Population Histories and Genomic Diversity of South American Natives

Abstract

South America is home to one of the most culturally diverse present-day native populations. However, the dispersion pattern, genetic substructure, and demographic complexity within South America are still poorly understood. Based on genome-wide data of 58 native populations, we provide a comprehensive scenario of South American indigenous groups considering the genomic, environmental, and linguistic data. Clear patterns of genetic structure were inferred among the South American natives, presenting at least four primary genetic clusters in the Amazonian and savanna regions and three clusters in the Andes and Pacific coast. We detected a cline of genetic variation along a west-east axis, contradicting a hard Andes-Amazon divide. This longitudinal genetic variation seemed to have been shaped by both serial population bottlenecks and isolation-by-distance. Results indicated that present-day South American substructures recapitulate ancient macroregional ancestries and western Amazonia groups show genetic evidence of cultural exchanges that led to language replacement in pre-contact times. Finally, demographic inferences pointed to a higher resilience of the western South American groups regarding population collapses caused by the European invasion and indicated pre-contact population reductions and demic expansions in South America.

Uncovering Signals of Positive Selection in Peruvian Populations from Three Ecological Regions

“…Additionally, when masking the non-native American genetic components, we also find some sharing of the coastal genetic component in northwestern rainforest individuals, which is consistent with the mixed ancestry profiles recently described by Borda et al . (2020) and Castro e Silva et al . (2022) .…”

A genomic perspective on South American human history

“…Hence, these groups would have occupied the Brazilian coast from at least 8 ka BP until the arrival of Tupi-Guarani groups and Macro-Jê speakers, not necessarily in that order, as evidenced by the presence of ceramics from the Tupiguarani and Taquara/Itararé traditions in the uppermost layers of some sambaqui, respectively (Gaspar et al, 2008). The relationship between the Sambaqui mound builders and the contemporary indigenous communities remains largely unknown due to the relatively small number of individual analyzed until now, however current evidence suggests a higher affinity between them and present-day Jê-speakers, in comparison to other eastern South American natives (Castro e Silva et al, 2020;Castro e Silva et al, 2022).…”

“…In this sense, archeological findings indicate that permanent settlements start to appear in the Andes circa 9 ka BP, while genetic analyses point to a long-standing genetic continuity in the Lake Titicaca region possibly from 3.8 or even 7 ka BP up until the present-day Aymara and Quechua speaking peoples of the same area (Lindo et al, 2018). Indeed, some level of long-term genetic continuity inside large continental areas -such as the Pacific coast, the Andes or the Amazonseem to be common, although sometimes the genetic affinity patterns between ancient and contemporary individuals suggest the occurrence of large scale population movements, at least among adjacent regions (Castro e Silva et al, 2022).…”

“…As previously stated, beginning approximately 9 ka BP, a new SNA group of people started to arrive, at least partially displacing the early migrants, as seen by their reduced affinity with the Anzick1 and their higher affinity with modern South American indigenous peoples (Posth et al, 2018;Moreno-Mayar et al, 2018b). There appears to be a robust genetic affinity between Jê-speaking communities in central and southern Brazil and ancient individuals from across the area, especially those from the early Holocene (Castro e Silva et al, 2020;Castro e Silva et al, 2022). Aside from that, Jê-speakers have an exclusive ancestry component, making them the most distinct group of eastern South Americans in terms of genetic structure, implying that they are descended from a different branch, possibly a more basal one, with higher genetic contributions from ancient populations from the region (Castro e Silva et al, 2020;Castro e Silva et al, 2022).…”

“…There appears to be a robust genetic affinity between Jê-speaking communities in central and southern Brazil and ancient individuals from across the area, especially those from the early Holocene (Castro e Silva et al, 2020;Castro e Silva et al, 2022). Aside from that, Jê-speakers have an exclusive ancestry component, making them the most distinct group of eastern South Americans in terms of genetic structure, implying that they are descended from a different branch, possibly a more basal one, with higher genetic contributions from ancient populations from the region (Castro e Silva et al, 2020;Castro e Silva et al, 2022).…”