The history books in school usually teach about the decline of indigenous American populations due to exploration, conquest, and massacre at the hand of European explorers. Though the Zapotec civilization had already mostly disappeared by the time the Europeans arrived in Mexico, historians had still attributed its people's near-complete disappearance to European activity. However, a recent mtDNA study shows that significant population decline occurred well before first European contact, suggesting that other factors were at play in gene flow decline.
This can, perhaps, be applied as an mtDNA study of more indigenous populations, so as to see the effects of contact with European populations more closely.
Source: Here
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