DNA analyses reveal genetic identities of world's first farmers

Conducting the first large-scale, genome-wide analyses of ancient human remains from the Near East, an international team led by Harvard Medical School has illuminated the genetic identities and population dynamics of the world's first farmers.

The study reveals three genetically distinct farming populations living in the Near East at the dawn of agriculture 12,000 to 8,000 years ago: two newly described groups in Iran and the Levant and a previously reported group in Anatolia, in what is now Turkey.

The findings, published in Nature on July 25, also suggest that agriculture spread in the Near East at least in part because existing groups invented or adopted farming technologies, rather than because one population replaced another.

"Some of the earliest farming was practiced in the Levant, including Israel and Jordan, and in the Zagros mountains of Iran--two edges of the Fertile Crescent," said Ron Pinhasi, associate professor of archaeology at University College Dublin and co-senior author of the study. "We wanted to find out whether these early farmers were genetically similar to one another or to the hunter-gatherers who lived there before so we could learn more about how the world's first agricultural transition occurred."

The team's analyses alter what is known about the genetic heritage of present-day people in western Eurasia. They now appear to have descended from four major groups: hunter-gatherers in what is now western Europe, hunter-gatherers in eastern Europe and the Russian steppe, the Iran farming group and the Levant farming group.

"We found that the relatively homogeneous population seen across western Eurasia today, including Europe and the Near East, used to be a highly substructured collection of people who were as different from one another as present-day Europeans are from East Asians," said David Reich, professor of genetics at Harvard Medical School and co-senior author of the study.

"Near East populations mixed with one another over time and migrated into surrounding regions to mix with the people living there until those initially quite diverse groups became genetically very similar," added Iosif Lazaridis, HMS research fellow in genetics and first author of the study.

Early adopters

Even as advances in ancient-DNA technology have made it possible to probe population mixing and large-scale migrations that occurred thousands of years ago, researchers have had trouble studying the genetic history of the Near East because the region's warm climate has degraded much of the DNA in unearthed bones.

The team overcame the problem of poor-quality DNA in part by extracting genetic material from ear bones that can yield up to 100 times more DNA than other bones in the body. The team also used a technique called in-solution hybridization to enrich for human DNA and filter out contaminant DNA from microbes.

The combined techniques allowed the researchers to gather high quality genomic information from 44 ancient Near Easterners who lived between 14,000 and 3,400 years ago: hunter-gatherers from before the invention of farming, the first farmers themselves and their successors.

By comparing the genomes to one another as well as to those of nearly 240 previously studied ancient people from nearby regions and about 2,600 present-day people, the researchers learned that the first farming cultures in the Levant, Iran and Anatolia were all genetically distinct. Farmers in the Levant and Iran were genetically similar, however, to earlier hunter-gatherers who had lived in the same areas.

"Maybe one group domesticated goats and another began growing wheat, and the practices were shared in some way," said Lazaridis. "These different populations all invented or adopted some facets of the farming revolution, and they all flourished."

The findings tell a different story from what researchers believe happened later in Europe, when the first farmers moved in from Anatolia and largely replaced the hunter-gatherer populations who'd been living there.

Mix and match

Over the following 5,000 years, the Near East farming groups mixed with one another and with hunter-gatherers in Europe.

"All this extraordinary diversity collapsed," said Reich. "By the Bronze Age, populations had ancestry from many sources and broadly resembled present-day ones."

The researchers also learned how descendants of each early farming group, even as they began to intermingle, contributed to the genetic ancestry of people in different parts of the world: Farmers related to the Anatolian group spread west into Europe, people related to the Levant group moved south into East Africa, people related to those in Iran or the Caucasus went north into the Russian steppe, and people related to both the farmers in Iran and hunter-gatherers from the steppe spread into South Asia.

"The Near East was the missing link to understanding many human migrations," said Pinhasi.

Finally, the study provides a few more clues about a hypothetical, even more ancient, population called the Basal Eurasians, an early diverging branch of the family tree of humans living outside Africa, whose existence Lazaridis has inferred from DNA analyses but whose physical remains have not yet been found.

"Every single group from the ancient Near East appears to have Basal Eurasian ancestry--up to around fifty percent in the earliest groups," said Lazaridis.

To the researchers' surprise, statistical analyses suggested that the Basal Eurasians may have had no Neanderthal DNA. Other non-African groups have at least 2 percent Neanderthal DNA.

The team believes this finding could help explain why West Eurasians have less Neanderthal DNA than East Asians, even though Neanderthals are known to have lived in west Eurasia.

"Admixture with Basal Eurasians may have diluted the Neanderthal ancestry in West Eurasians who have ancient Near Eastern farmer ancestry," said Reich. "Basal Eurasians may have lived in parts of the Near East that did not come into contact with the Neanderthals."

Going forward, said Pinhasi, "We're eager to study remains from the world's first civilizations, who succeeded the samples analyzed in the study. The people everyone reads about in history books are now within the reach of our genetic technology."

---

Story Source:

The above post is reprinted from materials provided by Harvard Medical School. Note: Materials may be edited for content and length.

New species of beaked whale confirmed by DNA

An international team of scientists who searched out specimens from museums and remote Arctic islands has identified a rare new species of beaked whale that ranges from northern Japan across the Pacific Ocean to Alaska's Aleutian Islands.

Japanese whalers call the enigmatic black whales "karasu," the Japanese word for raven. The new species is darker in color and about two-thirds the size of the more common Baird's beaked whale, but so scarce that even whalers rarely see them.

A DNA analysis of 178 beaked whales from around the Pacific Rim found eight known examples of the new species, the scientists reported today in the journal Marine Mammal Science. The eight included specimens from the Smithsonian Institution and Los Angeles County Museum of Natural History, a skeleton on display in an Alaska high school, and another that puzzled researchers trying to identify it when it washed up on an island in the Bering Sea.

"The challenge in documenting the species was simply locating enough specimens to provide convincing evidence," said Phillip Morin, a research molecular biologist at NOAA Fisheries' Southwest Fisheries Science Center, and lead author of the new study. "Clearly this species is very rare, and reminds us how much we have to learn about the ocean and even some of its largest inhabitants."

An earlier Japanese study had suggested that the black whales, sometimes considered a dwarf form of Baird's beaked whale, might represent a new species. That sent Morin in search of additional genetic samples to definitively answer the question and better understand the range of the elusive species.

He turned first to the Southwest Fisheries Science Center's marine mammal tissue collection, the largest in the world, and found two samples that appeared to represent a new species. One came from a whale found in Alaska's Aleutian Islands in 2004, whose skeleton now hangs on display at Unalaska High School. Then he and his colleagues pursued additional DNA samples from museums, research institutions and Japanese markets where whale meat is sold.

In 2014 scientists found a dead beaked whale on St. George Island, one of the Pribilof Islands in the Bering Sea. When it did not match any known species, they sent samples to Morin. Genetic tests later showed it to be the new species.

"We knew it was not any whale we knew from our area," said Michelle Ridgway, a marine ecologist with Oceanus Alaska who documented the whale in the Pribilofs and is a coauthor of the new research.

DNA analysis shows that the new species and Baird's beaked whale are each more closely related to Arnoux's beaked whale from the Southern Hemisphere than they are to each other. The genetic differences and smaller size indicate that the black whale is distinctive enough to represent a new species, the scientists found. Official recognition and naming of the species awaits a formal review of the animal's characteristics and differences from other beaked whales.

Beaked whales remain among the least known whales in the ocean, with several species identified only in the past few decades. They have beaks like dolphins, diving thousands of feet into deep underwater canyons and basins to feed on squid and bottom fish. Japan hunts Baird's beaked whales, the largest of the beaked whales at about 35 feet long.

"Japanese whalers have known about the black form but didn't consider it a separate species," said Erich Hoyt, a research fellow with Whale and Dolphin Conservation in the United Kingdom and co-director of the Russian Cetacean Habitat Project. He is a coauthor of the new research, and his research group contributed genetic samples from beaked whales in the Russian Far East.

"The implication of a new species of beaked whale is that we need to reconsider management of both species to be sure they're sufficiently protected, considering how rare the new one appears to be," Hoyt said. "Discovering a new species of whale in 2016 is exciting but it also reveals how little we know and how much more work we have to do to truly understand these species."

The eight known examples of the new species cluster around northern Japan and the Aleutian Islands and Bering Sea. That suggests that the species has a smaller range than Baird's beaked whale, which occurs throughout the North Pacific from Japan to Baja California.

Scars from the cookie-cutter-like bites of tropical sharks suggest that, like other beaked whales, the species may migrate to tropical waters.

"As much as we know about the genetic heritage of this animal, we still do not know very much about the animal itself," Morin said. "We can draw some indications from what we know about other beaked whales in terms of its range and behavior, but we still have many more questions than answers."

---

Story Source:

The above post is reprinted from materials provided by NOAA Fisheries West Coast Region. Note: Materials may be edited for content and length.

Giant Blobs of Rock, Deep Inside the Earth, Hold Important Clues About Our Planet

Two massive blob-like structures lie deep within Earth, roughly on opposite sides of the planet. The two structures, each the size of a continent and 100 times taller than Mount Everest, sit on the core, 1,800 miles deep, and about halfway to the center of Earth.

Arizona State University scientists Edward Garnero, Allen McNamara and Sang-Heon (Dan) Shim, of the School of Earth and Space Exploration, suggest these blobs are made of something different from the rest of Earth's mantle. The scientists' work appears in the June issue of Nature Geoscience.

"While the origin and composition of the blobs are yet unknown," said Garnero, "we suspect they hold important clues as to how Earth was formed and how it works today."

The blobs, he says, may also help explain the plumbing that leads to some massive volcanic eruptions, as well as the mechanism of plate tectonics from the convection, or stirring, of the mantle. This is the geo-force that drives earthquakes.

Deep stirring

Earth is layered like an onion, with a thin outer crust, a thick viscous mantle, a fluid outer core and a solid inner core. The two blobs sit in the mantle on top of Earth's core, under the Pacific Ocean on one side and beneath Africa and the Atlantic Ocean on the other.

Waves from earthquakes passing through Earth's deep interior have revealed that these blobs are regions where seismic waves travel slowly. The mantle materials that surround these regions are thought to be composed of cooler rocks, associated with the downward movement of tectonic plates.

The blobs, also called thermochemical piles, have long been depicted as warmer-than-average mantle materials, pushed upward by a slow churning of hot mantle rock. The new paper argues they are also chemically different from the surrounding mantle rock, and may partly contain material pushed down by plate tectonics. They might even be material left over from Earth's formation, 4.5 billion years ago.

Much is yet to be learned about these blobs. But the emerging view from seismic and geodynamic information is that they appear denser than the surrounding mantle materials, are dynamically stable and long-lived, and have been shaped by the mantle's large-scale flow. The scientists expect that further work on the two deep-seated anomalies will help clarify the picture and tell of their origin.

"If a neuroscientist found an unknown structure in the human brain, the whole community of brain scientists, from psychologists to surgeons, would actively pursue understanding its role in the function of the whole system," Garnero said.

"As the thermochemical piles come into sharper focus, we hope other Earth scientists will explore how these features fit into the big puzzle of planet Earth."

---

Story Source:

The above post is reprinted from materials provided by Arizona State University (ASU). Note: Materials may be edited for content and length.