Ancient DNA studies have had a major impact in archaeology and ecology. However, the vast majority of ancient DNA studies have been performed on samples from cold or temperate regions, where DNA preservation is generally much better than in non-temperate settings. With average annual temperatures over 25°C and high levels of ambient humidity, the Caribbean represents a particularly challenging environment for ancient DNA research, which explains why so few ancient DNA studies have been conducted in the region to date.
Nonetheless, previous studies have shown that ancient DNA does preserve in the Caribbean, in some cases possibly up to several thousand years; however, the factors influencing DNA preservation in this challenging environment are as yet not well understood. High-throughput sequencing data offer an excellent way to study the molecular preservation of archaeological specimens, using such indicators as the endogenous DNA content, average fragment lengths, molecular decay rates, and DNA fragmentation and deamination patterns.
Using low-coverage, high-throughput sequencing data from over 100 archaeological bone and tooth specimens from the Caribbean, we systematically explore the effects of temperature, age, microbial action, time since excavation, sample and soil type, and burial setting on DNA preservation. Results indicate that the level of DNA preservation varies dramatically across the region and that factors such as the burial setting, the age of the sample, and sample type can have a strong influence on the level of preservation.