In Europe, the first farmers of Europe, derived from Western Anatolian farmers, largely replaced Europe's original hunter-gatherers (who actually show continuity between the periods before and immediately after the Last Glacial Maximum), and in turn, received very substantial genetic admixture from late Copper Age/early Bronze Age Indo-Europeans from more or less where Ukraine is today. This diluted both first farmer ancestry, and the already highly diluted European hunter-gather ancestry that was admixed into those first farmer populations. In some places, like Britain, the population replacement of first farmers by Indo-Europeans was nearly complete.
Something similar apparently happened in East and Southeast Asia.
A new study established that the Americas did not break from this pattern, with some of its early agriculturists replacing pre-existing hunter-gatherer populations in a similarly genocidal pattern. If anything, this replacement was even more complete.
Sometime between 4000 BCE and 0 CE, in the Columbian highlands, probably coinciding with a new archaeological culture whose artifacts appear around 1000 BCE to 800 BCE, a millennium after maize cultivation began around 1800 BCE (but possibly before the full blown ceramic culture emerged), a clade of indigenous South American hunter-gatherers (with ancestry dating back to the initial wave of human settlement of South America) were replaced by a different group of indigenous South Americans.
The 1800 BCE date is from A. Gómez, et al., "A Holocene pollen record of vegetation change and human impact from Pantano de Vargas, an intra-Andean basin of Duitama, Colombia." 145 Rev. Palaeobot. Palynol. 143–157 (2007) (full paper available here), and really only definitively points to deforestation and Amaranth cultivation at that point in the highlands of Columbia.
The population that replaced them, which is genetically linked to the speakers of Chibchan languages and probably originated in Central America, has remained the dominant population of the region in genetic continuity with their ancestors since this population replacement occurred, although later populations admixed with them and brought new languages in some parts of the region.
There is no evidence that anyone from the pre-agricultural, pre-ceramic culture that was replaced in the Columbian highlands survived, or even significantly admixed with surviving populations.
The new agriculturalist culture did not really come into its own archaeologically until 1000 BCE to 800 BCE, so we can't know for sure if the replacement took place suddenly (although the lack of admixture between the new and old populations suggests that it did) or more gradually, or how long after maize cultivation, a thousand years earlier than this culture's pots appeared, the population replacement happened.
Conservatively, it happened in some short time period between 1800 BCE and 800 BCE (about 3,000 to 4,000 years after it happened in Europe). Realistically, it probably happened on the later side of that time range when other components of the emerging farmer culture, like pottery and possibly other key domesticated plants and/or animals, joined with improved maize cultivation to give rise to a technologically dominant new culture.
The introduction and discussion sections of a new study released May 28, 2025 in the journal Scientific Advances by Kim-Louise Krettek, et al., explain that:
Genetic studies on ancient and present-day Indigenous populations have substantially contributed to the understanding of the settlement of the Americas. Those studies revealed that the population ancestral to non-Arctic Native Americans derives from a genetic admixture between ancient East Asian and Siberian groups somewhere in North-East Asia before 20,000 years before the present (yr B.P.). Around 16,000 yr B.P., after its arrival in North America, this genetic ancestry split into two lineages known as northern Native American and southern Native American. While northern Native American ancestry is largely confined to ancient and current populations of North America, the southern Native American lineage expanded further south and constitutes the main ancestry component of ancient and present-day Indigenous South Americans.
Southern Native American ancestry diversified within North America into at least three sublineages, i.e., one related to the Clovis-associated Anzick-1 individual from western Montana (USA), one found in ancient California Channel Islands individuals and the last one representing the main ancestry source of modern-day Central and South Americans.
Each of these sublineages provided a wave of ancestry into the gene pool of ancient South Americans. Individuals from Chile and Brazil dating back to around 12,000 and 10,000 yr B.P., respectively, were more genetically related to the Anzick-1 genome than individuals from the eastern Southern American coast, Southern Cone and the Andes from 10,000 yr B.P. onward. In addition, the California Channel Islands ancestry was found in the Central Andes by 4200 yr B.P. and became widespread in the region thereafter. However, the exact timing of these population movements into the southern subcontinent remains largely unsolved to date.
The Isthmo-Colombian area, stretching from the coast of Honduras to the northern Colombian Andes, is critical to understanding the peopling of the Americas. Besides being the land bridge between North and South America, it is at the center of the three major cultural regions of Mesoamerica, Amazonia, and the Andes. At the time of European contact, the region was inhabited by a complex mosaic of human populations, mainly speakers of Chibchan, Chocoan, Carib, and Arawakan languages.
Among those populations, those who were speakers of Chibchan languages were the most widespread in the region in terms of demography, cultural diversity, and territorial distribution. Chibchan is a language family with multiple, highly distinct branches, many of which are still spoken today in different regions of the Isthmo-Colombian area. The homeland and antiquity of the Proto-Chibchan language and the ancestor of all Chibchan languages remain subjects of debate. High intrafamily variation in terms of lexicon and grammar suggests that the language family is ancient and began diversifying several thousand years ago. The locus of that incipient diversification, however, is still uncertain. Most scholars believe that this protolanguage began to diversify in Lower Central America, where the largest number of these languages is spoken today. However, some evidence suggests that Proto-Chibchan might have originated in South America and then diversified in Central America at a much later date.
Genetic studies of ancient and present-day Isthmo-Colombian Indigenous populations revealed a distinctive ancestry component primarily associated with speakers of Chibchan languages. However, whereas mitochondrial DNA (mtDNA) studies suggested a migration of Chibchan-related ancestry from Central America into Colombia and Venezuela, genome-wide studies favored an opposite, south-to-north population movement. According to the latter model, speakers of Chibchan languages from Central America are not direct descendants of the first settlers in the region but, instead, derive from a more recent back migration from South to Central America.
The southernmost region of the Isthmo-Colombian area is the Altiplano Cundiboyacense (hereafter Altiplano). This plateau with an average altitude of 2600 m in the Eastern Cordillera of the Colombian Andes was inhabited by ancient hunter-gatherer groups from the Late Pleistocene. During the Early and Middle Holocene phases of the Preceramic period (~11,500 to 4000 yr B.P.), populations on the Altiplano underwent multiple cultural transformations, most notably increased sedentism and a transition from a hunter-gatherer subsistence to the introduction of horticultural practices and forest management. However, it was not until the early Late Holocene, ~3800 yr B.P., that the first clear evidence of maize cultivation appeared.
During the subsequent Formative period (~3000 to 1000 yr B.P.), a distinct type of pottery emerged on the Altiplano that is referred to as the Herrera ceramic complex, also known in the literature as the Herrera period (2800 to 1200 yr B.P.). It is still highly debated whether Herrera-associated groups on the Altiplano derived from an in situ development of local hunter-gatherers or were a consequence of population dispersals into the region.
Around 1200 yr B.P., a cultural phase, known as the Muisca period, began on the Altiplano and lasted until the imposition of the Hispanic Colonial regime in the mid-16th century. Most available evidence is suggestive of population continuity with the preceding Herrera period. The Muisca period is characterized by a relatively continuous process of demographic growth, development of agriculture and trade, and social and political complexification. These factors played a considerable role in shaping the Muisca culture and gave rise to the Chibchan-speaking population that dominated the Altiplano until European colonization.
While several studies have reported mtDNA data from ancient Colombian individuals, genome-wide data from this region are still entirely lacking to date. In this study, we generated mtDNA and genome-wide data of 21 ancient individuals from two areas of the Altiplano (Bogotá plateau and Los Curos). Our data, spanning a time transect between around 6000 and 500 yr B.P., provide an opportunity to explore several key questions:
(i) Which southern Native American genetic ancestry do Preceramic individuals from the Altiplano derive from?
(ii) Were the cultural transformations associated with the Herrera and Muisca periods accompanied by migrations and demographic changes?
(iii) How is the genetic ancestry observed in speakers of Chibchan languages related to that of ancient individuals from the Altiplano?
(iv) What are the genetic relationships between the generated ancient genomes and the existing genomic data of present-day Indigenous communities from Colombia and neighboring regions?
In this study, we generated genome-wide data from 21 individuals spanning a time transect of almost 6000 years from the Altiplano, which represents the southern edge of the Isthmo-Colombian area. Our findings contribute to a better understanding of the population history of this area, a key region in the peopling process of South America. We show that the hunter-gatherer population from the Altiplano dated to around 6000 yr B.P. lack the genetic ancestry related to the Clovis-associated Anzick-1 genome and to ancient California Channel Island individuals, suggesting their affiliation to the southern Native American lineage that became the primary source of ancestry of South Americans by 9000 yr B.P.
However, unlike ancient genomes from the Andes and the Southern Cone that are associated with the same wave of ancestry, the analyzed Preceramic individuals from Colombia do not share distinct affinity with any ancient or modern-day population from Central and South America studied to date. Colombia_Checua_6000BP can thus be modeled as a previously undescribed distinct lineage deriving from the radiation event that gave rise to multiple populations across South America during its initial settlement.
The cultural transition between the Preceramic and Herrera periods is associated with a seemingly complete replacement of the local genetic profile. This challenges the model where local hunter-gatherers developed in situ as suggested by morphometric studies and an ancient mtDNA time transect. Instead, our study provides evidence for a major genetic turnover on the Altiplano occurring after 6000 yr B.P. but before 2000 yr B.P. Since the mechanisms and precise temporal scale of this replacement event remain uncertain, we cannot directly associate it with the emergence of maize cultivation ~3800 yr B.P. However, our data do support the archaeological hypothesis that the introduction of pottery associated with the Herrera ceramic complex was mediated through population dispersals.
Our results show that the incoming genetic ancestry on the Altiplano is related to ancient and present-day populations speaking Chibchan languages from Central America. This can be explained most parsimoniously by Chibchan-related migrations from Lower Central America to South America, rather than back-migration to the isthmus.
A separate study found evidence for a previously unknown south-to-north expansion of Chibchan-related ancestry from Lower Central America into the Mayan territories of Belize by 5600 yr B.P. Therefore, rather than modeling Central American populations associated with Chibchan languages as deriving from a mixture between North and South American ancestries, these results are consistent with an origin of Chibchan-related ancestries in Lower Central America, followed by bidirectional gene flow toward both Meso- and South America. This model of an original “Chibchan homeland” in Central America is supported not only by mtDNA studies on present-day populations who speak Chibchan languages but also from linguistic observations, indicating that the isthmus region exhibits the highest diversity within this language family.
From an archaeological perspective, the Chibchan-related ancestry is first identified in 2000-year-old individuals associated with Herrera ceramics. In addition, previously sequenced Ceramic-associated individuals from Venezuela dated to 2400 yr B.P. also showed a high affinity to Central American populations speaking Chibchan languages. Despite the similar ancestry pattern and temporal frame, the two populations do not appear to form a simple sister group. This could be in line with linguistic evidence that suggests multiple, distinct Chibchan language expansions into South America, but additional studies will be necessary to further clarify this issue.
After the arrival of the Chibchan-related ancestry, which completely reshaped the genetic landscape of the region, we find evidence of a long period of genetic continuity in the genetic profile of the local populations for over 1500 years (from at least 2000 to 500 yr B.P.). The stability in genetic ancestry encompasses the end of the Herrera period and the beginning of the Muisca period. This points to a scenario in which populations speaking languages from the Chibchan lineage would have settled the Altiplano before the emergence of traits normally associated with the Muisca culture, and it shows that this cultural transition took place without a substantial migration from regions with a distinct genetic ancestry composition. In addition, such a genetic continuity extends through different cultural phases within the Muisca period and persists until the Spanish colonization. Colonial linguistic documentation established that Muisca people spoke a now extinct Chibchan language. Our findings not only confirm their genetic link with speakers of Chibchan languages from Central America but also suggest that ancestral Chibchan languages, possibly basal to the Magdalenic branch that gave rise to the documented Muisca language, might have already been spoken on the Altiplano during the pre-Muisca Herrera period.
While the representation of Indigenous populations in our dataset is certainly not exhaustive, the observed spatial pattern in the genetic affinity of post-2000 yr B.P. ancient Colombians with present-day Indigenous populations raises questions regarding the uneven distribution of populations speaking Chibchan languages across the Isthmo-Colombian area at the time of the Hispanic colonization, also referred to as a Chibchan “archipelago”.
One possible explanation is that this distribution resulted from separate dispersals from Central America to different locations of northern South America rather than a single expansion wave, as suggested by the internal branching pattern of the Chibchan language family. However, it is also possible that the initial spread was more widespread and got later fragmented by post-Chibchan migration and admixture events. The observation that Chibchan-affiliated populations from northern Colombia have a significantly reduced genetic affinity to post-2000–yr B.P. ancient Colombians than to Lower Central Americans supports the role of population admixture in shaping the genetic diversity of northern South America.
Also, while the earlier South American hunter-gatherer clade that went extinct probably dated to the founding wave of the modern humans in South America, they did not have notable Australasian or Melanesian ancestry, disfavoring the existence of a dramatically genetically distinct founding population of the Americas that preceded the main founding wave of modern humans and has Australasian or Melanesian genetic affinities that ancient.
