Tag Archives: gene

Missing Y chromosome kept us apart from Neanderthals

The Y chromosome is a hindrance

Modern humans diverged from Neanderthals some 600,000 years ago – and a new study shows the Y chromosome might be what kept the two species separate.

It seems we were genetically incompatible with our ancient relatives – and male fetuses conceived through sex with Neanderthal males would have miscarried. We knew that some cross-breeding between us and Neanderthals happened more recently – around 100,000 to 60,000 years ago.

Neanderthal genes have been found in our genomes, on X chromosomes, and have been linked to traits such as skin colour, fertility and even depression and addiction. Now, an analysis of a Y chromosome from a 49,000-year-old male Neanderthal found in El Sidrón, Spain, suggests the chromosome has gone extinct seemingly without leaving any trace in modern humans.

This could simply be because it drifted out of the human gene pool or, as the new study suggests, it could be because genetic differences meant that hybrid offspring who had this chromosome were infertile – a genetic dead end.

Four gene mutations

Fernando Mendez of Stanford University, and his colleagues compared the Neanderthal Y chromosome with that of chimps, and ancient and modern humans.

They found mutations in four genes that could have prevented the passage of Y chromosome down the paternal line to the hybrid children.

“Some of these mutations could have played a role in the loss of Neanderthal Y chromosomes in human populations,” says Mendez.

For example, a mutation in one of the genes, KDM5D that plays a role in cancer suppression, has previously been linked to increased risk of miscarriages as it can elicit an immune response in pregnant mothers.

“That could be one reason why we don’t see Neanderthal Y chromosomes in modern human populations,” says Mark Pagel an evolutionary biologist at the University of Reading.

It could also be one factor keeping the two species as separate species.

The researchers also used the new DNA sequences to estimate the time when the most recent common ancestor of Neanderthal and modern human Y chromosomes existed. They came up with a figure of around 590,000 years ago, which agrees with other estimates for the split of the two groups.


Journal reference: The American Journal of Human Genetics, DOI: 10.1016/j.ajhg.2016.02.023


Deletion of a gene reduces body fat, slows down aging in mice

A single gene appears to play a crucial role in coordinating the immune system and metabolism, and deleting the gene in mice reduces body fat and extends lifespan, according to new research by scientists at the Jean Mayer USDA Human Nutrition Research Center (USDA HNRCA) on Aging at Tufts University and Yale University School of Medicine. Their results are reported online today in the Proceedings of the National Academy of Sciences.

Based on gene expression studies of fat tissue conducted at the USDA HNRCA, the Tufts University researchers initiated studies of the role of FAT10 in adipose tissue and metabolism. “No one really knew what the FAT10 gene did, other than it was ‘turned on’ by inflammation and that it seemed to be increased in gynecological and gastrointestinal cancers.” said co-author Martin S. Obin, Ph.D., an adjunct scientist in the Functional Genomics Core Unit at the USDA HNRCA at Tufts University. “Turning off the FAT10 gene produces a variety of beneficial effects in the mice, including reduced body fat, which slows down aging and extends lifespan by 20 percent.”
Typically, mice gain fat as they age. The authors observed that activation of the FAT10 gene in normal mice increases in fat tissue with age. Mice lacking FAT10 consume more food, but burn fat at an accelerated rate. As a result, they have less than half of the fat tissue found in normal, aged mice. At the same time their skeletal muscle ramps up production of an immune molecule that increases their response to insulin, resulting in reduced circulating insulin levels, protection against type 2 diabetes and longer lifespan.
The authors note that eliminating FAT10 will not fully address the dilemma of aging and weight gain. “Laboratory mice live in a lab under ideal, germ-free conditions,” said Obin, who is also an associate professor at the Friedman School of Nutrition Science and Policy at Tufts University. “Fighting infection requires energy, which can be provided by stored fat. Mice without the FAT10 gene might be too lean to fight infection effectively outside of the laboratory setting. More research is needed to know how to achieve that balance in mice and then hopefully, at some point, people.”
The possibilities for future research of FAT10 are exciting. Recent high-profile studies reported that FAT10 interacts with hundreds of other proteins in cells. Now the Tufts and Yale researchers have demonstrated that it impacts immune response, lipid and glucose metabolism, and mitochondrial function.
“Now there is dramatic road map for researchers looking at all of the proteins that FAT10 gets involved with,” said co-first and corresponding author Allon Canaan, Ph.D., an associate scientist in the Department of Genetics at Yale. “Blocking what FAT10 does to coordinate immunity and metabolism could lead to new therapies for metabolic disease, metabolic syndrome, cancer and healthy aging, because when we knock it out the net result is mice live longer.”
Canaan and colleagues initially developed the FAT10-deficient mouse to study the role of FAT10 in sepsis. In an attempt to increase sensitivity for sepsis, Canaan aged the FAT10 knockout mice and made the discovery that mice lacking the gene were lean and aged more slowly. The mice appear younger and more robust than comparably-aged normal mice, have better muscle tone, and do not develop age-related tumors.

More information: Canaan A; Defuria J; Perelman E; Schulz V; Seay M; Tuck D; Flavell R; Snyder M; Obin M; and Weissman S. “Extended Lifespan and Reduced Adiposity in Mice Lacking the FAT10 Gene.” Proceedings of the National Academy of Sciences. Published online ahead of print March 24, 2014. http://www.pnas.org/cgi/doi/10.1073/pnas.1323426111

Where Native Americans come from

Here is a sampling of the stone and bone tools buried with a baby who died some 12,600 years ago. They identify him as one of the Clovis people, a culture that dominated the United States and northern Mexico long ago.

M. Rasmussen et al.

DNA from an ancient baby’s skeleton shows that all Native Americans descend from a single gene pool. And their ancestral roots are in Asia, a new study finds.

The bones came from a roughly 12- to 18-month-old boy. He died about 12,600 years ago in what is now Montana. Construction workers uncovered the grave in 1968. It remains the only known burial site of a person from the Clovis culture. 

Clovis is the name of prehistoric people. They lived in what is now the United States and northern Mexico between about 13,000 and 12,600 years ago. They made a type of stone spear point that differs from stone tools found elsewhere in the world at the time.

The young boy had been covered in red ochre. It’s a natural pigment that had often been used in burial rituals at the time. More than 100 tools had been placed atop his body when it was buried. Those tools also had been dipped in red ochre.

Some were the stone spear points or tools used to make the spear points.. People had fashioned rods from elk antlers, a rare material in Montana at the time. The bone tools were 13,000 years old — hundreds of years older than the child’s parents. The bone rods had been deliberately broken before being placed with the boy’s body. That suggests these ancient tools could have been family “heirlooms,” the scientists say.

All of those details are fairly old. Decades old, at least.

What’s new are analyses of the Clovis child’s DNA. Just reported in the Feb. 13 Nature, they indicate that the Clovis people were ancestors of all present-day Native Americans. And like today’s Native Americans, the Clovis baby — known as Anzick-1 — can trace part of his heritage to a child known as the Mal’ta boy. He lived in Siberia 24,000 years ago. That link now suggests that all Native American populations share a common Asian heritage.


This is where the Clovis baby’s skeleton was unearthed. The pole (center left) marks the burial site, which look out towards scenic, snow-capped mountains.


From Asian — not European — roots

“This clearly shows that the homeland of the first Americans was Asia,” says study coauthor Michael Waters. He’s a geologist and archaeologist at Texas A&M University in College Station.

The study may put to rest an oft-reported idea that ancient Europeans crossed the Atlantic and established the Clovis culture. That idea has been known as the Solutrean hypothesis. The new analysis is “the last spade full of earth on the grave of the Solutrean hypothesis,” says Jennifer Raff. An anthropological geneticist, she works at the University of Texas at Austin. She had no role in the current analysis.

The study also may settle speculation about the Clovis people’s relationship to modern Native Americans. Clovis culture was widespread for 400 years after the last Ice Age. Other styles of tool making eventually replaced the distinctive stone spear points made by Clovis people. That was among clues indicating that other American settlers might have replaced the Clovis people.

“Their technology and tools vanished, but now we understand that their genetic legacy lives on,” says Sarah Anzick, a coauthor of the new study.

Anzick was 2 years old when the baby’s grave was found on her family’s land. Since then, she and her family have been stewards of the bones, keeping them respectfully preserved and locked away.

Respecting the bones

In time, Anzick became a molecular biologist, at one point working on the Human Genome Project. (Completed in April 2003, it gave scientists an ability to read a person’s full genetic blueprints.) Based on that experience, Anzick made it a personal goal to decipher the Clovis baby’s DNA.

So she traveled with the child’s bones to the lab of Eske Willerslev. He’s an evolutionary geneticist at the University of Copenhagen, in Denmark. There, she helped extract DNA from the skeleton and performed some of the initial tests. Willerslev and his colleagues completed the rest of the toddler’s genetic blueprints.

Their examination shows that about one-third of the Clovis baby’s genome traces back to the ancient Siberian people, says Willerslev. The remainder, he says, comes from an ancestral East Asian population. The new data suggest East Asians and Siberians interbred before the Clovis era. Their descendants would have become the founding population for all later Native Americans. 

About four out of five Native Americans, mainly those in Central and South America, probably descend directly from the Anzick baby’s people, Willerslev says. Other native peoples, such as those in Canada, are closely related to the Clovis child. They, however, come from a different branch of the family.

Anzick iand members of several Native American tribes are preparing to rebury the baby’s remains where his parents had left him more than 12 millennia ago. It’s at the base of a sandstone cliff. The site overlooks a creek with views of three mountain ranges.

Power Words

archaeology  The study of human history and prehistory through the excavation of sites and the analysis of artifacts and other physical remains. People who work in this field are known as archaeologists.

Clovis people  Prehistoric humans who inhabited much of North America between about 13,000 and 12,600 years ago. They are known primarily by the cultural artifacts they left behind, especially a type of stone point used on hunting spears. It’s called the Clovis point. It was named after Clovis, New Mexico, where someone first found this type of stone tool.

gene  A segment of DNA that codes, or holds instructions, for producing a protein. Offspring inherit genes from their parents. Genes influence how an organism looks and behaves.

evolutionary genetics  A field of biology that focuses on how genes — and the traits they lead to — change over long periods of time (potentially over millennia or more). People who work in this field are known as evolutionary geneticists

genome  The complete set of genes or genetic material in a cell or an organism.

geology  The study of Earth’s physical structure and substance, its history and the processes that act on it. People who work in this field are known as geologists.

Ice Age  Earth has experienced at least five major Ice Ages, which are prolonged periods of unusually cold weather experienced by much of the planet. During that time, which can last hundreds to thousands of years, glaciers and ice sheets expand in size and depth. The most recent Ice Age peaked 21,500 years ago, but continued until about 13,000 years ago.

molecular biology  The branch of biology that deals with the structure and function of molecules essential to life. Scientists who work in this field are called molecular biologists.

pigment  A material, like the natural colorings in paints and dyes, that alter the light reflected off of an object or transmitted through it. The overall color of a pigment typically depends on which wavelengths of visible light it absorbs and which ones it reflects. For example, a red pigment tends to reflect red wavelengths of light very well and typically absorbs other colors.

red ochre  A natural pigment often been used in ancient burial rituals.

Solutrean hypothesis The idea that ancient Europeans crossed the Atlantic and established the Clovis culture.

Stone Age  A prehistoric period, lasting millions of years and ending tens of thousands of years ago, when weapons and tools were made of stone or of materials such as bone, wood, or horn.