The Leicester skeleton had been buried without a coffin in soil that had been subject to the normal cycles of English weather for five centuries. These were not ideal preservation conditions. Nevertheless, sufficient DNA survived for analysis.
Mitochondrial DNA was the primary target for several reasons. First, each cell contains thousands of mitochondria, each carrying its own circular genome, meaning that mitochondrial DNA is far more abundant in a tissue sample than nuclear DNA. Where a cell might carry two copies of each nuclear chromosome, it might carry thousands of copies of the mitochondrial genome. This abundance means mitochondrial DNA is more likely to survive in ancient samples to a degree that allows sequencing.
Second, the mitochondrial genome is much smaller than the nuclear genome. The complete mitochondrial genome contains approximately 16,569 base pairs, compared to the roughly three billion base pairs in the complete nuclear genome. A smaller target is easier to sequence completely from degraded samples.
Third, the maternal inheritance pattern of mitochondrial DNA makes it uniquely valuable for genealogical matching. If you know an individual’s maternal lineage, you can predict their mitochondrial haplogroup and specific sequence — and if you find a living descendant through an unbroken female line, you have a direct comparator.
The contamination challenges in ancient DNA analysis are substantial. Modern human DNA is everywhere — in the air, on tools, on the hands of researchers — and if a sample is contaminated with modern DNA, it can overwhelm the ancient signal and produce false results. The field has developed protocols to address this: work in clean-room environments, use of protective clothing, sequencing of the same regions multiple times to check for consistency, and statistical methods that allow researchers to identify which DNA is ancient (based on characteristic damage patterns) and which might be modern contamination.