Tag: dna

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Ice Age Migration to America from China and Japan

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Scientists have used mitochondrial DNA to trace a female lineage from northern coastal China to the Americas. By integrating contemporary and ancient mitochondrial DNA, evidence was found of at least two migrations: one during the last ice age, and one during the subsequent melting period. Around the same time as the second migration, another branch of the same lineage migrated to Japan, which could explain Paleolithic archaeological similarities between the Americas, China, and Japan. The study appears May 9 in the journal Cell Reports (https://pubmed.ncbi.nlm.nih.gov/37164007/).

“The Asian ancestry of Native Americans is more complicated than previously indicated,” says first author Yu-Chun Li, a molecular anthropologist at the Chinese Academy of Sciences. “In addition to previously described ancestral sources in Siberia, Australo-Melanesia, and Southeast Asia, we show that northern coastal China also contributed to the gene pool of Native Americans.”

Though it was long assumed that Native Americans descended from Siberians who crossed over the Bering Strait’s ephemeral land bridge, more recent genetic, geological, and archeological evidence suggests that multiple waves of humans journeyed to the Americas from various parts of Eurasia.

To shed light on the history of Native Americans in Asia, a team of researchers from the Chinese Academy of Sciences followed the trail of an ancestral lineage that might link East Asian Paleolithic-age populations to founding populations in Chile, Peru, Bolivia, Brazil, Ecuador, Mexico, and California. The lineage in question is present in mitochondrial DNA, which can be used to trace kinship through the female line.

The researchers scoured over 100,000 contemporary and 15,000 ancient DNA samples from across Eurasia to eventually identify 216 contemporary and 39 ancient individuals belonging to the rare lineage. By comparing the accumulated mutations, geographic locations, and carbon-dated age of each of these individuals, the researchers were able to trace the lineage’s branching path. They identified two migration events from northern coastal China to the Americas, and in both cases, they think that the travelers probably set dock in America via the Pacific coast rather than by crossing the inland ice-free corridor (which would not have opened at the time).

The first radiation event occurred between 19,500 and 26,000 years ago during the Last Glacial Maximum, when ice sheet coverage was at its greatest and conditions in northern China were likely inhospitable for humans. The second radiation occurred during the subsequent deglaciation or melting period, between 19,000 and 11,500 years ago. There was a rapid increase in human populations at this time, probably due to the improved climate, which may have fueled expansion into other geographical regions.

The researchers also uncovered an unexpected genetic link between Native Americans and Japanese people. During the deglaciation period, another group branched out from northern coastal China and traveled to Japan. “We were surprised to find that this ancestral source also contributed to the Japanese gene pool, especially the indigenous Ainus,” says Li.

This discovery helps to explain archeological similarities between the Paleolithic peoples of China, Japan, and the Americas. Specifically, the three regions share similarities in how they crafted stemmed projectile points for arrowheads and spears. “This suggests that the Pleistocene connection among the Americas, China, and Japan was not confined to culture but also to genetics,” says senior author Qing-Peng Kong, an evolutionary geneticist at the Chinese Academy of Sciences.

Cell Press. “Evidence of Ice Age human migrations from China to the Americas and Japan.” ScienceDaily. ScienceDaily, 9 May 2023.

AR #103

Kennewick Man: the Japanese Connection

by Steven Sora

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Atoms Entangled Across Quan­tum Net­work

Trapped ions are one of the leading systems to build quantum computers and other quantum technologies. To link multiple such quantum systems, interfaces are needed through which the quantum information can be transmitted. In recent years, researchers led by Tracy Northup and Ben Lanyon at the University of Innsbruck’s Department of Experimental Physics have developed a method for doing this by trapping atoms in optical cavities such that quantum information can be efficiently transferred to light particles. The light particles can then be sent through optical fibers to connect atoms at different locations. Now, their teams, together with theorists led by Nicolas Sangouard of the Université Paris-Saclay, have for the first time entangled two trapped ions more than a few meters apart. (https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.130.050803)

The two quantum systems were set up in in two laboratories, one in the building that houses the Department of Experimental Physics and one in the building that houses the Institute of Quantum Optics and Quantum Information of the Austrian Academy of Sciences. “Until now, trapped ions were only entangled with each other over a few meters in the same laboratory. Those results were also achieved using shared control systems and photons (light particles) with wavelengths that aren’t suitable for travelling over much longer distances,” Ben Lanyon explains. After years of research and development, the Innsbruck physicists have now managed to entangle two ions across campus. “To do this, we sent individual photons entangled with the ions over a 500-meter fiber optic cable and superimposed them on each other, swapping the entanglement to the two remote ions,” says Tracy Northup, describing the experiment. “Our results show that trapped ions are a promising platform for realizing future distributed networks of quantum computers, quantum sensors and atomic clocks.”

https://www.uibk.ac.at/en/newsroom/2023/entangled-atoms-across-the-innsbruck-quantum-network/

AR #80

Entangled Minds & the Quantum Factor

by Patrick Marsolek

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Ancient Siberian DNA and the Bering Sea

The movement of people across the Bering Sea from North Asia to North America is a well-known phenomenon in early human history. Nevertheless, the genetic makeup of the people who lived in North Asia during this time has remained mysterious due to a limited number of ancient genomes analyzed from this region. Now, researchers reporting in Current Biology describe genomes from ten individuals up to 7,500 years old that help to fill the gap and show geneflow from people moving in the opposite direction from North America to North Asia.

Their analysis reveals a previously undescribed group of early Holocene Siberian people that lived in the Neolithic Altai-Sayan region, near to where Russia, China, Mongolia, and Kazakhstan come together. The genetic data show they were descendants of both paleo-Siberian and Ancient North Eurasian (ANE) people.

“We describe a previously unknown hunter-gatherer population in the Altai as early as 7,500 years old, which is a mixture between two distinct groups that lived in Siberia during the last Ice Age,” says Cosimo Posth at the University of Tübingen, Germany, and senior author of the study. “The Altai hunter-gatherer group contributed to many contemporaneous and subsequent populations across North Asia, showing how great the mobility of those foraging communities was.”

Posth notes that the Altai region is known in the media as the location where a new archaic hominin group, the Denisovans, was discovered. But the region also has importance in human history as a crossroad for population movements between northern Siberia, Central Asia, and East Asia over millennia.

The findings reveal the spread of ANA ancestry about 1,500 kilometers farther to the west than previously observed. In the Russian Far East, they also identified 7,000-year-old individuals with Jomon-associated ancestry, indicating links with hunter-gatherer groups from the Japanese Archipelago.

The data also are consistent with multiple phases of gene flow from North America to northeastern Asia over the last 5,000 years, reaching the Kamchatka Peninsula and central Siberia. The researchers note that the findings highlight a largely interconnected population throughout North Asia from the early Holocene onwards.

“The finding that surprised me the most is from an individual dated to a similar period as the other Altai hunter-gatherers but with a completely different genetic profile, showing genetic affinities to populations located in the Russian Far East,” says Ke Wang at Fudan University, China, and lead author of the study. “Interestingly, the Nizhnetytkesken individual was found in a cave containing rich burial goods with a religious costume and objects interpreted as possible representation of shamanism.”

Wang says the finding implies that individuals with very different profiles and backgrounds were living in the same region around the same time.

https://www.science.org/content/article/native-americans-and-their-genes-traveled-back-siberia-new-genomes-reveal

AR #135

Artificial Intelligence Identifies
Unknown Human Ancestor

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Problems with Mammoth Extinction Timeline

Exactly when mammoths went extinct has fascinated paleontologists for generations, perhaps because their decline coincided with the arrival of people to North and South America.

So it’s only natural to wonder if humans more than contributed to the extinction of these enormous beasts of the ice age more than 10,000 years ago.

A University of Cincinnati paleontologist refutes the latest timeline published in 2021 in the journal Nature that suggested mammoths met their end much more recently than we believed. An international team of researchers examined environmental DNA of mammoth remains and more than 1,500 arctic plants to conclude that a wetter climate quickly changed the landscape from tundra grassland steppe to forested wetlands that could not support many of these big grazing animals, driving mammoths to extinction as recently as 3,900 years ago.


But in a rebuttal paper to be published Dec. 1 in Nature, UC College of Arts and Sciences assistant professor Joshua Miller and co-author Carl Simpson at the University of Colorado Boulder argue that the environmental DNA used to establish their updated timeline is more complex than previously recognized.


“The issue is you have no idea how old that DNA is,” Miller said. “Sedimentary deposits are complex. Materials of different ages are routinely buried together.”


From recent discoveries like the baby mammoth found in Canada this year, we know that many ice age animals that died tens of thousands of years ago can become mummified in the arctic’s dry, cold environment. Miller said researchers can’t tell whether environmental DNA preserved in sediment was shed from a living or dead animal.
“DNA is shed from organisms all the time,” Miller said. “In fact, DNA continues to be shed long after the animal dies. In places where decomposition is slow, that means long-dead and even long-extinct species can continue to make their way into surrounding sediments. In the arctic and other cold-weather places, it can take thousands of years for something to decompose.”


They’re tantalizingly similar to animals that live among us today. We can almost touch them. That makes mammoths really alluring.


Joshua Miller, UC paleontologist

The researchers say the slow decomposition of animals in arctic regions could explain how mammoth DNA is showing up thousands of years later than the most recent mammoth fossil discovered. The paper notes that the mummified remains of elephant seals near Antarctica can be more than 5,000 years old.
In some remote parts of the arctic, it’s not unusual to find 2,000-year-old caribou antlers on the surface, Miller said. But the most recent mammoth fossils found in the Siberian area were entombed in permafrost 11,000 years ago.
Simpson said his work studying marine environments from recently eroded hillsides demonstrates how difficult it is to date ancient specimens.


“Seashells can sit on the seafloor for thousands of years. When you see shells on the beach, some could be from animals that died recently while others might be from shellfish that died millennia ago,” Simpson said. “This happens in the vertebrate record as well.”

https://www.uc.edu/news/articles/2022/11/uc-paleontologist-says-environmental-dna-paints-a-misleading-picture-of-mammoth-extinction.html

AR #112

The Coming of the Clones”

Patrick Marsolek

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The DNA of Infection-Fighting

Viral DNA in human genomes, embedded there from ancient infections, serve as antivirals that protect human cells against certain present-day viruses, according to new research.

The paper, “Evolution and Antiviral Activity of a Human Protein of Retroviral Origin,” published Oct. 28 in Science, provides proof of principle of this effect.

Previous studies have shown that fragments of ancient viral DNA – called endogenous retroviruses – in the genomes of mice, chickens, cats and sheep provide immunity against modern viruses that originate outside the body by blocking them from entering host cells. Though this study was conducted with human cells in culture in the lab, it shows that the antiviral effect of endogenous retroviruses likely also exists for humans.

The research is important because further inquiry could uncover a pool of natural antiviral proteins that lead to treatments without autoimmune side effects. The work reveals the possibility of a genome defense system that has not been characterized, but could be quite extensive.

Endogenous retroviruses account for about 8% of the human genome – at least four times the amount of DNA that make up the genes that code for proteins. Retroviruses introduce their RNA into a host cell, which is converted to DNA and integrated into the host’s genome. The cell then follows the genetic instructions and makes more virus.
In this way, the virus hijacks the cell’s transcriptional machinery to replicate itself. Typically, retroviruses infect cells that don’t pass from one generation to the next, but some infect germ cells, such as an egg or sperm, which opens the door for retroviral DNA to pass from parent to offspring and eventually become permanent fixtures in the host genome.

In order for retroviruses to enter a cell, a viral envelope protein binds to a receptor on the cell’s surface, much like a key into a lock. The envelope is also known as a spike protein for certain viruses, such as SARS-CoV-2.

The study shows how one human protein of retroviral origin blocks a cell receptor that allows viral entry and infection by a broad range of retroviruses circulating in many non-human species. In this way, Feschotte said, ancient retroviruses integrated into the human genome provide a mechanism for protecting the developing embryo against infection by related viruses.

Future work will explore the antiviral activity of other envelope-derived proteins encoded in the human genome, he said.

AR Issue #57

Sound & Genetic Healing

By Sol Luckman

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The Bottlenecks of Human History

By Robert Sanders

Human populations have waxed and waned over the millennia, with some cultures exploding and migrating to new areas or new continents, others dropping to such low numbers that their genetic diversity plummeted. In some small populations, inbreeding causes once rare genetic diseases to become common, despite their deleterious effects.

A new analysis of more than 4,000 ancient and contemporary human genomes shows how common such “founder events” were in our history. A founder event is when a small number of ancestral individuals gives rise to a large fraction of the population, often because war, famine or disease drastically reduced the population, but also because of geographic isolation — on islands, for example — or cultural practices, as among Ashkenazi Jews or the Amish.
More than half of the 460 groups represented by these individuals had experienced a population bottleneck somewhere in their past that decreased their genetic diversity and likely increased the incidence of recessive hereditary diseases.


The analysis by population geneticists at the University of California, Berkeley, is the first comprehensive look at founder events across a broad swath of human populations over the past 10,000 years or so of human history and pinpoints when these events occurred.


According to the authors, led by Priya Moorjani, an assistant professor of molecular and cell biology at UC Berkeley, the findings will be useful not only to archeologists and historians tracking the movement and mixing of populations around the world, but also to scientists and doctors studying human genetic variation. The genetic diseases of inbred populations have helped scientists find many disease-causing mutations in the human genome and discover the causes of numerous genetic and inherited diseases.


Moorjani, former UC Berkeley undergraduate Gillian Chu and first author Rémi Tournebize, now a postdoctoral fellow at the Instituto Gulbenkian de Ciência in Oeiras, Portugal, published their findings in June in the journal PLOS Genetics.

https://news.berkeley.edu/2022/06/23/bottlenecks-that-reduced-genetic-diversity-were-common-throughout-human-history/

AR #60

“Atlantis and the Neanderthals”

by Colin Wilson