Under certain conditions, skeletal specimens retain a sufficient number of DNA molecules to permit their recovery and analysis. DNA is the molecule of heredity and almost every human cell has a complete copy of their DNA. After an organism dies, the DNA molecules degrade rapidly, but sometimes, fragments of DNA are present in the biological remains (bone tissue, muscles, and hair, amongst others). The ability to recover DNA from ancient human remains potentially allows for addressing questions of importance to different scientific fields (Figure 1), such as estimation of sex, disease status, ancestry, diet, and individuation.
Sampling
Sampling of skeletal elements for molecular analysis is important in order to obtain reliable results. In the case of samples recovered in modern excavations, specific procedures should be employed in order to minimize the contamination and degradation of samples. The use of disposable latex gloves and masks during excavation should be recommended, while the use of preservatives and humidity (washing) should be avoided. When the molecular analysis is applied to museum collections, sampling should be made minimizing damage and the loss of morphological information, because this type of analysis is often destructive. Morphological information should be recorded through photographs, radiographs, and casts, at least for important specimens. It is often useful to first attempt to analyze fauna bones from the same layer as humans and, whenever possible, more than one sample is to be taken per individual, in order to replicate results in an independent laboratory.
Methodology
Working with ancient DNA (aDNA) involves a number of limitations, namely the scarcity and fragmentation of DNA that is recovered, and the risk of contamination. To avoid contamination, the processing of the samples in the laboratory involves the application of strict criteria, as detailed in the specialized literature, for the authentication of results. The major problem in aDNA analysis is contamination by exogenous DNA. Some potential sources of contamination, such as microorganisms or personal manipulating samples, are not difficult to detect and overcome, but laboratory contamination related to polymerase chain reaction (PCR) products is more difficult to avoid. The PCR preferentially amplifies well-preserved DNA molecules, which are more likely to be modern than ancient DNA. Products of previous PCR reactions may produce laboratory contamination. However, a number of techniques can be applied to reduce the chances of contamination.
The general methodology of aDNA analysis involves several stages. First, extraction and isolation of DNA from a bone or tooth sample. Second, a specific sequence of the DNA is amplified using PCR, an in vitro technique to produce many copies of this DNA, starting from only a few original molecules (DNA template). Finally, the amplified DNA sample is analyzed by enzymatic digestion (restriction fragment length polymorphism: RFLP) and/or sequencing, typically specific regions of mitochondrial DNA (mtDNA).
Limitations
Limitations of aDNA analysis are mainly related to the preservation of DNA, which seems to be influenced primarily by environmental factors rather than by time, at least for younger remains (up to 10 000 years). In general, samples recovered from environments with cooler temperatures, neutral or slightly alkaline pH, and dry conditions are best for DNA preservation, although samples found in wet anoxic conditions or frozen in permafrost have also yielded DNA. Typically, the quality and quantity of DNA is better from tooth than bone, and better from hard tissue than from soft tissue, due to the hydroxyapatite content that binds DNA and thus protects it from subsequent degradation. It is also well known that mtDNA (non-nuclear genome) is easier to retrieve than nuclear DNA, because the greater number of copies present in the cell favors their survival and recovery.
There is currently no clear consensus on the time limit regarding remains that may still contain DNA fragments. The Neanderthals fromFeldhofer (Germany) (40 000 years) and Vindija (Croatia) (42 000 years) are the oldest human remains analyzed to date.
See also: Bioarchaeology; DNA: Ancient; Forensic Archaeology; Paleodemography; Stable Isotope Analysis; Trace Element Analysis.
World History
