scholarly journals Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments

2018 ◽  
Vol 166 (4) ◽  
pp. 824-836 ◽  
Author(s):  
Maria A. Nieves-Colón ◽  
Andrew T. Ozga ◽  
William J. Pestle ◽  
Andrea Cucina ◽  
Vera Tiesler ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Ancient Dna ◽  
Skeletal Remains ◽  
Tropical Environments

scholarly journals Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments

2017 ◽  
Author(s):  
Maria A. Nieves-Colón ◽  
Andrew T. Ozga ◽  
William J. Pestle ◽  
Andrea Cucina ◽  
Vera Tiesler ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Ancient Dna ◽  
Extraction Methods ◽  
Optimal Choice ◽  
Skeletal Remains ◽  
Tissue Type ◽  
Dna Fragments ◽  
Illumina Hiseq ◽  
Tropical Environments ◽  
Significant Difference

ABSTRACTObjectivesThe tropics harbor a large part of the world’s biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semitropical sites in Tanzania, Mexico, and Puerto Rico (N=12).Materials and MethodsAll samples were extracted twice, built into double-stranded sequencing libraries, and shotgun sequenced on the Illumina HiSeq 2500. The first extraction protocol, Method D, was previously designed for recovery of ultrashort DNA fragments from skeletal remains. The second, Method H, modifies the first by adding an initial EDTA wash and an extended digestion and decalcification step.ResultsNo significant difference was found in overall ancient DNA yields or post-mortem damage patterns recovered from samples extracted with either method, irrespective of tissue type. However, Method H samples had higher endogenous content and more mapped reads after quality-filtering, but also higher clonality. In contrast, samples extracted with Method D had shorter average DNA fragments.DiscussionBoth methods successfully recovered endogenous ancient DNA. But, since surviving DNA in ancient or historic remains from tropical contexts is extremely fragmented, our results suggest that Method D is the optimal choice for working with samples from warm and humid environments. Additional optimization of extraction conditions and further testing of Method H with different types of samples may allow for improvement of this protocol in the future.

scholarly journals Ancient DNA Methods Improve Forensic DNA Profiling of Korean War and World War II Unknowns

Genes ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 129
Author(s):  
Elena I. Zavala ◽  
Jacqueline Tyler Thomas ◽  
Kimberly Sturk-Andreaggi ◽  
Jennifer Daniels-Higginbotham ◽  
Kerriann K. Meyers ◽  
...  
Keyword(s):  
World War Ii ◽  
Dna Extraction ◽  
Ancient Dna ◽  
Korean War ◽  
Skeletal Remains ◽  
Dna Profiling ◽  
Library Preparation ◽  
Forensic Dna ◽  
World War ◽  
Preparation Methods

The integration of massively parallel sequencing (MPS) technology into forensic casework has been of particular benefit to the identification of unknown military service members. However, highly degraded or chemically treated skeletal remains often fail to provide usable DNA profiles, even with sensitive mitochondrial (mt) DNA capture and MPS methods. In parallel, the ancient DNA field has developed workflows specifically for degraded DNA, resulting in the successful recovery of nuclear DNA and mtDNA from skeletal remains as well as sediment over 100,000 years old. In this study we use a set of disinterred skeletal remains from the Korean War and World War II to test if ancient DNA extraction and library preparation methods improve forensic DNA profiling. We identified an ancient DNA extraction protocol that resulted in the recovery of significantly more human mtDNA fragments than protocols previously used in casework. In addition, utilizing single-stranded rather than double-stranded library preparation resulted in increased attainment of reportable mtDNA profiles. This study emphasizes that the combination of ancient DNA extraction and library preparation methods evaluated here increases the success rate of DNA profiling, and likelihood of identifying historical remains.

scholarly journals The influence of sample quantity and lysis parameters on the success of ancient DNA extraction from skeletal remains

BioTechniques ◽  
2021 ◽  
Author(s):  
Alina Euskirchen ◽  
Larissa Hartmann ◽  
Janine Mazanec ◽  
Patrick Wittmeier ◽  
Susanne Hummel
Keyword(s):  
Mitochondrial Dna ◽  
Sample Preparation ◽  
Dna Extraction ◽  
Ancient Dna ◽  
Skeletal Remains ◽  
Sample Material ◽  
Chromosomal Dna ◽  
High Quality ◽  
Dna Analyses ◽  
Lysis Time

DNA extraction is of utmost importance in archaeobiology, as it determines the success of further DNA analyses. This study concentrates on the success of ancient DNA extraction using silica spin columns and PCR-based analysis from archaeological skeletal material and investigates the influence of sample quantity, lysis time and lysis temperature during sample preparation. The results show that lysis times ranging from 2 to 48 h are suitable, and that lysis should be carried out at a constant temperature of 56°C. Concerning sample quantity, 10 mg for mitochondrial DNA and 50 mg for chromosomal DNA are sufficient for high quality analyses. Thus invaluable sample material can be saved, and time of sample preparation can be reduced considerably.

scholarly journals Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 146
Author(s):  
Catarina Xavier ◽  
Mayra Eduardoff ◽  
Barbara Bertoglio ◽  
Christina Amory ◽  
Cordula Berger ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Ancient Dna ◽  
Extraction Method ◽  
Fragment Size ◽  
Molecular Genetic ◽  
Extraction Methods ◽  
Degraded Dna ◽  
Size Analysis ◽  
Dna Fragments ◽  
Dna Amount

The efficient extraction of DNA from challenging samples, such as bones, is critical for the success of downstream genotyping analysis in molecular genetic disciplines. Even though the ancient DNA community has developed several protocols targeting small DNA fragments that are typically present in decomposed or old specimens, only recently forensic geneticists have started to adopt those protocols. Here, we compare an ancient DNA extraction protocol (Dabney) with a bone extraction method (Loreille) typically used in forensics. Real-time quantitative PCR and forensically representative typing methods including fragment size analysis and sequencing were used to assess protocol performance. We used four bone samples of different age in replicates to study the effects of both extraction methods. Our results confirm Loreille’s overall increased gain of DNA when enough tissue is available and Dabney’s improved efficiency for retrieving shorter DNA fragments that is beneficial when highly degraded DNA is present. The results suggest that the choice of extraction method needs to be based on available sample, degradation state, and targeted genotyping method. We modified the Dabney protocol by pooling parallel lysates prior to purification to study gain and performance in single tube typing assays and found that up to six parallel lysates lead to an almost linear gain of extracted DNA. These data are promising for further forensic investigations as the adapted Dabney protocol combines increased sensitivity for degraded DNA with necessary total DNA amount for forensic applications.

Balaenoptera borealis Lesson, 1828: rediscovery of a holotype

Mammalia ◽  
2019 ◽  
Vol 83 (4) ◽  
pp. 343-351 ◽  
Author(s):  
Christian Haberland ◽  
Oliver Hampe ◽  
Marijke Autenrieth ◽  
Manja Voß
Keyword(s):  
World War Ii ◽  
Ancient Dna ◽  
Vertebral Column ◽  
Type Specimen ◽  
Skeletal Remains ◽  
Historical Research ◽  
Type Material ◽  
World War ◽  
Mitochondrial Haplotypes ◽  
The World

Abstract The whereabouts of the Balaenoptera borealis holotype, the skeleton of a 1819 stranded specimen, have been unknown since the World War II (WWII). Due to nomenclatural confusion, deficient documentation, and finally WWII bombing, which destroyed predominantly cetacean material in the Museum für Naturkunde Berlin (MfN), the type skeleton of the sei whale sank into oblivion. Construction activities enabled a recent search and study on the remaining whale material. Here, we provide evidence that the type specimen was not destroyed. On the basis of species-wide and individual characters of the type material such as the shape of cranial elements and the pattern of the maxillary foramina, we show that the skull and mandibles, the vertebral column (except the atlas), and the ribs of the holotype remain intact. Further evidence that these skeletal remains belong to the previously missing holotype is provided by the characteristics of the spine. In addition, we analyzed ancient DNA from bone samples and confirm they are B. borealis, and the occurrence of same mitochondrial haplotypes indicate that the bones belong to the same individual. Additionally, a blue inscription was discovered at the caudal epiphysis of a thoracic vertebra; historical research matched this inscription with the material belonging to the former Anatomical-Zootomical Museum, from which the holotype was once bought.

Evaluation Of A Powder-Free DNA Extraction Method For Skeletal Remains

2018 ◽  
Vol 63 (6) ◽  
pp. 1819-1823 ◽  
Author(s):  
Michelle Harrel ◽  
Carrie Mayes ◽  
David Gangitano ◽  
Sheree Hughes-Stamm
Keyword(s):  
Dna Extraction ◽  
Extraction Method ◽  
Skeletal Remains ◽  
Free Dna ◽  
Dna Extraction Method

scholarly journals Evolutionary history and palaeoecology of brown bear in North-East Siberia re-examined using ancient DNA and stable isotopes from skeletal remains

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Alba Rey-Iglesia ◽  
Ana García-Vázquez ◽  
Eve C. Treadaway ◽  
Johannes van der Plicht ◽  
Gennady F. Baryshnikov ◽  
...  
Keyword(s):  
Stable Isotopes ◽  
Ancient Dna ◽  
Evolutionary History ◽  
Brown Bear ◽  
Skeletal Remains ◽  
East Siberia ◽  
North East

scholarly journals Genome‐wide SNP typing of ancient DNA: Determination of hair and eye color of Bronze Age humans from their skeletal remains

2020 ◽  
Vol 172 (1) ◽  
pp. 99-109 ◽  
Author(s):  
Nicole Schmidt ◽  
Katharina Schücker ◽  
Ina Krause ◽  
Thilo Dörk ◽  
Michael Klintschar ◽  
...  
Keyword(s):  
Bronze Age ◽  
Ancient Dna ◽  
Skeletal Remains ◽  
Eye Color ◽  
Snp Typing ◽  
Genome Wide

An investigation into the effects of X-ray on the recovery of ancient DNA from skeletal remains

2016 ◽  
Vol 76 ◽  
pp. 1-8 ◽  
Author(s):  
Lars Fehren-Schmitz ◽  
Joshua Kapp ◽  
Kim Laura Ziegler ◽  
Kelly M. Harkins ◽  
Gary P. Aronsen ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Skeletal Remains ◽  
X Ray

scholarly journals Tooth Sampling from the inner pulp chamber for ancient DNA Extraction v1 (protocols.io.bakqicvw)

protocols.io ◽  
2019 ◽  
Author(s):  
Gunnar U ◽  
Aida Andrades ◽  
James A ◽  
Raphaela Stahl ◽  
Guido Brandt
Keyword(s):  
Dna Extraction ◽  
Ancient Dna ◽  
Pulp Chamber
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