Category Archive 'DNA'
18 Oct 2018

Liz Warren’s Indian Blood

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17 Oct 2018

DNA and Victim Status

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16 Oct 2018

Orrin Hatch’s DNA

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16 Oct 2018

The Onion Nails Pocahontas

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16 Oct 2018

Tweet of the Day

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04 Jun 2018

From Reddit

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19 Apr 2018

Oldest American Domestic Dogs

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Science News reports recent analysis proves dogs have lived with humans in North America longer than previously supposed and that the genetics of some dogs kept by early inhabitants of North America have not survived to the present day.

A trio of dogs buried at two ancient human sites in Illinois lived around 10,000 years ago, making them the oldest known domesticated canines in the Americas.

Radiocarbon dating of the dogs’ bones shows they were 1,500 years older than thought, zooarchaeologist Angela Perri said April 13 at the annual meeting of the Society for American Archaeology. The previous age estimate was based on a radiocarbon analysis of burned wood found in one of the animals’ graves. Until now, nearly 9,300-year-old remains of dogs eaten by humans at a Texas site were the oldest physical evidence of American canines.

Ancient dogs at the Midwestern locations also represent the oldest known burials of individual dogs in the world, said Perri, of Durham University in England. A dog buried at Germany’s Bonn-Oberkassel site around 14,000 years ago was included in a two-person grave. Placement of the Americas dogs in their own graves indicates that these animals were held in high regard by ancient people.

An absence of stone tool incisions on the three ancient dogs’ skeletons indicates that they were not killed by people, but died of natural causes before being buried, Perri said. …

She and her colleagues studied two of three dogs excavated at the Koster site in the 1970s and a dog unearthed at Stilwell II in 1960. These sites lie about 30 kilometers apart in west-central Illinois.

Perri’s team found that the lower jaws and teeth of the Stilwell II dog and one Koster dog displayed some similarities to those of modern wolves. Another Koster dog’s jaw shared some traits with present-day coyotes, possibly reflecting some ancient interbreeding.

A new genetic analysis positions the 10,000-year-old Illinois dogs in a single lineage that initially populated North America. Dog origins are controversial, but may date to more than 20,000 years ago (SN Online: 7/18/17). Ancient American dogs, including the Koster and Stilwell II animals, shared a common genetic ancestor, cell biologist Kelsey Witt Dillon of the University of California, Merced reported April 13 at the SAA meeting. That ancestor originated roughly 15,000 years ago after diverging from a closely related Siberian dog population about 1,000 years earlier, she said.

Dillon’s team, which includes Perri, studied 71 complete mitochondrial genomes and seven nuclear genomes of dogs from more than 20 North American sites, ranging in age from 10,000 to 800 years ago. Mitochondrial DNA is typically inherited from the mother, whereas nuclear DNA comes from both parents.

Much of the genetic blueprint of those ancient dogs is absent in present-day canines, Dillon said. Only a small number of U.S. and Asian dogs share maternal ancestry with ancient American dogs, suggesting the arrival of European breeds starting at least several hundred years ago reshaped dog DNA in the Americas, she proposed.

RTWT

12 Apr 2018

No Wonder There Are So Many Democrats!

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The BBC reports that the human part of humanity is outnumbered.

More than half of your body is not human, say scientists.

Human cells make up only 43% of the body’s total cell count. The rest are microscopic colonists.

Understanding this hidden half of ourselves – our microbiome – is rapidly transforming understanding of diseases from allergy to Parkinson’s.

The field is even asking questions of what it means to be “human” and is leading to new innovative treatments as a result.

“They are essential to your health,” says Prof Ruth Ley, the director of the department of microbiome science at the Max Planck Institute, “your body isn’t just you”.

No matter how well you wash, nearly every nook and cranny of your body is covered in microscopic creatures.

This includes bacteria, viruses, fungi and archaea (organisms originally misclassified as bacteria). The greatest concentration of this microscopic life is in the dark murky depths of our oxygen-deprived bowels.

Prof Rob Knight, from University of California San Diego, told the BBC: “You’re more microbe than you are human.”

Originally it was thought our cells were outnumbered 10 to one.

“That’s been refined much closer to one-to-one, so the current estimate is you’re about 43% human if you’re counting up all the cells,” he says.

But genetically we’re even more outgunned.

The human genome – the full set of genetic instructions for a human being – is made up of 20,000 instructions called genes.

But add all the genes in our microbiome together and the figure comes out between two and 20 million microbial genes.

RTWT

03 Dec 2017

NYC Has Solved the Rat Diversity Problem

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Uptown rats are genetically different from Downtown rats, and you can even easily differentiate West Village rats from East Village rats. I can only suppose that most Upper West Side rats are probably liberal and Jewish. The Atlantic:

Manhattan’s rats are genetically most similar to those from Western Europe, especially Great Britain and France. They most likely came on ships in the mid-18th century, when New York was still a British colony. [Fordhan University grad student Matthew] Combs was surprised to find Manhattan’s rats so homogenous in origin. New York has been the center of so much trade and immigration, yet the descendants of these Western European rats have held on.

When Combs looked closer, distinct rat subpopulations emerged. Manhattan has two genetically distinguishable groups of rats: the uptown rats and the downtown rats, separated by the geographic barrier that is midtown. It’s not that midtown is rat-free—such a notion is inconceivable—but the commercial district lacks the household trash (aka food) and backyards (aka shelter) that rats like. Since rats tend to move only a few blocks in their lifetimes, the uptown rats and downtown rats don’t mix much.

When the researchers drilled down even deeper, they found that different neighborhoods have their own distinct rats. “If you gave us a rat, we could tell whether it came from the West Village or the East Village,” says Combs. “They’re actually unique little rat neighborhoods.” And the boundaries of rat neighborhoods can fit surprisingly well with human ones.

Combs and a team of undergraduate students spent their summers trapping rats—beginning in Inwood at the north tip of Manhattan and working their way south. They got permission from the New York City Department of Parks and Recreation, which gave them access to big green spaces like Central Park as well as medians and triangles and little gardens that dot the city. And they asked local residents. “More often than not, they were very, very happy to show us exactly where they had rats.” says Combs. A crowdsourced map of rat sightings also proved very helpful.

Rats, although abundant, are not easily fooled into traps. They’re wary of new objects. To entice them, the bait was a potent combination of peanut butter, bacon, and oats. And the team placed their traps near places where rats had clearly crawled. They looked for rat holes, droppings, chew marks on trash cans, and sebum marks—aka the grease tracks rats leave when they traverse the same path to the garbage over and over again.

For the DNA analysis, Combs cut off an inch or so of the rats’ tails. (Over 200 of these tails are still saved in vials in a lab freezer.) The team also took tissue samples for other researchers interested in studying how rats spread diseases through the urban environment. And some of the rats they skinned and stuffed for the collections of the Yale University Peabody Museum of Natural History, where they will join stuffed rats from 100 years ago.

RTWT

01 Dec 2017

Yeti is Apparently a Bear

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Himalayan brown bear

Science:

Hikers in Tibet and the Himalayas need not fear the monstrous yeti—but they’d darn well better carry bear spray. DNA analyses of nine samples purported to be from the “abominable snowman” reveal that eight actually came from various species of bears native to the area.

In the folklore of Nepal, the yeti looms large. The creature is often depicted as an immense, shaggy ape-human that roams the Himalayan hinterlands. Purported sightings over the years, as well as scattered “remains” secreted away in monasteries or held by shamans, have hinted to some that the yeti is not merely a mythical boogeyman.

But science has not borne this out so far. Previous genetic analyses of a couple of hair samples collected in India and Bhutan suggested that one small stretch of their mitochondrial DNA (mtDNA)—the genetic material in a cell’s power-generating machinery that’s passed down only by females—resembled that of polar bears. That finding hinted that a previously unknown type of bear, possibly a hybrid between polar bears and brown bears, could be roaming the Himalayas, says Charlotte Lindqvist, an evolutionary biologist at the State University of New York in Buffalo.

To find out for sure, Lindqvist and her colleagues took a more thorough look at the mtDNA of as many samples of supposed yeti remains as she could get her hands on. Some were obtained when she worked with a U.K. production crew on the 2016 documentary Yeti or Not?, which sought to sift fact from folklore. The filmmakers got hold of a tooth and some hair collected on the Tibetan Plateau in the late 1930s, as well as a sample of scat from Italian mountaineer Reinhold Messner’s museum in the Tyrolean Alps. More recent samples included hair collected in Nepal by a nomadic herdsman and a leg bone found by a spiritual healer in a cave in Tibet. The team also analyzed samples recently collected from several subspecies of bears native to the area, including the Himalayan brown bear, the Tibetan brown bear, and the black bear. Altogether, the scientists analyzed 24 samples, including nine purported to be from yeti.

Of the nine “yeti” samples, eight turned out to be from bears native to the area, the researchers report today in the Proceedings of the Royal Society B. The other sample came from a dog.

RTWT

20 Oct 2017

Neanderthal DNA

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How Stuff Works:

Researchers at the Max Planck Institute for Evolutionary Anthropology in Germany analyzed the genetic data of 112,338 people of British ancestry who have Neanderthal DNA to conduct a study on the link between Neanderthal DNA and humans’ physical characteristics. Having access to a large cohort of study participants from the UK Biobank proved important, since there just isn’t much Neanderthal DNA floating around. (People of European and Asian descent get anywhere from 1–4 percent of their genes from Neanderthals, thanks to interbreeding thousands of years ago.)

Prior research has found that the ancient hominids may have influenced a variety of disease-related traits in humans. For instance, the presence of Neanderthal DNA is associated with the increased sensitivity to certain allergens and a higher risk for nicotine addiction. But in the new study, the researchers focused on nondisease phenotypes — the observable physical characteristics of an organism — in modern humans.

With the help of questionnaires given through UK Biobank, the researchers determined that the propensity to smoke and loneliness are associated with Neanderthal DNA. They also found that some Neanderthal alleles (variant forms of genes) contributed to lighter skin and hair tones in modern humans, while others contributed to darker tones. But breaking down the study’s results isn’t as easy as pointing to a certain shade of skin and linking it to Neanderthal DNA. Multiple alleles influence skin and hair color, and Neanderthals might’ve had a large range of skin and hair tones based on different pieces of genetic material, just like modern humans.

The researchers noted in the study that many of the Neanderthal-linked traits are related to sunlight exposure, including an allele that contributes to circadian rhythm and the tendency to be an “evening person.” In the study, non-African people living farther from the equator had higher frequencies of that allele. Indeed, Neanderthals had been living in northern environments with lower and more varying levels of ultraviolet radiation for thousands of years when modern humans came to the region from sunnier Africa.

So, if you stay up late and nap during the day? That might be the Neanderthal in you.

25 Jul 2017

“Ghost Species” Found To Have Contributed Genetic Material to Sub-Saharan Africans

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Homo erectus imagined by the Smithsonian.

Before It’s News:

The evolutionary history of a salivary protein may point to interbreeding between humans and an enigmatic ancient relative

In saliva, scientists have found hints that a “ghost” species of archaic humans may have contributed genetic material to ancestors of people living in Sub-Saharan Africa today.

The research adds to a growing body of evidence suggesting that sexual rendezvous between different archaic human species may not have been unusual.

Past studies have concluded that the forebears of modern humans in Asia and Europe interbred with other early hominin species, including Neanderthals and Denisovans. The new research is among more recent genetic analyses indicating that ancient Africans also had trysts with other early hominins.

“It seems that interbreeding between different early hominin species is not the exception — it’s the norm,” says Omer Gokcumen, PhD, an assistant professor of biological sciences in the University at Buffalo College of Arts and Sciences.

“Our research traced the evolution of an important mucin protein called MUC7 that is found in saliva,” he says. “When we looked at the history of the gene that codes for the protein, we see the signature of archaic admixture in modern day Sub-Saharan African populations.”

The research was published on July 21 in the journal Molecular Biology and Evolution. The study was led by Gokcumen and Stefan Ruhl, DDS, PhD, a professor of oral biology in UB’s School of Dental Medicine.

The scientists came upon their findings while researching the purpose and origins of the MUC7 protein, which helps give spit its slimy consistency and binds to microbes, potentially helping to rid the body of disease-causing bacteria.

As part of this investigation, the team examined the MUC7 gene in more than 2,500 modern human genomes. The analysis yielded a surprise: A group of genomes from Sub-Saharan Africa had a version of the gene that was wildly different from versions found in other modern humans.

The Sub-Saharan variant was so distinctive that Neanderthal and Denisovan MUC7 genes matched more closely with those of other modern humans than the Sub-Saharan outlier did.

“Based on our analysis, the most plausible explanation for this extreme variation is archaic introgression — the introduction of genetic material from a ‘ghost’ species of ancient hominins,” Gokcumen says. “This unknown human relative could be a species that has been discovered, such as a subspecies of Homo erectus, or an undiscovered hominin. We call it a ‘ghost’ species because we don’t have the fossils.”

Given the rate that genes mutate during the course of evolution, the team calculated that the ancestors of people who carry the Sub-Saharan MUC7 variant interbred with another ancient human species as recently as 150,000 years ago, after the two species’ evolutionary path diverged from each other some 1.5 to 2 million years ago.

RTWT

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