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Genetic studies link indigenous peoples in the Amazon and Australasia

Native Americans living in the Amazon bear an unexpected genetic connection to indigenous people in Australasia, suggesting a previously unknown wave of migration to the Americas thousands of years ago, a new study has found.

“It’s incredibly surprising,” said David Reich, Harvard Medical School professor of genetics and senior author of the study. “There’s a strong working model in archaeology and genetics, of which I have been a proponent, that most Native Americans today extend from a single pulse of expansion south of the ice sheets–and that’s wrong. We missed something very important in the original data.”

Previous research had shown that Native Americans from the Arctic to the southern tip of South America can trace their ancestry to a single “founding population” called the First Americans, who came across the Bering land bridge about 15,000 years ago. In 2012, Reich and colleagues enriched this history by showing that certain indigenous groups in northern Canada inherited DNA from at least two subsequent waves of migration.

The new study, published July 21 in Nature, indicates that there’s more to the story.

Pontus Skoglund, first author of the paper and a postdoctoral researcher in the Reich lab, was studying genetic data gathered as part of the 2012 study when he noticed a strange similarity between one or two Native American groups in Brazil and indigenous groups in Australia, New Guinea and the Andaman Islands.

“That was an unexpected and somewhat confusing result,” said Reich, who is also an associate member of the Broad Institute of Harvard and MIT and a Howard Hughes Medical Investigator. “We spent a really long time trying to make this result go away and it just got stronger.”

Skoglund and colleagues from HMS, the Broad and several universities in Brazil analyzed publicly available genetic information from 21 Native American populations from Central and South America. They also collected and analyzed DNA from nine additional populations in Brazil to make sure the link they saw hadn’t been an artifact of how the first set of genomes had been collected. The team then compared those genomes to the genomes of people from about 200 non-American populations.

The link persisted. The Tupí-speaking Suruí and Karitiana and the Ge-speaking Xavante of the Amazon had a genetic ancestor more closely related to indigenous Australasians than to any other present-day population. This ancestor doesn’t appear to have left measurable traces in other Native American groups in South, Central or North America.

The genetic markers from this ancestor don’t match any population known to have contributed ancestry to Native Americans, and the geographic pattern can’t be explained by post-Columbian European, African or Polynesian mixture with Native Americans, the authors said. They believe the ancestry is much older–perhaps as old as the First Americans.

In the ensuing millennia, the ancestral group has disappeared.

“We’ve done a lot of sampling in East Asia and nobody looks like this,” said Skoglund. “It’s an unknown group that doesn’t exist anymore.”

The team named the mysterious ancestor Population Y, after the Tupí word for ancestor, “Ypykuéra.”

Reich, Skoglund and colleagues propose that Population Y and First Americans came down from the ice sheets to become the two founding populations of the Americas.

“We don’t know the order, the time separation or the geographical patterns,” said Skoglund.

Researchers do know that the DNA of First Americans looked similar to that of Native Americans today. Population Y is more of a mystery.

“About 2 percent of the ancestry of Amazonians today comes from this Australasian lineage that’s not present in the same way elsewhere in the Americas,” said Reich.

However, that doesn’t establish how much of their ancestry comes from Population Y. If Population Y were 100 percent Australasian, that would indeed mean they contributed 2 percent of the DNA of today’s Amazonians. But if Population Y mixed with other groups such as the First Americans before they reached the Americas, the amount of DNA they contributed to today’s Amazonians could be much higher–up to 85 percent.

To answer that question, researchers would need to sample DNA from the remains of a person who belonged to Population Y. Such DNA hasn’t been obtained yet. One place to look might be in the skeletons of early Native Americans whose skulls some researchers say have Australasian features. The majority of these skeletons were found in Brazil.

Reich and Skoglund think that some of the most interesting open questions about Native American population history are about the relationships among groups after the initial migrations.

“We have a broad view of the deep origins of Native American ancestry, but within that diversity we know very little about the history of how those populations relate to each other,” said Reich.

This work was supported by the National Science Foundation (HOMINID grant BCS-1032255), the National Institutes of Health (GM100233), the Simons Foundation (grant 280376), the Howard Hughes Medical Institute, the Conselho Nacional de Desenvolvimento Científico e Tecnológico and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brazil), the Wenner-Gren Foundation and the Swedish Research Council (VR grant 2014-453).

Native Americans living in the Amazon bear an unexpected genetic connection to indigenous people in Australasia, suggesting a previously unknown wave of migration to the Americas thousands of years ago, a new study has found.

Battling ‘biopiracy’, scientists catalog the Amazon’s genetic wealth

TORONTO (Thomson Reuters Foundation) – In a bid to stop “biopiracy”, researchers are building a giant database to catalog genetic material from the world’s largest rainforest.

From the rubber in car tires, to cosmetics and medicines, genetic material contained in the Amazon region has contributed to discoveries worth billions of dollars.

Communities living there, however, have rarely benefited from the genetic wealth extracted from their land – a form of theft that legal experts call “biopiracy”.

Instead, forest-dwellers often remain impoverished, which can drive them to find other ways to make money, such as illegal logging, according to Dominic Waughray, who heads the Amazon Bank of Codes project for the World Economic Forum.

“At the heart of the conservation debate is: how do you find a way for a person in the forest to get more cash in their hand right now from preserving that habitat rather than cutting it down?” said Waughray.

One solution involves compelling investors to pay royalties to local communities when using genetic sequences from organisms extracted from the forest, he said. The Amazon Bank of Codes will facilitate those payments.

But first those genetic sequences need to be mapped and stored online, which is what the project backers aim to do as early as 2020.

Smart phones and digital payment tools will make it possible for outside investors to directly pay local residents to use genetic material extracted from their land, Waughray said.

DEEP HISTORY

Spread across nine countries, including Brazil, Colombia and Peru, the Amazon is home to one in 10 known species on earth, according to the World Wildlife Fund, a conservation group.

That makes the region vulnerable to biopiracy, which is the unlawful appropriation or commercial use of biological materials native to a particular country without providing fair financial compensation to its people or government.

“The history of biopiracy runs deep in the Amazon basin,” Waughray said, citing early colonialists taking rubber trees from the region to create lucrative plantations in Malaysia.

In a more recent case, Brazilian prosecutors launched an investigation into a California-based company earlier this year, accusing it of using genetic components of the tropical acai berry in its nutritional supplements without paying for them.

Pharmaceutical companies have also used the yellow-and-green Kambo frog to create anti-inflammatory drugs without distributing benefits to local residents, Brazil’s environmental enforcement agency said in 2011.

In India, attempts to patent products such as basmati rice and properties of the spice turmeric, for medical use, have sparked protests.

“The phenomenon has given rise to a huge outcry to have a more ethical approach to the use of biological resources,” said Ikechi Mgbeoji, a professor of intellectual property law at Toronto’s York University.

Internationally, the Nagoya Protocol, which came into force in 2014, governs how companies and researchers should equitably share benefits from genetic material, said Valerie Normand, an official from the U.N. Convention on Biological Diversity.

The agreement was “implemented precisely because developing countries, which are largely hot spots for biodiversity, were concerned about the misappropriation of their genetic resources,” Normand told the Thomson Reuters Foundation.

BANKING ON BIODIVERSITY

The Amazon Bank of Codes will use blockchain – decentralized digital technology allowing users to track the origins and transfers of information – to catalog specific pieces of genetic material contained in plants and animals.

If a company or researcher wants to use a piece of genetic code for a new medicine, study or product, they can access the bank and see exactly where in the Amazon it came from, said Waughray.

Governments, indigenous groups, non-governmental organizations and others, are discussing how the fees paid to use a genetic sequence will be distributed, said Waughray.

Critics, however, worry the project could actually make it easier for companies to steal genetic material.

“This will become a one-stop shop for digital biopiracy,” said Jim Thomas from the Montreal-based ETC Group, a technology watchdog.

Companies may use the database of genetic codes to go prospecting to find information they need, and then slightly alter it or find another way to avoid paying royalties, he said.

“It used to be companies would send people into the Amazon to gather material,” said Thomas.

“Then they would negotiate over whether they would be able to move that material out of the country. Now, you won’t even have to leave Toronto to scan the DNA.”

The Amazon Code Bank does not offer a “silver bullet” for combating the theft of genetic resources, Waughray said.

“Mischievous developers” could abuse the program, similar to illicit downloads of artists’ digital music from the internet.

But having a clear set of rules, and a way to track people who violate them, is far better than the status quo where powerful companies can pirate intellectual property from Amazonian communities, he added.

Genetic mapping of the Amazon could also usher in a “fourth industrial revolution”, he said.

Less than 15 percent of the world’s estimated species of plants and land animals have been genetically classified, and less than 0.1 percent have had their DNA thoroughly sequenced, according to the World Economic Forum.

Yet, these small percentages have delivered all modern knowledge about biology and the wealth stemming from it.

Genetically mapping 10 percent of the planet’s species could trigger a wave of innovation based on biotechnology that could change lives all over the world, said Waughray.

For example, he said, Amazonian ants could prove crucial in developing self-driving cars.

“Ants zoom around tropical forests and collect leaves . but there’s never an ant jam or an ant crash.”

The insects move at consistent speeds, and know the distances between one another, based on pheromones, which are chemicals the creatures release into the environment to affect the behavior of others around them.

“That code becomes very valuable when companies are trying to develop self-driving cars,” said Waughray.

Reporting by Chris Arsenault, Editing by Jared Ferrie. Please credit the Thomson Reuters Foundation, the charitable arm of Thomson Reuters, that covers humanitarian news, women’s and LGBT+ rights, human trafficking, property rights and climate change.

In a bid to stop "biopiracy", researchers are building a giant database to catalog genetic material from the world's largest rainforest.