The Hill Above The Valley<\/p>\n
The Checua River valley lies in the high plains north of Bogot\u00e1, at an elevation just above 2,500 meters, in the crumpled highland terrain of Colombia’s Eastern Cordillera.<\/p>\n
The view from the hill where the ancient people lived is wide and uncluttered \u2014 the kind of visibility that hunters value, where you can see across grassland and wetland for a long distance and watch for game moving at the edges of the morning mist.<\/p>\n
In 1992, archaeologists excavating on that hill found human bones.<\/p>\n
Not a single burial, but the partial remains of roughly thirty individuals spread across the site.<\/p>\n
One skull was nearly complete.<\/p>\n
The bones were old \u2014 old in the way that bones from this part of South America rarely are, old in the way that archaeological sites at this elevation almost never yield, old enough to sit in the shadowy territory of deep prehistory where the questions about who lived here and how they fit into the larger story of human migration become genuinely difficult to answer.<\/p>\n
What happened to those remains, and to the DNA eventually extracted from them, is one of the more scientifically significant findings to emerge from South American archaeology in recent years.<\/p>\n
A research team led by Kim-Louise Krettek of the Senckenberg Center for Human Evolution and Paleoenvironment in Germany, working with Colombian scientists including Andrea Casas-Vargas of the Universidad Nacional de Colombia and a range of international collaborators, spent years working through the biological material from that site and four others on the Bogot\u00e1 Altiplano.<\/p>\n
They extracted ancient DNA.<\/p>\n
They sequenced genomes.<\/p>\n
They ran the resulting data through the analytical frameworks that modern population genetics uses to place ancient individuals in relation to other populations \u2014 living and dead \u2014 and to trace the threads of ancestry that connect them.<\/p>\n
The results were published in May 2025 in the journal Science Advances under the title “A 6000-year-long genomic transect from the Bogot\u00e1 Altiplano reveals multiple genetic shifts in the demographic history of Colombia.”<\/p>\n
The paper is dense with statistics, populated with genetic comparisons, and written for specialists.<\/p>\n
But what it describes is extraordinary.<\/p>\n
The seven oldest individuals in the study \u2014 people who had lived on that high Colombian plateau roughly 6,000 years ago \u2014 represented a genetic lineage that no one had found before.<\/p>\n
Not in any ancient South American genome.<\/p>\n
Not in any ancient Central American genome.<\/p>\n
<\/p>\n
Not in any living Indigenous American population included in the researchers’ comparative dataset.<\/p>\n
A previously undocumented branch of the early South American population radiation, sitting in a high-altitude valley in Colombia, preserved in the bones of hunter-gatherers who had lived there thousands of years before anyone thought to look.<\/p>\n
And the genetic signature of those people \u2014 the specific ancestral fingerprint that distinguished the Checua hunter-gatherers from every other population in the study’s comparison set \u2014 showed no detectable contribution to the later ancient populations from the same region, or to any of the present-day South American populations the researchers tested.<\/p>\n
The lineage, as far as the current evidence goes, vanished from the genetic record.<\/p>\n
What happened to it, and how, and why, is a question that the 2025 paper opened without closing.<\/p>\n
The Gap On The Map<\/p>\n
To understand why this finding mattered, start with a map.<\/p>\n
Ancient DNA research \u2014 the extraction and sequencing of genetic material from prehistoric human remains \u2014 has transformed the study of human prehistory over the past fifteen years.<\/p>\n
The technology that made this possible was the development of next-generation sequencing: the ability to read millions of short, degraded DNA fragments simultaneously, reassembling them computationally into something that reflects the genetic makeup of the ancient individual who left them behind.<\/p>\n
Using these methods, researchers have built an increasingly detailed picture of how the Americas came to be populated.<\/p>\n
They have sequenced genomes from early North Americans, including the famous Anzick-1 individual associated with the Clovis culture in Montana, one of the oldest genomes yet recovered from the Western Hemisphere.<\/p>\n
They have analyzed individuals from the Pacific Coast of North America, including ancient inhabitants of the California Channel Islands, who represent a distinct ancestral lineage.<\/p>\n
They have sequenced genomes from ancient Peruvians, ancient Brazilians, ancient Argentinians, ancient Chileans, ancient Bolivians.<\/p>\n
The Americas, as a subject of ancient DNA study, are increasingly well-mapped \u2014 but with significant regional gaps.<\/p>\n
<\/p>\n
Colombia was one of the largest of those gaps.<\/p>\n
This is not because Colombia is archaeologically unimportant.<\/p>\n
The opposite is true.<\/p>\n
The Bogot\u00e1 Altiplano \u2014 the high plateau of Colombia’s Eastern Cordillera \u2014 has been inhabited continuously for more than eleven thousand years, making it one of the most uninterrupted archaeological sequences in the Americas.<\/p>\n
The later cultures of this plateau include the Muisca, one of the most complex societies in pre-Columbian South America, who built a hierarchical chiefdom system, practiced elaborate goldworking, and maintained the trade networks that created the legend of El Dorado.<\/p>\n
The Altiplano has been excavated by Colombian archaeologists for decades.<\/p>\n
<\/p>\n
The record is rich.<\/p>\n
But until 2025, no ancient human genome from Colombia had ever been published in peer-reviewed literature.<\/p>\n
The reasons are practical.<\/p>\n
Ancient DNA requires well-preserved biological material.<\/p>\n
The humid tropical and subtropical conditions that characterize much of Colombia are generally hostile to long-term DNA preservation \u2014 moisture and heat accelerate the bacterial degradation that destroys genetic material.<\/p>\n
Even at the relatively cooler, higher-altitude environment of the Bogot\u00e1 Altiplano, preservation is uncertain.<\/p>\n
The extraction of useful genetic data from ancient bones requires finding individuals whose dental or skeletal material has retained enough molecular information to be read.<\/p>\n
<\/p>\n
The 2025 paper reported that the research team had achieved this.<\/p>\n
Working with material from five archaeological sites on the Altiplano, they recovered genome-wide data from 21 ancient individuals spanning roughly 5,500 years of the plateau’s occupation.<\/p>\n
The study represented an eleven-fold increase in the ancient DNA sample size available for Colombia, starting from essentially zero.<\/p>\n
The oldest of those individuals came from Checua.<\/p>\n
The Site And The People Who Lived There<\/p>\n
Checua is an open-area settlement site \u2014 not a cave, not a rock shelter, but an outdoor location where people lived on a hill in the Checua River valley, in what is now the municipality of Nemoc\u00f3n in Cundinamarca Department, roughly forty kilometers north of the center of Bogot\u00e1.<\/p>\n
<\/p>\n
The site sits at an elevation of approximately 2,577 meters above sea level.<\/p>\n
The Bogot\u00e1 Altiplano is high country by any global standard \u2014 this is the terrain of the Eastern Andes, elevated well above the warm lowlands to the east and west, exposed to the temperature extremes and thin air that characterize Andean highland environments.<\/p>\n
The people who lived here in the Preceramic period were adapted to altitude in ways that their lowland contemporaries elsewhere in the Americas were not.<\/p>\n
The first significant excavations at Checua were conducted in 1992 under the direction of archaeologist Ana Mar\u00eda Groot.<\/p>\n
<\/p>\n
The discoveries were significant from the beginning: the remains of approximately thirty individuals, representing one of the most substantial early-Holocene human assemblages then known from northern South America.<\/p>\n
One skull survived in nearly complete condition \u2014 a rarity in outdoor sites where preservation is often fragmentary.<\/p>\n
Additional excavation and collection work continued between 1987 and 2003.<\/p>\n
The physical characteristics of the Checua individuals were noted by researchers.<\/p>\n
Jos\u00e9 Vicente Rodr\u00edguez Cuenca, a physical anthropology expert and co-author of the 2025 genetics study, observed that the skulls from the site were more elongated in their proportions than those of populations associated with later periods on the same plateau.<\/p>\n
This observation is archaeologically interesting, and it connects to broader discussions in physical anthropology about variation in skull morphology among ancient American populations.<\/p>\n
<\/p>\n
It is important to state explicitly: elongated skull shape does not indicate a different biological species, a lost race, or a separate origin outside the Americas.<\/p>\n
Variation in cranial morphology among ancient populations reflects a range of biological factors \u2014 normal within-population variation, differences between populations that have been geographically separated for extended periods, and possibly cultural practices in some cases.<\/p>\n
The Checua individuals were fully anatomically modern human beings.<\/p>\n
The skull morphology observation is one physical characteristic among many, and it was the DNA \u2014 not the skull shape \u2014 that revealed the most significant information about who these people were.<\/p>\n
Dental pathology was also noted.<\/p>\n
<\/p>\n
Some of the Checua individuals showed abscesses in the upper front jaw area, consistent with tooth loss from infection.<\/p>\n
Researchers suggested this might be connected to dietary patterns, potentially involving reliance on root vegetables and tubers rather than the more abrasive grain-based diets associated with later agricultural periods.<\/p>\n
The Altiplano experienced volcanic activity during prehistoric periods, and researchers noted that eruptions may have periodically damaged surface crops and pushed early inhabitants toward underground food sources.<\/p>\n
The Checua site preserves evidence not just of bodies but of habitation.<\/p>\n
Postholes \u2014 the preserved outlines of the wooden posts that would have supported structures \u2014 suggest that the people who lived here were building shelters, not simply camping in the open.<\/p>\n
<\/p>\n
This points toward some degree of sedentism or repeated seasonal return to a fixed location, rather than purely mobile nomadic existence.<\/p>\n
However, the nature and permanence of this occupation remains a subject of archaeological interpretation.<\/p>\n
The broader archaeological context of Checua is the Preceramic period of the Bogot\u00e1 Altiplano \u2014 roughly 11,500 to 4,000 years before the present \u2014 a long span during which the population of the plateau was hunter-gatherers who had not adopted the pottery-making and formal agriculture that would come later.<\/p>\n
This period saw multiple environmental changes, including the retreat of the Ice Age climates that had characterized the region during the terminal Pleistocene, the evolution of the Altiplano’s vegetation from open grassland toward more closed forest and wetland environments, and the gradual intensification of human land use as populations stabilized.<\/p>\n
<\/p>\n
The Checua individuals in the 2025 study date to approximately 6,000 years before the present \u2014 well within this Preceramic window, roughly halfway through the period before pottery appears on the plateau.<\/p>\n
They were hunter-gatherers living in a world without ceramics, without formal agriculture, and without the social complexity that would develop much later with the Herrera and Muisca periods.<\/p>\n
They were, in the genetic analysis, something quite specific.<\/p>\n
What Ancient DNA Actually Requires<\/p>\n
Before going further into what the genome analysis showed, it is worth spending some time on what ancient DNA work actually involves \u2014 because the gap between popular understanding and scientific reality is significant, and because understanding the methodology helps clarify what conclusions can and cannot be drawn.<\/p>\n
The extraction of DNA from ancient human remains begins with the selection of the best possible source material.<\/p>\n
<\/p>\n
DNA degrades over time through bacterial action, chemical reactions with water and oxygen, and the physical fragmentation of the long molecular chains that carry genetic information.<\/p>\n
In most burial environments, by the time thousands of years have passed, only short fragments of DNA survive \u2014 and most of what can be extracted is the DNA of the bacteria and fungi that colonized the remains after death, not the DNA of the human who left those remains behind.<\/p>\n
The most reliable source of ancient human DNA has proven to be the petrous bone \u2014 the dense, compact portion of the temporal bone that houses the inner ear.<\/p>\n
The petrous bone is the hardest bone in the human body, and its density creates a physical barrier that slows bacterial invasion and preserves the cellular material inside better than softer skeletal elements.<\/p>\n
<\/p>\n
Ancient DNA researchers now routinely target the petrous bone when it is available, drilling into it to extract a small amount of powder that can then be processed in specialized laboratory environments.<\/p>\n
Teeth are also excellent sources.<\/p>\n
The dense outer casing of enamel protects the biological material inside, and dental pulp \u2014 the soft tissue at the center of the tooth \u2014 can preserve DNA in good condition for thousands of years.<\/p>\n
The 2025 Colombia study used both of these approaches.<\/p>\n
The research team extracted DNA from the petrous portion of temporal bones and from teeth, applying the standard protocols developed over the past decade of ancient DNA research.<\/p>\n
Once extracted, the DNA must be processed in strictly controlled laboratory environments to prevent contamination \u2014 the introduction of modern DNA from the researchers themselves or from ambient sources.<\/p>\n
<\/p>\n
Ancient DNA work is conducted in cleanrooms designed to minimize airborne particles, using equipment and surfaces that have been thoroughly decontaminated.<\/p>\n
The researchers themselves must take precautions including wearing protective gear to prevent their own DNA from entering the sample.<\/p>\n
The resulting raw material \u2014 a mixture of short, degraded DNA fragments from the ancient individual and from the various organisms that colonized the remains over time \u2014 is then sequenced and subjected to bioinformatic analysis.<\/p>\n
Computational methods distinguish authentic ancient human DNA from contamination by looking for the specific chemical damage patterns that accumulate in DNA over long periods: particular changes to the nucleotide bases that characterize genuine ancient sequences rather than modern contamination.<\/p>\n
Authenticating ancient DNA is not simple, and the field has developed increasingly sophisticated methods for doing so.<\/p>\n
<\/p>\n
The study reported genome-wide data from 21 individuals \u2014 meaning that they were able to recover information from across the entire genome, not just from a few specific genetic markers.<\/p>\n
This genome-wide data is what allows the detailed population genetic comparisons that the paper’s conclusions depend on.<\/p>\n
Of the 21 individuals, seven were associated with the Checua site and the Preceramic period dating to approximately 6,000 years before present.<\/p>\n
Nine came from a site called Laguna de la Herrera, dating to approximately 2,000 years before present and associated with the Herrera ceramic complex.<\/p>\n
Three individuals came from sites called Las Delicias and Soacha, associated with both early and late Muisca culture and dating to approximately 1,200 and 520 years before present respectively.<\/p>\n
<\/p>\n
Two more came from a site called Purnia in the Los Curos area, associated with Guane populations, dating to approximately 530 years before present.<\/p>\n
This five-site, 21-individual, 5,500-year time span is what the researchers called a “genomic transect” \u2014 a time series of genetic snapshots from the same geographic region, allowing them to track how the population’s genetics changed over time.<\/p>\n
What the transect revealed was unexpected at every major step.<\/p>\n
The Americas Before Colombia: The Necessary Background<\/p>\n
To understand what the Checua individuals’ genomes revealed about their position in American prehistory, it is necessary to understand something about the broader story of how the Americas came to be populated.<\/p>\n
This is a story that ancient DNA research has significantly revised and complicated over the past decade, and the Colombia findings fit within that revised picture in ways that matter.<\/p>\n
<\/p>\n
The first Americans came from Asia.<\/p>\n
This basic fact has been established by multiple independent lines of evidence \u2014 genetics, archaeology, and linguistics \u2014 and is not seriously disputed.<\/p>\n
The specific route was the Bering land bridge: a broad swath of land, hundreds of miles wide from north to south, that connected what is now Siberia to what is now Alaska during the last Ice Age, when global sea levels were much lower because so much of the world’s water was locked in glacial ice.<\/p>\n
This land connection \u2014 geologists call it Beringia \u2014 enabled the migration of people from northeastern Asia into North America at some point during the late Pleistocene.<\/p>\n
<\/p>\n
The timing of this migration has been one of the most contested questions in American prehistory.<\/p>\n
The oldest well-established human presence in the Americas was once thought to date to roughly 13,000 years before present, associated with the Clovis culture \u2014 people who left distinctive fluted stone spear points at sites scattered across North America.<\/p>\n
But evidence for pre-Clovis human presence has accumulated over the past several decades, with sites in Chile, Oregon, and New Mexico now providing robust evidence for people in the Americas as early as 14,500 to 23,000 years ago or even earlier, depending on the site and the analysis.<\/p>\n
The ancient DNA record has added crucial dimensions to this story.<\/p>\n
<\/p>\n
One of the most important findings has been the identification of at least two distinct founding genetic lineages in the Americas.<\/p>\n
The first \u2014 and better documented \u2014 is the lineage associated with the Anzick-1 individual from Montana, who was buried approximately 12,600 years ago along with Clovis artifacts.<\/p>\n
Anzick-1 represents the ancestral population most closely connected to what researchers call “southern Native American” ancestry \u2014 the lineage that gave rise to most of the Indigenous populations of South America and much of North America.<\/p>\n
The second founding lineage is associated with populations sometimes called “Ancient Beringian” or “related to the California Channel Island ancient individuals” \u2014 populations that appear to have diverged from the main founding lineage early in the peopling process and that are more closely connected to some North American populations than to the South American pattern.<\/p>\n
<\/p>\n
By roughly 9,000 years before present, what researchers call the “southern Native American” lineage \u2014 the one associated with Anzick-1 and related individuals \u2014 had become the dominant ancestral source for populations across South America.<\/p>\n
The ancient genomes from the Andes, from Amazonia, from the southern cone of the continent, largely reflect this common ancestry, with variations reflecting the specific population histories of different regions.<\/p>\n
Into this framework, the Checua individuals introduced an unexpected complication.<\/p>\n
The seven Preceramic hunter-gatherers from Checua showed no affinity to the Anzick-1 genome \u2014 that is, they did not carry the ancestry associated with the Clovis-related founding lineage.<\/p>\n
This was not entirely surprising, since other ancient South American populations also show reduced affinity to Anzick-1, instead being connected to different aspects of the founding radiation.<\/p>\n
<\/p>\n
The more startling finding came from the broader comparisons.<\/p>\n
The Checua individuals were also not closely matched to any other ancient genome in the researchers’ comparison dataset.<\/p>\n
Not to ancient individuals from Brazil.<\/p>\n
Not to ancient individuals from Peru.<\/p>\n
Not to ancient individuals from Chile.<\/p>\n
Not to ancient individuals from Argentina.<\/p>\n
Not to ancient individuals from Panama.<\/p>\n
Not to any present-day South American population included in the analysis.<\/p>\n
<\/p>\n
The researchers modeled the Checua population as a deeply divergent branch of the initial South American radiation \u2014 a lineage that split early from the ancestors of other South American populations and then apparently went its own way, developing a distinct genetic character on the Colombian Altiplano.<\/p>\n
This is what the paper meant when it called the Checua individuals “a previously unknown basal lineage.” Basal, in population genetics, means closer to the root of the population tree \u2014 an early branch that diverged before later differentiation produced the populations that are more familiar from other ancient South American genomes.<\/p>\n
Basal is not a synonym for primitive or simpler; it is a structural description of where a group sits in the branching diagram of population relationships.<\/p>\n
The Checua lineage was basal to the rest of the South American variation in the study’s comparison set.<\/p>\n
<\/p>\n
They were early.<\/p>\n
They were distinct.<\/p>\n
And in later samples from the same plateau, their specific genetic signature could no longer be found.<\/p>\n
What “Basal Lineage” Actually Means<\/p>\n
The language of population genetics can be precise in ways that mislead if not carefully explained.<\/p>\n
The term “basal lineage” carries a specific technical meaning that is easy to misread in either direction \u2014 toward mystification (a lost race, a mystery people with no relatives) or toward dismissal (just another Native American group, nothing special).<\/p>\n
The truth is more nuanced than either of those readings.<\/p>\n
<\/p>\n
When researchers analyze the genomes of a large set of populations and construct a statistical tree showing how they are related, some populations sit close to the trunk \u2014 they branched off early, before the other populations had diverged from each other.<\/p>\n
These early-branching populations are described as basal to the later ones.<\/p>\n
They share ancestry with all other populations in the tree, but they share their most recent common ancestry with a broad, early ancestor rather than with any specific later group.<\/p>\n
The Checua individuals occupy this basal position relative to other ancient South American populations in the researchers’ comparison set.<\/p>\n
Their genomes contain the signal of early South American ancestry \u2014 they share the broad foundation that connects all Native American populations, ultimately traceable back through the founding migrations from Asia.<\/p>\n
<\/p>\n
But they lack the specific shared genetic signatures that would tie them to any particular later branch of South American population history.<\/p>\n
To put it another way: they were ancient South Americans, part of the same broad family as all other Native Americans.<\/p>\n
But they were a branch of that family that split off early, before the differentiation that produced the specific ancestral patterns visible in later Andean, Amazonian, or southern-cone populations.<\/p>\n
They were not genetically unrelated to other Native Americans \u2014 they were related in a deep, early way, like a distant cousin who shares great-great-grandparents but whose family has been on a separate path since before any living person can remember.<\/p>\n
This is why it is wrong to say the Checua people were “not Native American” or “had no relatives in the Americas.” Their ancestry traces back to the same founding migrations that gave rise to all other Indigenous peoples of the Western Hemisphere.<\/p>\n
<\/p>\n
The novelty is that they represented a specific branch of that ancestry that diverged earlier than the branches documented in other ancient South American genomes, and that their specific genetic signature was not detectable in the later populations that the researchers studied.<\/p>\n
It is also why the framing of “vanished ancestry” or “lineage that disappeared from the genetic record” requires precise qualification.<\/p>\n
The paper does not claim that every biological descendant of the Checua people died without reproducing, or that the lineage was completely exterminated and left no living biological descendants anywhere on Earth.<\/p>\n
What it establishes, based on the populations included in the study’s comparison dataset, is that the specific genetic signature of the Checua group was not detectable in:<\/p>\n
– The nine Herrera-period individuals from the same plateau, dated approximately 2,000 years before present.
\n– The three Muisca-period individuals, dated approximately 1,200 and 520 years before present.
\n– The present-day South American populations included in the analysis.<\/p>\n
<\/p>\n
Future studies with larger datasets, including populations from other regions that were not part of this comparison, might detect traces of Checua-related ancestry that the current analysis could not find.<\/p>\n
The absence of a detectable signal in the populations studied so far is not the same as proof of total biological extinction.<\/p>\n
What it does mean is that the demographic history of the Bogot\u00e1 Altiplano was more dynamic than anyone had realized \u2014 that the genetic character of the people living on this plateau changed substantially, and apparently completely, between roughly 6,000 and 2,000 years ago.<\/p>\n
The Plateau At 6,000 Years Before Present<\/p>\n
<\/p>\n
Stepping back from the genetics for a moment, it is worth trying to understand what the world of the Checua people actually looked like \u2014 because the environmental and ecological context of their lives helps explain why this plateau was both an attractive place to live and a setting in which demographic change could occur.<\/p>\n
Six thousand years before the present corresponds to a period sometimes called the middle Holocene \u2014 the roughly five-thousand-year stretch between the end of the Ice Age and the beginning of the period in which agriculture and complex societies became widespread across much of the world.<\/p>\n
In much of the Americas, this was a period of substantial environmental change: the continent was still adjusting to the end of the Pleistocene, with ecosystems shifting as climates warmed, animal populations changed, and plant communities reorganized.<\/p>\n
The Bogot\u00e1 Altiplano at 6,000 years before present was a high grassland and wetland landscape, distinctly different from the tropical environments at lower elevations to the east and west.<\/p>\n
<\/p>\n
The plateau sits at roughly 2,600 meters above sea level \u2014 the same elevation as the city of Bogot\u00e1 today \u2014 in a basin created by the complex geological history of the Andes.<\/p>\n
The climate was cooler and more variable than at lower elevations, with cold nights and a climate that supported grassland, high-altitude wetlands called ci\u00e9nagas, and the forests that grew at the edges of the basin and in protected valleys.<\/p>\n
The animal life of the middle Holocene Altiplano included deer, which would have been a primary prey animal for hunter-gatherers.<\/p>\n
The wetlands supported abundant bird life.<\/p>\n
The rivers and lakes provided fish.<\/p>\n
<\/p>\n
The highland forest offered a range of plant foods, including tubers and roots that could be harvested year-round even when surface crops were unreliable.<\/p>\n
The people who lived here at 6,000 years before present were not the first.<\/p>\n
The Altiplano has yielded evidence of human occupation stretching back to at least 11,500 years before present at sites like Tibit\u00f3, one of the oldest dated archaeological sites on the plateau, where tools were found alongside the bones of extinct Pleistocene animals.<\/p>\n
The Checua individuals at 6,000 years were thus part of a long lineage of Altiplano occupation, though whether there was biological continuity between the earliest inhabitants and the Checua-period people cannot yet be determined from the current genetic data.<\/p>\n
By 6,000 years before present, the cultural pattern on the Altiplano had evolved toward the construction of more substantial settlements.<\/p>\n
<\/p>\n
The postholes at Checua suggest that people were building structures \u2014 perhaps not permanent year-round habitations, but more substantial than simple windbreaks or temporary shelters.<\/p>\n
The presence of habitation floors indicates that the site was used repeatedly and for extended periods.<\/p>\n
The economy was hunter-gatherer, based on hunting deer and other game, fishing, gathering wild plant foods, and exploiting the rich resources of the high-altitude wetland environment.<\/p>\n
Agriculture was not yet established on the plateau \u2014 the first clear evidence for maize cultivation does not appear until around 3,800 years before present, well after the period represented by the Checua individuals.<\/p>\n
These were people who knew their landscape intimately.<\/p>\n
<\/p>\n
They had developed the knowledge of the plateau’s seasonal patterns, the habits of its animals, the locations of reliable water sources and the best spots for hunting and gathering across the mountain year.<\/p>\n
That knowledge would have been transmitted from parents to children over generations, accumulated into the specialized ecological intelligence that hunter-gatherer communities in high-altitude environments around the world characteristically develop.<\/p>\n
They were, by any reasonable measure, a successful population \u2014 one that had lived on this demanding plateau for generations, had developed the physiological adaptations and cultural knowledge that high-altitude life requires, and had established recognizable patterns of settlement and subsistence.<\/p>\n
And then, at some point in the following two to four thousand years, the genetic signature that identifies them as a distinct lineage stopped appearing in the archaeological record of the plateau.<\/p>\n
<\/p>\n
The Gap: 6,000 To 2,000 Years Before Present<\/p>\n
Here is where the mystery deepens, and where the honest scientific answer requires acknowledging real uncertainty.<\/p>\n
Between the Checua individuals at approximately 6,000 years before present and the Herrera-period individuals at approximately 2,000 years before present, there is a gap of roughly four thousand years in the genomic dataset.<\/p>\n
The study does not have genetic data from Altiplano individuals who lived in between \u2014 at 5,000, 4,000, or 3,000 years before present.<\/p>\n
This means that researchers cannot say precisely when the Checua-related ancestry disappeared from the local genetic record, or how gradually or abruptly the transition occurred.<\/p>\n
<\/p>\n
The transition happened sometime in that four-thousand-year window, but the specific timing and the rate of change are unknown from the current evidence.<\/p>\n
This limitation is important for evaluating any claims about what happened to the Checua people.<\/p>\n
The data supports the conclusion that by 2,000 years before present, the genetic ancestry of the Altiplano population had shifted dramatically \u2014 the Herrera-period individuals look genetically very different from the Checua group.<\/p>\n
But the data does not support specific claims about events during the intervening period.<\/p>\n
What could have caused such a shift?<\/p>\n
<\/p>\n
Researchers and commentators have suggested several possibilities, none of which can be confirmed from the current evidence:<\/p>\n
Migration and replacement: A population from outside the plateau \u2014 in this case, eventually identified as having Central American-related ancestry \u2014 moved into the region and became demographically dominant, either displacing the earlier inhabitants through competition or absorbing them through intermarriage in proportions that diluted the Checua genetic signal below detectable levels.<\/p>\n
Population decline followed by replacement: The Checua-related population may have experienced a significant demographic decline \u2014 due to disease, climate stress, resource depletion, or other factors \u2014 that left the plateau partially depopulated, creating conditions in which incoming populations could establish themselves without resistance.<\/p>\n
Disease: Epidemic disease has been a powerful mechanism of population replacement in the Americas.<\/p>\n
<\/p>\n
While the diseases most strongly associated with Native American population collapse are the Old World pathogens introduced by European contact after 1492, there is no reason to assume that pathogen exposure was previously unknown as a demographic force.<\/p>\n
Novel diseases can spread through networks of human contact independently of colonialism.<\/p>\n
Climate stress: The middle to late Holocene on the Bogot\u00e1 Altiplano saw significant environmental changes, including volcanic activity that the research co-authors mentioned in discussions of the Checua population.<\/p>\n
Volcanic eruptions can disrupt local food systems, forcing populations to relocate or change their subsistence strategies in ways that might favor incoming groups with different agricultural capabilities.<\/p>\n
Kim-Louise Krettek, the study’s first author, stated in comments reported by news outlets that the genetic material of the Checua people disappeared completely from what the team could detect in individuals from the region around 2,000 years old.<\/p>\n
<\/p>\n
She described it as a “complete exchange of the population” in the area around Bogot\u00e1, based on the genetic evidence available.<\/p>\n
Andrea Casas-Vargas, the Colombian co-author, noted that the group “might have died out because of climate conditions, disease, or lack of food,” while acknowledging that these are speculative possibilities rather than documented causes.<\/p>\n
The researchers are clear in the paper itself that the replacement mechanism is not established by their data.<\/p>\n
The study documents that genetic replacement occurred.<\/p>\n
It does not identify a cause.<\/p>\n
What the study does establish is the direction of the incoming ancestry \u2014 and this is one of the paper’s most significant findings.<\/p>\n
<\/p>\n
The Arrival From The North: Central American Ancestry<\/p>\n
By approximately 2,000 years before present, the Altiplano individuals in the study \u2014 the nine Herrera-period individuals from the Laguna de la Herrera site \u2014 showed a genetic profile dramatically different from the Checua group.<\/p>\n
The Herrera-period individuals showed affinities to ancient populations from Panama, and to present-day Chibchan-language-speaking populations from the Isthmus of Panama and adjacent regions of Central and northwestern South America.<\/p>\n
The Chibchan language family is one of the most geographically widespread in the region connecting Central America to the northern Andes.<\/p>\n
<\/p>\n
It includes languages spoken by communities from Costa Rica and Panama through Colombia and into Venezuela.<\/p>\n
The geographic spread of Chibchan languages has long been recognized as evidence of a historically significant population expansion, but the genetic basis and direction of that expansion has been debated.<\/p>\n
The 2025 Colombia study provides direct genetic evidence supporting a southward or southeastward movement of people carrying Central American-related ancestry into the Bogot\u00e1 Altiplano by around 2,000 years before present.<\/p>\n
The Herrera-period individuals showed genetic profiles consistent with an origin in or connection to the population complex of the Isthmus of Panama and adjacent lowland areas.<\/p>\n
<\/p>\n
The Herrera ceramic complex \u2014 the Formative-period pottery tradition that appears on the Altiplano around 2,800 to 1,200 years before present \u2014 has long been debated by archaeologists.<\/p>\n
There were two competing hypotheses: either the Herrera ceramic tradition developed in situ from the local hunter-gatherer population through independent innovation, or it was introduced from outside the region by incoming populations.<\/p>\n
The genetic evidence from the 2025 study provides strong support for the second hypothesis.<\/p>\n
The people associated with the Herrera ceramic complex on the Bogot\u00e1 Altiplano were not genetically continuous with the Preceramic hunter-gatherers.<\/p>\n
Their ancestry profile looks Central American, not like a local continuation of the Checua population.<\/p>\n
<\/p>\n
This is a significant conclusion for the archaeology of the northern Andes.<\/p>\n
It means that the introduction of the Herrera ceramic tradition was not simply a cultural adoption \u2014 the spread of new pottery-making knowledge among an existing population.<\/p>\n
It was accompanied by, and possibly caused or enabled by, an actual movement of people.<\/p>\n
The nature of that movement \u2014 its scale, its pace, whether it involved peaceful coexistence with or violent displacement of the existing inhabitants, what social forms it took \u2014 cannot be determined from the genetic data alone.<\/p>\n
Genetics tells us that ancestry changed.<\/p>\n
<\/p>\n
It does not tell us the human story of how that change happened.<\/p>\n
The Herrera Period And What It Left Behind<\/p>\n
The Herrera ceramic complex is one of the defining cultural horizons of the Bogot\u00e1 Altiplano, and understanding it is essential to appreciating the full significance of the 2025 genetic findings.<\/p>\n
Herrera ceramics are distinctive: handmade pottery with specific decorative conventions, shapes, and firing techniques that archaeologists have used to identify sites associated with this cultural tradition across a broad area of the northern Andes and adjacent lowlands.<\/p>\n
The Herrera period on the Altiplano spans roughly 2,800 to 1,200 years before present, a period during which the plateau underwent significant transformations.<\/p>\n
<\/p>\n
The most important of these transformations was agricultural intensification.<\/p>\n
While maize cultivation first appeared on the Altiplano around 3,800 years before present, the Herrera period saw its expansion and the development of more complex food production systems.<\/p>\n
The populations of the Herrera period appear to have been more sedentary than their Preceramic predecessors, living in larger settlements and maintaining more systematic relationships with their agricultural landscapes.<\/p>\n
The Laguna de la Herrera site \u2014 from which the nine Herrera-period individuals in the 2025 study were analyzed \u2014 is situated along what was historically a lake environment on the western edge of the Bogot\u00e1 savanna.<\/p>\n
Lake and wetland margins are productive environments for sedentary agricultural communities, offering abundant water, rich soils, and diverse food resources from both aquatic and terrestrial ecosystems.<\/p>\n
<\/p>\n
The genetic profile of the Herrera-period individuals, as established by the 2025 study, shows the shift in ancestry that the researchers documented: ancestry related to Central American populations and Chibchan-language communities, replacing the earlier Checua-related ancestry entirely.<\/p>\n
No detectable component of the Checua group’s distinct genetic signature was found in the Herrera individuals.<\/p>\n
This represents a complete genetic turnover \u2014 the most dramatic finding in the paper’s analysis of the Altiplano time series.<\/p>\n
Whatever processes brought the Herrera-period population to the plateau, they effectively replaced the earlier genetic ancestry without apparent continuation of the earlier lineage.<\/p>\n
Or at least, that is what the available data shows.<\/p>\n
The caveat about the four-thousand-year gap in the genomic record applies here as well.<\/p>\n
<\/p>\n
Without genetic data from individuals who lived on the plateau between 6,000 and 2,000 years before present, researchers cannot know whether the transition was abrupt or gradual, or whether intermediate stages might show more complex patterns of mixing and replacement.<\/p>\n
The Muisca: Continuity Through Cultural Change<\/p>\n
The most famous culture of the Bogot\u00e1 Altiplano is not the Preceramic hunter-gatherers of Checua, nor even the Herrera-period agriculturalists who replaced them.<\/p>\n
It is the Muisca \u2014 the chiefdom society whose sophisticated political organization, elaborate religious practices, and spectacular goldwork made such an impression on the first European explorers that they became central to the legend of El Dorado.<\/p>\n
The Muisca achieved their greatest cultural elaboration between roughly 600 and 1600 CE \u2014 approximately 1,400 to 400 years before present.<\/p>\n
<\/p>\n
At their height, the Muisca chiefdoms controlled most of the Altiplano Cundiboyacense, organized complex redistribution economies, constructed salt-mining operations, and maintained the trading networks that circulated gold, emeralds, cotton, and other goods across a wide region of the northern Andes.<\/p>\n
The question of the Muisca’s origins \u2014 where they came from and how they related to the earlier populations of the plateau \u2014 has been debated by archaeologists and historians.<\/p>\n
Were the Muisca the descendants of the Herrera-period populations, or did they represent a new intrusion?<\/p>\n
And what was the relationship between the Muisca cultural complex and the genetic ancestry of the people who created it?<\/p>\n
The 2025 genetic study addressed these questions directly, analyzing three individuals associated with Muisca culture \u2014 from the Las Delicias site (approximately 1,200 years before present) and the Soacha site (approximately 520 years before present) \u2014 and comparing their genomes to the Herrera-period and Checua-period populations.<\/p>\n
<\/p>\n
The finding was clear: despite the dramatic cultural changes that separate the Herrera and Muisca periods \u2014 changes in political organization, ceramic styles, ritual practices, and economic complexity \u2014 the Muisca-period individuals showed genetic continuity with the Herrera-period individuals, not with the earlier Checua group.<\/p>\n
This is an important negative result in its own right.<\/p>\n
Some researchers had speculated that the rise of Muisca cultural complexity might have involved a new population influx that brought the social innovations associated with Muisca chiefdoms.<\/p>\n
The genetic data does not support this.<\/p>\n
The people who built the Muisca chiefdoms appear to have been the biological descendants of the Herrera-period population, carrying the same Central American-related ancestry that had replaced the Checua lineage roughly two thousand years earlier.<\/p>\n
Culture changed dramatically between the Herrera and Muisca periods.<\/p>\n
<\/p>\n
The genes did not.<\/p>\n
This finding illustrates a pattern that ancient DNA research has documented repeatedly in various parts of the world: cultural transformation and genetic replacement are not always linked.<\/p>\n
People can change their cultural practices dramatically while maintaining biological continuity with their predecessors.<\/p>\n
Conversely, major genetic changes \u2014 as occurred between the Checua and Herrera periods \u2014 can accompany cultural change, but this is not inevitable.<\/p>\n
The Muisca case is an example of cultural elaboration without genetic discontinuity.<\/p>\n
<\/p>\n
The Checua-to-Herrera transition is an example of both cultural and genetic change occurring together.<\/p>\n
Ancient DNA allows researchers to distinguish between these different patterns in ways that archaeology alone cannot.<\/p>\n
The Two Guane Individuals<\/p>\n
The 2025 study also included two individuals from the Los Curos site in the Purnia area, associated with the Guane population of the northern Santander region of Colombia.<\/p>\n
These individuals dated to approximately 530 years before present \u2014 the early colonial period \u2014 and provided a genetic data point from a population geographically adjacent to but culturally distinct from the Muisca.<\/p>\n
The Guane were known to Spanish colonizers as a distinct people occupying the region north of the main Muisca territories.<\/p>\n
<\/p>\n
They had their own language, their own social organization, and their own relationship to the highland environments of the Eastern Cordillera.<\/p>\n
The 2025 study’s inclusion of Guane individuals extended the geographic scope of the genetic analysis beyond the Bogot\u00e1 Altiplano proper and provided a comparative perspective on how the regional genetic landscape varied across culturally distinct groups.<\/p>\n
The genetic analysis of the Guane individuals from Purnia suggested some differences from the Altiplano population, consistent with the idea that the populations of the northern Santander region had a somewhat distinct demographic history from those of the Bogot\u00e1 savanna.<\/p>\n
However, the Guane individuals also showed affinities to the Central American-related ancestry documented in the Herrera and Muisca-period Altiplano individuals, suggesting that the broader regional pattern of Central American ancestry replacement applied across a wider area than just the Bogot\u00e1 Altiplano.<\/p>\n
<\/p>\n
This extends the significance of the study’s findings: the movement of Central American-related ancestry that replaced the Checua hunter-gatherers was not a purely local phenomenon limited to the Bogot\u00e1 basin.<\/p>\n
It was part of a larger demographic transformation affecting at least the broader northern Andes and Eastern Cordillera of Colombia.<\/p>\n
The Chibchan Connection And Its Implications<\/p>\n
The identification of Central American-related ancestry \u2014 specifically, affinities to ancient Panamanian individuals and to present-day Chibchan-speaking communities \u2014 as the replacement ancestry on the Bogot\u00e1 Altiplano connects the 2025 Colombia findings to a broader conversation about the Chibchan language family and its demographic history.<\/p>\n
Chibchan languages are spoken today by communities scattered across a large geographic area: from the Bribri and Cabecar of Costa Rica, through the Kuna (Guna) of Panama, to the Wiwa, Arhuaco, Kogi, and Kankuamo of the Sierra Nevada de Santa Marta in Colombia, to the Tunebo\/U’wa of the eastern Colombian Andes.<\/p>\n
<\/p>\n
The geographic fragmentation of Chibchan communities reflects a history of significant demographic change since European contact, including population decline from disease and displacement, and the loss of many formerly Chibchan-speaking communities.<\/p>\n
Linguists and anthropologists have long debated the origin and spread of the Chibchan languages.<\/p>\n
The geographic center of Chibchan linguistic diversity \u2014 the Isthmus of Panama and adjacent regions \u2014 has been proposed as the homeland from which Chibchan languages spread both northward into Central America and southward into the northern Andes.<\/p>\n
The 2025 genetics study provides independent genetic support for a southward or southeastward movement of Chibchan-related populations into the Bogot\u00e1 Altiplano.<\/p>\n
The genetic affinities of the Herrera-period and Muisca-period individuals to ancient Panamanians and to present-day Chibchan-speaking communities is consistent with a population expansion from the Isthmus of Panama region into the northern Andes, accompanied by or associated with the spread of Chibchan languages.<\/p>\n
<\/p>\n
Whether the Muisca themselves spoke a Chibchan language is a question that historical records confirm: Muysccubun, the language of the Muisca, is classified as a Chibchan language.<\/p>\n
Its extinction \u2014 Muysccubun ceased to be spoken as a living language in the nineteenth century, replaced by Spanish \u2014 has made the documentation of this connection more challenging, but its Chibchan affiliation is well-established.<\/p>\n
The genetics thus align with the linguistics: the people who established the Herrera cultural tradition and whose descendants built the Muisca chiefdoms spoke Chibchan languages and carried genetics consistent with an ultimate origin in the Isthmus of Panama \/ Costa Rica \/ Panama region.<\/p>\n
This does not mean that the Muisca were simply transplanted Panamanians.<\/p>\n
<\/p>\n
The journey from the Isthmus of Panama to the Bogot\u00e1 Altiplano \u2014 across lowland forests, up the slopes of the Andes, into the high cold plateau \u2014 would have taken many generations and involved significant adaptation to new environments.<\/p>\n
The Herrera and Muisca cultures were distinctly Colombian and distinctly Andean in their development; the Central American ancestry connection refers to a deep ancestral source, not to a recent or direct cultural derivation.<\/p>\n
But the genetic findings do support the idea that the northern Andes were a destination for population movements from the north \u2014 from the region where Central and South America connect \u2014 and that those movements fundamentally transformed the demographic character of the Bogot\u00e1 Altiplano some two thousand years ago.<\/p>\n
A Second Opening: What The Study Changes<\/p>\n
<\/p>\n
At this point in the story, it is worth stepping back and considering what the 2025 Science Advances paper actually changes in our understanding of South American prehistory.<\/p>\n
Before this study, Colombia was a blank space in the ancient DNA map of the Americas.<\/p>\n
The country that sits at the junction of Central and South America \u2014 the geographic entry point into the larger continent \u2014 had yielded zero published ancient human genomes.<\/p>\n
This was not because Colombia was archaeologically unimportant; the opposite was true.<\/p>\n
It was because the environmental conditions had made ancient DNA work difficult, and because the scientific infrastructure to conduct such work had not been available in Colombia.<\/p>\n
The 2025 study changed all of that simultaneously.<\/p>\n
<\/p>\n
It provided the first ancient genomic data from Colombia \u2014 not just one genome, but 21, covering 5,500 years of the Altiplano’s occupation.<\/p>\n
It addressed multiple major questions in one dataset.<\/p>\n
Most significantly, it documented a previously unknown early branch of South American population history \u2014 a lineage that diverged early from the common ancestor of other South American populations and that was established on the Bogot\u00e1 Altiplano by at least 6,000 years before present.<\/p>\n
The discovery of this previously undocumented lineage matters for several reasons beyond its intrinsic interest.<\/p>\n
First, it demonstrates that the genetic diversity of ancient South America was greater than the existing dataset had suggested.<\/p>\n
<\/p>\n
The Checua lineage shows that the early peopling of South America was not a simple, single expansion from a single source population that spread uniformly across the continent.<\/p>\n
Different regions harbored genetically distinct populations that had been separated long enough to develop distinct genetic characters.<\/p>\n
Colombia’s high plateau was home to one such population \u2014 one that left no visible trace in any of the other ancient genomes studied.<\/p>\n
Second, it raises questions about what other regions might harbor similarly distinct populations.<\/p>\n
If the Bogot\u00e1 Altiplano \u2014 which has been archaeologically studied for decades \u2014 was home to a genetically distinct population that was unknown to science until 2025, what other corners of South America might yield comparable surprises?<\/p>\n
Western Colombia, the Pacific lowlands, the Caribbean coast, the eastern lowlands of the Llanos \u2014 these regions remain almost entirely uncharted from an ancient DNA perspective.<\/p>\n
<\/p>\n
Third, it provides direct genetic evidence for the linguistic and cultural expansion associated with the Chibchan language family, demonstrating that the spread of Chibchan languages into the northern Andes was accompanied by substantial genetic change \u2014 the movement of people, not merely the adoption of cultural innovations by existing populations.<\/p>\n
Fourth, it raises fundamental questions about the demographic dynamics of northern South America between 6,000 and 2,000 years before present \u2014 a four-thousand-year period during which, the data suggest, a complete genetic turnover occurred on the Altiplano, but for which the specific causes and mechanisms remain unknown.<\/p>\n
The Question Of What “Disappeared” Means<\/p>\n
Any honest account of the Checua findings must grapple carefully with the language of disappearance.<\/p>\n
The lineage, as the study’s authors note, “does not contribute genetically to ancient or present-day South American populations” \u2014 a finding that has been summarized in popular coverage as the ancestry having “disappeared,” “vanished,” or the population having “completely replaced.”<\/p>\n
<\/p>\n
These characterizations are accurate in a limited sense: the Checua genetic signature is not detectable in the populations included in the study’s comparison dataset.<\/p>\n
But “disappeared” and “vanished” are stronger claims than the evidence strictly supports, for several reasons.<\/p>\n
The comparison dataset, while extensive, is not exhaustive.<\/p>\n
Present-day South American populations show high genetic diversity, and many communities across western Colombia, Venezuela, Ecuador, and adjacent regions were not included in the comparison.<\/p>\n
It is possible \u2014 not certain, but possible \u2014 that traces of Checua-related ancestry survive in populations that were not sampled.<\/p>\n
The four-thousand-year gap in the ancient DNA timeline means that intermediate steps in the transition are invisible to the current analysis.<\/p>\n
<\/p>\n
A gradual process of admixture, during which Checua-related ancestry was progressively diluted as new populations arrived, would eventually produce a signal below detection thresholds without requiring every biological descendant to die without reproducing.<\/p>\n
The genetic detection threshold matters.<\/p>\n
When researchers describe ancestry as “not detectable,” they mean not detectable at the statistical level of their analysis.<\/p>\n
Small amounts of ancestry from a distant source \u2014 ancestry that has been diluted across many generations of admixture \u2014 can fall below detection thresholds even when it technically persists in the genomes of living populations.<\/p>\n
None of this undermines the core finding that the Checua genetic signature underwent a dramatic transition between 6,000 and 2,000 years before present.<\/p>\n
The finding is real and significant.<\/p>\n
<\/p>\n
But characterizing it as proof of complete biological extinction, with zero living descendants anywhere, would exceed what the evidence can support.<\/p>\n
The more scientifically defensible language \u2014 which the 2025 paper itself uses \u2014 is that the Checua lineage “does not contribute genetically” to the populations studied, and that its ancestry is “not detectable” in later Colombian groups or in present-day South Americans included in the analysis.<\/p>\n
This is different from saying that every biological descendant of every Checua individual died without children.<\/p>\n
It means that whatever happened to the Checua population \u2014 whether replacement, dilution, migration, disease, or some combination \u2014 the specific genetic character that distinguishes them as a lineage cannot be found in the places where researchers looked.<\/p>\n
<\/p>\n
Whether it might be found somewhere else \u2014 in populations not yet studied, in regions not yet sampled \u2014 is an open scientific question.<\/p>\n
The Altiplano As A Corridor<\/p>\n
Understanding the Bogot\u00e1 Altiplano’s geographic role in the broader Americas helps explain why the demographic history documented in the 2025 study matters beyond the specific region.<\/p>\n
The Colombian Andes form the entry point into South America from the north.<\/p>\n
Anyone moving overland from Central America into South America must cross or go around the mountains and lowlands of Colombia.<\/p>\n
The Andes divide here into multiple ranges \u2014 the Cordillera Occidental, the Cordillera Central, and the Cordillera Oriental \u2014 with valleys and passes that channel movement and population flow.<\/p>\n
<\/p>\n
The Bogot\u00e1 Altiplano, on the Cordillera Oriental, is one of the major highland basins of this system.<\/p>\n
At 2,600 meters above sea level, it is cool enough to be productive for highland agriculture but not so high that human occupation becomes physiologically difficult.<\/p>\n
Its rich soils, fed by the volcanic geology of the Andes, supported intensive agriculture in the Muisca period and continue to do so today \u2014 the Bogot\u00e1 savanna is one of the most agriculturally productive areas in Colombia.<\/p>\n
As a highland corridor, the Altiplano offered a route for movement between the northern Andes and the broader South American highlands to the south.<\/p>\n
<\/p>\n
The Eastern Cordillera extends southward from Colombia into Ecuador, Peru, and Bolivia, forming the backbone of the Andes along which populations could theoretically move for thousands of kilometers.<\/p>\n
Any population expanding southward from Central America along the highland spine of the Andes would have passed through or near the Bogot\u00e1 Altiplano.<\/p>\n
The genetic evidence from the 2025 study is consistent with exactly this kind of movement: people with Central American-related ancestry arriving on the Bogot\u00e1 Altiplano and establishing themselves as the dominant genetic population.<\/p>\n
Whether they moved further southward, and whether their genetic signature can be traced into the Ecuadorian or Peruvian highlands, is a question that requires ancient DNA data from those regions.<\/p>\n
The Altiplano’s role as a corridor also helps explain why a distinct and isolated lineage might have developed there.<\/p>\n
<\/p>\n
If the Checua population became isolated on the plateau \u2014 separated from other South American populations by the geography of the Andes and the ecological barriers of the surrounding lowlands \u2014 they could have evolved a distinct genetic character over the thousands of years of their occupation.<\/p>\n
Geographic isolation is one of the most powerful drivers of genetic differentiation, and the high-altitude environment of the Andes can create effective barriers even in the absence of long distances.<\/p>\n
The Checua lineage’s deeply divergent position in the population tree is consistent with a history of geographic isolation on the plateau.<\/p>\n
How long that isolation lasted before the 6,000-year-before-present individuals whose genomes were sequenced, and how the Checua population initially became established on the plateau, are questions that would require older ancient DNA from the same region to answer.<\/p>\n
The Archaeology Behind The Genetics: More Than One Site<\/p>\n
<\/p>\n
The 2025 study’s five-site approach represents one of the most ambitious ancient DNA projects ever undertaken in northern South America, and the archaeological context of each site matters for interpreting the genetic findings.<\/p>\n
Checua, as discussed, is the Preceramic open-area site in Nemoc\u00f3n where the seven oldest individuals in the study were found.<\/p>\n
The site’s elongated-skull individuals and the dental pathology observations add physical anthropological data to the genetic picture, though the physical characteristics should not be overinterpreted as evidence of a separate origin or unusual biology.<\/p>\n
Laguna de la Herrera is the Herrera-period site from which nine individuals were analyzed.<\/p>\n
This site is located along the margins of what was historically a lake environment on the western Bogot\u00e1 savanna \u2014 a productive setting for the early agricultural communities associated with the Herrera ceramic complex.<\/p>\n
<\/p>\n
The site preserves evidence of the transition from hunter-gatherer to agricultural settlement on the plateau.<\/p>\n
Las Delicias and Soacha provided Muisca-period individuals.<\/p>\n
The Soacha site \u2014 from the municipality of the same name, just south of Bogot\u00e1 \u2014 is associated with the late Muisca period, roughly 500 years before present, and thus overlaps with the earliest Spanish contact.<\/p>\n
The Las Delicias site represents the earlier Muisca period, approximately 1,200 years before present.<\/p>\n
The Purnia site in the Los Curos area provided the two Guane individuals, extending the study’s geographic scope northward from the Bogot\u00e1 basin.<\/p>\n
The five-site approach allowed the researchers to construct their genomic time series \u2014 their “transect” \u2014 tracking genetic change across the full documented period of Altiplano occupation in their dataset.<\/p>\n
<\/p>\n
The selection of sites spanning from the Preceramic through the Muisca period ensured that the major cultural transitions on the plateau were represented in the genetic record.<\/p>\n
What the time series revealed was not gradual change but apparent discontinuity: a sharp break in the genetic record between the Preceramic and Herrera periods, with no detectable genetic continuity between the two populations.<\/p>\n
Whether future research will fill in this gap \u2014 identifying individuals from the intervening 4,000 years who show intermediate genetic profiles \u2014 remains to be seen.<\/p>\n
Finding and successfully extracting DNA from individuals who lived on the Altiplano between 6,000 and 2,000 years before present would be enormously valuable for understanding the timing and mechanism of the transition.<\/p>\n
What The Study Does Not Say<\/p>\n
<\/p>\n
In the coverage of this research, several claims have been made that go beyond what the study’s evidence supports.<\/p>\n
Clarifying what the study does not say is as important as describing what it does say.<\/p>\n
The study does not say that the Checua individuals were a different species.<\/p>\n
They were fully anatomically modern human beings \u2014 Homo sapiens \u2014 whose genomes, for all their divergence from other South American populations, were unmistakably within the range of human genetic diversity.<\/p>\n
Population genetics routinely finds distinct lineages within the human species; distinctness at the population level is not the same as biological speciation.<\/p>\n
The study does not say that the Checua people had no relatives anywhere in the Americas.<\/p>\n
<\/p>\n
Their genomes indicate that they were part of the early South American radiation \u2014 the broader founding of South American populations from the migration out of Beringia and through North America.<\/p>\n
They share this deep ancestry with all other Native Americans.<\/p>\n
The distinctness is in their specific branch of that early radiation, not in being outside it entirely.<\/p>\n
The study does not identify the mechanism by which the Checua genetic signature was replaced.<\/p>\n
The paper documents the fact of replacement.<\/p>\n
It does not establish whether replacement occurred through violent conflict, disease, absorption through intermarriage, outmigration of the Checua population, or some combination.<\/p>\n
Saying that there was a “complete exchange of the population” describes a genetic outcome, not a historical cause.<\/p>\n
<\/p>\n
The study does not establish that no living person carries any ancestry related to the Checua group.<\/p>\n
The populations included in the comparison were extensive but not complete.<\/p>\n
Ancient populations that were not included in the study’s reference panel might carry traces of Checua-related ancestry that the current analysis could not detect.<\/p>\n
The study does not represent the final word on the demographic history of Colombia or the northern Andes.<\/p>\n
It represents a major first step \u2014 the first published ancient genomic dataset from Colombia \u2014 that opens many more questions than it closes.<\/p>\n
The four-thousand-year gap in the genomic time series, the limited coverage of other Colombian regions, and the absence of data from neighboring Venezuela, Ecuador, and Panama all mean that the full picture will require substantially more work to emerge.<\/p>\n
<\/p>\n
The First Colombian Ancient Genomes And What They Required<\/p>\n
The 2025 study’s significance extends beyond its specific scientific findings to what it represents institutionally and methodologically.<\/p>\n
This was the first published ancient genomic dataset from Colombia \u2014 a country that has been archaeologically active for decades and that sits at one of the most important junctions in New World prehistory.<\/p>\n
The lead author, Kim-Louise Krettek, is affiliated with the Senckenberg Center for Human Evolution and Paleoenvironment in Germany, one of the world’s leading centers for ancient genomic research.<\/p>\n
The co-lead author, Andrea Casas-Vargas, is at the Universidad Nacional de Colombia \u2014 representing the growing capacity of Colombian scientific institutions to participate in international ancient DNA research.<\/p>\n
<\/p>\n
The involvement of Colombian researchers was not incidental.<\/p>\n
They brought knowledge of the archaeological context, the institutional relationships with Colombian heritage institutions that allowed access to the ancient materials, and the local expertise that makes it possible to navigate the complex permissions and collaborative frameworks that archaeological research in Colombia requires.<\/p>\n
Jos\u00e9 Vicente Rodr\u00edguez Cuenca’s contributions as a physical anthropologist, William Usaqu\u00e9n’s work in biological anthropology, and the other Colombian contributors to the study represent an integration of international methodological expertise with local scientific and archaeological knowledge.<\/p>\n
This kind of international collaboration is increasingly the model for ancient DNA research in Latin America and in other regions where the materials of interest are held by national institutions and where the scientific capacity to analyze those materials is distributed across multiple countries and institutions.<\/p>\n
<\/p>\n
The 2025 Colombia study exemplifies how this collaboration can work and what it can produce.<\/p>\n
The extraction of genome-wide data from 21 ancient Colombian individuals required years of laboratory work, the optimization of ancient DNA extraction protocols for the specific preservation conditions of Altiplano archaeological sites, and the application of bioinformatic methods to authenticate and analyze the resulting data.<\/p>\n
The success of the effort represents not just scientific achievement but institutional and logistical accomplishment.<\/p>\n
Cosimo Posth, the study’s senior author, is a leading ancient DNA researcher whose work spans Europe, Asia, and the Americas.<\/p>\n
His involvement alongside Colombian and German co-authors reflects the increasingly global and interdisciplinary character of ancient genomics.<\/p>\n
<\/p>\n
The Broader South American Genomic Picture<\/p>\n
The Checua findings connect to a set of broader patterns that have been emerging from ancient DNA research across South America over the past several years.<\/p>\n
The early population history of South America was more complex than previously appreciated.<\/p>\n
Ancient genomes from Brazil, Argentina, Chile, and Peru have revealed that the continent’s prehistoric population was not a single, homogeneous group that spread from a single source.<\/p>\n
Instead, the genetic record shows multiple distinct lineages, some of which show complex patterns of mixture, divergence, and replacement.<\/p>\n
<\/p>\n
One important finding from other South American ancient DNA studies has been the identification of what some researchers call a “Population Y” or “Australasian-related” signal in some early South American genomes \u2014 a genetic component that appears to connect some early South Americans to populations from Southeast Asia or Australia, suggesting either a distinct founding migration or a more complex pre-Beringian ancestry than the simple North America-to-South America model assumes.<\/p>\n
The Colombia study did not detect this signal in the Checua individuals, though the limited coverage and specific comparison populations used mean that this absence should be interpreted cautiously.<\/p>\n
Other ancient South American genomes \u2014 including some from early Amazonian sites and from the southern cone \u2014 show high levels of affinity to the “southern Native American” lineage associated with Anzick-1 and the Clovis-related founding population.<\/p>\n
The Checua individuals’ lack of affinity to this lineage suggests that they represent a distinct trajectory within the early South American radiation \u2014 one that diverged from the common ancestor of other South Americans before the southern Native American ancestry pattern became established.<\/p>\n
<\/p>\n
The geographic pattern emerging from ancient DNA work suggests that the early South Americans were more diverse than their later descendants \u2014 that the continent’s population history involved significant replacement and homogenization over time, with some early lineages (like the Checua group) disappearing from the genetic record while later expansions (like the Herrera-related Central American movement) established more widespread patterns.<\/p>\n
The Colombian findings fit into this emerging picture as a specific regional case study \u2014 documentation of how one small region at the junction of the two Americas underwent two major demographic transitions in the space of a few thousand years, ending with the population whose descendants built one of pre-Columbian South America’s most sophisticated societies.<\/p>\n
What Future Research Might Reveal<\/p>\n
The 2025 Colombia study opened many more questions than it answered, and the researchers themselves were explicit about the directions in which future work should go.<\/p>\n
<\/p>\n
The most pressing need is for ancient DNA from the four-thousand-year gap in the Altiplano time series.<\/p>\n
Individuals who lived on the plateau between roughly 6,000 and 2,000 years before present would allow researchers to determine when the genetic transition began, how long it took, and whether it involved gradual admixture or abrupt replacement.<\/p>\n
Finding well-preserved individuals from this period and extracting usable DNA from them would be technically challenging but enormously informative.<\/p>\n
Geographic expansion of the ancient DNA sample is equally important.<\/p>\n
The 2025 study covers the Bogot\u00e1 Altiplano and the adjacent Guane territory \u2014 a small portion of Colombia’s diverse geography.<\/p>\n
<\/p>\n
Western Colombia, the Caribbean coast, the Pacific lowlands, the Amazonian regions, and the northern Sierra Nevada de Santa Marta are all essentially uncharted from an ancient DNA perspective.<\/p>\n
Each of these regions has its own distinctive archaeological record and its own Indigenous populations, and each might reveal distinct population histories.<\/p>\n
The Isthmus of Panama and neighboring Costa Rica are particularly important for understanding the source of the Central American ancestry documented in the Herrera-period Altiplano individuals.<\/p>\n
Greater coverage of ancient genomes from these areas would allow researchers to trace the specific population movements that brought Central American ancestry into the northern Andes, identifying when those movements began, what direction they took, and how rapidly they transformed the genetic landscape.<\/p>\n
Venezuela and Ecuador, which occupy the geographic corridor between Colombia and other well-studied regions of South America, are also poorly represented in the ancient DNA record.<\/p>\n
<\/p>\n
Understanding how population movements propagated through these intermediate regions is crucial for connecting the Bogot\u00e1 Altiplano findings to the broader South American picture.<\/p>\n
The question of whether any living populations carry detectable traces of Checua-related ancestry also deserves investigation.<\/p>\n
The comparison populations included in the 2025 study were extensive, but not exhaustive.<\/p>\n
More comprehensive sampling of contemporary Indigenous communities from Colombia and adjacent regions, combined with larger ancient genomic datasets from early periods, might detect signals of Checua-related ancestry that the current analysis could not resolve.<\/p>\n
Finally, the study’s findings about the persistence of Central American ancestry through the Muisca period raise questions about what happened to that ancestry after Spanish contact.<\/p>\n
<\/p>\n
The colonial period was demographically catastrophic for the Muisca and other Indigenous peoples of the Altiplano; disease, displacement, and forced labor resulted in severe population decline.<\/p>\n
Whether the genetic heritage of the Herrera-Muisca population survives in any modern communities \u2014 and in what proportions and distributions \u2014 is a question that modern genomic studies of contemporary populations could address.<\/p>\n
The People Who Will Never Be Named<\/p>\n
There is something that the science cannot give to the Checua people, and it is worth naming honestly.<\/p>\n
We cannot know their names.<\/p>\n
We cannot know the language they spoke, the stories they told about themselves and their world, the names they gave to the hills and valleys of the Checua River valley, or the words they used for the animals they hunted and the plants they gathered.<\/p>\n
<\/p>\n
We cannot know how they understood their own history \u2014 whether they had traditions that reached back to the time of their arrival on the plateau, or what those traditions might have said about where they came from.<\/p>\n
The bones and the genomes tell us things that are genuinely remarkable: that they were a distinct lineage, that they had been on that plateau for a long time, that they were part of the early South American radiation but had taken their own path within it.<\/p>\n
This is knowledge that no previous generation of scientists possessed, and it is knowledge that changes our understanding of the deep human history of northwestern South America.<\/p>\n
But it is not a full human story.<\/p>\n
<\/p>\n
It is a molecular record \u2014 a record of ancestry and relatedness, of divergence and isolation, of the population-level patterns that emerge when you compare genomes across thousands of years of human history.<\/p>\n
The inner life of the Checua people, their social organization, their relationships with the landscape and with neighboring communities, their response to whatever forces eventually displaced their genetic presence from the plateau \u2014 these things are not in the bones, and the ancient DNA cannot speak to them.<\/p>\n
What the science can do is witness their existence.<\/p>\n
Before 2025, the Checua people were not known to science in any molecular sense.<\/p>\n
Their bones had been excavated, their physical characteristics documented, their archaeological context investigated.<\/p>\n
<\/p>\n
But their place in the genetic landscape of the Americas was unknown.<\/p>\n
They were, in the language of population genetics, an uncharacterized lineage \u2014 a group whose specific position in the family tree of South American populations had never been determined.<\/p>\n
Now it has been.<\/p>\n
The Checua individuals from the Bogot\u00e1 Altiplano, the seven hunter-gatherers who lived on that high Colombian plateau roughly 6,000 years ago, have been placed \u2014 with all appropriate scientific uncertainty \u2014 in the family tree of the Americas.<\/p>\n
They were early South Americans who took an independent path from the common ancestor they shared with other South American populations.<\/p>\n
<\/p>\n
They developed on that plateau, left the material traces that archaeologists have been studying for decades, and eventually \u2014 for reasons the science cannot yet determine \u2014 stopped leaving the genetic traces that would have carried their specific lineage forward into later populations.<\/p>\n
To witness them, in this limited but real way, is something.<\/p>\n
The Resolution: A More Complex Map<\/p>\n
The founding story of the Americas is not a single story.<\/p>\n
That is the fundamental lesson of the past decade of ancient DNA research, and the 2025 Colombia study is one of its clearest demonstrations.<\/p>\n
The peopling of two continents was not a single population flowing steadily southward from a single source, differentiating gradually into regional variants.<\/p>\n
It was a series of distinct movements, radiations, isolations, extinctions, and replacements \u2014 a demographic history as complicated and event-filled as any other major chapter of human prehistory.<\/p>\n
<\/p>\n
The Checua people were one chapter of that history \u2014 a chapter that had not been read before.<\/p>\n
Their genomes preserve the signature of an early South American population that took an independent trajectory on the Bogot\u00e1 Altiplano, developing a distinct genetic character that does not appear in the later populations of the same plateau or in the present-day South American populations included in the comparison dataset.<\/p>\n
By approximately 2,000 years before present, that genetic character had been replaced.<\/p>\n
The people of the Herrera period carried ancestry related to Central American populations \u2014 the Isthmus of Panama, the Chibchan-speaking communities of that region \u2014 that bore no detectable trace of the earlier Checua lineage.<\/p>\n
<\/p>\n
The mechanism of this replacement remains unknown: migration, disease, climate stress, or some combination of forces could all be consistent with the genetic evidence.<\/p>\n
The later history of the plateau \u2014 the elaboration of the Herrera ceramic tradition, the development of Muisca chiefdom society, the construction of the sophisticated political and economic networks that made the Muisca one of the most complex pre-Columbian societies north of the Inca \u2014 unfolded in a population that carried the Central American ancestry, not the earlier Checua lineage.<\/p>\n
The Muisca, famous for their gold work and their religious ceremonies and the El Dorado legend they inspired, were the cultural and biological descendants of populations that had come from the north.<\/p>\n
And the people who had lived on that plateau for the preceding four thousand years \u2014 the Checua lineage \u2014 were not their ancestors, at least not in any way that the current genetic tools can detect.<\/p>\n
<\/p>\n
What this means for our understanding of the Americas is that the demographic map of the continent was more dynamic, more subject to change, and more complicated than the archaeological record alone could reveal.<\/p>\n
Before ancient DNA, the best available evidence suggested that the populations of the Bogot\u00e1 Altiplano were broadly related to the other highland populations of the Andes, part of a continuous human occupation stretching from northern Colombia to the southern tip of South America.<\/p>\n
The genetics reveals instead a history of distinct populations, genetic replacement, and demographic transformation \u2014 a history invisible to archaeology because the bones of the Herrera-period and Muisca-period individuals gave no visible indication of their genetic distance from their Preceramic predecessors.<\/p>\n
The Checua people were part of that story.<\/p>\n
<\/p>\n
They were not a mystery race or an alien intrusion or a lost civilization in any sensational sense.<\/p>\n
They were hunter-gatherers who lived on a high Colombian plateau for generations, developed a genetic character distinct from other South Americans, and left a record \u2014 in bone and ultimately in DNA \u2014 that persisted until science could finally read it.<\/p>\n
The reading has been done.<\/p>\n
The story is partial \u2014 incomplete in the four-thousand-year gap, incomplete in the populations not yet sampled, incomplete in the mechanisms it cannot identify.<\/p>\n
But it is real.<\/p>\n
<\/p>\n
The Bogot\u00e1 Altiplano, standing at the junction of the Americas, preserves in its earth a record of multiple human beginnings and endings.<\/p>\n
The Checua people are one of those beginnings \u2014 visible now, for the first time, through the molecular traces they left behind.<\/p>\n
Whether traces of their lineage persist in living populations not yet studied is a question that future research will address.<\/p>\n
Whether the mechanisms of their replacement will ever be fully understood depends on finding biological material from the four-thousand-year gap that separates their 6,000-year-old record from the 2,000-year-old record of the people who followed them.<\/p>\n
What is not in question is that they were here.<\/p>\n
<\/p>\n
That they were part of the early human story of the Americas \u2014 a branch of the founding radiation that took a path distinct from the other branches, lived on a Colombian plateau for thousands of years, and then, somehow, stopped appearing in the genetic record of the world they had inhabited.<\/p>\n
Their genomes answered one question with precision: who were these people in genetic terms?<\/p>\n
They were a previously uncharacterized, deeply divergent lineage deriving from the initial South American radiation.<\/p>\n
This is a scientific answer.<\/p>\n
It is a real answer.<\/p>\n
And it changes the map.<\/p>\n
What it does not answer \u2014 and what remains the legitimate open question at the end of this story \u2014 is exactly how, in the four thousand years between 6,000 and 2,000 years before present, a population that had been established on one of South America’s most significant highland corridors lost its detectable presence in the genetic record, and what the specific human experiences of that transition were for the people who lived through it.<\/p>\n
That question will require more bones, more DNA, and more time.<\/p>\n
<\/p>\n
The search has begun.<\/p>\n
The Altiplano Cundiboyacense As A Geographic Entity<\/p>\n
The Bogot\u00e1 Altiplano \u2014 formally the Altiplano Cundiboyacense \u2014 is not simply the elevated plateau on which Bogot\u00e1 sits.<\/p>\n
It is a geographic and ecological complex extending through two of Colombia’s highland departments, Cundinamarca and Boyac\u00e1, encompassing an area of roughly 25,000 square kilometers of high-altitude terrain within the folds and basins of the Eastern Cordillera.<\/p>\n
The basin that contains Bogot\u00e1 is the most prominent of these highland environments \u2014 a broad, relatively flat space at roughly 2,600 meters above sea level, ringed by higher peaks and drained by the Bogot\u00e1 River.<\/p>\n
<\/p>\n
But the Altiplano Cundiboyacense extends further north into Boyac\u00e1, where additional basins and valleys at comparable elevations were also centers of prehistoric occupation, and where the Muisca maintained territorial presence during their period of greatest political influence.<\/p>\n
The Altiplano is unusual in the context of the Andes.<\/p>\n
Unlike the narrow, steep valleys that characterize much of the Andean highland, the Bogot\u00e1 basin and the adjacent Boyac\u00e1 highlands offer relatively flat terrain, productive volcanic soils, and an agricultural climate suited to potato cultivation and, after its introduction, maize.<\/p>\n
These characteristics made the Altiplano one of the most densely occupied highland regions in pre-Columbian South America, supporting population densities that exceeded those of many comparable highland environments elsewhere in the continent.<\/p>\n
The geographic enclosure of the plateau \u2014 bounded by the mountains of the Eastern Cordillera on multiple sides, with relatively difficult access through the passes and slopes that connect the plateau to the lowlands below \u2014 created conditions favorable to both cultural distinctiveness and genetic isolation.<\/p>\n
<\/p>\n
A population established on the Altiplano would have had limited but not zero contact with neighboring groups at lower elevations, maintaining some degree of genetic and cultural exchange while developing its own specific characteristics over time.<\/p>\n
For the Checua lineage, this geographic context is potentially important.<\/p>\n
If the plateau’s relatively enclosed geography contributed to the development of a distinct genetic character over thousands of years of occupation, then the dramatic genetic shift documented between the Preceramic and Herrera periods implies that whatever movement brought the Central American-related ancestry to the Altiplano was substantial enough to overcome this geographic isolation.<\/p>\n
The routes by which people could have moved from the Central American isthmus to the Bogot\u00e1 Altiplano are not direct or easy.<\/p>\n
<\/p>\n
The most plausible corridor runs along the Caribbean coast of northwestern Colombia and then inland through the lower slopes of the Andes, eventually ascending the Eastern Cordillera to reach the Altiplano.<\/p>\n
This route would have involved crossing multiple ecological zones \u2014 tropical lowlands, subtropical montane forest, cool highland environments \u2014 and adapting to the physiological demands of increasing altitude.<\/p>\n
Alternatively, movement could have occurred through the western slope of the Andes, down through the Cauca Valley that separates the Cordillera Occidental from the Cordillera Central, and then across to the Eastern Cordillera.<\/p>\n
Or through the lowland llanos to the east of the mountains, with ascending access through the eastern passes of the Cordillera.<\/p>\n
The specific routes taken by the populations who brought Central American ancestry to the Altiplano remain unknown.<\/p>\n
<\/p>\n
Genetic data from archaeological sites along these potential corridors would help trace the specific paths of population movement.<\/p>\n
The Muisca: What Came After<\/p>\n
The Muisca are worth understanding in some depth, because they are the endpoint of the demographic sequence that the 2025 study documented \u2014 the people who occupied the Bogot\u00e1 Altiplano when European colonizers arrived in 1537, and who have remained present (though transformed by colonialism) in the region to this day.<\/p>\n
The Muisca chiefdoms were among the most politically complex societies in pre-Columbian South America outside of the central Andean civilizations of Peru and Bolivia.<\/p>\n
At the time of Spanish contact, the Altiplano was governed by multiple competing chiefdoms, the two largest of which were centered on the towns of Bogot\u00e1 (in the southern Bogot\u00e1 basin) and Hunza (in the Boyac\u00e1 region to the north, near modern Tunja).<\/p>\n
<\/p>\n
A third important chiefdom was centered on Sogamoso, site of a major religious center dedicated to the sun deity Su\u00e9.<\/p>\n
The Muisca political system was not a unified empire but a network of hierarchically organized chiefdoms in which paramount chiefs \u2014 the zipa of Bogot\u00e1 and the zaque of Hunza \u2014 exercised authority over subsidiary chiefs who in turn administered local communities.<\/p>\n
This hierarchical structure was maintained through tribute systems, marriage alliances, ritual relationships, and the control of access to prestige goods.<\/p>\n
The material culture of the Muisca is perhaps best known through their goldwork \u2014 the tumbaga artifacts (alloys of gold and copper) that Muisca artisans produced in extraordinary numbers and varieties.<\/p>\n
<\/p>\n
Muisca gold objects, including the famous muisca raft (a tunjo depicting a ceremony that is now interpreted as the origin of the El Dorado legend) are among the most celebrated artifacts from pre-Columbian South America.<\/p>\n
The Muisca controlled access to emeralds from the Muzo mines in western Boyac\u00e1 and to salt from the enormous salt deposits at Zipaquir\u00e1 and Nemoc\u00f3n \u2014 the same Nemoc\u00f3n where the Checua site is located.<\/p>\n
This point deserves emphasis: the Checua archaeological site, where the ancient hunter-gatherers with the previously unknown genetic lineage were found, lies in the same municipality as one of the Muisca’s most important salt mining centers.<\/p>\n
The geographic continuity between the early Preceramic occupation and the later Muisca presence masks a complete genetic discontinuity.<\/p>\n
<\/p>\n
The people who mined salt at Nemoc\u00f3n in the Muisca period were not genetically related, in any detectable way, to the hunter-gatherers who had lived on the same plateau four thousand years earlier.<\/p>\n
The Muisca maintained elaborate ritual and ceremonial practices, including the ceremony at Lake Guatavita in which gold and emeralds were cast into the sacred lake as offerings \u2014 the ceremony that inspired the El Dorado legend.<\/p>\n
Muisca cosmology was sophisticated and well-documented by colonial-era Spanish sources, though the accuracy and completeness of those sources is debated by scholars.<\/p>\n
The Muisca were also the creators of the architecture and infrastructure that organized the plateau’s landscape \u2014 roads, causeways across wetland areas, terracing for agriculture, and the planned layouts of settlement sites that archaeologists have been documenting for decades.<\/p>\n
The genetic evidence from the 2025 study places all of this Muisca achievement in the context of the Central American-related ancestry that had replaced the earlier Checua lineage approximately two thousand years before Spanish contact.<\/p>\n
<\/p>\n
The Muisca’s cultural achievements \u2014 their political complexity, their goldwork, their religious system, their salt trade \u2014 were the products of a population that had arrived on the plateau relatively recently in geological terms, carrying a genetic heritage rooted in the Isthmus of Panama and the Chibchan-speaking world.<\/p>\n
This does not diminish those achievements.<\/p>\n
It contextualizes them within a deeper demographic history that was invisible until the genetic analysis made it visible.<\/p>\n
Colombia As Entry Point: The Geographic Stakes<\/p>\n
Colombia’s significance in the story of human movement through the Americas extends far beyond the specific findings of the 2025 study.<\/p>\n
The country occupies a unique geographic position that makes it one of the most important regions for understanding how human populations moved between the two American continents.<\/p>\n
The conventional depiction of the Americas as two separate continents joined by a narrow land bridge at Panama obscures something important: that land bridge \u2014 the Isthmus of Panama and the Dari\u00e9n region \u2014 is in fact the boundary zone between Central and South America, not the boundary between North America and South America in any geological or ecological sense.<\/p>\n
<\/p>\n
Colombia is where the Andes begin, where the Caribbean and Pacific coasts of South America start, where the great river basins of the Orinoco and Amazon originate.<\/p>\n
For populations moving southward from North America into South America during the period of the initial peopling of the Americas, Colombia was the first major landscape they would have encountered after crossing the Dari\u00e9n.<\/p>\n
The country’s extraordinary geographic diversity \u2014 high-altitude Andean highlands, Caribbean lowlands, Pacific rainforests, Amazonian basins, llanos grasslands \u2014 means that any population moving through it would have faced immediate choices about which ecological zones to occupy and what routes to follow southward.<\/p>\n
The lack of ancient DNA data from Colombia before 2025 thus represented a significant gap in our understanding of how the initial peopling of South America proceeded.<\/p>\n
<\/p>\n
The routes taken by the founders of South American populations \u2014 whether they moved primarily along the Pacific coast, through the Andes, through the Caribbean lowlands, or through the interior \u2014 could not be clearly addressed without genetic data from the relevant transitional region.<\/p>\n
The 2025 study does not fully close this gap.<\/p>\n
Its oldest individuals date to approximately 6,000 years before present \u2014 thousands of years after the initial peopling of the continent, which most researchers place at or before 15,000 years before present.<\/p>\n
The study cannot directly address the routes and populations involved in the initial founding of South America.<\/p>\n
What it does provide is a baseline for the genetic character of the Altiplano population at 6,000 years before present, demonstrating that the population of this region at that time was already a distinct lineage with a long history of separate development from other South American groups.<\/p>\n
The depth of the Checua lineage’s divergence from other ancient South American populations implies that the differentiation between the Checua lineage and the ancestors of other South Americans occurred long before the 6,000-year-before-present individuals whose genomes were analyzed \u2014 potentially thousands of years earlier.<\/p>\n
<\/p>\n
This in turn implies that the founding of South America involved rapid divergence of populations into distinct regional lineages shortly after the initial entry into the continent.<\/p>\n
The ancestors of the Checua people must have separated from the common ancestor of other South Americans and established themselves on the Colombian highlands well before 6,000 years before present for the degree of genetic distinctiveness observed in the 2025 study to have developed.<\/p>\n
The Comparison Populations And Why They Matter<\/p>\n
The conclusions about the Checua lineage’s distinctiveness depend entirely on who it was compared to.<\/p>\n
Understanding which populations were included in the researchers’ comparison dataset \u2014 and which were not \u2014 is essential for evaluating the strength of the “no detectable affinity” conclusion.<\/p>\n
<\/p>\n
The 2025 study compared the Checua individuals against a comprehensive set of ancient genomes from across the Americas, including individuals from North America, Central America, and multiple South American regions.<\/p>\n
The ancient North American genomes included the Anzick-1 individual from Montana (associated with Clovis culture and approximately 12,600 years old), ancient individuals from California’s Channel Islands (early coastal inhabitants of North America), and various other North American ancient genomes.<\/p>\n
Ancient Central American genomes included individuals from Panama that provided the comparison population most closely matched by the Herrera-period Altiplano individuals.<\/p>\n
Ancient South American genomes included individuals from Brazil, Peru, Chile, Argentina, and other regions across the continent.<\/p>\n
<\/p>\n
The modern comparison populations included a wide range of present-day Indigenous communities from across South America, including Chibchan-speaking populations from Panama and Colombia.<\/p>\n
The finding that the Checua individuals showed no detectable specific affinity to any of these comparison populations is striking precisely because of the breadth of the comparison.<\/p>\n
Researchers often find that ancient individuals show closest affinity to modern or ancient populations from the same geographic region; the absence of such an affinity for the Checua individuals, despite being compared against populations from across the Americas, indicates a genuine genetic distinctiveness.<\/p>\n
However, the comparison was not exhaustive.<\/p>\n
<\/p>\n
Some populations that might carry signals related to Checua ancestry were not included.<\/p>\n
Ancient genomes from the Caribbean islands, from the Venezuelan highlands, from western Colombia, and from the Ecuadorian highlands were not available for the comparison.<\/p>\n
Present-day communities from some of these regions were also not included.<\/p>\n
It is possible \u2014 not certain, but possible \u2014 that expanding the comparison to include these populations would reveal specific affinities that the current analysis could not detect.<\/p>\n
This caveat does not undermine the study’s core finding, but it does define its boundaries.<\/p>\n
<\/p>\n
The Checua lineage shows no specific affinity to the populations compared in this study.<\/p>\n
Whether it shows affinity to populations not yet sampled is an open question.<\/p>\n
The Physical Evidence Alongside The Genetic<\/p>\n
The genetic analysis that forms the centerpiece of the 2025 study exists alongside a much longer tradition of physical anthropological research on the remains from Checua and other Altiplano sites.<\/p>\n
The relationship between the two types of evidence is important to understand.<\/p>\n
Physical anthropology \u2014 the study of human skeletal remains to determine biological characteristics \u2014 has been applied to Colombian archaeological material for many decades.<\/p>\n
<\/p>\n
Jos\u00e9 Vicente Rodr\u00edguez Cuenca, one of the co-authors of the 2025 genetics study, has spent much of his career studying the physical characteristics of pre-Columbian populations from the Bogot\u00e1 Altiplano, and his expertise in the physical characteristics of the Checua remains was an important contribution to the broader research project.<\/p>\n
The physical characteristics observed in the Checua individuals \u2014 elongated skull proportions, specific dental pathology, and the overall robusticity of the skeleton \u2014 provide complementary information to the genetic analysis.<\/p>\n
But it is crucial to understand that physical characteristics alone cannot establish genetic relationships between populations.<\/p>\n
The history of physical anthropology includes a long and problematic tradition of using skull shape and other morphological characteristics to make claims about racial or ethnic identity, biological superiority, and population relationships.<\/p>\n
These claims were not only scientifically flawed but were used to justify harmful ideologies and policies.<\/p>\n
<\/p>\n
Modern physical anthropology is far more careful about the relationship between morphological characteristics and population identity, and the genetics field has demonstrated that populations can show similar skull morphologies while being genetically quite distant, and vice versa.<\/p>\n
The elongated skull proportions observed in some of the Checua individuals do not indicate a separate species, a different biological origin, or unusual biology.<\/p>\n
They reflect the normal variation in skull morphology that exists across human populations.<\/p>\n
The researchers who described this characteristic were observing a physical feature that distinguishes the Checua population from later Altiplano populations in that specific morphological dimension.<\/p>\n
This observation is consistent with the genetic finding of distinctiveness, but it does not add independent evidence of any specific ancestry or origin.<\/p>\n
<\/p>\n
The dental pathology \u2014 the abscesses and tooth loss from infection noted by Rodr\u00edguez Cuenca \u2014 provides information about diet and health that is consistent with the archaeological interpretation of a hunter-gatherer population that relied heavily on root vegetables and tubers.<\/p>\n
This dietary interpretation is plausible given the ecological context and the evidence for volcanic disruption of surface crops, but it should be understood as a hypothesis rather than a definitively established fact.<\/p>\n
The Living Communities Of The Bogot\u00e1 Altiplano Today<\/p>\n
The demographic history documented in the 2025 study does not exist in isolation from the living communities of the Bogot\u00e1 Altiplano.<\/p>\n
Understanding the relationship between the ancient genetic findings and the contemporary human geography of the region requires some care.<\/p>\n
<\/p>\n
The Muisca people, whose ancestors the 2025 study’s genetic data traces through the Herrera and Muisca periods, did not disappear with the Spanish conquest.<\/p>\n
The Muisca population was devastated by the disease, displacement, forced labor, and cultural suppression that accompanied colonization, but biological and cultural continuity persisted.<\/p>\n
Descendants of the pre-Columbian Muisca communities are present in the Bogot\u00e1 Altiplano today, organized in communities (cabildos) that have successfully pursued legal recognition of their identity and territorial rights within the Colombian legal framework.<\/p>\n
The Muisca communities of today \u2014 including those in Suba, Bosa, Engativ\u00e1, Cota, Ch\u00eda, Tocancip\u00e1, Tenjo, and other municipalities of the Cundinamarca Department \u2014 are engaged in processes of cultural revitalization, including the reconstruction and teaching of Muysccubun, the Muisca language that ceased to be spoken in the nineteenth century.<\/p>\n
These communities maintain connections to the archaeological and historical record of the Altiplano, and the findings from the 2025 genetic study are part of a scientific conversation that affects their understanding of their own history.<\/p>\n
<\/p>\n
Other Indigenous communities present in Colombia today include Chibchan-speaking groups in the Sierra Nevada de Santa Marta \u2014 the Wiwa, Arhuaco, Kogi, and Kankuamo \u2014 who represent the northern extension of the Chibchan-related ancestry that the 2025 study documented in the Herrera-period Altiplano population.<\/p>\n
The genetic affinities between the ancient Herrera-period individuals and present-day Chibchan speakers provide a direct link between the findings of the 2025 study and living Indigenous communities.<\/p>\n
The relationship between genetic research findings and Indigenous communities is not without complexity.<\/p>\n
Indigenous communities have legitimate interests in how their history is described and interpreted by scientists, and the history of genetics research on Indigenous peoples includes instances of data being collected without adequate community consultation or used in ways that communities found harmful or disrespectful.<\/p>\n
The 2025 Colombia study involved Colombian researchers who brought institutional connections to Colombian academic and heritage institutions, and who were embedded in the professional and community networks that archaeological research in Colombia requires.<\/p>\n
<\/p>\n
The involvement of Colombian scientists \u2014 particularly Andrea Casas-Vargas, who has engaged directly with Colombian communities about the research \u2014 represents an effort to ensure that the findings are communicated to and through the communities most directly affected by them.<\/p>\n
The Comparative Scale Of The Discovery<\/p>\n
To appreciate the significance of the 2025 Colombia study, it helps to place it in the context of ancient DNA research globally.<\/p>\n
The ancient DNA revolution \u2014 the ability to sequence genomes from thousands-year-old human remains \u2014 has transformed the study of human prehistory over the past fifteen years.<\/p>\n
In Europe, ancient DNA has documented population replacements, migrations, and demographic transformations that were invisible to archaeology.<\/p>\n
In Asia, ancient genomes have revealed the deep roots of modern populations and the connections between ancient and contemporary communities.<\/p>\n
<\/p>\n
In Africa, ancient DNA has begun to illuminate the deep population history of the continent where all modern humans originated.<\/p>\n
In the Americas, ancient DNA research has been growing but remains uneven in its geographic coverage.<\/p>\n
North America has the most extensive ancient genomic dataset, with hundreds of ancient individuals analyzed from sites ranging from Alaska to Florida.<\/p>\n
South America has seen significant progress, with important studies from Peru, Chile, Argentina, and Brazil documenting the population history of the Andes, the southern cone, and Amazonia.<\/p>\n
But major regions remain almost entirely unsampled.<\/p>\n
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Colombia was, until 2025, a complete blank.<\/p>\n
Venezuela is largely uncharted.<\/p>\n
Bolivia has limited coverage.<\/p>\n
Ecuador and western Colombia are essentially unknown.<\/p>\n
These gaps matter because they represent regions where unique population histories \u2014 comparable to what the 2025 study documented for the Bogot\u00e1 Altiplano \u2014 might be preserved in the archaeological record and accessible through ancient DNA analysis.<\/p>\n
The Checua discovery demonstrates that even well-studied archaeological regions can harbor surprising genetic diversity that was invisible to any method other than ancient genomics.<\/p>\n
The eleven-fold increase in Colombian ancient genomic coverage that the 2025 study represents \u2014 from zero to 21 individuals \u2014 illustrates how much can be learned from what was previously a complete gap.<\/p>\n
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Comparable studies in the uncharted regions of the Americas have the potential to reveal demographic histories that are currently completely unknown to science.<\/p>\n
The Petrous Bone And The Science Of Recovery<\/p>\n
The technical success of the 2025 study deserves some additional attention, because the extraction of genome-wide data from 6,000-year-old remains in a tropical highland environment was not a foregone conclusion.<\/p>\n
The petrous bone \u2014 the dense inner-ear portion of the temporal bone \u2014 has become the standard target for ancient DNA extraction in archaeological research over the past decade.<\/p>\n
The decision to focus on the petrous bone was driven by a series of studies that demonstrated its superiority as a DNA source: the bone’s extraordinary density creates a physical barrier that resists bacterial invasion, and the cells within the cochlea (the spiral structure of the inner ear housed within the petrous) appear to contain unusually high amounts of DNA even in ancient remains.<\/p>\n
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For remains from tropical or subtropical regions, where warm and humid conditions accelerate biological degradation, the petrous bone’s protective qualities become even more important.<\/p>\n
DNA preservation in tropical soils is generally poor; many ancient specimens from the tropics have yielded no usable genetic material despite extensive extraction attempts.<\/p>\n
The success of the 2025 Colombia study in recovering genome-wide data from seven Preceramic individuals at 6,000 years before present suggests that the cool, high-altitude conditions of the Bogot\u00e1 Altiplano provided preservation conditions significantly better than those in tropical lowland regions.<\/p>\n
The combination of high altitude (reducing temperature), relatively low humidity compared to lowland tropical environments, and the specific soil chemistry of the Altiplano may have combined to create conditions favorable for DNA preservation over millennia.<\/p>\n
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This has implications for future research: the high-altitude archaeological sites of the Colombian Andes and neighboring regions may prove to be significantly more productive for ancient DNA recovery than lowland sites in the same geographic region.<\/p>\n
The bioinformatic analysis applied to the recovered DNA is equally sophisticated.<\/p>\n
Distinguishing authentic ancient sequences from modern contamination, assembling short degraded fragments into coherent genome-wide datasets, and applying the population genetic tests (f-statistics, D-statistics, ADMIXTURE analysis, and related methods) that the study’s conclusions depend on all require specialized expertise and computational infrastructure.<\/p>\n
The fact that this expertise was combined successfully \u2014 bringing together the field expertise to identify and sample the archaeological material, the laboratory expertise to extract and sequence the DNA, and the computational expertise to analyze the results \u2014 demonstrates the increasingly sophisticated infrastructure of ancient DNA research and the capacity of international collaborations to mobilize that infrastructure for high-priority scientific questions.<\/p>\n
The Headline Versus The Reality<\/p>\n
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Articles about this research \u2014 including from major scientific news outlets \u2014 have described the Checua people using phrases like “ghost lineage,” “complete population replacement,” “lineage that vanished,” and “unknown group of humans.” These framings are attention-grabbing and not entirely inaccurate, but they require the kind of careful qualification that has been attempted throughout this account.<\/p>\n
“Ghost lineage” is a term sometimes used in population genetics for a population that contributed ancestry to known groups but is not itself represented by any sampled ancient or modern genome.<\/p>\n
The Checua lineage is not quite this in the technical sense \u2014 it IS represented by sampled ancient genomes (the seven Preceramic individuals from Checua).<\/p>\n
But the term captures something real about the relationship between the Checua population and the later populations of the same plateau: they were there, and then their genetic signature was gone.<\/p>\n
“Complete population replacement” is the phrase Kim-Louise Krettek used in some media communications, and it accurately describes what the genetic data shows within the study’s comparison framework.<\/p>\n
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The genetic ancestry changed completely between the Preceramic period at 6,000 years before present and the Herrera period at 2,000 years before present, with no detectable contribution from the earlier lineage to the later population.<\/p>\n
This is what “complete replacement” means in genetic terms.<\/p>\n
“Lineage that vanished” is accurate in the sense that the lineage is not detectable in the populations studied.<\/p>\n
It is potentially misleading in that it could be read as implying the physical extinction of every biological descendant \u2014 which is not what the evidence establishes.<\/p>\n
“Unknown group of humans” is accurate in that the Checua lineage was genuinely unknown to genetic science before the 2025 study.<\/p>\n
The archaeology had documented these people; the genetics had not.<\/p>\n
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The most important thing to understand about all of these framings is that they describe the current state of the scientific knowledge, not an exhaustive truth about what happened.<\/p>\n
The knowledge will expand as more ancient genomes are analyzed from more sites across Colombia and neighboring regions.<\/p>\n
Some of the framings that currently seem dramatic may become more nuanced \u2014 or more extreme \u2014 as the larger picture becomes clearer.<\/p>\n
The Open Question At The Center<\/p>\n
Here is the thing that the 2025 Science Advances paper could not answer, despite answering so much else.<\/p>\n
The genetic evidence documents that the Checua lineage existed on the Bogot\u00e1 Altiplano at approximately 6,000 years before present, that it was genetically distinct from other South American populations, and that by approximately 2,000 years before present its detectable signal had been replaced by ancestry related to Central American populations.<\/p>\n
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The evidence also documents that the Central American-related ancestry persisted through the Muisca period despite major cultural changes.<\/p>\n
What the evidence does not document is the human experience of that transition.<\/p>\n
Not the specific years in which it began and ended.<\/p>\n
Not the population-level events \u2014 migration, disease, displacement, absorption \u2014 that produced the genetic outcome.<\/p>\n
Not the perspective of any individual or community that was part of the change.<\/p>\n
Not the specific choices, pressures, or historical accidents that shaped the course of demographic events on the plateau over four thousand years.<\/p>\n
These are the questions that the science opened without closing.<\/p>\n
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They are the questions that motivate the next phase of research \u2014 the search for ancient individuals from the gap period between 6,000 and 2,000 years before present, the expansion of geographic coverage to neighboring regions, the more comprehensive sampling of contemporary populations that might carry traces of Checua-related ancestry.<\/p>\n
The science has achieved something remarkable: it has made visible, for the first time, a distinct early branch of South American population history that was completely unknown before 2025.<\/p>\n
The seven Preceramic individuals from Checua \u2014 people who lived on a Colombian highland, hunted deer in the mountain grasslands, returned to the same settlement hill on the valley floor year after year, and left their bones in the earth of the Altiplano \u2014 have now been placed in the genetic family tree of the Americas.<\/p>\n
Their placement is not simple or neat.<\/p>\n
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They sit in a position that the researchers describe as a previously unknown basal lineage, distinct from other ancient South American populations, with no detectable contribution to the later peoples of the same region.<\/p>\n
This is simultaneously a clear scientific result and a source of new questions.<\/p>\n
The clearest of those new questions is: what happened in the four thousand years between when the Checua people are last visible in the genetic record and when the Central American-related ancestry appears as the new dominant profile on the plateau?<\/p>\n
The answer to that question is not in the 2025 paper.<\/p>\n
It is in the ground \u2014 in the bones of people who lived on the Bogot\u00e1 Altiplano between 6,000 and 2,000 years before present, in sites that may or may not have been identified, in remains that may or may not have preserved enough biological material for ancient DNA extraction.<\/p>\n
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Finding that answer is now one of the most important objectives in the ancient genomics of the Americas.<\/p>\n