This approach, developed in the 2000s and refined through the following decade, involves sequencing millions of short DNA fragments simultaneously.

Rather than trying to recover long, intact stretches of DNA — which ancient specimens rarely preserve — next-generation sequencing can work with the short, degraded fragments that ancient remains typically contain.

The resulting sequence data must then be carefully filtered.

Ancient DNA from a burial site will be contaminated with the DNA of bacteria, fungi, and in many cases the modern researchers who have handled the material.

Distinguishing genuine ancient human DNA from these sources requires sophisticated bioinformatics — computational methods for separating authentic ancient sequences from contamination, identifying the characteristic chemical damage patterns that mark ancient DNA, and assembling the short fragments into coherent genetic information.