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Ancient Peruvian Sequence Data Argue Against Population Replacement by Wari Empire

NEW YORK (GenomeWeb) – The ancient expansion of the Wari culture, from Peru's central highlands to a large swath of sites in the region, does not appear to have led to substantial changes in the mitochondrial genome sequences of populations found in Lima at the time, according to a new study in PLOS One.

Researchers from Australia, Peru, the US, and Germany sequenced nearly three dozen ancient mitochondrial genomes from the Huaca Pucllana archeological site in Lima, Peru, representing individuals from three cultures that lived in the region as far back as 1,500 years ago. Rather than supporting the replacement of one culture by another, their results indicate that the Wari Empire's influence on Peruvian culture was likely a consequence of cultural diffusion.

"The results indicate that genetic diversity shifted only slightly through time, ruling out a complete population discontinuity or replacement driven by the Wari imperialist hegemony, at least in the region around present-day Lima," senior authors Bastien Llamas and Wolfgang Haak, both affiliated with the University of Adelaide's Australian Centre for Ancient DNA, and their co-authors wrote.

The availability of ancient samples at the Huaca Pucllana site made is possible to characterize genetic diversity within, and relationships between, the Lima, Wari, and Ychsma cultures, they explained, which predated current Columbian cultures in the region.

For example, the team had access to samples from the 100 to 650 CE window when the early intermediate Lima group lived in the region, along with samples from individuals in an imperialist Wari Empire that became predominant during the transitional Middle Horizon period from 650 to 1100. It also looked at more than a dozen individuals from a Late Intermediate group called Ychsma that lived in the region after the Wari, until the mid-1400s.

As such, the Huaca Pucllana site "provides the exceptional opportunity to study a 1,000 years of pre-Inca history, including the impact of the Wari imperialist expansion on Peru's Central Coast cities," first author Guido Valverde, with the Australian Centre for Ancient DNA, said in a statement.

Using hybridization capture-based enrichment and an Illumina HiSeq 2000 instrument, the researchers attempted to sequence 52 Huaca Pucllana samples, coming up with complete mitochondrial genome sequences for 34 of the ancient individuals: 15 representatives from the Ychsma group, 10 Wari individuals, and nine Lima individuals.

The team identified 28 haplotypes in the ancient mitochondrial genomes, falling in four main Native American mitochondrial DNA founder haplogroups. These haplotypes were distinct from those found in present-day Peruvians, though similar haplotype diversity was detected in the Lima, Wari, and Ychsma individuals.

"[A]ncient Peruvians from Huaca Pucllana did not undergo dramatic changes in genetic ancestry over approximately 1,000 years," the researchers wrote. "These results suggest population continuity through time, with no major demographic turnovers."

The team noted that additional samples and more in-depth sequencing should provide a more complete view of relationships between populations in ancient Peru and their possible influence on the populations now found in the area.