Ancient DNA evidence reveals two unknown migrations from North to South America

An international research team has used genome-wide ancient DNA data to revise Central and South American history. Their analysis of DNA from 49 individuals spanning about 10,000 years in Belize, Brazil, the Central Andes, and southern South America has concluded that the majority of Central and South American ancestry arrived from at least three different streams of people entering from North America, all arising from one ancestral lineage of migrants who crossed the Bering Strait some time before 15,000 years ago.

Ancient DNA evidence reveals two unknown migrations from North to South America
Graphic showing the geographic movement of populations discussed in the study
[Credit: Posth et al./Cell]

The evidence, presented in the journal Cell, shows that within this one ancestral lineage, there were two previously undocumented streams of gene flow from North to South America, one of which was later displaced in a major population replacement that began at least 9,000 years ago.
“Our work multiplied the number of ancient genomes available from these areas by about 20, giving us a much more comprehensive picture of indigenous history in the Americas,” says co-senior author David Reich, a geneticist at Harvard Medical School and the Howard Hughes Medical Institute. “This broader dataset reveals a common origin of North, Central, and South Americans as well as two previously unknown genetic exchanges between North and South America.”

“Nearly all Central and South Americans arose from a star-like radiation of the first lineage into at least three branches,” says co-lead author Cosimo Posth, an archaeogeneticist from the Max Planck Institute for the Science of Human History. “That means that nearly all the ancestry of Central and South Americans came from the same source population, albeit one that had already diversified prior to its spread into South America. With DNA evidence largely based on present-day people, those multiple gene flow events are undetectable, highlighting the power of ancient DNA data.”

Ancient DNA evidence reveals two unknown migrations from North to South America
The exterior of the rock shelter site of Lapa do Santo in Brazil
[Credit: André Strauss]

The genome analysis also yielded new insights on the Clovis culture-related people, who were mainly distributed across North America from about 13,000 years ago. Archaeological evidence from Clovis sites shows that the spread of Clovis artefacts did not expand throughout South America. But when the researchers used genome-sequencing technology to generate and compare genomes from a previously published ~13,000-year-old Clovis-related genome in Montana to the earliest genomes analyzed from South and Central America dating to between ~9,000 and ~11,000 years ago, they noticed significant shared ancestry. That suggested that the people who spread the Clovis culture also left a major impact much father south through people producing non-Clovis-specific stone tools.
“We weren’t expecting to find a relation to people associated with the Clovis culture in South America,” says co-first author Nathan Nakatsuka, a PhD student in Reich’s lab at Harvard. “But it seems the expansion of the Clovis-associated lineage extended to parts of Central and South America.”

Ancient DNA evidence reveals two unknown migrations from North to South America
Excavation in progress at the rock shelter site of Lapa do Santo in Brazil, where an individual dating
to approximately ~9,600 years ago was found [Credit: André Strauss]

The paper concludes that this Clovis-related lineage contributed substantially to a group of 9,000-10,000-year-old individuals from Lagoa Santa in Brazil, inconsistent with the hypothesis that the people from this site derived from a separate migration from Asia. The authors also detected the Clovis-related genetic affinity in an even older, almost ~11,000-year-old individual from Chile and a slightly younger, more than ~9,000-year-old individual from Belize.
Beginning around ~9,000 years ago with ancient samples in Peru, however, the authors detected an almost complete disappearance of the Clovis culture-associated ancestry in Central and South America, documenting a remarkable population replacement. The large-scale population replacement is a process that was not widely expected by archaeologists,” says Reich. “This is an exciting example of how ancient DNA studies can reveal events in the past that were not confirmed and thus can stimulate new work in archaeology.”

Ancient DNA evidence reveals two unknown migrations from North to South America
Where two, 7,400 year old indiivduals were found [Credit: Keith Prufer,
Bladen Paleoindian and Archaic Archaeological Project]

The researchers also showed that after this major population turnover, there was striking continuity compared to other parts of the world like Eurasia and Africa. “There is remarkable continuity between earlier and later skeletons with South Americans today,” says Posth. “For example, modern-day Quechua and Aymara from the Central Andes can trace their ancestry back to the ancient people of the Cuncaicha site from 9,000 years ago onwards. This is a longer-standing continuity than you see in other continents.”
The researchers recognize that there is much more work to do to fully flesh out the history of the Americas.

“We’re very enthusiastic about the prospects for a much richer understanding of American population history, but this is still a vast region full of geographic and chronological holes,” says Reich. “We’d like to collect more genetic material from earlier and later sites and from more countries, such as Colombia, Venezuela, and other parts of Brazil. We also want to examine the evolution of genetic traits over time.”

Source: Cell Press [November 08, 2018]

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History of early settlement and survival in Andean highlands revealed by ancient genomes

A multi-center study of the genetic remains of people who settled thousands of years ago in the Andes Mountains of South America reveals a complex picture of human adaptation from early settlement, to a split about 9,000 years ago between high and lowland populations, to the devastating exposure to European disease in the 16th-century colonial period.

History of early settlement and survival in Andean highlands revealed by ancient genomes
One the burial context sampled at Jiskairumoko. The image shows one of the individuals encountered during
excavation. The human remains have been removed in this image [Credit: Mark Aldenderfer]

Led by Anna Di Rienzo, PhD, and John Lindo, PhD, JD, from the University of Chicago; Mark Aldenderfer, PhD, from the University of California, Merced; and Ricardo Verdugo from the University of Chile, the researchers used newly available samples of DNA from seven whole genomes to study how ancient Andean people – including groups that clustered around Lake Titicaca in Peru and Bolivia, 12,000 feet above sea level – adapted to their environment over the centuries.

In the journal Science Advances, they compared their seven historical genomes to 64 modern-day genomes from a current highland Andean population, the agropastoral Aymara of Bolivia, and the lowland hunter-gatherer Huilliche-Pehuenche in coastal Chile.

The goals were (1) to date the initial migration to the Andean highlands, (2) to identify the genetic adaptations to the high-altitude environment that allowed that settlement, (3) to estimate the impact of the European contact starting in the 1530s that caused the near annihilation of many lowland communities of South America.

“We have very ancient samples from the high Andes,” said Di Rienzo. “Those early settlers have the closest affinity to the people who now live in that area. This is a harsh, cold, resource-poor environment, with low oxygen levels, but people there adapted to that habitat and the agrarian lifestyle.”

The study, “The Genetic prehistory of the Andean highlands 7,000 years BP through European contact,” uncovered several unexpected features.

History of early settlement and survival in Andean highlands revealed by ancient genomes
The location of ancient samples near Lake Titicaca, elevation 3812 metres, in what is now Peru and Bolivia
[Credit: John Lindo et al. 2018]

The researchers found that highland Andeans experienced much smaller than expected population declines following contact with European explorers who first came to South America in the 1530s. In the lowlands, demographic modeling and historical records infer that up to 90 percent of residents may have been wiped-out after the arrival of Europeans. But the people living in the upper Andes had only a 27-percent population reduction.

Even though the highlanders lived in altitudes above 8,000 feet, which meant reduced oxygen, frequent frigid temperatures and intense ultra-violet radiation, they did not develop the responses to hypoxia seen in natives of other high-altitude settings, such as Tibet.

The Andeans may have adapted to high altitude hypoxia “in a different way, via cardiovascular modifications,” the researchers suggest. They found evidence of alterations in a gene called DST, which is associated with the formation of cardiac muscle. Andean highlanders tend to have enlarged right ventricles. This may have improved oxygen intake, enhancing blood flow to the lungs.

But the strongest adaptation signal the researchers found was in a gene called MGAM (maltase-glucoamylase) an intestinal enzyme. It plays an important role in the digestion of starchy foods such as potatoes — a food native to the Andes. A recent study suggests that the potato may have been domesticated in the region at least 5,000 years ago. Positive selection on the MGAM gene, the authors note, “may represent an adaptive response to greater reliance upon starchy domesticates.”

The early presence of this variant in Andean peoples suggests “a significant shift in diet from one that was likely more meat based to one more plant based,” said UC Merced’s Aldenderfer, an anthropologist. “The timing of the appearance of the variant is quite consistent with what we know of the paleo-ethno-botanical record in the highlands.”

History of early settlement and survival in Andean highlands revealed by ancient genomes
Entry into the Americas 20 ka ago. High/low altitude split 8750 years.
European contact 1532 AD [Credit: John Lindo et al. 2018]

Although Andean settlers consumed a high-starch diet after they started to farm, their genomes did not develop additional copies of the starch related amylase gene, commonly seen in European farming populations.

A comparison of the ancient genomes with their living descendants also revealed selection for immune-related genes soon after the arrival of Europeans, suggesting that Andeans who survived may have had an advantage with regard to the newly introduced European pathogens.

“Contact with Europeans had a devastating impact on South American populations, such as the introduction of disease, war, and social disruption,” explained Lindo. “By focusing on the period before that, we were able to distinguish environmental adaptations from adaptations that stemmed from historical events.”

“In our paper,” said Aldenderfer, “there was none of this prioritization of genes at the expense of archaeological data. We worked back and forth, genetics and archeology, to create a narrative consistent with all of the data at hand.”

Source: University of Chicago Medical Center [November 08, 2018]

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HiPOD (8 November 2018): Ridges in Terra Sabaea   – The…

HiPOD (8 November 2018): Ridges in Terra Sabaea

   – The objective of this observation is to determine the nature of ridges on a crater floor.  They may represent inverted terrain. (256 km above the surface. Black and white is less than 5 km across; enhanced color is less than 1 km.)

NASA/JPL/University of Arizona