The DNA recovered from the ancient specimens is called ancient DNA (aDNA). The time period of the aDNA collected from the target specimen can range from 100 years to million years. Some of the sources of aDNA are: mummified tissues, archeological skeletons, iced animal and plant remains, and sediments from oceans, rivers and lakes. The major advantage of studying aDNA is that it will provide insights into the history. With that it can help to resolve long standing disputes, confusions or curiosities. For example, comprehending evolutionary processes, determining how humans migrated from one continent to others, and understanding interactions between diseases and humans.
There are two main challenges of investigating aDNA, i.e. degradation and contamination of the genetic material. Degradation of aDNA is caused by the time lapses after the individual was dead, and the environment it was recovered from. Scientists have found a correlation between the age of specimen and degradation of aDNA. With the same age the rate of degradation can vary depending on the environmental conditions, for example, the rate of degradation is slow in a frozen condition, while it is accelerated in the hot and humid conditions. The other important factor to consider about degradation of aDNA is the type of DNA. The rate of degradation is twice as much higher for nuclear DNA (nDNA) than that for mitochondrial DNA (mtDNA). There are two main reasons behind the slower degradation rate of mtDNA as compared to the nDNA. One is due to the double membrane cover of mitochondria as opposed to the single membrane cover of nucleus. The membranes are known for protecting DNA from autolysis. The other reason is that the mtDNA occurs in a higher copy numbers than the nDNA. Because of the lower degradation rate, most of the studies about ancient samples are based on mtDNA.
Contamination of DNA is another big challenge the scientists face while investigating aDNA. Contamination means introduction of foreign DNA to the targeted specimen. Because living organisms continuously shed DNA-bearing tissues such as hair, saliva, blood, skin, urine, feces and other tissues, there is high chance that the DNA of the ancient specimen is contaminated over the time period. Another major source of contamination is DNA from microorganisms found in the specimen. With the laboratory precautions and statistical methods, it is possible to differentiate sequences of targeted specimen from the contaminated sequences.
Because of the degraded and limited genetic materials available for the ancient samples, earlier it was thought that getting meaningful genome information of such samples is impossible. However, due to recent advancements in next generation sequencing technology, scientists have been able to reconstruct the complete or near complete genomes of certain ancient specimens including neanderthal, wooly mamoth, and palaeo eskimos. Since the advancement of sequencing technology is happening at such a fast pace, the precision of getting sequence data at lower cost is also increasing at the same speed. Therefore, we can expect significant increase in the number of studies covering the genomics of even more ancient specimens in the near future.