Ancient DNA preservation in the Caribbean

Abstract

Ancient DNA (aDNA) analysis has transformed how we study human migration, species dispersals and environmental change, but poor preservation remains a major challenge. This is especially true in tropical settings, where hot and humid conditions accelerate DNA decay. Because aDNA work is destructive, knowing how long DNA survives and under what conditions is crucial for selecting samples likely to yield meaningful data while minimizing damage. Here, we analyse low-coverage shotgun data from over 300 human samples from 33 archaeological sites (3300–400 cal. BP) in the Caribbean to evaluate the effects of sample age, sample type and burial context on DNA preservation. Preservation varied markedly both between and within sites, with sample type and burial context exerting strong effects. Macroscopic inspection, though imperfect, proved a useful first line predictor of molecular preservation. Decay-rate modelling indicates that DNA decays roughly 4× faster in the Caribbean than in temperate regions and about 14× faster than in subpolar settings. Under these conditions we predict that recovery from remains significantly older than approximately 5000 years will be challenging. Encouragingly, this window encompasses most of the region's human history, indicating that much of it remains accessible to aDNA analysis, provided suitable samples can be found and appropriate excavation and post-excavation protocols are followed.