Molecules of DNA are ubiquitous in the environment and a rich source of biological information, but because DNA degrades rapidly in tropical climates studies of ancient DNA in the Caribbean have been limited until recently. ...

This thesis seeks to address the deficit of ancestral human references from the tropics, specifically the Caribbean, by adding genetic (genomic and microbiomic) information from the ancient Puerto Rican Amerindian population ...

The gut microbiome plays essential functions in human health. Environmental disruptions such as changes in diet or lifestyle can exert a significant effect on a population&rsquo;s microbiomes, resulting in several diseases. The study of the ancient microbiota preserved in archaeological samples (paleomicrobiology) is a window for characterizing these possible changes. Recent advances advocate for the consideration of the human microbiome while studying the evolution of humans. However, while more efforts have been made to incorporate microbiome in the evolution of humans, only bacterial communities have been evaluated, whilst fungal communities have been neglected. In addition to the fungal component, regional and temporal variations in dietary habits remain to be defined.<br /> <br /> In this thesis, one of the missing pieces of the puzzle is considered: the mycobiome. Metagenomics approaches were applied for characterizing the fecal mycobiome in thousand-year-old coprolites from pre-Columbian Caribbean cultures, and to elucidate the diets and lifestyles of two pre-Columbian cultures, i.e., the Huecoid and Saladoid, prior to the arrival of Europeans. For this purpose, ancient DNA in coprolites retrieved from the pre-Columbian Huecoid and Saladoid deposits in Vieques, Puerto Rico were analyzed using shotgun metagenomic sequencing. In addition, ancient DNA sequences from the Huecoid and Saladoid coprolites were compared with those detected in coprolites from other ancient cultures, as well as extant feces from more modern cultures. To date, relatively little is known about the Huecoid and Saladoid ethnic groups and their cultural heritage.<br /> <br /> The Saladoid gut mycobiome exhibited a higher alpha-diversity than that of the Huecoid. This result is further supported by the well-distributed relative abundance of fungal genera in the Saladoid coprolites compared to the Huecoid coprolites. The gut mycobiome of the Huecoid and Saladoid coprolites was similar at the phylum level, with Ascomycota representing the most abundant phyla, followed by Basidiomycota and Mucoromycota. However, the gut mycobiome composition at the genus level was highly different between the Huecoid and Saladoid coprolites, and the former resembled the ancestral gut mycobiome of Mexico. The gut mycobiome's α-diversity, as well as the composition and structure, distinguished the ancient and extant populations, with the pre-Columbian cultures harboring a lower total diversity and higher relative abundance of Aspergillus spp., whereas the extant populations were enriched with Mucor spp. and Malassezia spp. Despite differences in diet and lifestyles, certain fungal genera were present in most of the samples. Overall, these results suggest that the gut mycobiome reflects changes related to modern lifestyles. DNA from plants and phytopathogenic fungi from coprolites also showed that the Huecoid and Saladoid exhibited preferences in food items. The diet of the Huecoid culture included sweet potato, chili peppers, peanuts, and maize, and the edible maize smut, Ustilago spp., was likely consumed as well. In contrast, the Saladoid culture consumed chili peppers and papaya, and likely chewed tobacco (or ingested it in some way), for its narcotic and hallucinogenic effects. However, the Huecoid and the Saladoid diets were significantly more similar to each other than to the diets of present-day cultures. These results suggest that present-day diets diverge from ancient diets due to different available nutritional flora, social environments, and historical periods.<br /> <br /> Our work revealed the gut mycobiome and dietary practices of pre-Columbian cultures, uncovered an unprecedented link between human lifestyles and ethnicity, and the diversity and composition of the gut mycobiome and diet. Results further support differences in diet and lifestyles among pre-Columbian Caribbean cultures (the Huecoid and Saladoid) with similar ecological conditions before the Spanish conquest, and these dietary differences were linked to shifts in the gut mycobiome. We demonstrate and emphasize that DNA sequence data from coprolites complement archaeological data and provide information otherwise impossible to obtain....