The second and third migratory waves from Siberia, which are thought to have led to the Athabaskan, Aleut, Inuit, and Yupik people, apparently did not reach farther than the southern United States and Canada, respectively.

The micro-satellite diversity and distributions of Y-chromosome lineages specific to South America suggest that certain Amerindian populations have been isolated since the initial colonization of the region.

All ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate.

However, an ancient signal of shared ancestry with the Indigenous peoples of Australia and Melanesia was detected among the Native populations of the Amazon region.

The most conspicuous remains of these societies are vast mounds of discarded shellfish, known as sambaquis, found at some coastal sites that were continuously inhabited for more than 5,000 years.

Additionally, substantial "black earth" (terra preta) deposits in several places along the Amazon are believed to be ancient garbage dumps (middens).

Recent excavations of these deposits in the middle and upper Amazon have uncovered remains of massive settlements, containing tens of thousands of homes, indicating a complex social and economic structure.

Many researchers believed that the Andes were populated by Paleoindian migrants from North America, who gradually moved south after being hunters on the plains.

[19] The Native Americans of the Amazon rainforest may have used their method of developing and working in terra preta to make the land suitable for the large-scale agriculture needed to support large populations and complex social formations, such as chiefdoms.

In addition to the Tupi and Tapuia, two other Indigenous mega-groups were commonly identified in the interior: the Caribs, who inhabited much of what is now northwestern Brazil, including both shores of the Amazon River up to the delta, and the Nuaraque group, whose constituent tribes inhabited several areas, including most of the upper Amazon (west of present-day Manaus) and significant pockets in modern Amapá and Roraima states.

When the Portuguese explorers first arrived in Brazil in April 1500, they found, to their astonishment, a wide coastline rich in resources and teeming with hundreds of thousands of Indigenous people living in a "paradise" of natural abundance.

The diseases spread rapidly along Indigenous trade routes, likely leading to the annihilation of entire tribes without direct contact with Europeans.

Groups of fierce explorers organized expeditions known as "bandeiras" (flags) into the interior to claim territory for the Portuguese crown and to search for gold and precious stones.

[30] Jesuit priests, such as Fathers José de Anchieta and Manuel da Nóbrega, studied and recorded the Indigenous languages and founded mixed settlements, such as São Paulo dos Campos de Piratininga, where colonists and Amerindians lived side by side, spoke the same Língua Geral (common language), and freely intermarried.

Due to a complex diplomatic situation involving Portugal, Spain, and the Vatican, the Jesuits were expelled from Brazil, and their missions were confiscated and sold.

There are documented accounts of smallpox being used as a biological weapon by some Brazilian villagers seeking to eliminate nearby Amerindian tribes, not always aggressively.

Local farmers, desiring more land for their cattle farms, gave clothing from sick villagers (which would normally have been burned to prevent further infection) to the Timbira.

The promise of wealth from reservation lands attracted cattle ranchers and settlers, who continued encroaching on Indigenous territories, with the SPI facilitating this intrusion.

[citation needed] Due largely to the efforts of the Villas-Bôas brothers, Brazil's first Indigenous reserve, the Xingu National Park, was established by the federal government in 1961.

During the social and political upheaval of the 1960s, reports of mistreatment of Amerindians increasingly reached Brazil's urban centers and began to affect public opinion.

The same year, the government established the Fundação Nacional do Índio (National Indian Foundation), known as FUNAI, which is responsible for protecting the interests, cultures, and rights of Indigenous peoples in Brazil.

[36] However, the exploitation of rubber and other Amazonian natural resources has led to a new cycle of invasion, expulsion, massacres, and death, which continues to this day.

[40][39][41][42][43] Since the 1980s, exploitation of the Amazon Rainforest for mining, logging, and cattle ranching had surged, which poses a severe threat to the region's Indigenous population.

Settlers illegally encroaching on Indigenous land continue to destroy the environment necessary for traditional ways of life, provoke violent confrontations, and spread disease.

"[48] Within hours of taking office in January 2019, Bolsonaro made two major changes to FUNAI, affecting its responsibility to identify and demarcate Indigenous territories.

[56] On May 5, 2020, following an investigation by Human Rights Watch (HRW), Brazilian lawmakers released a report examining violence against Indigenous people, Afro-Brazilian rural communities, and others involved in illegal logging, mining, and land grabbing.

Brazil has one of the highest levels of income inequality in the world,[58] and a significant portion of its population includes Indigenous tribes migrating towards urban areas, both by choice and due to displacement.

As a result, their claims to Indigenous Territories (TIs), which often involve the demarcation of large areas of land and may dispossess established local communities, can be challenged by others.

Even neighboring kinship groups might dispute these claims, arguing that those making them are not "real Indians" due to factors like historical intermarriage (miscegenation), cultural assimilation, and stigma against self-identifying as Indigenous.

Additionally, claims to TIs can be opposed by major landowning families from the rubber era or by peasants working the land, who might instead prefer the concept of extractive reserve.