed achieving self-extinction for 86 and 74%of the tested samples; in addition, 45 and 25% reductions of total heat release and heat release rate peak under 35 kW/m 2 have been found with respect to untreated cotton. These findings may be attributed to themorphology of the low molecular size DNA coating, which shows a greater penetration into the microfibrillar surfaces of the component fibres within the fabric and to its higher thermal stability in air.

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“…Fragmentation is thought to be driven mainly by depurination, i.e., the loss of guanines and adenines, which leaves chemically instable abasic sites that lead to hydrolysis of the DNA backbone via β-elimination (Lindahl 1993;Briggs et al 2007). DNA fragmentation causes an excess of short molecules (Pääbo 1989;Glenn et al 1999;Poinar et al 2003), which can be described in many samples as an inverse exponential relationship between fragment length and abundance (Handt et al 1994;Schwarz et al 2009;Adler et al 2011;Allentoft et al 2012;Orlando et al 2013). In extremely poorly preserved material, such as the Sima de los Huesos remains, almost no authentic ancient DNA fragments longer than 45 bp can be detected (Meyer et al 2014), underlining the importance of recovering short DNA fragments from highly degraded material.…”

mentioning

confidence: 99%

Extending the spectrum of DNA sequences retrieved from ancient bones and teeth

Glocke

Meyer

2017

Genome Res.

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The number of DNA fragments surviving in ancient bones and teeth is known to decrease with fragment length. Recent genetic analyses of Middle Pleistocene remains have shown that the recovery of extremely short fragments can prove critical for successful retrieval of sequence information from particularly degraded ancient biological material. Current sample preparation techniques, however, are not optimized to recover DNA sequences from fragments shorter than ∼35 base pairs (bp). Here, we show that much shorter DNA fragments are present in ancient skeletal remains but lost during DNA extraction. We present a refined silica-based DNA extraction method that not only enables efficient recovery of molecules as short as 25 bp but also doubles the yield of sequences from longer fragments due to improved recovery of molecules with singlestrand breaks. Furthermore, we present strategies for monitoring inefficiencies in library preparation that may result from co-extraction of inhibitory substances during DNA extraction. The combination of DNA extraction and library preparation techniques described here substantially increases the yield of DNA sequences from ancient remains and provides access to a yet unexploited source of highly degraded DNA fragments. Our work may thus open the door for genetic analyses on even older material.

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Survival and recovery of DNA from ancient teeth and bones

Cited by 164 publications

References 64 publications

Genetic Affiliation of Pre-Hispanic and Contemporary Mayas through Maternal Linage

Genetic Affiliation of Pre-Hispanic and Contemporary Mayas through Maternal Linage

DNA coatings on cotton fabrics: Effect of molecular size and pH on flame retardancy

Extending the spectrum of DNA sequences retrieved from ancient bones and teeth

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