3074. New Studies Suggest Ancient Populations Expanded Across the Americas Approximately 13,000 Years Ago

By Lizzie Wade, Science, November 8, 2018

The Suruí from the Brazilian Amazon carry traces of Australasian ancestry, now confirmed to have arrived in South America more than 10,400 years ago. 

 Craig Stennett/Alamy Stock Photo 

For decades, scientists could describe the peopling of the Americas only in broad strokes, leaving plenty of mysteries about when and how people spread across the continents. Now, state-of-the-art ancient DNA methods, applied to scores of new samples from around the Americas, are filling in the picture. Two independent studies, published in Cell and online in Science, find that ancient populations expanded rapidly across the Americas about 13,000 years ago. They also emphasize that the story continued in the thousands of years since, revealing previously undocumented, large-scale movements between North and South America.

The data include 64 newly sequenced ancient DNA samples from Alaska to Patagonia, spanning more than 10,000 years of genetic history. "The numbers [of samples] are just extraordinary," says Ben Potter, an archaeologist at the University of Alaska in Fairbanks. Prior to these studies, only six genomes older than 6000 years from the Americas had been sequenced. As a result, says Jennifer Raff, an anthropological geneticist at the University of Kansas in Lawrence, "The [genetic] models that we've been using to explain the peopling of the Americas have always been oversimplified."

Eske Willerslev, an evolutionary geneticist at the University of Copenhagen who led the Scienceteam, worked closely with the Fallon Paiute-Shoshone Tribe in Nevada to gain access to some of the new samples. The tribe had been fighting to repatriate 10,700-year-old remains found in Nevada's Spirit Cave and had resisted destructive genetic testing. But when Willerslev visited the tribe in person and vowed to do the work only with their permission, the tribe agreed, hoping the result would bolster their case for repatriation.

It did. Willerslev found that the remains from Spirit Cave are most closely related to living Native Americans. That strengthened the Fallon Paiute-Shoshone Tribe's claim to the bones, which were returned to them in 2016 and reburied. Willerslev's study validates that "this is our homeland, these are our ancestors," says Rochanne Downs, the tribe's cultural coordinator.

Willerslev added the Spirit Cave data to 14 other new whole genomes from sites scattered from Alaska to Chile and ranging from 10,700 to 500 years old. His data join an even bigger trove published in Cell by a team led by population geneticist David Reich of Harvard Medical School in Boston. They analyzed DNA from 49 new samples from Central and South America dating from 10,900 to 700 years old, at more than 1.2 million positions across the genome. All told, the data decisively dispel suggestions, based on the distinctive skull shape of a few ancient remains, that early populations had a different ancestry from today's Native Americans. "Native Americans truly did originate in the Americas, as a genetically and culturally distinctive group. They are absolutely indigenous to this continent," Raff says.

The two studies also provide an unprecedented view of how ancient Americans moved across the continent beginning about 13,000 years ago. Previous genetic work had suggested the ancestors of Native Americans split from Siberians and East Asians about 25,000 years ago, perhaps when they entered the now mostly drowned landmass of Beringia, which bridged the Russian Far East and North America. Some populations stayed isolated in Beringia, and Willerslev sequenced one new example of such an "Ancient Beringian," 9000-year-old remains from Alaska's Seward peninsula. Meanwhile, other groups headed south. At some point, those that journeyed south of the ice sheets split into two groups—"Southern Native Americans" and "Northern Native Americans" (also sometimes called Ancestral A and B lineages), who went on to populate the continents.

By looking for genetic similarities between far-flung samples, both papers add detail—some of it puzzling—to this pattern. The 12,700-year-old Anzick child from Montana, who is associated with the mammoth-hunting Clovis culture, known for their distinctive spear points, provided a key reference point. Willerslev detected Anzick-related ancestry in both the Spirit Cave individual—who is associated with western stemmed tools, a tradition likely older than Clovis—and 10,000-year-old remains from Lagoa Santa in Brazil. Reich's team found an even closer relationship between Anzick and 9300- to 10,900-year-old samples from Chile, Brazil, and Belize.

Those close genetic affinities at similar times but across vast distances suggest people must have moved rapidly across the Americas, with little time to evolve into distinct genetic groups. Reich's team argues that Clovis technology might have spurred this rapid expansion. But anthropological geneticist Deborah Bolnick of the University of Connecticut in Storrs notes the Anzick-related ancestry group may have been broader than the Clovis people, and doubts that the culture was a driver.

Willerslev also finds traces of this Anzick-related ancestry in later samples from South America and Lovelock Cave in Nevada. But in Reich's data it fades starting about 9000 years ago in much of South America, suggesting "a major population replacement," he says.

After that population turnover in South America, both teams see striking genetic continuity in many regions. But that doesn't mean no one moved around. Reich's group sees a new genetic signal entering the central Andes about 4200 years ago, carried by people who are most closely related to ancient inhabitants of the Channel Islands, off Southern California. Meanwhile, Willerslev's team detects ancestry related to the present-day Mixe, an Indigenous group from Oaxaca in Mexico, spreading to South America about 6000 years ago and North America about 1000 years ago. Neither of these migrations replaced local communities, but rather mixed with them. Both teams say they could be seeing the same signal, but "without comparing the data, it's really hard to tell," says archaeogeneticist Cosimo Posth of the Max Planck Institute for the Science of Human History in Jena, Germany, the first author of the Cell paper.

Just as mysterious is the trace of Australasian ancestry in some ancient South Americans. Reich and others had previously seen hints of it in living people in the Brazilian Amazon. Now, Willerslev has provided more evidence: telltale DNA in one person from Lagoa Santa in Brazil, who lived 10,400 years ago. "How did it get there? We have no idea," says geneticist José Víctor Moreno-Mayar of the University of Copenhagen, first author of the Willerslev paper.

The signal doesn't appear in any other of the team's samples, "somehow leaping over all of North America in a single bound," says co-author and archaeologist David Meltzer of Southern Methodist University in Dallas, Texas. He wonders whether that Australasian ancestry was confined to a small population of Siberian migrants who remained isolated from other Native American ancestors throughout the journey through Beringia and the Americas. That suggests individual groups may have moved into the continents without mixing.

Delighted as they are with the data in the new studies, scientists want more. Meltzer points out that none of the new samples can illuminate what's happening at pre-Clovis sites such as Chile's Monte Verde, which was occupied 14,500 years ago. And Potter notes that, "We have a huge, gaping hole in the central and eastern North American [sampling] record. … These papers aren't the final words."

3028. Luigi Cavalli-Sforza, 96, Who Tracked Genes Through History, Dies

By Denise Grady, The New York Times, September 19, 2018

Luigi Luca Cavalli-Sforza in 2006. He was a pioneer in using genetic information to help trace human evolution, history, and patterns of migration.CreditCredit Photo: Basso Cannarsa/Agence Opale, via Alamy

Millions of people in recent years have sent off samples of their saliva to DNA-testing companies like 23andMe and Ancestry.com hoping to find out where their forebears came from and whether they have mystery relatives in some distant land, or even around the corner.

The trend itself can be traced to an Italian physician and geneticist, Luigi Luca Cavalli-Sforza, who died on Aug. 31 at his home in Belluno, Italy, at 96. He laid the foundation for such testing, having honed his skills more than 60 years ago using blood types and 300 years of church records to study heredity in the villagers of his own country.

Dr. Cavalli-Sforza was a pioneer in using genetic information to help trace human evolution, history and patterns of migration. The founder of a field that he called genetic geography, he was renowned for synthesizing information from diverse disciplines — genetics, archaeology, linguistics, anthropology and statistics — to explain how human populations fanned out over the earth from their original home in Africa.

David Reich, a professor of genetics at Harvard Medical School, said in an interview that Dr. Cavalli-Sforza was the first scientist to predict that there would be “enough information in genes to determine where people came from in the world and who they’re most closely related to.

“A fair number of reasonable people,” he added, “thought it wouldn’t be possible.”

Dr. Cavalli-Sforza was a professor at Stanford University from 1970 to 1992 and continued to do research for more than a decade after retiring.

Described by colleagues as endlessly curious and fearless about venturing into unexplored zones, he studied fruit flies, bacteria, Italian marriage records, human blood groups, African Pygmies and the political and religious views of American college students and their parents, analyzing his own findings with merciless statistical rigor. Cultural traits and how they spread fascinated him, and late in life he began to study variations in hand gestures in different parts of Italy.

With Marcus Feldman, a biologist and colleague at Stanford, he founded a field called cultural evolution, which treats language, values, customs and other social phenomena as traits that evolved, just as physical traits do.

One major question their work answered concerned the spread of agriculture about 10,000 years ago as populations shifted from hunting and gathering to farming. Did people in one region visit an area with farming and then take the skills home? Apparently not. Overall, the genetic studies revealed, it was the farmers themselves who moved, taking their knowledge of agriculture with them.

Cultural evolution “exploded into a legitimate discipline,” Dr. Feldman said in a telephone interview. “There’s now a cultural evolution society.”

Dr. Cavalli-Sforza also studied genetic changes in the Y chromosome, the determinant of male gender, which is passed from fathers to sons. He traced the changes to one male ancestor, who lived in Africa 70,000 to 100,000 years ago.

His work, along with that of colleagues, indicated that genetically there is no such thing as race: Individuals within a population group differ genetically from one another just as much as they differ from people in other groups. He denounced efforts to suggest that superficial traits like skin color or hair texture had any underlying connection to intelligence, behavior or character.

In 1973, Dr. Cavalli-Sforza publicly debated William B. Shockley, a Stanford engineering professor who had shared the 1956 Nobel Prize in Physics for inventing the transistor and who had become notorious for declaring that blacks were less intelligent than whites.

Dr. Cavalli-Sforza came under fire from some quarters after proposing, in the 1990s, what he called a Human Genome Diversity Project. The plan was to collect blood, hair or saliva to provide DNA from populations all over the world, including aboriginal groups that were declining in numbers. The project would create cell lines that could be stored and used later by researchers.

Although many scientists favored the plan, opponents said it smacked of colonialism, racism and “biopiracy” — meaning that if the samples led to medical or pharmaceutical breakthroughs, the people who donated their DNA would never see the health benefits or the profits.

Some critics even maintained that the samples could be used to create biological weapons that might target specific ethnic groups.

But Dr. Cavalli-Sforza stuck to his guns. The project went on, though not on the scale that he had planned. He had hoped for 10,000 samples but wound up with about 1,000 samples from some 50 populations; the samples are stored in Paris at the Center for the Study of Human Polymorphisms.

“That group of samples has been an incredible resource that has been studied in many, many ways,” Dr. Reich said.

Luigi Luca Cavalli was born in Genoa, Italy, on Jan. 25, 1922, the only child of Pio Cavalli and Attilia (Manacorda) Cavalli. His father represented American companies that sold washing machines and dishwashers in Europe; he also wrote a book on advertising, “La Spada dell’America” (“America’s Sword”), published in 1919.

Luigi Cavalli added Sforza to his surname as an adult after his father had died, taking it from his maternal step-grandfather, who had adopted him.

He earned a medical degree from the University of Pavia in 1944. Studying medicine during World War II might have saved his life, he later told colleagues: Italy did not draft medical students.

Dr. Cavalli-Sforza worked as a physician in Italy for two years. Medicine then was not advanced, antibiotics were unavailable, and the work “was really more a job for a priest,” he told Dr. Feldman in a videotaped interview in 2006.

“You couldn’t help anybody,” he said. “You just saw people dying, and you couldn’t do anything to help them.”

The experience prompted him to move away from clinical medicine toward microbiology and then genetics.

In 1946 he married Alba Ramazzotti, a niece of one of his professors. She had studied biology but did not pursue a career in it.

Dr. Cavalli-Sforza became an assistant professor at the University of Cambridge in Britain in 1948 and worked with Ronald Fisher, a top expert on bacterial genetics and statistics. It was a turning point. Trained in clinical medicine, not basic science, Dr. Cavalli-Sforza seized the opportunity to learn what he needed to know to forge ahead in research.

“He loved working with numbers,” Dr. Feldman said in the telephone interview. “He was strongly influenced by the period he spent with Fisher at Cambridge. That period led him to have this feel for numbers, and their use in revealing patterns.”

From 1951 to 1970 Dr. Cavalli-Sforza taught at the University of Parma as well as at the University of Pavia, where he led the genetics department.

In the early 1950s, he was part of a team that helped explain the mechanics of a phenomenon that was newly discovered at the time: sex between bacteria — that is, their ability to swap genetic material. The finding was important because it helped explain the spread of genes that enable bacteria to resist antibiotics.

But humans interested him more than bacteria did. A student of his, a priest named Antonio Moroni, told him that Roman Catholic parishes in Italy kept detailed marriage records that went back generations; some included notations of marriages between cousins. Dr. Cavalli-Sforza realized that the records, compiled in books, could be a gold mine. For one thing, the marriages between relatives could reveal the effects of inbreeding.

DNA testing was not available then, but tests for A, B and O blood groups — an inherited trait — could be done. He began collecting blood samples from people all over the country. Pairing blood types and information from the books going back 300 years enabled him and his research partners to show that random genetic changes — known as genetic drift — played a bigger role in human evolution than scientists had realized.

Dr. Cavalli-Sforza moved to Stanford University in 1970, but only after being assured that he would not have to head a department.

From 1966 to 1985 he made 11 trips to Africa to study Pygmies, who were still hunter-gatherers at the time. He later edited and wrote part of a book about them and their culture.

“These people are exactly like me — brothers, really,” he told Dr. Feldman in the video interview. “And yet they were living in such a completely different way.”

His experience with the Pygmies had a profound effect on his thinking, igniting a determination to “understand why cultures can be so different,” he said.

“He was adopted into a Pygmy extended family and was very proud of it,” said Mary-Claire King, a geneticist at the University of Washington. “They gave him a name. He told me it translated as ‘Great White Elephant.’ He just loved living with the Pygmies.”

Dr. Cavalli-Sforza was the author or co-author of hundreds of scientific articles and nine books. His masterwork was “The History and Geography of Human Genes,” a 1,000-page account of where humans originated and where they went, based on his tracking of various genetic traits around the world.

His wife died in 2015. He is survived by a daughter, Violetta Cavalli-Sforza; three sons, Tommaso, Francesco and Matteo, who confirmed the death; and three grandchildren.

“He embodied the idea of the scientist as a citizen of the world,” Dr. King said. “He was very comfortable everywhere. He’d be in Africa, all over Europe, in Asia. He had a real sensitivity to cultures, and he picked up languages. He had the capacity to think very well and bring you into his thinking and make you feel like you were part of his understanding, in so many fields.”

The ability to sequence DNA gives geneticists far more power today than they had when Dr. Cavalli-Sforza did much of his research.

“He did so much just with blood groups,” Dr. King said. “Suppose people like Luca had the kinds of modern tools we have now?”