“That genetic traces of the original population disappear completely is unusual, especially in South America,” said geneticist Andrea Casas-Vargas of Colombia’s National University in a recent interview. But that is exactly what an international research team has found in the highlands north of Bogotá, Colombia a region historically the door between North and South America. The revelation, based on the exhaustive examination of ancient DNA, is redefining our knowledge of how the Americas were populated and what was lost in the process.
It starts 6,000 years ago on the Altiplano Cundiboyacense, where a band of hunter-gatherers lived in isolation. Their remains, excavated from archaeological locations like Checua and Laguna de la Herrera, have produced a genetic trace that is distinctive from any ancient or existing population of the Americas. As University of Tübingen anthropologist Kim-Louise Krettek put it, “We couldn’t find descendants of these early hunter-gatherers of the Colombian high plains the genes were not passed on. That means in the area around Bogotá there was a complete exchange of the population.”
The technical achievement behind this find is itself a wonder of contemporary science. Scientists isolated DNA from the petrous part of the temporal bone and teeth, taking advantage of advances in ancient DNA (aDNA) recovery which make it possible to examine even teeny-tiny, degraded bits. The process involves a series of chemical digestions, silica column purifications, and the construction of double-stranded, double-indexed libraries, which are then sequenced using high-throughput Illumina platforms. Authenticity checks such as estimating mitochondrial and X-chromosomal contamination ensure that the results reflect ancient genomes, not modern intrusions.
The results, published in Science Advances, are as clear as they are unexpected. Seven Preceramic hunter-gatherers’ DNA creates a new, previously unrecognized branch geneticists speak of a basal lineage of the early South American radiation. They have no genetic affinity with the North American Clovis-linked Anzick-1 genome or with California Channel Islands ancestry that would later extend down through the Andes. Rather, they are a distinct genetic branch of human beings in the Americas, which then died off approximately 2,000 years ago.
Then came a sudden and dramatic replacement. By 2,000 years ago, the genetic marks of the early settlers had been eliminated, with a population whose roots lay to the north, to Central America. This new population, who were linked to the Herrera ceramic complex, introduced not only sophisticated ceramics and maize cultivation but also a genetic makeup closely linked to Chibchan language speakers a native people still found in Central America and parts of Colombia today.
The change is seen in the genome-wide information of 21 people over 6,000 years. Following the disappearance of the first hunter-gatherers, the area had more than 1,500 years of genetic continuity despite cultures changing from the Herrera to the Muisca famous for social sophistication and farming ability. This continuity lasted up to the time of the Europeans’ arrival in the 16th century.
The methodology of the study is a testament to the might of contemporary genomics in archaeology. Principal components analysis (PCA) and f-statistics were applied by researchers to contrast ancient genomes against a worldwide reference panel and ascertain that the preceramic group was genetically different from preceding and subsequent populations. Uniparental markers mitochondrial DNA and Y-chromosome haplogroups also helped spell out the tale. All male samples were in Y-chromosome haplogroup Q1b1a, the most common paternal lineage among Native Americans, but the subclades and mitochondrial haplogroups depicted a scenario of small isolated groups with minimal inbreeding evidence.
These results refute earlier models which posited that cultural innovations such as the use of pottery resulted from local innovation and not migration. The genetic information now show a huge migration from modern-day Panama and Costa Rica, which substantiates the notion that the Chibchan-related ancestry began in Lower Central America and migrated south (science.org). This expansion is replicated in linguistic variation: Chibchan languages, which have numerous branches, are densest in Central America, hinting at an ancient and profound homeland.
The destiny of the original hunter-gatherers is still a mystery. They vanished without leaving behind descendants genetically apparently in contrast to the high genetic continuity that is present elsewhere in South America. The explanation may vary from disease and warfare to a slow process of assimilation, but as Casas-Vargas observed, “the researchers don’t speculate on” the reasons.
For archaeology and science buffs, the importance is immense. Not only does this study fill a critical void in peopling the Americas, but it illustrates how improvements in ancient DNA recovery and sequencing are re-writing human history. The Altiplano Cundiboyacense, previously a mere stopover on migration routes, now stands as a platform for epic demographic transformations exposed, finally, through the quiet witness of ancient genomes.
