Indigenous populations of the Americas experienced high mortality rates during the early contact period as a result of infectious diseases, many of which were introduced by Europeans. Most of the pathogenic agents that caused these outbreaks remain unknown. Through the introduction of a new metagenomic analysis tool called MALT, applied here to search for traces of ancient pathogen DNA, we were able to identify Salmonella enterica in individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in southern Mexico. This cemetery is linked, based on historical and archaeological evidence, to the 1545-1550 CE epidemic that affected large parts of Mexico. Locally, this epidemic was known as 'cocoliztli', the pathogenic cause of which has been debated for more than a century. Here, we present genome-wide data from ten individuals for Salmonella enterica subsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever. We propose that S. Paratyphi C be considered a strong candidate for the epidemic population decline during the 1545 cocoliztli outbreak at Teposcolula-Yucundaa.

A mid-sixteenth-century cemetery was investigated at the colonial Mixtec site of Teposcolula Yucundaa and is shown to be related to the cocoliztli pandemic of 1544–1550. This is the earliest colonial epidemic cemetery to be identified in Mexico. Through archaeogenetic and oxygen stable isotope analysis it is demonstrated that the interred individuals were local Mixtecs, and mortuary analysis sheds light on both Christian and traditional religious practices at the site. Mitochondrial haplogroup frequencies support long-term genetic continuity in the region, and carbon stable isotopes of bone collagen and enamel carbonates suggest no decrease in maize consumption during the early colonial period, despite historical evidence for a changing agricultural economy and increased wheat production at the site. The Teposcolula cemetery provides a rich and complex perspective on early colonial life in the Mixteca Alta and reaffirms the importance of archaeological and bioarchaeological evidence in investigating complex social and biological processes of the past.

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This report presents the results to date of a three-year archaeological investigation of the Postclassic and early Spanish Colonial Mixtec City of Yucundaa, PuebloViejo de Teposcolula, Oaxaca. It is the first project in Oaxaca to focus specifically on a major prehispanic city and its dramatic transformation during the first three decades of the colonial period. Given the dearth of conventional historical documentation relating to Yucundaa, the site itself serves as a “primary text,” the major source of information regarding its development and operation. The project attempts to define the major components of the settlement, and to examine each as comprehensively as possible in order to form a coherent view of the city's structure and function. At the conclusion of the third season, the encouraging results serve to demonstrate the utility of a well-planned excavation program that from its inception attempts to examine an entire Postclassic-Colonial settlement and the great transformation occurring there between A.D. 1521 and 1550. The research methods, as well as information and insights derived from the project, will provide stimulus and a useful model for the study of other Mesoamerican urban settlements.

BackgroundIdentification of historic pathogens is challenging since false positives and negatives are a serious risk. Environmental non-pathogenic contaminants are ubiquitous. Furthermore, public genetic databases contain limited information regarding these species. High-throughput sequencing may help reliably detect and identify historic pathogens.ResultsWe shotgun-sequenced 8 16th-century Mixtec individuals from the site of Teposcolula Yucundaa (Oaxaca, Mexico) who are reported to have died from the huey cocoliztli (‘Great Pestilence’ in Nahautl), an unknown disease that decimated native Mexican populations during the Spanish colonial period, in order to identify the pathogen. Comparison of these sequences with those deriving from the surrounding soil and from 4 precontact individuals from the site found a wide variety of contaminant organisms that confounded analyses. Without the comparative sequence data from the precontact individuals and soil, false positives for Yersinia pestis and rickettsiosis could have been reported.ConclusionsFalse positives and negatives remain problematic in ancient DNA analyses despite the application of high-throughput sequencing. Our results suggest that several studies claiming the discovery of ancient pathogens may need further verification. Additionally, true single molecule sequencing’s short read lengths, inability to sequence through DNA lesions, and limited ancient-DNA-specific technical development hinder its application to palaeopathology.

Cultivated cochineal (Dactylopius coccus) produces carminic acid, a valuable red dye used to color textiles, cosmetics, and food. Extant native D. coccus is largely restricted to two populations in the Mexican and the Andean highlands, although the insect's ultimate center of domestication remains unclear. Moreover, due to Mexican D. coccus cultivation's near demise during the 19th century, the genetic diversity of current cochineal stock is unknown. Through genomic sequencing, we identified two divergent D. coccus populations in highland Mexico: one unique to Mexico and another that was more closely related to extant Andean cochineal. Relic diversity is preserved in the crops of small-scale Mexican cochineal farmers. Conversely, larger-scale commercial producers are cultivating the Andean-like cochineal, which may reflect clandestine 20th century importation.

Indigenous populations of the Americas experienced high mortality rates during the early contact period as a result of infectious diseases, many of which were introduced by Europeans. Most of the pathogenic agents that caused these outbreaks remain unknown. Using a metagenomic tool called MALT to search for traces of ancient pathogen DNA, we were able to identify Salmonella enterica in individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in southern Mexico. This cemetery is linked to the 1545-1550 CE epidemic locally known as "cocoliztli", the cause of which has been debated for over a century. Here we present two reconstructed ancient genomes for Salmonella enterica subsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever. We propose that S. Paratyphi C contributed to the population decline during the 1545 cocoliztli outbreak in Mexico.One Sentence Summary: Genomic evidence of enteric fever identified in an indigenous population from early contact period Mexico.

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