The genome of a Late Pleistocene human from a Clovis burial site in western Montana

Abstract

Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 14C years BP (13,000 to 12,600 calendar years BP)1,2. Nearly fifty years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology3. However, both the origins and genetic legacy of the people who manufactured Clovis tools remain debated. It is argued that these people ultimately derived from Asia and were directly related to contemporary Native Americans2. An alternative, Solutrean, hypothesis posits that the Clovis predecessors immigrated from Southwestern Europe during the Last Glacial Maximum (LGM)4. Here, we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705±35 14C years BP (CAMS-80538; c. 12,707–12,556 calendar years BP) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4× and show that the gene flow from the Siberian Upper Palaeolithic Mal′ta individual5 into Native American ancestors is also shared by the Anzick-1 individual and thus happened prior to 12,600 years BP. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that pre-dates the Anzick-1 individual.

Solutrean hypothesis: genetics, the mammoth in the room

“…Moving first to the Rasmussen et al (2014) claim introduced above: "…our genome analysis refutes the possibility that Clovis originated via a European (Solutrean) migration to the Americas." While not explaining the basis of their SH genomic refutation, the authors do actually find evidence for Pleistocene West Eurasian autosomal admixture in the Americas, which would be predicted by the SH.…”

“…One of the possible explanatory models Rasmussen et al (2014) tested for this anomaly of NA ancestry was articulated as: "The NA groups carry ancestry from a previously undocumented stream of gene flow from the Old World." Testing the model of "undocumented stream of gene flow", they looked for and found "…no evidence for Siberian gene flow into the Northern Amerinds".…”

Partial uracil–DNA–glycosylase treatment for screening of ancient DNA

“…These are often built in the presence of the enzymes uracil -DNAglycosylase (UDG), which cleaves deaminated cytosines (uracils), and Endo VIII [13], which cuts at the resulting abasic sites, driving down the rate of ancient DNA errors. While we focus here on UDG-treated libraries, non-UDGtreated libraries can also be of value for analyses that are tuned to handle ancient DNA damage [14,15]. Moreover, non-UDG-treated libraries have a particular advantage for analysis of contaminated samples, where restriction to damaged molecules can greatly reduce contamination [16,17].…”

Ancient DNA and human history

“…The first complete genomic sequence from a Native American was presented by Rasmussen et al (44). The individual, called Anzick-1, was associated with Clovis artifacts and is about 12,600 y old.…”