Posts Tagged ‘DNA’

by Michelle Z. Donahue

A baby girl who lived some 11,500 years ago survived for just six weeks in the harsh climate of central Alaska, but her brief life is providing a surprising and challenging wealth of information to modern researchers.

Her genome is the oldest-yet complete genetic profile of a New World human. But if that isn’t enough, her genes also reveal the existence of a previously unknown population of people who are related to—but older and genetically distinct from— modern Native Americans.

This new information helps sketch in more details about how, when, and where the ancestors of all Native Americans became a distinct group, and how they may have dispersed into and throughout the New World.

The baby’s DNA showed that she belonged to a population that was genetically separate from other native groups present elsewhere in the New World at the end of the Pleistocene. Ben Potter, the University of Alaska Fairbanks archaeologist who unearthed the remains at the Upward River Sun site in 2013 , named this new group “Ancient Beringians.”

The discovery of the baby’s bones, named Xach’itee’aanenh T’eede Gaay, or Sunrise Child-Girl in a local Athabascan language, was completely unexpected, as were the genetic results, Potter says

Found in 2006 and accessible only by helicopter, the Upward River Sun site is located in the dense boreal forest of central Alaska’s Tanana River Valley. The encampment was buried under feet of sand and silt, an acidic environment that makes the survival of organic artifacts exceedingly rare. Potter previously excavated the cremated remains of a three-year-old child from a hearth pit in the encampment, and it was beneath this first burial that the six-week-old baby and a second, even younger infant were found.

A genomics team in Denmark, including University of Copenhagen geneticist Eske Willerslev, performed the sequencing work on the remains, comparing the child’s genome with the genes of 167 ancient and contemporary populations from around the world. The results appeared today in the journal Nature.

“We didn’t know this population even existed,” Potter says. “Now we know they were here for many thousands of years, and that they were really successful. How did they do it? How did they change? We now have examples of two genetic groups of people who were adapting to this very harsh landscape.”

The genetic analysis points towards a divergence of all ancient Native Americans from a single east Asian source population somewhere between 36,000 to 25,000 years ago—well before humans crossed into Beringia, an area that includes the land bridge connecting Siberia and Alaska at the end of the last ice age. That means that somewhere along the way, either in eastern Asia or in Beringia itself, a group of people became isolated from other east Asians for about 10,000 years, long enough to become a unique strain of humanity.

The girl’s genome also shows that the Beringians became genetically distinct from all other Native Americans around 20,000 years ago. But since humans in North America are not reliably documented before 14,600 years ago, how and where these two groups could have been separated long enough to become genetically distinct is still unclear.

The new study posits two new possibilities for how the separation could have happened.

The first is that the two groups became isolated while still in east Asia, and that they crossed the land bridge separately—perhaps at different times, or using different routes

A second theory is that a single group moved out of Asia, then split into Beringians and ancient Native Americans once in Beringia. The Beringians lingered in the west and interior of Alaska, while the ancestors of modern Native Americans continued on south some time around 15,700 years ago.

“It’s less like a tree branching out and more like a delta of streams and rivers that intersect and then move apart,” says Miguel Vilar, lead scientist for National Geographic’s Genographic Project. “Twenty years ago, we thought the peopling of America seemed quite simple, but then it turns out to be more complicated than anyone thought.”

John Hoffecker, who studies the paleoecology of Beringia at the University of Colorado-Boulder, says there is still plenty of room for debate about the geographic locations of the ancestral splits. But the new study fits well with where the thinking has been heading for the last decade, he adds.

“We think there was a great deal more diversity in the original Native American populations than is apparent today, so this is consistent with a lot of other evidence,” Hoffecker says.

However, that same diversity—revealed through research on Native American cranial morphology and tooth structure—creates its own dilemma. How does a relatively small group of New World migrants, barricaded by a challenging climate with no access to fresh genetic material, evolve such a deep bank of differences from their east Asian ancestors? It certainly doesn’t happen over just 15,000 years, Hoffecker insists, referring to the estimated date of divergence of ancient Native Americans from Beringians.

“We’ve been getting these signals of early divergence for decades—the first mitochondrial work in the 1990s from Native Americans were coming up with estimates of 30, 35, even 40,000 years ago,” Hoffecker says. “They were being dismissed by everybody, myself included. Then people began to suspect there were two dates: one for divergence, and one for dispersal, and this study supports that.”

“Knowing about the Beringians really informs us as to how complex the process of human migration and adaptation was,” adds Potter. “It prompts the scientist in all of us to ask better questions, and to be in awe of our capacity as a species to come into such a harsh area and be very successful.”

https://news.nationalgeographic.com/2018/01/alaska-dna-ancient-beringia-genome/

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by Lisa Ryan

As genetic-ancestry kits increase in popularity, more white nationalists have been taking the spit-in-a-cup tests to prove their heritage — and many are left disappointed by results showing they aren’t as “white” as they had hoped, STAT News reports.

A new study from researchers at the University of California, Los Angeles, and the Data & Society Research Institute examined comments left in 12 million posts on the website Stormfront, left by more than 300,000 users. The team was able to find 70 discussion threads, where 153 users posted about their test results from companies like 23andMe and Ancestry.com — with more than 3,000 posts in response.

Sociologist Aaron Panofsky explained to STAT News that many of the white nationalists would post their results, even if they were upset to learn they weren’t completely “white” — which was surprising because “they will basically say if you want to be a member of Stormfront you have to be 100 percent white European, not Jewish.”

Only a third of people who posted their ancestry results were pleased with what they discovered — a commenter with the username Sloth even wrote, “Pretty damn pure blood.” Those who found themselves with results that weren’t 100 percent white European dealt with their disappointment by rejecting the test or disputing the results with the help of other users. Some would say they knew their genealogy better than whatever a genetic test may reveal; certain users also apparently tried to discredit the tests as a Jewish conspiracy.

Panofsky notes that there is “mainstream critical literature” on these tests that ague people should be cautious about the results. J. Scott Roberts, an associate professor at the University of Michigan who wasn’t involved in the study, told STAT News, “The science is often murky in those areas and gives ambiguous information. They try to give specific percentages from this region, or x percent disease risk, and my sense is that that is an artificially precise estimate.” However, STAT News points out that Ancestry.com and 23andMe are “meticulous” in how they analyze a person’s genetic material, and exclude outliers that can distort a person’s genetic data.

https://www.yahoo.com/news/study-finds-many-white-nationalists-172104845.html

by Andy Greenberg

WHEN BIOLOGISTS SYNTHESIZE DNA, they take pains not to create or spread a dangerous stretch of genetic code that could be used to create a toxin or, worse, an infectious disease. But one group of biohackers has demonstrated how DNA can carry a less expected threat—one designed to infect not humans nor animals but computers.

In new research they plan to present at the USENIX Security conference on Thursday, a group of researchers from the University of Washington has shown for the first time that it’s possible to encode malicious software into physical strands of DNA, so that when a gene sequencer analyzes it the resulting data becomes a program that corrupts gene-sequencing software and takes control of the underlying computer. While that attack is far from practical for any real spy or criminal, it’s one the researchers argue could become more likely over time, as DNA sequencing becomes more commonplace, powerful, and performed by third-party services on sensitive computer systems. And, perhaps more to the point for the cybersecurity community, it also represents an impressive, sci-fi feat of sheer hacker ingenuity.

“We know that if an adversary has control over the data a computer is processing, it can potentially take over that computer,” says Tadayoshi Kohno, the University of Washington computer science professor who led the project, comparing the technique to traditional hacker attacks that package malicious code in web pages or an email attachment. “That means when you’re looking at the security of computational biology systems, you’re not only thinking about the network connectivity and the USB drive and the user at the keyboard but also the information stored in the DNA they’re sequencing. It’s about considering a different class of threat.”

A Sci-Fi Hack
For now, that threat remains more of a plot point in a Michael Crichton novel than one that should concern computational biologists. But as genetic sequencing is increasingly handled by centralized services—often run by university labs that own the expensive gene sequencing equipment—that DNA-borne malware trick becomes ever so slightly more realistic. Especially given that the DNA samples come from outside sources, which may be difficult to properly vet.

If hackers did pull off the trick, the researchers say they could potentially gain access to valuable intellectual property, or possibly taint genetic analysis like criminal DNA testing. Companies could even potentially place malicious code in the DNA of genetically modified products, as a way to protect trade secrets, the researchers suggest. “There are a lot of interesting—or threatening may be a better word—applications of this coming in the future,” says Peter Ney, a researcher on the project.

Regardless of any practical reason for the research, however, the notion of building a computer attack—known as an “exploit”—with nothing but the information stored in a strand of DNA represented an epic hacker challenge for the University of Washington team. The researchers started by writing a well-known exploit called a “buffer overflow,” designed to fill the space in a computer’s memory meant for a certain piece of data and then spill out into another part of the memory to plant its own malicious commands.

But encoding that attack in actual DNA proved harder than they first imagined. DNA sequencers work by mixing DNA with chemicals that bind differently to DNA’s basic units of code—the chemical bases A, T, G, and C—and each emit a different color of light, captured in a photo of the DNA molecules. To speed up the processing, the images of millions of bases are split up into thousands of chunks and analyzed in parallel. So all the data that comprised their attack had to fit into just a few hundred of those bases, to increase the likelihood it would remain intact throughout the sequencer’s parallel processing.

When the researchers sent their carefully crafted attack to the DNA synthesis service Integrated DNA Technologies in the form of As, Ts, Gs, and Cs, they found that DNA has other physical restrictions too. For their DNA sample to remain stable, they had to maintain a certain ratio of Gs and Cs to As and Ts, because the natural stability of DNA depends on a regular proportion of A-T and G-C pairs. And while a buffer overflow often involves using the same strings of data repeatedly, doing so in this case caused the DNA strand to fold in on itself. All of that meant the group had to repeatedly rewrite their exploit code to find a form that could also survive as actual DNA, which the synthesis service would ultimately send them in a finger-sized plastic vial in the mail.

The result, finally, was a piece of attack software that could survive the translation from physical DNA to the digital format, known as FASTQ, that’s used to store the DNA sequence. And when that FASTQ file is compressed with a common compression program known as fqzcomp—FASTQ files are often compressed because they can stretch to gigabytes of text—it hacks that compression software with its buffer overflow exploit, breaking out of the program and into the memory of the computer running the software to run its own arbitrary commands.

A Far-Off Threat
Even then, the attack was fully translated only about 37 percent of the time, since the sequencer’s parallel processing often cut it short or—another hazard of writing code in a physical object—the program decoded it backward. (A strand of DNA can be sequenced in either direction, but code is meant to be read in only one. The researchers suggest in their paper that future, improved versions of the attack might be crafted as a palindrome.)

Despite that tortuous, unreliable process, the researchers admit, they also had to take some serious shortcuts in their proof-of-concept that verge on cheating. Rather than exploit an existing vulnerability in the fqzcomp program, as real-world hackers do, they modified the program’s open-source code to insert their own flaw allowing the buffer overflow. But aside from writing that DNA attack code to exploit their artificially vulnerable version of fqzcomp, the researchers also performed a survey of common DNA sequencing software and found three actual buffer overflow vulnerabilities in common programs. “A lot of this software wasn’t written with security in mind,” Ney says. That shows, the researchers say, that a future hacker might be able to pull off the attack in a more realistic setting, particularly as more powerful gene sequencers start analyzing larger chunks of data that could better preserve an exploit’s code.

Needless to say, any possible DNA-based hacking is years away. Illumina, the leading maker of gene-sequencing equipment, said as much in a statement responding to the University of Washington paper. “This is interesting research about potential long-term risks. We agree with the premise of the study that this does not pose an imminent threat and is not a typical cyber security capability,” writes Jason Callahan, the company’s chief information security officer “We are vigilant and routinely evaluate the safeguards in place for our software and instruments. We welcome any studies that create a dialogue around a broad future framework and guidelines to ensure security and privacy in DNA synthesis, sequencing, and processing.”

But hacking aside, the use of DNA for handling computer information is slowly becoming a reality, says Seth Shipman, one member of a Harvard team that recently encoded a video in a DNA sample. (Shipman is married to WIRED senior writer Emily Dreyfuss.) That storage method, while mostly theoretical for now, could someday allow data to be kept for hundreds of years, thanks to DNA’s ability to maintain its structure far longer than magnetic encoding in flash memory or on a hard drive. And if DNA-based computer storage is coming, DNA-based computer attacks may not be so farfetched, he says.
“I read this paper with a smile on my face, because I think it’s clever,” Shipman says. “Is it something we should start screening for now? I doubt it.” But he adds that, with an age of DNA-based data possibly on the horizon, the ability to plant malicious code in DNA is more than a hacker parlor trick.

“Somewhere down the line, when more information is stored in DNA and it’s being input and sequenced constantly,” Shipman says, “we’ll be glad we started thinking about these things.”

https://www.wired.com/story/malware-dna-hack/?mbid=nl_81017_p1&CNDID=50678559

The animation on the left comes from a series of images taken by Eadweard Muybridge of the mare, Annie G, galloping. The frames were encoded in genetic material and stored in living bacteria. The animation on the right shows the frames after multiple generations of bacterial growth, recovered by sequencing the bacterial genomes.
Photograph: Seth Shipman

His groundbreaking photos showed life in motion, from cantering bison to leapfrogging boys, and settled an argument that had long divided trainers and riders: do all four hooves of a racehorse ever leave the floor at once?

Now, more than a century later, the stills and animations of Eadweard Muybridge, the eccentric Englishman and father of the motion picture, have had a modern makeover. Where Muybridge captured his pictures on photographic plates, Harvard scientists have set them in DNA.

There is more to the feat than showing off. If cells can be made to store information, the applications are vast. Microbes could be turned into living sentinels to monitor environmental pollution. Meanwhile, neurons could be programmed to record how the brain develops in a living animal.

“We encoded images and a movie into DNA in a living cell which is fun, but it’s not really the point of the system,” said Seth Shipman, a geneticist at Harvard Medical School. “What we’re trying to develop is a molecular recorder that can sit inside living cells and collect data over time.”

To build the prototype molecular recorder, the Harvard team hacked the immune defences that protect bacteria from invading viruses. When a bacterium is breached by an intruding virus, it releases enzymes to chop up the virus’s genetic code. To make sure it is prepared for future attacks, the bacterium remembers the invader by adding a chunk of the virus’s genetic code to its own genome. Over time, the bacterium’s genome expands, like bits of food stuck on a kebab skewer, to incorporate more and more chunks of DNA from viral intruders.

Shipman and his colleagues created strands of synthetic DNA in the lab that encoded in the letters G, T, C and A, the positions and shades of pixels found in an image of a hand and five pictures of a galloping horse taken by Muybridge in the 1880s. The scientists then fed the strands of DNA to E. coli bacteria. The bugs treated the strips of DNA like invading viruses and dutifully added them to their own genomes.

The researchers left the bugs in a dish for a week during which time they grew and divided into new bacterial cells. Shipman then collected some of the bacteria and read out their genomes. He found that the synthetic strands of DNA, which carried all the information needed to reconstruct either the hand image or the pictures of the galloping horse, had been spliced into the bugs’ genetic code.

“We delivered the material that encoded the horse images one frame at a time,” Shipman said. “Then, when we sequence the bacteria, we looked at where the frames were in the genome. That told us the order in which the frames should then appear.” Even though the bugs had grown and divided over the week, they had retained the synthetic strands of DNA which Shipman used to reconstruct the images with 90% accuracy.

“What this shows us is that we can get the information in, we can get the information out, and we can understand how the timing works too,” he said. Details of the work are reported in Nature.

Muybridge pioneered motion pictures with help from a contraption called the zoopraxiscope which projected sequences of images held on spinning glass discs. He dedicated much of his life to unveiling the beauty of animals in motion, even through the disruption of 1874 when he tracked down his younger wife’s lover, shot him point black, and was acquitted on the grounds of justifiable homicide, despite the jury having dismissed his plea of insanity brought on by a head injury suffered in a stagecoach crash in Texas 14 years earlier.

Eadweard by name and weird by nature, Muybridge was born Edward Muggeridge in Kingston upon Thames in 1830, but adopted what he believed to be the original AngloSaxon form of his name. His work on horses, including the images of the mare, Annie G, which Shipman stored in bacteria, was commissioned by Leland Stanford, a businessman, racehorse-owner and former governor of California, to settle a longstanding debate over whether a racehorse ever lifted all four hooves off the ground at once. In other work, Muybridge captured the precise motion of a nude woman turning around in surprise and another hopping on the spot.

While bacteria might not be great for storing data for thousands of years, the bugs could work well when information only has to be kept for days, weeks or months, Shipman said. Because bacteria thrive happily in the environment, the bugs could be spread on soil where they could keep a running record of heavy metals and other pollutants.

But that is only one potential use. Living cells could also be made to record what happens inside them or in the tissues and fluids that surround them. A neuroscientist by training, Shipman said that scientists have long struggled to understand brain development because it is hard to make measurements without interfering with the process. “If we had cells that recorded information inside the brain, the whole organ could develop and you could go in and retrieve the data once it’s all done,” he said.

https://www.theguardian.com/science/2017/jul/12/scientists-pioneer-a-new-revolution-in-biology-by-embeding-film-on-dna#img-3

by Jason Daley

Fiinding bones from early humans and their ancestors is difficult and rare—often requiring scientists to sort through the sediment floor of caves in far-flung locations. But modern advances in technology could completely transform the field. As Gina Kolta reports for The New York Times, a new study documents a method to extract and sequence fragments of hominid DNA from samples of cave dirt.

The study, published this week in the journal Science, could completely change the type of evidence available to study our ancestral past. Researchers from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, collected 85 sediment samples from seven archeological sites in Belgium, Croatia, France, Russia and Spain, covering a span of time from 550,000 to 14,000 years ago.

As Lizzie Wade at Science reports, when the team first sequenced the DNA from the sediments, they were overwhelmed. There are trillions of fragments of DNA in a teaspoon of dirt, mostly material from other mammals, including woolly mammoth, woolly rhinoceroses, cave bears and cave hyenas. To cut through the clutter and examine only hominid DNA, they created a molecular “hook” made from the mitochondrial DNA of modern humans. The hook was able to capture DNA fragments that most resembled itself, pulling out fragments from Neanderthals at four sites, including in sediment layers where bones or tools from the species were not present. They also found more DNA from Denisovans, an enigmatic human ancestor found only in single cave in Russia.

“It’s a great breakthrough,” Chris Stringer, anthropologist at the Natural History Museum in London tells Wade. “Anyone who’s digging cave sites from the Pleistocene now should put [screening sediments for human DNA] on their list of things that they must do.”

So how did the DNA get there? The researchers can’t say exactly, but it wouldn’t be too difficult. Humans shed DNA constantly. Any traces of urine, feces, spit, sweat, blood or hair would all contain minute bits of DNA. These compounds actually bind with minerals in bone, and likely did the same with minerals in the soil, preserving it, reports Charles Q. Choi at LiveScience.

There’s another—slightly scarier—option for the DNA’s origins. The researchers found a lot of hyena DNA at the study sites, Matthias Meyer, an author of the study tells Choi. “Maybe the hyenas were eating human corpses outside the caves, and went into the caves and left feces there, and maybe entrapped in the hyena feces was human DNA.”

The idea of pulling ancient DNA out of sediments is not new. As Kolta reports, researchers have previously successfully recovered DNA fragments of prehistoric mammals from a cave in Colorado. But having a technique aimed at finding DNA from humans and human ancestors could revolutionize the field. Wade points out that such a technique might have helped produce evidence for the claim earlier this week that hominids were in North America 130,000 years ago.

DNA analysis of sediments might eventually become a routine part of archeology, similar to radio carbon dating, says Svante Pääbo, director of the Evolutionary Genetics department at the Max Planck Institute for Evolutionary Anthropology, in the press release. The technique could also allow researchers to start searching for traces of early hominids at sites outside of caves.

“If it worked, it would provide a much richer picture of the geographic distribution and migration patterns of ancient humans, one that was not limited by the small number of bones that have been found,” David Reich, Harvard geneticist tells Kolta. “That would be a magical thing to do.”

As Wade reports, the technique could also solve many mysteries, including determining whether certain tools and sites were created by humans or Neanderthals. It could also reveal even more hominid species that we have not found bones for, creating an even more complete human family tree.

Read more: http://www.smithsonianmag.com/smart-news/new-technique-pulls-ancient-human-dna-out-cave-soil-180963084/#5gzaxagh8RYmlP6s.99

A 13,000-year-old bison fossil has shown the most likely migration route of some of the first native Americans.

DNA from the bison remains has narrowed down when an ice-free corridor opened up along the Rocky Mountains during the late Pleistocene.

That corridor was a vital route for migrations between what is now Alaska and Yukon in the far north and the rest of the North American continent.

Researchers had previously suspected this was the way migrating humans and animals must have travelled, but were unclear about how and when it was used.

But now, a new study published in Proceedings of the National Academy of Sciences, shows the route was fully open by about 13,000 years ago.

While this route was closed when the very first humans moved south of the ice sheets into North America around 15,000 years ago (they probably took a Pacific coastal route), it is thought it later became a well-travelled thoroughfare in both directions.

“The opening of the corridor provided new opportunities for migration and the exchange of ideas between people living north and south of the ice sheets,” said Peter Heintzman, of UC Santa Cruz, who led the DNA analysis.

His coauthor Beth Shapiro, also from UC Santa Cruz, has previously shown that bison populations north and south of the ice sheets were genetically distinct by the time the corridor opened.

So, armed with that knowledge, the researchers have been able track the movement of northern bison southward, and southern bison northward.

“The radiocarbon dates told us how old the fossils were, but the key thing was the genetic analysis, because that told us when bison from the northern and southern populations were able to meet within the corridor,” Heintzman said.

https://cosmosmagazine.com/life-sciences/ice-age-bison-dna-sheds-light-human-migration

The elusive octopus genome has finally been untangled, which should allow scientists to discover answers to long-mysterious questions about the animal’s alienlike physiology: How does it camouflage itself so expertly? How does it control—and regenerate—those eight flexible arms and thousands of suckers? And, most vexing: How did a relative of the snail get to be so incredibly smart—able to learn quickly, solve puzzles and even use tools?

The findings, in Nature, reveal a vast, unexplored landscape full of novel genes, unlikely rearrangements—and some evolutionary solutions that look remarkably similar to those found in humans.

With the largest-known genome in the invertebrate world—similar in size to that of a house cat (2.7 billion base pairs) and with more genes (33,000) than humans (20,000 to 25,000)—the octopus sequence has long been known to be large and confusing. Even without a genetic map, these animals and their cephalopod cousins (squids, cuttlefishes and nautiluses) have been common subjects for neurobiology and pharmacology research. But a sequence for this group of mollusks has been “sorely needed,” says Annie Lindgren, a cephalopod researcher at Portland State University who was not involved in the new research. “Think about trying to assemble a puzzle, picture side down,” she says of octopus research to date. “A genome gives us a picture to work with.”

Among the biggest surprises contained within the genome—eliciting exclamation point–ridden e-mails from cephalopod researchers—is that octopuses possess a large group of familiar genes that are involved in developing a complex neural network and have been found to be enriched in other animals, such as mammals, with substantial processing power. Known as protocadherin genes, they “were previously thought to be expanded only in vertebrates,” says Clifton Ragsdale, an associate professor of neurobiology at the University of Chicago and a co-author of the new paper. Such genes join the list of independently evolved features we share with octopuses—including camera-type eyes (with a lens, iris and retina), closed circulatory systems and large brains.

Having followed such a vastly different evolutionary path to intelligence, however, the octopus nervous system is an especially rich subject for study. “For neurobiologists, it’s intriguing to understand how a completely distinct group has developed big, complex brains,” says Joshua Rosenthal of the University of Puerto Rico’s Institute of Neurobiology. “Now with this paper, we can better understand the molecular underpinnings.”

Part of octopuses’ sophisticated wiring system—which extends beyond the brain and is largely distributed throughout the body—controls their blink-of-an-eye camouflage. Researchers have been unsure how octopuses orchestrate their chromatophores, the pigment-filled sacs that expand and contract in milliseconds to alter their overall color and patterning. But with the sequenced genome in hand, scientists can now learn more about how this flashy system works—an enticing insight for neuroscientists and engineers alike.

Also contained in the octopus genome (represented by the California two-spot octopus, Octopus bimaculoides) are numerous previously unknown genes—including novel ones that help the octopus “taste” with its suckers. Researchers can also now peer deeper into the past of this rarely fossilized animal’s evolutionary history—even beyond their divergence with squid some 270 million years ago. In all of that time octopuses have become adept at tweaking their own genetic codes (known as RNA editing, which occurs in humans and other animals but at an extreme rate in octopuses), helping them keep nerves firing on cue at extreme temperatures. The new genetic analysis also found genes that can move around on the genome (known as transposons), which might play a role in boosting learning and memory.

One thing not found in the octopus genome, however, is evidence that its code had undergone wholesale duplication (as the genome of vertebrates had, which allowed the extra genes to acquire new functions). This was a surprise to researchers who had long marveled at the octopus’s complexity—and repeatedly stumbled over large amounts of repeated genetic code in earlier research.

The size of the octopus genome, combined with the large number of repeating sequences and, as Ragsdale describes, a “bizarre lack of interest from many genomicists,” made the task a challenging one. He was among the dozens of researchers who banded together in early 2012 to form the Cephalopod Sequencing Consortium, “to address the pressing need for genome sequencing of cephalopod mollusks,” as they noted in a white paper published later that year in Standards in Genomic Sciences.

The full octopus genome promises to make a splash in fields stretching from neurobiology to evolution to engineering. “This is such an exciting paper and a really significant step forward,” says Lindgren, who studies relationships among octopuses, which have evolved to inhabit all of the world’s oceans—from warm tidal shallows to the freezing Antarctic depths. For her and other cephalopod scientists, “having a whole genome is like suddenly getting a key to the biggest library in the world that previously you could only look into by peeking through partially blocked windows.”

http://www.scientificamerican.com/article/octopus-genome-reveals-secrets-to-complex-intelligence/