Abstract

Paleofeces or coprolites are often used to reconstruct diet at archaeological sites, usually using macroscopic analyses or targeted DNA amplification and sequencing. Here we present an integrative analysis of dog coprolites, combining macroscopic analyses, stable isotope measurements, and DNA shotgun sequencing to examine diet and health status. Dog coprolites used in this study were recovered from the Janey B. Goode and East Saint Louis archaeological sites, both of which are located in the American Bottom, an extensive Mississippi River floodplain in Southwestern Illinois. Based on the context of recovery, coprolites are assigned to the Late Woodland and Terminal Late Woodland periods (ca. 600–1050 AD). Given the scarcity of human remains from this time period, these dog coprolites can be useful as a proxy for understanding human diet during the Late Woodland period. We find that the Late Woodland dogs consumed a variety of fish as well as bird and plant taxa, possibly including maize, and also harbored intestinal parasites and pathogenic bacteria. By sequencing the fecal microbiome of the coprolites, we find some similarities to modern dog microbiomes, as well as specific taxa that can be used to discriminate between modern and ancient microbiomes, excluding soil contaminants. As dogs are often used as a surrogate to assess human diet, humans living with these dogs likely had a similar diet and were affected by similar parasites. These analyses, when integrated, show a more comprehensive view of ancient dog and human diet and health in the region during the initial expansion of maize agriculture than any individual method could alone.

Highlights

  • Paleofeces or coprolites are often used to reconstruct diet at archaeological sites, usually using macroscopic analyses or targeted DNA amplification and sequencing

  • Genomic sequencing of additional species, such as native plant taxa, and under-represented microbiome diversity, would help confirm the identity of the DNA reads recovered from coprolites, as well as enable the identification of additional taxa. This integrative analysis of coprolites demonstrates the value of using multiple methods to assess the diet, microbiome, and health of an individual from a single sample

  • Specific dietary components and parasites can be identified through DNA sequencing and macroscopic analyses, while stable isotope analysis can shed light on large-scale trends in diet

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Summary

Introduction

Paleofeces or coprolites are often used to reconstruct diet at archaeological sites, usually using macroscopic analyses or targeted DNA amplification and sequencing. Known as coprolites and paleofeces, has been recovered from archaeological contexts worldwide and contain a wealth of information about the organism that produced them and the environment they lived i­n1. The stable carbon and nitrogen isotope composition (δ13C and δ15N) of feces and coprolites can be used to reconstruct diet isotopic ­composition[11,12,13,14,15], and ancient bat guano and soil samples that likely contain fecal matter have been used to identify changes in climate, population demographics, and d­ iet[16,17,18,19]. Shotgun sequencing or metagenomics (which sequences all DNA in the sample) have been used in a small number of coprolite studies, but they either focused on specific t­axa[29,34] or only analyzed mitochondrial DNA reads following ­sequencing[22]

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