Improved DNA extraction from ancient bones using silica-based spin columns

Yang, Dongya; Eng, Barry; Waye, John S.; Dudar, J. Christopher; Saunders, Shelley R.

doi:10.1002/(sici)1096-8644(199804)105:4<539::aid-ajpa10>3.0.co;2-1

Cited by 530 publications

(157 citation statements)

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“…R. Soc. B 283: 20160130 extracted using silica spin columns based on Yang et al [22], with the inclusion of 1 M urea in the extraction buffer. mtDNA was amplified using overlapping fragments spanning 643 base pairs of the control region.…”

Section: (B) Dna Extraction and Sequencingmentioning

confidence: 99%

The colonization history of British water vole (Arvicola amphibius(Linnaeus, 1758)): origins and development of the Celtic fringe

et al. 2016

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The terminal Pleistocene and Early Holocene, a period from 15 000 to 18 000 Before Present (BP), was critical in establishing the current Holarctic fauna, with temperate-climate species largely replacing cold-adapted ones at midlatitudes. However, the timing and nature of this process remain unclear for many taxa, a point that impacts on current and future management strategies. Here, we use an ancient DNA dataset to test more directly postglacial histories of the water vole (Arvicola amphibius, formerly A. terrestris), a species that is both a conservation priority and a pest in different parts of its range. We specifically examine colonization of Britain, where a complex genetic structure can be observed today. Although we focus on population history at the limits of the species' range, the inclusion of additional European samples allows insights into European postglacial colonization events and provides a molecular perspective on water vole taxonomy.

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Section: (B) Dna Extraction and Sequencingmentioning

confidence: 99%

The colonization history of British water vole (Arvicola amphibius(Linnaeus, 1758)): origins and development of the Celtic fringe

et al. 2016

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“…Samples were ground to fine-grained powder and DNA was extracted according a modified protocol from Yang et al, 1998. Fifty to 100 mg of powder was incubated overnight in a water bath at 56°C in a digestion solution of 0.5 M EDTA pH 8 (Invitrogen, Carlsbad, CA, USA), 0.5% SDS and 0.1 mg ml − 1 Proteinase K. DNA was extracted through silica-based spin columns (Minielute PCR Purification Kit, Qiagen, Inc., CA, USA) with a final elution volume of 50-100 μl.…”

Section: Dna Extraction and Amplificationmentioning

confidence: 99%

Like a pig out of water: seaborne spread of domestic pigs in Southern Italy and Sardinia during the Bronze and Iron Ages

et al. 2016

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Southern Italy has a long history of human occupation and passage of different cultures since the Early Holocene. Repeated, ancient introductions of pigs in several geographic areas in Europe make it difficult to understand pig translocation and domestication in Italy. The archeozoological record may provide fundamental information on this, hence shedding light on peopling and on trading among different ancient cultures in the Mediterranean. Yet, because of the scanty nature of the fossil record, ancient remains from human-associated animals are somewhat rare. Fortunately, ancient DNA analysis as applied to domestic species proved to be a powerful tool in revealing human migrations. Herein, we analyzed 80-bp fragment of mitochondrial DNA control region from 27 Sus scrofa ancient samples retrieved from Southern Italian and Sardinian archeological sites, spanning in age from the Mesolithic to the Roman period. Our results surprisingly indicate the presence of the Near Eastern haplotype Y1 on both Italy's major islands (Sardinia and Sicily) during the Bronze Age, suggesting the seaborne transportation of domestic pigs by humans at least during 1600-1300 BC. The presence of the Italian E2 clade in domestic contexts shows that the indigenous wild boar was effectively domesticated or incorporated into domestic stocks in Southern Italy during the Bronze Age, although the E2 haplotype has never been found in modern domestic breeds. Pigs belonging to the endemic E2 clade were thus traded between the Peninsula and Sardinia by the end of the second millennium BC and this genetic signature is still detected in Sardinian feral pigs.

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“…The samples were then homogenized in a swing mill (RETSCH). DNA was extracted according to two different protocols (see Yang et al [39]), and by use of the InViSorb Forensic Kit I (InViTek). Although cattle tibiae are rather large bones, the variety of methods applied here consumed a significant amount of material.…”

Section: Dna Analysismentioning

confidence: 99%