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09/18/13 5:23 AM

#209951 RE: F6 #209017

DNA Double Take


DNA sequencing elements displayed on a monitor.
Noah Berger for The New York Times





John Hersey


A DNA sample. Sequencing has become faster and relatively cheaper in the last 20 years.
Kathy Kmonicek for The New York Times


By CARL ZIMMER
Published: September 16, 2013

From biology class to “C.S.I.,” we are told again and again that our genome is at the heart of our identity. Read the sequences in the chromosomes of a single cell, and learn everything about a person’s genetic information — or, as 23andme [ https://www.23andme.com/ ], a prominent genetic testing company, says on its Web site, “The more you know about your DNA, the more you know about yourself.”

But scientists are discovering that — to a surprising degree — we contain genetic multitudes. Not long ago, researchers had thought it was rare for the cells in a single healthy person to differ genetically in a significant way. But scientists are finding that it’s quite common for an individual to have multiple genomes. Some people, for example, have groups of cells with mutations that are not found in the rest of the body. Some have genomes that came from other people.

“There have been whispers in the matrix about this for years, even decades, but only in a very hypothetical sense,” said Alexander Urban [ http://urbanlab.stanford.edu/ ], a geneticist at Stanford University. Even three years ago, suggesting that there was widespread genetic variation in a single body would have been met with skepticism, he said. “You would have just run against the wall.”

But a series of recent papers by Dr. Urban and others has demonstrated that those whispers were not just hypothetical. The variation in the genomes found in a single person is too large to be ignored. “We now know it’s there,” Dr. Urban said. “Now we’re mapping this new continent.”

Dr. James R. Lupski [ http://www.bcm.edu/genetics/?pmid=10944 ], a leading expert on the human genome at Baylor College of Medicine, wrote in a recent review [ http://www.sciencemag.org/content/341/6144/358.summary ] in the journal Science that the existence of multiple genomes in an individual could have a tremendous impact on the practice of medicine. “It’s changed the way I think,” he said in an interview.

Scientists are finding links from multiple genomes to certain rare diseases, and now they’re beginning to investigate genetic variations to shed light on more common disorders.

Science’s changing view is also raising questions about how forensic scientists should use DNA evidence to identify people. It’s also posing challenges for genetic counselors, who can’t assume that the genetic information from one cell can tell them about the DNA throughout a person’s body.

Human Blueprint

When an egg and sperm combine their DNA, the genome they produce contains all the necessary information for building a new human. As the egg divides to form an embryo, it produces new copies of that original genome.

For decades, geneticists have explored how an embryo can use the instructions in a single genome to develop muscles, nerves and the many other parts of the human body. They also use sequencing to understand genetic variations that can raise the risk of certain diseases. Genetic counselors can look at the results of genetic screenings to help patients and their families cope with these diseases — altering their diet, for example, if they lack a gene for a crucial enzyme.

The cost of sequencing an entire genome has fallen so drastically in the past 20 years — now a few thousand dollars, down from an estimated $3 billion for the public-private partnership that sequenced the first human genome [ http://www.genome.gov/11006943 ] — that doctors are beginning to sequence the entire genomes of some patients [ http://www.nytimes.com/2013/02/19/health/dna-analysis-more-accessible-than-ever-opens-new-doors.html ]. (Sequencing can be done in as little as 50 hours.) And they’re identifying links between mutations and diseases that have never been seen before.

Yet all these powerful tests are based on the assumption that, inside our body, a genome is a genome is a genome. Scientists believed that they could look at the genome from cells taken in a cheek swab and be able to learn about the genomes of cells in the brain or the liver or anywhere else in the body.

In the mid-1900s, scientists began to get clues that this was not always true. In 1953, for example, a British woman donated a pint of blood. It turned out that some of her blood was Type O and some was Type A. The scientists who studied her concluded that she had acquired some of her blood from her twin brother in the womb [ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2028470/?page=1 ], including his genomes in his blood cells.

Chimerism, as such conditions came to be known, seemed for many years to be a rarity. But “it can be commoner than we realized,” said Dr. Linda Randolph [ http://www.chla.org/site/apps/kb/cs/contactdisplay.asp?c=ipINKTOAJsG&b=3832751&sid=6eIFLWMtGcLJJPPxHpF&r=1 ], a pediatrician at Children’s Hospital in Los Angeles who is an author of a review of chimerism [ http://onlinelibrary.wiley.com/doi/10.1002/ajmg.a.35957/abstract ] published in The American Journal of Medical Genetics in July.

Twins can end up with a mixed supply of blood when they get nutrients in the womb through the same set of blood vessels. In other cases, two fertilized eggs may fuse together. These so-called embryonic chimeras may go through life blissfully unaware of their origins.

One woman discovered she was a chimera as late as age 52. In need of a kidney transplant [ http://health.nytimes.com/health/guides/surgery/kidney-transplant/overview.html ], she was tested so that she might find a match. The results indicated that she was not the mother of two of her three biological children. It turned out that she had originated from two genomes. One genome gave rise to her blood and some of her eggs; other eggs carried a separate genome.

Women can also gain genomes from their children. After a baby is born, it may leave some fetal cells behind in its mother’s body, where they can travel to different organs and be absorbed into those tissues. “It’s pretty likely that any woman who has been pregnant is a chimera,” Dr. Randolph said.

Everywhere You Look

As scientists begin to search for chimeras systematically — rather than waiting for them to turn up in puzzling medical tests — they’re finding them in a remarkably high fraction of people. In 2012, Canadian scientists performed autopsies on the brains of 59 women. They found neurons with Y chromosomes in 63 percent of them. The neurons likely developed from cells originating in their sons.

In The International Journal of Cancer in August, Eugen Dhimolea of the Dana-Farber Cancer Institute in Boston and colleagues reported that male cells can also infiltrate breast tissue [ http://onlinelibrary.wiley.com/doi/10.1002/ijc.28077/abstract ]. When they looked for Y chromosomes in samples of breast tissue, they found it in 56 percent of the women they investigated.

A century ago, geneticists discovered one way in which people might acquire new genomes. They were studying “mosaic animals,” rare creatures with oddly-colored patches of fur. The animals didn’t inherit the genes for these patches from their parents. Instead, while embryos, they acquired a mutation in a skin cell that divided to produce a colored patch.

Mosaicism, as this condition came to be known, was difficult to study in humans before the age of DNA sequencing. Scientists could only discover instances in which the mutations and the effects were big.

In 1960, researchers found that a form of leukemia is a result of mosaicism [ http://health.nytimes.com/health/guides/disease/mosaicism/overview.html ]. A blood cell spontaneously mutates as it divides, moving a big chunk of one chromosome to another.

Later studies added support to the idea that cancer is a result of mutations in specific cells. But scientists had little idea of how common cases of mosaicism were beyond cancer [ http://health.nytimes.com/health/guides/disease/cancer/overview.html ].

“We didn’t have the technology to systematically think about them,” said Dr. Christopher Walsh [ http://specialists.childrenshospital.org/Default.asp?pageID=PHY000797 ], a geneticist at Children’s Hospital in Boston who recently published a review on mosaicism and disease [ http://www.sciencemag.org/content/341/6141/1237758.abstract ] in Science. “Now we’re in the midst of a revolution.”

Benign Differences

The latest findings make it clear that mosaicism is quite common — even in healthy cells.

Dr. Urban and his colleagues, for example, investigated mutations in cells called fibroblasts, which are found in connective tissue. They searched in particular for cases in which a segment of DNA was accidentally duplicated or deleted. As they reported last year, 30 percent of the fibroblasts carried at least one such mutation [ http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11629.html ].

Michael Snyder [ http://snyderlab.stanford.edu/ ] of Stanford University and his colleagues searched for mosaicism by performing autopsies on six people who had died of causes other than cancer. In five of the six people they autopsied, the scientists reported last October [ http://www.pnas.org/content/109/44/18018.full ], they found cells in different organs with stretches of DNA that had accidentally been duplicated or deleted.

Now that scientists are beginning to appreciate how common chimerism and mosaicism are, they’re investigating the effects of these conditions on our health. “That’s still open really, because these are still early days,” Dr. Urban said.

Nevertheless, said Dr. Walsh, “it’s safe to say that a large proportion of those mutations will be benign.” Recent studies on chimeras suggest that these extra genomes can even be beneficial. Chimeric cells from fetuses appear to seek out damaged tissue and help heal it, for example.

But scientists are also starting to find cases in which mutations in specific cells help give rise to diseases other than cancer. Dr. Walsh, for example, studies a childhood disorder of the brain called hemimegalencephaly, in which one side of the brain grows larger than the other, leading to devastating seizures [ http://health.nytimes.com/health/guides/symptoms/seizures/overview.html ].

“The kids have no chance for a normal life without desperate surgery to take out half of their brain,” he said.

Dr. Walsh has studied the genomes of neurons removed during those surgeries. He and his colleagues discovered that some neurons in the overgrown hemisphere have mutations [ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460551/ ] to one gene. Two other teams of scientists have identified mutations on other genes, all of which help to control the growth of neurons. “We can get our hands on the mechanism of the disease,” said Dr. Walsh.

Other researchers are now investigating whether mosaicism is a factor in more common diseases, like schizophrenia [ http://health.nytimes.com/health/guides/disease/schizophrenia-disorganized-type/overview.html ]. “This will play itself out over the next 5 or 10 years,” said Dr. Urban, who with his colleagues is studying it.

Moving Cautiously

Medical researchers aren’t the only scientists interested in our multitudes of personal genomes. So are forensic scientists. When they attempt to identify criminals or murder victims by matching DNA, they want to avoid being misled by the variety of genomes inside a single person.

Last year, for example, forensic scientists at the Washington State Patrol Crime Laboratory Division described how a saliva sample and a sperm sample [ http://www.fsigenetics.com/article/S1872-4973%2812%2900086-5/abstract ] from the same suspect in a sexual assault case didn’t match.

Bone marrow transplants can also confound forensic scientists. Researchers at Innsbruck Medical University in Austria took cheek swabs from 77 people who had received transplants up to nine years earlier. In 74 percent of the samples, they found a mix of genomes [ http://link.springer.com/article/10.1007%2Fs00414-012-0687-5 ] — both their own and those from the marrow donors, the scientists reported this year. The transplanted stem cells [ http://topics.nytimes.com/top/news/health/diseasesconditionsandhealthtopics/stemcells/index.html ] hadn’t just replaced blood cells, but had also become cells lining the cheek.

While the risk of confusion is real, it is manageable, experts said. “This should not be much of a concern for forensics,” said Manfred Kayser, a professor of Forensic Molecular Biology [ http://www.erasmusmc.nl/fmb/staff/?lang=en ] at Erasmus University in Rotterdam. In the cases where mosaicism or chimerism causes confusion, forensic scientists can clear it up by other means. In the Austrian study, for example, the scientists found no marrow donor genomes in the hair of the recipients.

For genetic counselors helping clients make sense of DNA tests, our many genomes pose more serious challenges. A DNA test that uses blood cells may miss disease-causing mutations in the cells of other organs. “We can’t tell you what else is going on,” said Nancy B. Spinner, a geneticist at the University of Pennsylvania, who published a review about the implications of mosaicism for genetic counseling in the May issue of Nature Reviews Genetics.

That may change as scientists develop more powerful ways to investigate our different genomes and learn more about their links to diseases. “It’s not tomorrow that you’re going to walk into your doctor’s office and they’re going to think this way,” said Dr. Lupski. “It’s going to take time.”

© 2013 The New York Times Company

http://www.nytimes.com/2013/09/17/science/dna-double-take.html [ http://www.nytimes.com/2013/09/17/science/dna-double-take.html?pagewanted=all ] [with comments]

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F6

01/04/14 6:03 AM

#216288 RE: F6 #209017

For That Zeus Bug in Your Life


David Plunkert


A male zeus bug clings to the back of a female. Her nuptial gift to him is a place to stay while they mate, complete with board -- a proteinaceous wax secreted from glands on her back.
Photo Researchers



Bonobos may be alone among apes in preferring to share food with strangers over friends and family. Researchers suggest they use the gifts to expand their social networks.
Jingzhi Tan


By NATALIE ANGIER
Published: December 23, 2013

Here are some last-minute gift ideas to suit even the most discriminating individuals on your list.

For the female scorpionfly: an extremely large, glittering, nutrient-laced ball of spit, equivalent to 5 percent to 10 percent of a male fly’s body mass. Gentlemen: Too worn down by the holidays to cough up such an expensive package? Try giving her a dead insect instead. You can always steal it back later.

For the male Zeus bug: a monthlong excursion aboard the luxury liner that is the much larger female’s back, with its scooped-out seat tailored to his dimensions and a pair of dorsal glands to supply the passenger with all the proteinaceous wax he can swallow.

For the bonobo you’ve just met: half your food, at least. Just shovel it over. Sharing is fun!

For the bonobos you’ve known your whole life: Eh, maybe nothing this year. It’s not like they’ll stop being your friend if you “forget” to toss them a banana.

We may denounce the hyper-consumerism of the Christmas season until we’re Hanukkah [ http://topics.nytimes.com/top/reference/timestopics/subjects/h/hanukkah/index.html ] blue in the face, but much of our economy relies on the strength of the gift-giving impulse, and with good reason: The drive to exchange presents is ancient, transcultural and by no means limited to Homo sapiens. Researchers have found striking examples of gift-giving across the phyletic landscape, in insects, spiders, mollusks, birds and mammals.

Many of these donations fall under the rubric of nuptial gifts, items or services offered up during the elaborate haggle of animal courtship to better the odds that one’s gametes will find purchase in the next generation. Hungry? Why don’t you go ahead and chew on the droplets oozing from my hind-leg spur while I just take a few moments to deposit a sperm packet in the neighborhood of your genitals?

Nuptial gifts can also be a gift for researchers, allowing them to precisely quantify a donor animal’s investment in mating and reproduction, and to track the subtleties of sexual competition and collusion by analyzing the chemical composition of a given bag of courtship swag.

“This is an incredibly cool and important topic in sexual selection that we’re just beginning to explore,” said Sara M. Lewis, a professor of biology at Tufts University who has written extensively about nuptial gifts. “The bright side of nuptial gifts is, here’s a way that males can contribute things that are essential to his mate and to his future offspring.

“On the other hand, the gifts can be a source of sexual conflict, a way of manipulating the female into doing what he wants,” she said. “So there is a lot of back and forth over evolutionary time.”

Other researchers are studying how animals use gifts socially, to foster alliances or appease dominant members of the group. Grooming among primates is considered a form of gift-giving, and in most cases, it’s the subordinates who do the tick-picking: betas groom alphas, females groom males.

A nuptial or other animal gift is, by definition, something that is voluntarily given, Dr. Lewis said. “But that doesn’t mean it’s voluntarily received,” she added. “We’ve all gotten gifts that we didn’t want and wished we could return.”

One example of a possibly unwelcome gift, she said, is the snail’s love dart. Land snails like the ones in a garden are hermaphroditic, meaning they produce both eggs and sperm, and they mate by swapping sperm with other snails, often promiscuously. This is why, before copulation, a snail will try to pierce its partner with a love dart, a harpoonlike structure made of calcium carbonate and produced in the snail’s genital region.

Barely an eighth of an inch long, coated in mucus and ejected with considerable force, the dart may penetrate anywhere on the other snail’s body: through the shell, the head, even the eye. And when it does, it delivers a “gift” of potent hormones, which scientists have lately determined offer little obvious benefit to the recipient but help promote the retention of the donor’s sperm over that of competing snails. No mere victim, the punctured mollusk retorts with a flirty fléchette of its own, at which point the dueling Cupids will copulate.

In most cases, though, a male’s nuptial gift is something the female wants or needs. Martin Edvardsson, an evolutionary biologist at Australian National University, studies Callosobruchus maculatus, a small, spotted beetle that is a major pest on beans and stored grains. Given their chosen meal plan, the beetles have little access to water, and the females get very thirsty while making eggs. What does a girl have to do to get a drink around here? Mate with a male.

As it turns out, a male sequesters most of the liquid he encounters as a larva inside a bean and adds it to his ejaculate. Should a parched female solicit him, he’ll mount and pump in the stored water along with his sperm packet, for seven or eight minutes at a time. The emission is a veritable cataract.

“When I’ve given talks, I use props,” Dr. Edvardsson said. “I’ll bring in four two-liter containers of milk” — proportionally speaking, that is the human equivalent of the male beetle’s ejaculate — “and I’ll hold up a little soy sauce packet from a takeout restaurant”: the actual volume of a human ejaculate. Dr. Edvardsson and his colleagues have shown that the thirstier a female beetle is, the more often she mates; and the more water she secures, the more eggs she lays.

Gifts can be costly to make or acquire. The salivary mass that a male scorpionfly secretes to lure in a peckish female is packed with so much protein and nutrients that a less-robust suitor may forgo the effort and resort to offering a female a dead insect instead. Unlike a spitball, that has the benefit of being reclaimable, at least in part, after mating is through.

Among Pisaura mirabilis garden spiders, males risk their lives to give gifts. The first thing they do as adults is look for suitable prey, which they kill and wrap carefully in silk. They then march through the forest looking for females, their bulky gifts held high in their mouthparts.

Reporting recently in the journal Animal Behaviour [ http://www.sciencedirect.com/anbehav/article/pii/S0003347212001224 ], Pavol Prokop of Trnava University in Slovakia and Michael R. Maxwell of National University in La Jolla, Calif., showed that gift-carrying cut down on a spider’s running speed by 60 percent, potentially putting the poor male — along with his precious bundle — at heightened risk of being eaten.

Among the thrush-sized great gray shrikes, males apportion their gifts according to what they can get away with. To their regular mates, they bestow modest courtship gifts of insects or other arthropods, impaled on a little stick like a cocktail hors d’oeuvres. But to woo a potential mistress for a fleeting extra-pair copulation, the male impales and presents meatier fare — a lizard, a mouse, a small songbird.

On occasion, females are the ones playing Santa Claus. In the semiaquatic Zeus beetle, the female is about twice the size of the male. Not only does she allow a male to piggyback on top of her for weeks at a time, she also has a depression on her back seemingly designed to accommodate him while he feeds on rich wax that she secretes for his convenience. The reason for her generosity remains puzzling, but scientists suspect it evolved to prevent more onerous problems, like constant male harassment or chronic theft of her food stores.

As they reported this year in the journal PLoS One [ http://www.ncbi.nlm.nih.gov/pubmed/?term=bonobos+share+with+strangers ], Jingzhi Tan and Brian Hare of Duke University and their colleagues showed that bonobos, those chimpanzee kin much celebrated for their peaceable ways and their nondomineering males, may be alone among apes, if not among animals generally, in preferring to share food with strangers over friends and family.

When wild-born bonobos were placed in a room and supplied with treats like slices of apples and bananas, and given the choice of opening a gate to admit either a familiar or an unknown bonobo, the provisioned bonobo would lift the latch of the stranger’s enclosure and then push food in the unfamiliar ape’s direction as though saying, “Eat, eat!”

“The first time we watched this on a video, it was so shocking, like seeing an alien on Mars,” Dr. Hare said.

The researchers propose that bonobos use food gifts to expand their social network, which could enhance their own odds of survival and reproductive success.

“If I’ve got an established relationship with somebody, me sharing food won’t change that relationship at all,” Dr. Hare said. “But if it’s somebody I haven’t met before, why not get the new relationship off to a good start?”

But bonobo xenophilia has its limits. In experiments where the bonobos could allow strangers into a food room but could not interact with them physically, they didn’t bother opening the door. What good does it do me if you don’t know what a good friend I can be?

*

Podcast: Science Times
Not sure what to get that bonobo on your list? Turns out they already give gifts — like many other animals. Holbrook Kohrt always wanted to be a doctor, but his brush with death decided what type of doctor he became. Is there nuance hidden inside “Valley Girl speak” — and is it used exclusively by women?
The Gift-Giving of Animals, a Doctor With Research in His Blood, Are You Uptalking to Me?
[26:07, embedded]

*

© 2013 The New York Times Company

http://www.nytimes.com/2013/12/24/science/for-that-zeus-bug-in-your-life.html [ http://www.nytimes.com/2013/12/24/science/for-that-zeus-bug-in-your-life.html?pagewanted=all ] [with comments]

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fuagf

10/23/14 11:09 PM

#229282 RE: F6 #209017

Man’s Genome From 45,000 Years Ago Is Reconstructed

OCT. 22, 2014


In 2012, Dr. Paabo and his colleagues took samples from this thigh bone to search for DNA. To their surprise,
it held a number of genetic fragments. Credit Bence Viola/Max-Planck-Institute for Evolutionary Anthropology

Carl Zimmer

Scientists have reconstructed the genome of a man who lived 45,000 years ago, by far the oldest genetic record ever obtained from modern humans. The research, published .. http://www.nature.com/nature/journal/v514/n7523/full/nature13810.html .. on Wednesday in the journal Nature, provided new clues to the expansion of modern humans from Africa about 60,000 years ago, when they moved into Europe and Asia.

And the genome, extracted from a fossil thighbone found in Siberia, added strong support to a provocative hypothesis: Early humans interbred with Neanderthals.

“It’s irreplaceable evidence of what once existed that we can’t reconstruct from what people are now,” said John Hawks, a paleoanthropologist at the University of Wisconsin who was not involved in the study. “It speaks to us with information about a time that’s lost to us.”

Related Coverage

A Conversation With Svante Paabo: Searching for Answers in Very Old DNA JUNE 23, 2014
http://www.nytimes.com/2014/06/24/science/searching-for-answers-in-very-old-dna.html

The discoveries were made by a team of scientists led by Svante Paabo, a geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Over the past three decades .. http://www.nytimes.com/2014/04/20/books/review/neanderthal-man-by-svante-paabo.html, Dr. Paabo and his colleagues have developed tools for plucking out fragments of DNA from fossils and reading their sequences.

Early on, the scientists were able only to retrieve tiny snippets of ancient genes. But gradually, they have invented better methods for joining the overlapping fragments together, assembling larger pieces of ancient genomes that have helped shed light on the evolution of humans and their relatives.

In December, they published .. http://www.nytimes.com/2013/12/19/science/toe-fossil-provides-complete-neanderthal-genome.html?pagewanted=all .. the entirety of a Neanderthal genome extracted from a single toe bone. Comparing Neanderthal to human genomes, Dr. Paabo and his colleagues found that we share a common ancestor, which they estimated lived about 600,000 years ago.

Recently, Dr. Paabo and his colleagues got an opportunity to test their new methods on an exceptional human bone.

In 2008, a fossil collector named Nikolai V. Peristov was traveling along the Irtysh River in Siberia, searching for mammoth tusks in the muddy banks. Near a settlement called Ust'-Ishim, he noticed a thighbone in the water. Mr. Peristov fished it out and brought it to scientists at the Russian Academy of Sciences.

The Russian researchers identified the bone as a modern human, not a Neanderthal. To determine its age, they sent samples to the University of Oxford. Scientists there measured the breakdown of radioactive carbon and determined the bone was about 45,000 years old — making it the oldest modern human fossil ever found outside of Africa and the Near East.

In 2012, Dr. Paabo and his colleagues took samples from the bone to search for DNA. To their surprise, it held a number of genetic fragments.

“This is an amazing and shocking and unique sample,” said David Reich, a geneticist at Harvard Medical School and co-author of the new study.

Video - The Neanderthal Inside Us

Svante Paabo is a Swedish biologist who studies evolutionary genetics. Video by Erik Olsen on Publish Date June 23, 2014. Photo by David Reich/Nature.

The researchers used the DNA fragments to create a high-resolution copy of the man’s complete genome. A Y chromosome revealed that the thighbone belonged to a man.

The scientists then compared the genome of the so-called Ust'-Ishim man to those of ancient and living people.

They found that his DNA was more like that of non-Africans than that of Africans. But the Ust'-Ishim man was no more closely related to ancient Europeans than he was to East Asians.
Continue reading the main story
Continue reading the main story

He was part of an earlier lineage, the scientists concluded — a group that eventually gave rise to all non-African humans.

Homo sapiens, our own species, appeared in Africa around 200,000 years ago. Previous studies, both on genes and on fossils, have suggested that they then expanded through the Near East to the rest of the Old World.

The Ust'-Ishim man’s genome suggests he belonged to a group of people who lived after the African exodus, but before the split between Europeans and Asians.

Dr. Paabo and his colleagues also found that the Ust'-Ishim man had pieces of Neanderthal DNA in his genome, just as living non-Africans do. But his Neanderthal DNA had some important differences.

Fossils indicate that Neanderthals spread across Europe and Asia before becoming extinct an estimated 40,000 years ago. Today, the Neanderthal DNA in each living non-African human is broken up into short segments sprinkled throughout the genome.

Dr. Paabo and his colleagues have hypothesized that this arrangement is a result of how cells divide.

During the development of eggs and sperm, each pair of chromosomes swaps pieces of their DNA. Over the generations, long stretches of DNA get broken into smaller ones, like a deck of cards repeatedly shuffled.

Over thousands of generations, the Neanderthal DNA became more fragmented. Dr. Paabo and his colleagues predicted, however, that Neanderthal DNA in the Ust'-Ishim man’s genome would form longer stretches.

And that’s exactly what they found. “It was very satisfying to see that,” Dr. Paabo said.

By comparing the Ust'-Ishim man’s long stretches of Neanderthal DNA with shorter stretches in living humans, Dr. Paabo and his colleagues estimated the rate at which they had fragmented. They used that information to determine how long ago Neanderthals and humans interbred.

Previous studies, based only on living humans, had yielded an estimate of 37,000 to 86,000 years. Dr. Paabo and his colleagues have now narrowed down that estimate drastically: Humans and Neanderthals interbred 50,000 to 60,000 years ago, according to the new data.

The findings raised questions about research suggesting that humans in India and the Near East dated back as far as 100,000 years ago. Some scientists believe that humans expanded out of Africa in a series of waves.

But Christopher Stringer, a paleoanthropologist at the Natural History Museum, said that the new study offered compelling evidence that living non-Africans descended from a group of people who moved out of Africa about 60,000 years ago.

Any humans that expanded out of Africa before then probably died out, Mr. Stringer said.

Correction: October 22, 2014

An earlier version of this article referred incorrectly to the museum in London at which
Christopher Stringer works. It is the Natural History Museum, not the National History Museum.


http://www.nytimes.com/2014/10/23/science/research-humans-interbred-with-neanderthals.html?_r=1

See also:

inbreeding apparently wasn't very taboo for neanderthals...
http://investorshub.advfn.com/boards/read_msg.aspx?message_id=95141274

'Jews a Race' Genetic Theory Comes Under Fierce Attack by DNA Expert
http://investorshub.advfn.com/boards/read_msg.aspx?message_id=95562636

First CRISPR-Tinkered Primates Born
http://investorshub.advfn.com/boards/read_msg.aspx?message_id=96748295

fuagf

12/15/14 5:02 PM

#230454 RE: F6 #209017

Did our DNA arrive from space?

Not much can survive being blasted out of Earth’s atmosphere but
it seems that the blueprint for life is tougher than we thought.


Viviane Richter reports.


Cora Thiel and Oliver Ullrich salvage DNA molecules from the outer shell of the payload
section of the TEXUS rocket

Credit: Adrian Mettauer

Could the blueprint for life have come from space? Yes, according to an experiment carried out by molecular biologist Cora Thiel and space biotechnologist Oliver Ullrich at the University of Zurich. The team daubed DNA into the surface crevices of a European space rocket and found much of it survived re-entry intact. Their astonishing results were published recently in PLOS ONE.

Are they believable? “Well, maybe… ”, says astrobiologist Penelope Boston, who is also director of the Cave and Karst Studies Program at the New Mexico Institute of Mining and Technology. “One would have to try and replicate these conditions in a laboratory. This finding will stimulate people to do that.”

“That DNA is so durable is a great surprise,” says Malcolm Walter, founding director of the Australian Centre for Astrobiology. For Walter, the findings are consistent with the idea that life in our solar system could first have developed on Mars, spreading to Earth at a later date.

While simple organic molecules such as amino acids are known to survive interplanetary journeys buried inside meteorites, it is more surprising that a complex molecule such as DNA would have a chance. Tough bacterial spores are incinerated as meteorites burn in the Earth’s atmosphere. But DNA is a hardy molecule. Held together by multiple hydrogen bonds in a stable helix, it has shown astonishing durability – for instance surviving 38,000 years in dry bones in a cave in Croatia to reveal the entire genome of a Neanderthal.

So Thiel and Ullrich put DNA to the test on the outer surface of a TEXUS-49 rocket. They daubed DNA into different niches, some of it in the grooves of screw heads, and launched the rocket 268 kilometres into space at the Esrange Space Centre in Kiruna, the northern-most town in Sweden. During the 13-minute return journey the DNA experienced incinerating temperatures of up to 1000°C mimicking the conditions DNA might experience on the back of a meteorite.

Astonishingly, up to half the DNA could be recovered after the journey. Stretching belief even further, up to a third of it was so unscarred the code was still readable. The DNA carried the code for making a green fluorescent protein. When placed inside mouse cells they followed the code and glowed green.

“We were completely surprised to find so much intact and functionally active DNA,” says Thiel. The team believes that the extreme, dry conditions in the vacuum of space stabilised the DNA on the rocket.

The results could shed new light on the origins of life in our Solar System. One theory is that genetic material first formed on Mars and inoculated Earth after an asteroid impact sprayed chunks of rock into space. In the Solar System’s early days Mars appears to have had a more hospitable environment for the emergence of life. It was wet and had the right amounts of the metals boron and molybdenum in its seas to stabilise the assembly of RNA, a flimsy molecule believed to be the ancestor of DNA. The discovery that DNA may be capable of making the journey between the neighbouring planets adds a supporting piece of evidence to the case. “DNA is tough when it’s dry. If I put you on Mars, you won’t survive. But your DNA might,” says Steve Benner, group leader at the Foundation for Applied Molecular Evolution in Florida.

But also there’s a flipside to the discovery. If bits of DNA can survive an incoming trip they may also survive an outgoing one. While space probes and surface landers are carefully cleaned before launch, Thiel is worried DNA from Earth could contaminate landing sites on other planets or moons. When looking for life there, we don’t want to find something we’ve taken along for the ride. “It’s impossible to remove everything,” agrees Walter. Working out how to get rid of unwanted hitchhikers will now receive more attention.

See also in COSMOS: The Neanderthals live on in us .. warning nudity ..
https://cosmosmagazine.com/life-sciences/neanderthals-live-us

Viviane Richter is a science writer based in Melbourne.

https://cosmosmagazine.com/life-sciences/did-our-dna-arrive-space