Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples

Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results. We studied a set of methods used to generate ancient genome data from archaeological human samples from different sites and periods, and with varying levels of preservation. In these experiments we compared two sample preparation techniques, two silica-based DNA extraction protocols, and two aDNA library preparation protocols. Finally, we explored the efficiency of whole-genome capture (WGC) on aDNA libraries with different characteristics by comparing a set of protocol modifications.