Retroviral DNA Sequences as a Means for Determining Ancient Diets.

For ages, specialists from varying fields have studied the diets of the primeval inhabitants of our planet, detecting diet remains in archaeological specimens using a range of morphological and biochemical methods. As of recent, metagenomic ancient DNA studies have allowed for the comparison of the fecal and gut microbiomes associated to archaeological specimens from various regions of the world; however the complex dynamics represented in those microbial communities still remain unclear. Theoretically, similar to eukaryote DNA the presence of genes from key microbes or enzymes, as well as the presence of DNA from viruses specific to key organisms, may suggest the ingestion of specific diet components. In this study we demonstrate that ancient virus DNA obtained from coprolites also provides information reconstructing the host's diet, as inferred from sequences obtained from pre-Columbian coprolites. This depicts a novel and reliable approach to determine new components as well as validate the previously suggested diets of extinct cultures and animals. Furthermore, to our knowledge this represents the first description of the eukaryotic viral diversity found in paleofaeces belonging to pre-Columbian cultures

Description of coprolite samples employed in study.

1<p>Prefix SV indicates the sampling site was in the Sorcé Estate (S) the Island of Vieques (V) Puerto Rico. The remaining characters refer to the specific excavation site from which the specimens were obtained (e.g., YTA-1_I-5-6_) and archaeological depth (e.g., 60 cm).</p><p>Description of coprolite samples employed in study.</p

Similarities (A) and differences (B) found in the microbial fecal communities of the Huecoid and Saladoid cultures.

<p>Similarities (A) and differences (B) found in the microbial fecal communities of the Huecoid and Saladoid cultures.</p

Location and obtainment of coprolites used in this study.

<p>Panels (a) and (b) show the sampling sites, located in Sorcé, Vieques, an island off the eastern coast of Puerto Rico. Panel (c) shows the Huecoid and Saladoid archaeological study sites (namely AGRO-I and AGRO-II, respectively). Panel (d) shows a coprolite extracted from these archeological sites.</p

Coprolite sequence statistics.

<p>Coprolite sequence statistics.</p

Relative abundance of fungi in coprolite samples.

<p>Panel (a) shows the proportions of fungi detected in Huecoid and Saladoid samples. Panel (b) shows the comparison of the proportions of yeasts detected in both cultures.</p

Comparison of Saladoid and Huecoid microbiota to the fecal microbiota of representative, extant indigenous cultures.

<p>Panel (a) shows the PCoA of coprolites and the fecal microbiota from extant indigenous cultures plotting PC1 vs. PC2. Panel (b) shows the PCoA of coprolites and the fecal microbiota from extant indigenous cultures plotting PC3 vs. PC2. Panel (c) shows the pie charts of taxa represented in coprolites and extant indigenous cultures.</p

Taxonomic comparison of Huecoid and Saladoid Microbiomes.

<p>Figure was generated using summarize_taxa_through_plots.py workflow of QIIME 1.8. Results are illustrated at the Order level. Extant Amazonian stools microbiome was included for comparisons. Mean values for each culture represent taxa obtained from 8 Huecoid coprolite cores, 7 Saladoid samples, and 5 adult, extant Amazonian stools.</p

Procrustes analysis compares the 16S microbiome found in the cores and respective cortices of coprolite samples.

<p>Samples 6,10, 4, 9 and 8 are of Huecoid origin. Samples 1, 2, 3, 5 ND 7 are of Saladoid origin. Samples identified with number “0” were obtained from coprolite cores and those with the number “1” are from cortical surfaces of the coprolite.</p

Rarefaction plots the 16S rRNA gene microbiome of the coprolite samples.

<p>Rarefaction plots for Huecoid (4B, 6B, 8B, 10B, 11B, 12B, 13B) and Saladoid (1B, 2B, 3B, 5B, 7B, 9B, 14B, 15B) coprolites are shown. Plots were generated using the chao1metic of QIIME 1.8 <i>alpha_rarefaction.py</i> with a sampling depth of 5,000. All 15 samples were obtained from the core region (B) of each coprolite.</p