Ancient DNA reveals the complex genetic prehistory of the Americas

American Association for the Advancement of Science

A comprehensive, hemisphere-spanning study of ancient DNA suggests a highly complex peopling of the American continents - one that cannot be explained by simple models or patterns of dispersal. The study involved an analysis of ancient American genomes unearthed in locations spanning from Alaska to Patagonia.

While there has been much focus on the timing and number of initial migrations into North and South America, less attention has been paid to the subsequent expansion throughout the American continents. Previous genomic studies have suggested that the first American populations diverged from their Siberian and East Asian ancestors nearly 25,000 years ago, and subsequently split into distinct North American and South American populations about 10,000 years later. However, the expansion of the first Americans remains a contentious topic and has been difficult to understand from analysis of present-day populations.

Víctor Moreno-Mayar and colleagues sequenced the genomes of 15 ancient Americans from locations spanning the Americas, and six of which were more than 10,000 years old. The results reveal a complex picture of population expansion and diversification. According to Moreno-Mayar et al., people spread out rapidly, yet unevenly, throughout the Americas, and diversified into multiple populations, some of which were unknown before this analysis -visible only in the genetic record. Interestingly, the authors identified the presence of a Late Pleistocene (about 11,700 BP) population with Australasian ancestry evident only in South America, which left no apparent genetic traces in North America.

In addition, the authors find evidence of a smaller Mesoamerican-related population expansion evident through a geographically widespread admixture of genetic material. While the study's results fill some gaps in our understanding of early Americans and reveal a complex population history, the authors note that the peopling of the Americas is likely more complicated still, as evidenced by the identification of unknown groups here.

In a separate study published in Science Advances, which focuses on the genetic prehistory of the South American Andes, John Lindo and colleagues find that the genetic and cultural adaptation to the harsh extremes of high-altitude Andean environments, in the region's first settlers and those who endured to meet Europeans, was a complex, yet relatively fast process.

Archaeological evidence suggests that the first permanent human occupation of the Andean highlands began upwards of 12,000 years before present (BP). Due to the stresses of living at high altitudes, such as cold temperatures, low oxygen and strong UV radiation, the selective pressures on human genes and social processes likely led to unique biological and social adaptations, research has suggested.

Even so, the genetics of highland Andean populations is not well-understood. To further explore the population history of Andean highlanders, John Lindo and colleagues compiled a time series of ancient genomes, derived from archaeological remains spanning three distinct cultural periods dating from 6,800 to 1,400 years BP. These sequences were then compared to others from both lowland and highland prehistoric and modern South American populations, as well as to sequences from ancient Native Americans from farther afield.

Lindo et al.'s analysis suggests that permanent highland populations were established in the Andes between 9,200 and 8,200 years BP, a date younger than what has been reported by studies using modern genomes alone. Surprisingly, say the authors, genetic traits modified due to environmental stressors did not include genes related to adaptation to hypoxia (oxygen deficiency). Rather, genes associated with the blood and heart were likely modified, a finding confirming previous hypotheses that native Andeans may have adapted to high altitudes via cardiovascular modifications.

The strongest signature of environmental modification on genes was associated with starch digestion, an adaptive response to a reliance on agriculture and the starchy potato diet that characterized the region for millennia, the authors suggest. Furthermore, Lindo et al. demonstrate how European contact may have affected Andean genetics within the last 500 years by identifying positive selection for genes directly associated with resistance to diseases likely brought by the first Europeans.