The study shows a striking absence of the pre-Columbian genetic lineages in modern Indigenous Americans; showing extinction of these lineages with the arrival of the Spaniards.
"Surprisingly, none of the genetic lineages we found in almost 100 ancient humans were present, or showed evidence of descendants, in today's Indigenous populations," said joint lead author Bastien Llamas, from University of Adelaide's Australian Centre for Ancient DNA (ACAD).
Shortly after the initial colonisation, populations were established that stayed geographically isolated from one another, and that a major portion of these populations later became extinct following European contact, he said.
"This closely matches the historical reports of a major demographic collapse immediately after the Spaniards arrived in the late 1400s," Llamas said.
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Researchers from University of Adelaide, University of California at Santa Cruz (UCSC) and Harvard Medical School, studied maternal genetic lineages by sequencing whole mitochondrial genomes extracted from bone and teeth samples from 92 pre-Columbian - mainly South American - human mummies and skeletons.
"Our genetic reconstruction confirms that the first Americans entered around 16,000 years ago via the Pacific coast, skirting around the massive ice sheets that blocked an inland corridor route which only opened much later," said Alan Cooper, Director of ACAD.
"They spread southward remarkably swiftly, reaching southern Chile by 14,600 years ago," said Cooper.
"Genetic diversity in these early people from Asia was limited by the small founding populations which were isolated on the Beringian land bridge for around 2,400 to 9,000 years," said Lars Fehren-Schmitz, from UCSC.
"This long isolation of a small group of people brewed the unique genetic diversity observed in the early Americans," he said.
The study was published in the journal Science Advances.