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I recently came across an article indicating that the half life of DNA in the most ideal situations is 521 years (http://www.nature.com/news/dna-has-a-521-year-half-life-1.11555). However, since human's DNA is 99.9% identical (and 98% identical to chimps), I can't quite understand how DNA evidence is often used in old samples. There has been DNA extracted from 100,000 year old Neanderthals, and DNA evidence has been used in cases over 50 years old.

However, with a 521 year half life, after only 0.75 years, there would only be 99.9% of the DNA left. Surely if 99.9% of a human's DNA is identical after only this short amount of time wouldn't it be impossible to distinguish any sample from any other? After 50 years only 93% would remain the same, meaning it would be much less similar to a human than just any chimp I would think.

And the 100,000 year old Neanderthal would only have 1.6*10^-57 % of the original sample left. How is there possibly any sort of useful information left?

All in all, how can DNA be distinguished from other samples when they are all so similar and the half life is so low?

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    $\begingroup$ This question belongs on the biology site - to answer it you have to understand how DNA is compared / identified. It's not about the bits that are different, but about certain (shortish) unique sequences that are the same. Such sequences will continue to exist when much of the DNA has mutated - especially when you recognize there is usually material from multiple cells which will not have degraded in the same way. Still - I suggest you ask a biologist. $\endgroup$
    – Floris
    Sep 8, 2014 at 3:10

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The original article cited in your reference is available here for free. After a quick skim, I saw that their study was based on fossils of a single species (Moas) all taken within a 5 km radius. Thus, it's possible the fossils were preserved under relatively similar conditions, despite different preservation ages. So, it's not yet clear how their results would compare to other species and varying preservation conditions (which they address to some extent).

Regardless, DNA does degrade in fossils yet scientists have been able to recover very high quality sequences from fossils, such as Neanderthals. This is because the samples contain many copies of the DNA. If bonds in one copy of the DNA break in several places it is very unlikely that another copy will break in the exact places.

There are a number of different techniques but in essence scientists simply amplify and sequence a very large number of the DNA fragments. Each fragment is relatively short compared to the total amount of DNA but the large number of fragments ensures (within reason) that the entire genome is covered. Complex computer algorithms are used to align the different fragments with each other. You can read about the techniques used in one of the major Neanderthal genome studies by Green et al. (2008).

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