Successful reconstruction of whole mitochondrial genomes from ancient Central America and Mexico

Ana Y Morales-Arce,M Anne Katzenberg,Ana T Duggan,Adam K Benfer,Geoffrey Mccafferty,Christina Warinner,Courtney A Hofman

doi:10.1038/s41598-017-18356-0

Abstract

The northern and southern peripheries of ancient Mesoamerica are poorly understood. There has been speculation over whether borderland cultures such as Greater Nicoya and Casas Grandes represent Mesoamerican outposts in the Isthmo-Colombian area and the Greater Southwest, respectively. Poor ancient DNA preservation in these regions challenged previous attempts to resolve these questions using conventional genetic techniques. We apply advanced in-solution mitogenome capture and high-throughput sequencing to fourteen dental samples obtained from the Greater Nicoya sites of Jícaro and La Cascabel in northwest Costa Rica (n = 9; A.D. 800–1250) and the Casas Grandes sites of Paquimé and Convento in northwest Mexico (n = 5; A.D. 1200–1450). Full mitogenome reconstruction was successful for three individuals from Jícaro and five individuals from Paquimé and Convento. The three Jícaro individuals belong to haplogroup B2d, a haplogroup found today only among Central American Chibchan-speakers. The five Paquimé and Convento individuals belong to haplogroups C1c1a, C1c5, B2f and B2a which, are found in contemporary populations in North America and Mesoamerica. We report the first successfully reconstructed ancient mitogenomes from Central America, and the first genetic evidence of ancestry affinity of the ancient inhabitants of Greater Nicoya and Casas Grandes with contemporary Isthmo-Columbian and Greater Southwest populations, respectively.

Highlights

The contemporary indigenous populations of Central America and Mexico present marked cultural, linguistic and genetic variation due to their diverse origins[1,2,3,4,5]
We explore the potential of these techniques for the recovery of ancient DNA (aDNA) from fourteen individuals at four archaeological sites in Central America and Mexico: Jícaro and La Cascabel, Greater Nicoya, in northwest Costa Rica (A.D. 800–1250) and the sites of Paquimé and Convento, Casas Grandes, in northwest Mexico (A.D. 700–1450) (Table 1; Fig. 2)
We demonstrate that sequence capture-enrichment coupled with high-throughput sequencing (HTS) enables the successful recovery of full mitogenomes from Central American and Mexican skeletal material, including samples for which conventional PCR-based techniques were unsuccessful

Summary

Introduction

The contemporary indigenous populations of Central America and Mexico present marked cultural, linguistic and genetic variation due to their diverse origins[1,2,3,4,5]. The pre-Contact distribution, movement, and autochthonous genetic diversity of populations within Central America and Mexico remain unclear[19,20] This is true for cultural borderland regions, such as those inhabited by the ancient Greater Nicoya and Casas Grandes cultures. At the time of European contact, early Spanish chroniclers documented speakers of Mesoamerican languages in Greater Nicoya; in the 1900s linguists confirmed that these languages belong to the Oto-Manguean and Nahua linguistic families of Chorotega-mangue, Subtiavas, and Nicaraos[28] Based on these lines of evidence, archaeologists have argued that the main incursions of Oto-Manguean and Nahua-speaking Mesoamerican populations shared a common origin and dispersal by way of a migration from Central Mexico[23,25,27,29]. The recovery of ancient mitochondrial genomes may clarify the genetic relationships of Postclassic Greater Nicoya inhabitants, including groups that are not longer extant

Methods

Results

Conclusion