DNA, even when well preserved, will not last for more than a few hundred thousand years. Therefore the description of DNA sequences in million year old dinosaur remains is due to contamination from modern ambient DNA, which is widespread in labs and elsewhere. The PCR will amplify any DNA, modern or prehistoric.
There are however certain clues to the age of DNA remains. The first is fragmentation. Ancient DNA fragments are between 50 and 500 bases long due to degradation. In fact most are no longer than 100 nucleotides.
Second, and most reliable is the observation that at both ends of DNA (5' and 3'), Cytosine (C) is deaminated to Uracil (U). This is an effect that occurs after death due to bacterial cytosine deaminase. This latter enzyme is not present in mammals (not to be confused with AID or activation induced cytidine deaminase, which is present during development and plays a major role in the affinity maturation and somatic hypermutation of B cells, in effect giving B cells their antigen specificity).
Thus if an archaeological remains has a high proportion of uracil bases in DNA- remember, this base is only present in RNA, it indicates that the specimen is thousands of years old. Archaeologists use an enzyme called uracil-DNA- glycosylase (UDG) to break the bond between deoxyribose sugar and uracil and remove the uracil bases.
Not doing so leads to a curious phenomenon. The PCR used to amplify the DNA remains reads the uracil as thymine (T), since thymine is the native DNA base, not uracil. Hence, on the supplementary (anti-sense) strand, it puts an adenine in place of the guanine (which paired with the original cytosine). The uracil on the sense strand is now replaced with thymine to pair with adenine. The original C-G pairing has therefore now been replaced by an A-T pair. Thus there is miscoding caused by the PCR process manifesting as "transition " of C to T and G to A. (In contrast, when a purine is replaced by pyrimidine base, it is described as "transversion").
There can be blocking lesions caused by the formation of non-physiological chemical bonds between say DNA & protein, which can make it difficult for PCR to read through the ancient DNA. This is difficult to overcome.
Archaeologists have databases comprising thousands of single nucleotide polymorphisms (SNPs) mapped from certain lineages such as Armenian farmers or Iranian invaders which they then compare with the putative SNPs from the sequenced DNA sample to see if there is a match.
Here, mitochondrial DNA, which is of course maternal derived (the sperm does not contain mitochondria) is more useful than nuclear DNA in lineage tracing. Although mitochondrial DNA shares the same predisposition for degradation with time elapsed since death as nuclear DNA, there are far more copies of a given DNA sequence in mitochondria than in chromosomes. Thus, while the nucleus will only have two copies of a given allele (on the 2 chromosomes), each mitochondrion has 10-100 copies- a phenomenon known as heteroplasmy, which explains why mitochondrial mutations cause such variable phenotypes unlike mutations that occur in chromosomes. Mitochondrial DNA therefore is favoured by archaeologists for lineage tracing.
Are there any other ways to determine where a long dead person originated, apart from DNA sequencing? As it happens, there is.
The isotopes of Strontium which are deposited in bone and teeth (dentine and enamel) during development are a reflection of the area where the person grew up in. There are 4 isotopes of Strontium- Sr84, Sr86, Sr87 and Sr88. Sr 87 is not a natural isotope. It is formed by beta decay from Rubidium 87. The rocks and water and therefore, by extension, the remains of a person or animal growing up in a certain area will always display a specific Sr87:Sr88 ratio that is native to that area. When that person migrates to a different geographical area, his teeth, which are often well preserved thousands of years after death, will still carry the signature Sr87:Sr88 ratio of the area where he or she grew up in , as the signature is established in the developing teeth or bones, and does not change after death.
It is thus possible to say that the woman's remains found in a Harappan valley, in fact grew up in Iran.
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