Ancient DNA Species Barcoding of Avian Remains from the Caribbean

Abstract

Ancient DNA (aDNA) offers opportunities to identify bird species from archaeological remains, yet recovering authentic DNA from tropical environments faces significant technical challenges: light bone texture reduces DNA preservation, and hot, humid climates accelerate degradation. In Caribbean archaeological contexts, approximately 75% of avian remains remain unidentified when using only morphological methods, limiting our understanding of pre-Columbian bird diversity and exploitation. This research studies aDNA approaches for Caribbean bird species identification. 

We selected six avian bone samples for DNA extraction. We tested the samples with universal COI barcoding mtDNA markers (175bp) that resulted in failure of PCR amplifications. Subsequently, a new PCR setup with a shorter 12S rDNA fragment (140bp) and enhanced PCR conditions (higher Taq concentration and lower annealing temperature) resulted in a 50% success rate (3/6 samples). Compared with ancient avian DNA from other regions, our Caribbean samples contain less DNA, confirming severe degradation in the Caribbean. 

Our preliminary data show that Caribbean avian DNA can still be analyzed, but efforts are needed to increase the PCR success rate. Many avian bone samples can be identified to family or genus through zooarchaeological (morphological) examination, which can allow us to design more efficient and specific PCR primers for extremely short fragments under 100bp. New primers are being designed to test on the extracted DNA samples and more avian remains. 

This study provides methodological insights for advancing aDNA studies of avian remains in challenging tropical archaeological contexts, with direct applications to understanding indigenous subsistence practices and paleoenvironmental reconstruction across the Caribbean.