scholarly journals Optimized Bone Sampling Protocols for the Retrieval of Ancient DNA from Archaeological Remains

10.3791/63250 ◽  
2021 ◽  
Author(s):  
Cody E. Parker ◽  
Kirsten I. Bos ◽  
Wolfgang Haak ◽  
Johannes Krause
Keyword(s):  
Ancient Dna ◽  
Archaeological Remains ◽  
Sampling Protocols

Anthropological Applications of Ancient DNA: Problems and Prospects

2006 ◽  
Vol 71 (2) ◽  
pp. 365-380 ◽  
Author(s):  
Connie J. Mulligan
Keyword(s):  
Ancient Dna ◽  
Archaeological Remains ◽  
Research Strategies ◽  
Exogenous Dna ◽  
Extensive Training ◽  
Excellent Preservation ◽  
Successful Analysis ◽  
Adna Analysis ◽  
Widespread Interest ◽  
Careful Design

The analysis of DNA extracted from archaeological specimens to address anthropological questions is becoming increasingly common. Despite widespread interest in ancient DNA (aDNA), the difficulties inherent in aDNA analysis are not generally appreciated by researchers outside of the field. The majority of samples subjected to aDNA analysis often fail to produce results, and successful analysis is typically limited to specimens that exhibit excellent preservation. Contamination of samples with exogenous DNA is an ongoing problem and requires careful design of research strategies to limit and identify all DNA contaminants. Overall, aDNA analysis is a highly specialized and technical field that requires extensive training and can be quite expensive. Thus, each aDNA study should be carefully planned with significant input from archaeologists, physical anthropologists, linguists, and related researchers and should focus on well-preserved samples that are likely to produce a clear answer to a question that is not amenable to nongenetic analysis. In this manuscript, I explain the problems and prospects of various anthropological applications of aDNA technology. I present a series of previously published studies, which are of general anthropological interest, to illustrate the strengths and weaknesses of aDNA methods in each case. I also provide a checklist of questions to evaluate the utility of archaeological remains for aDNA analysis and to provide guidelines when designing an aDNA study.

scholarly journals HOPS: Automated detection and authentication of pathogen DNA in archaeological remains

2019 ◽  
Author(s):  
Ron Hübler ◽  
Felix M. Key ◽  
Christina Warinner ◽  
Kirsten I. Bos ◽  
Johannes Krause ◽  
...  
Keyword(s):  
High Throughput ◽  
Ancient Dna ◽  
High Throughput Screening ◽  
Large Scale ◽  
Sequence Data ◽  
Evolutionary Relationship ◽  
Molecular Data ◽  
Clinical Samples ◽  
Archaeological Remains ◽  
Archaeological Material

AbstractHigh-throughput DNA sequencing enables large-scale metagenomic analyses of complex biological systems. Such analyses are not restricted to present day environmental or clinical samples, but can also be fruitfully applied to molecular data from archaeological remains (ancient DNA), and a focus on ancient bacteria can provide valuable information on the long-term evolutionary relationship between hosts and their pathogens. Here we present HOPS (HeuristicOperations forPathogenScreening), an automated bacterial screening pipeline for ancient DNA sequence data that provides straightforward and reproducible information on species identification and authenticity. HOPS provides a versatile and fast pipeline for high-throughput screening of bacterial DNA from archaeological material to identify candidates for subsequent genomic-level analyses.

scholarly journals The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics

2020 ◽  
Vol 54 (1) ◽  
pp. 563-581
Author(s):  
Ludovic Orlando
Keyword(s):  
Ancient Dna ◽  
Evolutionary History ◽  
Economic Value ◽  
Domestic Horse ◽  
Human History ◽  
Archaeological Remains ◽  
Animal Kingdom ◽  
Sequencing Technologies ◽  
Sport Industry ◽  
Horse Domestication

The domestication of the horse some 5,500 years ago followed those of dogs, sheep, goats, cattle, and pigs by ∼2,500–10,000 years. By providing fast transportation and transforming warfare, the horse had an impact on human history with no equivalent in the animal kingdom. Even though the equine sport industry has considerable economic value today, the evolutionary history underlying the emergence of the modern domestic horse remains contentious. In the last decade, novel sequencing technologies have revolutionized our capacity to sequence the complete genome of organisms, including from archaeological remains. Applied to horses, these technologies have provided unprecedented levels of information and have considerably changed models of horse domestication. This review illustrates how ancient DNA, especially ancient genomes, has inspired researchers to rethink the process by which horses were first domesticated and then diversified into a variety of breeds showing a range of traits that are useful to humans.

scholarly journals Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity

2014 ◽  
Vol 281 (1781) ◽  
pp. 20133236 ◽  
Author(s):  
Romy Müller ◽  
Charlotte A. Roberts ◽  
Terence A. Brown
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Ancient Dna ◽  
Dna Typing ◽  
Nucleotide Polymorphisms ◽  
Archaeological Remains ◽  
Single Nucleotide ◽  
Genetic Groups ◽  
Single Location ◽  
History Of ◽  
Multiple Samples

The evolutionary history of the Mycobacterium tuberculosis complex (MTBC) has previously been studied by analysis of sequence diversity in extant strains, but not addressed by direct examination of strain genotypes in archaeological remains. Here, we use ancient DNA sequencing to type 11 single nucleotide polymorphisms and two large sequence polymorphisms in the MTBC strains present in 10 archaeological samples from skeletons from Britain and Europe dating to the second–nineteenth centuries AD. The results enable us to assign the strains to groupings and lineages recognized in the extant MTBC. We show that at least during the eighteenth–nineteenth centuries AD, strains of M. tuberculosis belonging to different genetic groups were present in Britain at the same time, possibly even at a single location, and we present evidence for a mixed infection in at least one individual. Our study shows that ancient DNA typing applied to multiple samples can provide sufficiently detailed information to contribute to both archaeological and evolutionary knowledge of the history of tuberculosis.

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