Sampling Skeletal Remains for Ancient DNA (aDNA): A Measure of Success

2006 ◽  
Vol 40 (3) ◽  
pp. 31-49 ◽  
Author(s):  
Mark D. Leney
Keyword(s):  
Ancient Dna ◽  
Skeletal Remains

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.

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 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 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 Pre-Clovis occupation of the Americas identified by human fecal biomarkers in coprolites from Paisley Caves, Oregon

2020 ◽  
Vol 6 (29) ◽  
pp. eaba6404 ◽  
Author(s):  
Lisa-Marie Shillito ◽  
Helen L. Whelton ◽  
John C. Blong ◽  
Dennis L. Jenkins ◽  
Thomas J. Connolly ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Skeletal Remains ◽  
Lipid Biomarkers ◽  
Radiocarbon Date ◽  
Human Occupation ◽  
Human Skeletal Remains ◽  
People First ◽  
Alternative Sources ◽  
Lithic Artifacts ◽  
Fecal Biomarkers

When and how people first settled in the Americas is an ongoing area of research and debate. The earliest sites typically only contain lithic artifacts that cannot be directly dated. The lack of human skeletal remains in these early contexts means that alternative sources of evidence are needed. Coprolites, and the DNA contained within them, are one such source, but unresolved issues concerning ancient DNA taphonomy and potential for contamination make this approach problematic. Here, we use fecal lipid biomarkers to demonstrate unequivocally that three coprolites dated to pre-Clovis are human, raise questions over the reliance on DNA methods, and present a new radiocarbon date on basketry further supporting pre-Clovis human occupation.

scholarly journals Ancient DNA: a review of its past, present and future potential in archaeology

1993 ◽  
Vol 11 (1) ◽  
Author(s):  
Linda M. Gibbs
Keyword(s):  
Nucleic Acids ◽  
Ancient Dna ◽  
Deoxyribonucleic Acid ◽  
Skeletal Remains ◽  
Extensive Review ◽  
Human Skeletal Remains ◽  
Archaeological Material ◽  
Future Potential ◽  
Biomolecular Analysis

This paper provides an extensive review of past and current research involving the biomolecular analysis of nucleic acids. In particular, it focuses on deoxyribonucleic acid (DNA) or ancient DNA that can be recovered from historic and prehistoric human skeletal remains and other archaeological material remains. It also critically assesses the problems that any investigation of ancient DNA poses and points to specific areas for future investigation.

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 Genetic contributions to variation in human stature in prehistoric Europe

2019 ◽  
Author(s):  
Samantha L. Cox ◽  
Christopher B. Ruff ◽  
Robert M. Maier ◽  
Iain Mathieson
Keyword(s):  
Bronze Age ◽  
Geographic Variation ◽  
Ancient Dna ◽  
Bending Strength ◽  
Skeletal Remains ◽  
Upper Paleolithic ◽  
Mineral Density ◽  
The Past ◽  
Relative Contribution ◽  
Over Time

AbstractThe relative contributions of genetics and environment to temporal and geographic variation in human height remain largely unknown. Ancient DNA has identified changes in genetic ancestry over time, but it is not clear whether those changes in ancestry are associated with changes in height. Here, we directly test whether changes over the past 38,000 years in European height predicted using DNA from 1071 ancient individuals are consistent with changes observed in 1159 skeletal remains from comparable populations. We show that the observed decrease in height between the Early Upper Paleolithic and the Mesolithic is qualitatively predicted by genetics. Similarly, both skeletal and genetic height remained constant between the Mesolithic and Neolithic and increased between the Neolithic and Bronze Age. Sitting height changes much less than standing height–consistent with genetic predictions–although genetics predicts a small Bronze Age increase that is not observed in skeletal remains. Geographic variation in stature is also qualitatively consistent with genetic predictions, particularly with respect to latitude. Finally, we hypothesize that an observed decrease in genetic heel bone mineral density in the Neolithic reflects adaptation to the decreased mobility indicated by decreased femoral bending strength. This study provides a model for interpreting phenotypic changes predicted from ancient DNA and demonstrates how they can be combined with phenotypic measurements to understand the relative contribution of genetic and developmentally plastic responses to environmental change.SignificanceMeasurements of prehistoric human skeletal remains provide a record of changes in height and other anthropometric traits, over time. Often, these changes are interpreted in terms of plastic developmental response to shifts in diet, climate or other environmental factors. These changes can also be genetic in origin but, until recently, it has been impossible to separate the effects of genetics and environment. Here we use ancient DNA to directly estimate genetic changes in phenotypes and to identify changes driven not by genetics, but by environment. We show that changes over the past 35,000 years are largely predicted by genetics, but also identify specific shifts that are more likely to be environmentally driven.

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