Lost City of the Incas

Fig. 3. Genomic structure and diversity of the individuals from Machu Picchu.
(A) f4 statistics of the type f4(Mbuti, X; Ollantaytambo/San Sebastian, MPindividual) using the HumOrg dataset (26). X represents either one of the Andean ancestry clusters or selected non-Central Andean groups from South and Central America (complete overview, see fig. S3 and table S3). (B) Conditional heterozygosity estimates (HE). Narrow and thicker black bars, ±1.96 and 3 SEs, respectively.
We used qpWave and qpADM to test whether any of the Machu Picchu retainers can be modeled as sharing the same ancestral population with any of the groups representing the regional Andean ancestry clusters (34) and any non-Andean South American ancestry cluster (33, 40, 41) or as a two-way admixture of the two (Fig. 1 and Supplementary Text). To the limits of our statistical resolution, we discerned that 17 of 30 individuals can be linked to a single ancestral source shared with one of the mentioned regional ancestry groups (P > 0.05 for rank 0; Fig. 4 and table S4). Six of these individuals (20%), all biologically female, exhibit ancestry associated with modern-day groups from the Peruvian North and Central Western Amazon. Additional tests indicate that these individuals share more genetic drift with groups living along the eastern piedmont of the Central Peruvian Andes, such as the Matsigenka, Shipibo, Piros, and the Ashaninka, than with groups inhabiting the northwestern Peruvian Amazon (figs. S2 and S4, table S5, and Supplementary Text). The Ashaninka are one of the contemporary tropical forest groups geographically closest to Machu Picchu, living in the lower Urubamba drainage and the lowlands of the Departments of Junín and Ucayali, north of Machu Picchu (Fig. 1).




Fig. 4. Ancestry modeling for Machu Picchu individuals.
Estimated ancestries for 30 individuals buried at Machu Picchu sorted by median date (table S1), considering qpWave and qpADM results. For admixed individuals, we only display only the model with the highest P value (including SE), but, in most cases competing models (P > 0.05) were observed (table S6). The light blue/middle blue candy stripes indicate that it was not possible to differentiate between PeruNorthCoast and PeruCentralCoast ancestry.

Four individuals from Machu Picchu (three males and one female) exhibit ancestry associated with pre-Hispanic and modern-day individuals from the Peruvian Northern and Central Coast (table S4). One male individual shares the same ancestry with San Sebastian_LIP, representing the Cusco region, while only six individuals (four males and two females) exhibit ancestry associated with the ancestral inhabitants of the Urubamba Valley (Ollantaytambo_LIP) and the broader SouthPeruHighland ancestry group. This does not necessarily mean that these six individuals were locals because the regional ancestry cluster SouthPeruHighland includes individuals from Ayacucho and Huancavelica, with some individuals in this group found at archaeological sites up to 260 km west of Ollantaytambo in the upper reaches of the Nasca drainage (Fig. 1).
We fitted two-way mixture models for the 13 remaining individuals (Fig. 4). In many cases, we observed multiple competing models, with several Andean sources fitting, while non-Andean sources were less problematic (table S6). The difficulty of determining distinct Andean sources when the number of SNPs is low is best explained by the low genetic differentiation among the Andean regional groups, most of whom share very recent ancestry (34, 40). Five male individuals were modeled as mixtures between two Andean sources, such as NorthHighland-SouthHighland or SouthHighland-TiticacaBasin (Fig. 3). For all other individuals, the models with the highest support (highest P value) suggest mixtures between an Andean and a non-Andean source (Fig. 4, table S6, and Supplementary Text). For two of the individuals, the models suggest a mixture of Central Andean ancestry (~63 to 70%) with a source from the Peruvian Amazon (~30 to 37%) that is closely related to the ancestry for the previously described six individuals of Amazonian ancestry. However, there are also two individuals for which the best fitting models (table S6) were a mixture of Andean ancestry (~30 to 40%) and ancestry associated with groups from the southeastern Amazon and Gran Chaco region of Bolivia, Brazil, Argentina, and Paraguay (~60 to 70%) such as the Chané, Guarani, Karitiana, and Xavante. We cannot exclude that the observed admixture reflects an unsampled regional ancestry, such as groups from the Eastern Slopes of the Bolivian Andes, rather than an admixture event in Inca times. Archaeological and ethnohistoric sources confirm interactions between the Inca and the ancestors of the Chané in the foothills of the Bolivian Andes, making both models plausible (42, 43).
Four individuals (three females and one male) can be modeled as a mixture between a genomic source sharing ancestry with modern-day eastern Ecuadorian Kichwa speakers (33) and ancestry from the Peruvian North Coast (Fig. 4, table S6, and Supplementary Text). Additional tests indicated that these individuals are genetically homogenous (table S7); thus, we grouped them to increase our statistical power and found that a model considering a mixture of 46 ± 6% Ecuadorian-Kichwa–associated ancestry and 54 ± 6% NorthPeruCoast ancestry produces the highest P value (P = 0.41). However, alternative models considering other Andean sources (NorthHighland and CentralCoast) are supported as well (table S6). There are no published ancient or modern-day genomes from individuals living in the Ecuadorian highlands or along the Ecuadorian coast, which limits our ability to assess whether the observed admixture indicates a recent admixture event or whether it reflects the genetic ancestry of an unsampled group somewhere in Ecuador. Similar to the previous case, the intensive interactions between Ecuadorian populations and the Inca make such an alternative possible (2, 44, 45).
On the basis of our results, Machu Picchu was substantially more genetically diverse—measured as conditional heterozygosity for nuclear DNA and nucleotide diversity for mtDNA—than contemporary rural villages in the Andes (Fig. 3 and fig. S5). Among the yanacona of Machu Picchu, we observe genetic ancestries that represent all regions comprising the Inca Empire, except Central Chile/Western Argentina, which represents the southern frontier. This observation is consistent with previous analyses of the Machu Picchu burials that indicated that many individuals exhibited nonlocal isotopic signatures (Sr and O) or cultural indicators (12, 20, 21) not associated with local cultural traditions (table S1).
The rate of variation at polymorphic sites observed for Machu Picchu seems to remain consistently high throughout the site’s occupation (Fig. 2) (25). Individuals of nonregional (Ollantaytambo, Cusco) genetic ancestry and nonlocal strontium 87Sr/86Sr are found throughout the burial population across radiocarbon ages (e.g., MP63 and MP107; table S1). When combined with the genetic diversity estimates, this pattern suggests that the addition of yanacona and former aclla to the Machu Picchu community continued after the death of Pachacuti. This is consistent with historical evidence that yanacona were gifted to royal estates after the death of the founder (11, 14) because the mummies who founded their royal estates continued to be recognized as the owners of the estates and were expected to entertain mummies from other lineages and their guests.
We observe a significant difference (P = 0.0157) when we compare the genetic ancestries of biologically male and female individuals, with most male individuals exhibiting ancestries associated with highland regions, while female individuals exhibit more diverse nonhighland ancestries (Fig. 4 and table S1). The genetic diversity observed at Machu Picchu also exceeds the diversity observed for the only genetically studied communities of mitimaes (i.e., ethnic groups forcibly resettled by the Inca state) from the Chincha Valley on the central Peruvian coast (46). This pattern is consistent with the conclusion that the burial population at Machu Picchu was composed of yanacona and former aclla (17) rather than mitimaes. The presence of individuals exhibiting ancestries associated with Amazonia (e.g., MP4b), Ecuador (e.g. MP9b), and the Peruvian North Coast (MP42b) in the earliest occupation phases of Machu Picchu (Fig. 4 and table S1) may suggest that the expansion of the Inca Empire occurred earlier or differently from models derived from historical sources. This observation is consistent with the increasing view among Inca specialists that the historicist chronology dominant since 1945 is untenable in light of recent archaeological evidence from Cusco and distant Inca provinces (2, 6, 42, 47, 48) (see Supplementary Text).
The early presence of individuals exhibiting ancestry associated with, for example, Ashaninka and other Arawak speaking groups along the eastern Andean piedmont is exciting but expected. Archaeological, ethnohistorical, linguistic, and genetic sources indicate that the inhabitants of this region interacted with the adjacent highlands even before the Inca (33, 40, 49–51), and recent studies suggest a complementary relationship between the Inca and these groups, rather than one dominated by conflict and conquest (49). All individuals buried at Machu Picchu exhibiting this ancestry have been determined to be biologically female, suggesting that some might have been gifted as wives to favored individuals, a process recorded in historical sources (13, 16).
The relationship between the Inca and populations of the former Kingdom of Chimor on the Peruvian North Coast and Ecuadorian groups such as the Cañaris were more bellicose, and the presence of some of the individuals at Machu Picchu with ancestries from these regions may be explained by their incorporation as yanacona who were craft specialists skilled in metal working. The identification of unfinished metal objects and production debris have allowed archaeologists to identify metal working as one of the activities present at Machu Picchu but apparently lacking at many other royal estates (8, 52).