How Humans’ Ability to Digest Milk Evolved from Famine and Disease

A landmark study is the first major effort to quantify how lactose tolerance developed

#archaeology, #evolution, #genetics, #social-sciences

‘Frog Skin’ Cell Type Found in Mammal Mouths

Salivary glands make unexpected use of tiny ionocytes, essential to frogs and fish

#advances, #biology, #genetics

Why is Monkeypox Evolving So Fast?

The virus circulating in the current outbreak has mutated 50 times in the past four years

#biology, #epidemiology, #genetics, #health

Genomic Sequencing Is Critical to Our Understanding of COVID

With infections still surging, the United States needs to invest in this technology to prepare for the next variants 

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#biology, #genetics

New Abortion Laws Could Make Prenatal Genetic Screening Harder to Do

States that outlaw abortions after a certain number of weeks could make it difficult or impossible to terminate a pregnancy because of a serious genetic disorder

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#biology, #genetics, #health, #reproduction

Sequencing Cat Genomes Could Help Breed Healthier Kitties

A study of more than 11,000 felines reveals the benefits of genetic testing before breeding

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#animals, #biology, #genetics, #health

Ancient Women’s Teeth Reveal Origins of 14-Century Black Death

A medieval cemetery yields DNA evidence of the deadly pandemic bacterium’s Central Asian ancestor

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#archaeology, #biology, #genetics

Ancient Women’s Teeth Reveal Origins of 14th-Century Black Death

A medieval cemetery yields DNA evidence of the deadly pandemic bacterium’s Central Asian ancestor

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#archaeology, #biology, #genetics

How Parachute Frogs Took to the Sky

Broad-webbed feet help them glide through rain-forest canopies

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#advances, #biology, #genetics

Mutations thought to be harmless turn out to cause problems

The genetic code. Note that a lot of the amino acids (the outer layer, in grey) are encoded by several sets of three-base codes that share the first two letters.

Enlarge / The genetic code. Note that a lot of the amino acids (the outer layer, in grey) are encoded by several sets of three-base codes that share the first two letters. (credit: Wikipedia)

Mutations are the raw ingredient of evolution, providing variation that sometimes makes an organism more successful in its environment. But most mutations are expected to be neutral and have no impact on an organism’s fitness. These can be incredibly useful since these incidental changes help us track evolutionary relationships without worrying about selection for or against the mutation affecting its frequency. All of the genetic ancestry tests, for example, rely heavily on tracking the presence of these neutral mutations.

But this week, a paper provided evidence that a significant category of mutations isn’t as neutral as we thought they were. The big caveat is that the study was done in yeast, which is a weird organism in a couple of ways, so we’ll have to see if the results hold in others.

True neutral?

One of the reasons that most mutations are neutral is that most of our DNA doesn’t seem to be doing anything useful. Only a few percent of the human genome is composed of the portion of genes that encode proteins, and only some of the nearby DNA is involved in controlling the activity of those genes. Outside of those regions, mutations don’t do much, either because the DNA there has no function or because the function isn’t very sensitive to having a precise sequence of bases in the DNA.

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#biology, #evolution, #genetics, #science

‘Superworms’ Eat–and Survive on–Polystyrene

Identifying the gut microbes in plastic-munching beetle larvae illuminates bacteria that could help degrade plastic waste

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#biochemistry, #biology, #genetics

Stress Management Helped Wolves Become Dogs

Genetic mutations related to production of the stress hormone cortisol may have played a role in the process of canine domestication

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#animals, #biology, #genetics

Insights from Pregnancy Could Help Fight Cancer

The placenta’s invasion of the uterus holds clues to cancer resistance

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#advances, #biology, #genetics, #physiology, #sexgender

Scientists Must Consider the Risk of Racist Misappropriation of Research

The Buffalo massacre shooter contorted genetic studies to support his hateful views

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#ethics, #genetics, #social-sciences

Science Must Not Be Used to Foster White Supremacy

It’s scientists’ responsibility to reveal the inherent biases of studies used to disparage Black people and other groups

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#biology, #genetics

What Genetics Can–and Cannot–Reveal about an Individual’s COVID Risk

Genome-wide association studies can sleuth out genetic markers that raise or lower COVID risk, but they miss social factors

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#biology, #genetics, #health, #health-care, #public-health

Study of reproducibility issues points finger at the mice

Study of reproducibility issues points finger at the mice

Enlarge (credit: David Aubrey)

Over the last decade or so, the science community has been concerned about what has been called the “reproducibility crisis”: the apparent failure of some significant experiments to produce the same results when they’re repeated. That failure has led to many suggestions about what might be done to improve matters, but we still don’t fully understand why experiments are failing to reproduce results.

A few recent studies have attempted to pinpoint the underlying problem. A new study approached reproducibility failure by running a set of identical behavioral experiments in several labs in Switzerland and Germany. It found that many of the differences come down to the lab itself. But there’s also variability in the results that can’t be ascribed to any obvious cause and may just arise from differences between individual mice.

Try and try again

The basic outline of the work is pretty simple: Get three labs to perform the same set of 10 standard behavioral experiments on mice. But the researchers took a number of additional steps to allow a detailed look at the underlying factors that might drive variation in experimental results. The experiments were done on two different mouse strains, both of which had been inbred for many generations, limiting genetic variability. All the mice were ordered from the same company. They were housed in identical conditions and were tested while they were the same age.

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#behavioral-science, #biology, #genetics, #mice, #reproducibility, #science

All’s not lost for the vaquita—even though its gene pool is shallow

Image of two animals swimming.

Enlarge / The vaquita’s population is small, but it may have purged most of its harmful mutations in the past. (credit: David Schneider)

With only around 10 individuals left in the world, a tiny porpoise called the vaquita is facing extinction. Somewhat surprisingly, despite the relative shallowness of its gene pool, inbreeding isn’t likely to be an issue for the porpoise. This is according to a new study by the National Marine Fisheries Service, National Oceanic and Atmospheric Administration (NOAA), University of California, San Francisco, and other groups around the globe.

The vaquita, also known as the California harbor porpoise, is the smallest cetacean and makes its home in the northern part of the Gulf of California. Over the decades, the diminutive mammals have been caught as bycatch in gillnets, and these accidental drownings have devastated their population. Ultimately, gillnets (and other random deaths) are the biggest risk the incredibly small population faces, said Jacqueline Robinson, one of the authors of the paper and postdoctoral scholar at the UCSF Institute for Human Genetics.

The reasoning goes that vaquitas have had a small population size for thousands of years and have experienced catastrophic population decline. This is a similar situation to one faced by the Channel Island Fox. “But through protection, conservation action, and captive breeding, those fox populations were able to rapidly recover and reach their pre-decline population sizes,” Robinson told Ars.

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#california, #conservation, #genetics, #science, #vaquita

Genetics goes to the dogs, finds there’s not much to breed behavior

Image of a white dog with a smile.

Enlarge / In the case of the samoyed, selection for physical characteristics produced a dog that sure looks happy. (credit: Zhao Hui)

Many dog breeds are purely about appearance—think poodles and the Pekingese. But plenty of other breeds are devoted to specific tasks, like racing greyhounds. For many of these tasks, physical appearance isn’t enough: behavior also matters. Things like herding by sheepdog breeds or fetching by various retrievers.

It’s not surprising that many people ascribe these behaviors—and a wide variety of other, less useful ones—to their dog’s breed and its underlying genetics. Now, a large team of US-based researchers has looked into whether this belief is accurate. And, with a few exceptions, they find that it’s not. With a huge panel of volunteer dog owners, they show that the genetics of dog behavior is built from lots of small, weak influences, and every breed seems to have some members that just don’t behave as we expect.

Dogs, meet Darwin

The work is based on a citizen science project called Darwin’s Ark. Participants were asked to give details about their dog, including whether it belonged to an established breed (either certified or inferred). They were also asked to fill out short surveys that collectively asked about 117 different behaviors. Overall, they obtained data on some 18,000 dogs, about half of them from purebreds.

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#biology, #dogs, #evolution, #genetics, #science

Dogs’ Personalities Aren’t Determined by Their Breed

A new genetic study shows generalizing breeds as affectionate or aggressive doesn’t hold up

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#biology, #genetics

A Single Gene in One Species Can Cause Other Species to Go Extinct

This “keystone” variant of a gene could make or break a food web in an experimental system

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#biology, #ecology, #genetics

Completing the Human Genome Sequence (Again)

The Telomere-to-Telomere consortium just sequenced the tricky final 10 percent of the essentially complete human genome

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#biology, #genetics

Desert Plants’ Adaptations Help Them Thrive

Genes found in the flora could help crops and biofuels survive more drastic extremes

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#advances, #biology, #genetics

First Gene Therapy for Tay-Sachs Disease Successfully Given to Two Children

About 1 in 300 people in the general population carry the Tay-Sachs disease gene

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#genetics, #health

Gene Variant May Have Helped Ancient Humans Survive Starvation

When there’s no food, it pays to be small

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#advances, #biology, #genetics

Secrets of Ultrarare Black Tigers Revealed

Scientists cracked the puzzle behind the mutant tigers’ markings and documented their spread

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#advances, #biology, #genetics

Ranking the Risk of Heart Disease

By accounting for the additive effect of multiple genetic variants, researchers can develop a system that improves their ability to identify the most vulnerable

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#biology, #genetics

Humans Are Doomed to Go Extinct

Habitat degradation, low genetic variation and declining fertility are setting Homo sapiens up for collapse 

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#biology, #evolution, #genetics, #reproduction

Genes Reveal How Some Rockfish Live Up to 200 Years

Scientists surveyed dozens of species’ genomes to uncover keys to longevity

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#animals, #biology, #genetics

Ancient DNA from Sitting Bull’s scalp lock confirms living great-grandson

Hair from Lakota Sioux leader Sitting Bull’s scalp lock, from which DNA was extracted for analysis.

Enlarge / Hair from Lakota Sioux leader Sitting Bull’s scalp lock, from which DNA was extracted for analysis. (credit: Eske Willerslev)

An international team of scientists has confirmed the lineage of a living descendent of the famous Lakota Chief Sitting Bull via a new method of DNA analysis designed to track familial lineage using ancient DNA fragments. According to the authors of a new paper published in the journal Science Advances, this is the first time that such an analysis has been used to confirm a link between deceased and living people—in this case, Sitting Bull and his great-grandson, Ernie LaPointe.

The team’s method should be broadly applicable to any historical question involving even the limited genetic data gleaned from ancient DNA. “In principle, you could investigate whoever you want—from outlaws like Jesse James to the Russian tsar’s family, the Romanovs,” said co-author Eske Willerslev of the University of Cambridge. “If there is access to old DNA, typically extracted from bones, hair or teeth, they can be examined in the same way.”

Sitting Bull (Tȟatȟáŋka Íyotake) was a Lakota leader who is best known for his defeat of Lt. Col. George Armstrong Custer‘s 7th Cavalry at the Battle of the Little Big Horn (aka, the Battle of the Greasy Grass) on June 25-26, 1876. Various tribes had been joining Sitting Bull’s camp over the preceding months, drawn by his spiritual leadership and seeking safety in numbers against US troops. Their number soon grew to more than 10,000. Custer’s men were badly outnumbered when they attacked the camp and were forced to retreat. The Sioux warriors ultimately killed Custer and most of his men in what was later dubbed Custer’s Last Stand.

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#american-history, #dna-analysis, #gaming-culture, #genealogy, #genetics, #history, #science, #sitting-bull

Poaching drove the evolution of tusk-free elephants

Image of three elephants

Enlarge (credit: Bisakha Datta / Getty Images)

In the wake of severe poaching problems, some wildlife authorities have resorted to removing the horns of rhinos in order to eliminate the reason they’re poached in the first place. It turns out that, in the wake of a severe poaching event, evolution came up with a similar solution.

A 15-year-long civil war in Mozambique set off a burst of poaching that ultimately killed 90 percent of a national park’s elephant population. In the wake of that, tuskless elephants were seen in the park. That’s surprising, since tusks play an important role in elephants’ foraging and defenses against predators. Now, researchers have revealed that the lack of tusks was the result of genetic changes and have even identified the genes that were likely behind it.

A change of face

Over the course of the Mozambican Civil War, the population of elephants in Gorongosa National Park dropped from 2,542 to just 242. But the remaining population contained a significant number of elephants that lacked tusks. Models of the population and rates of tusklessness suggest that animals without them were roughly five times more likely to survive than their fellows with tusks.

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#biology, #elephants, #evolution, #genetics, #genomics, #poaching, #science

The Blueprints of Health

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#from-the-editor, #genetics, #health

New genomic analysis sorts out when Polynesians reached which islands

A lush tropical island.

Enlarge / The Island of Rarotonga, which the new study suggests was settled around 830 CE by people arriving from the vicinity of Samoa. (credit: Matthew Williams-Ellis / Getty Images)

The spread of the Polynesian culture across the Pacific was the greatest migration in humanity’s history. All indications are that the Polynesians started in Taiwan and made it to the Americas while settling on islands from Hawaii to New Zealand along the way. Many of those islands retained trade routes for centuries, even if the islands themselves were tiny and difficult to consistently find in the vast expanse of the Pacific.

Reconstructing the route the Polynesians took has proven challenging. Very little ancient DNA has survived in the warm, often humid environments of the tropics. Artifacts have been dated, but it’s not clear how closely they relate to the arrival of an island’s population, and often they don’t indicate where that population came from. Post-colonial travel has complicated the genetics and linguistic evidence that might otherwise help us sort things out.

Now, a large international team of researchers has come up with an entirely new way of analyzing the genomes of modern Polynesians, based on the effect that a long series of settlement events would have on genomes. The results provide a detailed map of which islands were settled in what order, and it even provides an estimate on the dates of when Polynesians arrived.

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#genetics, #genomics, #human-genetics, #migration, #polynesia, #science

‘Guerilla’ Artist Daisy Ginsberg Re-creates Scent of Extinct Flowers

Ginsberg collaborates with synthetic biologists to create eau de Leucadendron and her latest: artwork for insects

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#biology, #biotech, #genetics, #technology

Too Many Scientists Still Say Caucasian

Racist ideas of categories for human identity continue to warp research and medicine

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#genetics, #inequality, #social-sciences

Maryland and Montana are restricting police access to DNA databases

Maryland and Montana have become the first U.S. states to pass laws that make it tougher for law enforcement to access DNA databases.

The new laws, which aim to safeguard the genetic privacy of millions of Americans, focus on consumer DNA databases, such as 23andMe, Ancestry, GEDmatch and FamilyTreeDNA, all of which let people upload their genetic information and use it to connect with distant relatives and trace their family tree. While popular — 23andMe has more than three million users, and GEDmatch more than one million — many are unaware that some of these platforms share genetic data with third parties, from the pharmaceutical industry and scientists to law enforcement agencies.

When used by law enforcement through a technique known as forensic genetic genealogy searching (FGGS), officers can upload DNA evidence found at a crime scene to make connections on possible suspects, the most famous example being the identification of the Golden State Killer in 2018. This saw investigators upload a DNA sample taken at the time of a 1980 murder linked to the serial killer into GEDmatch and subsequently identify distant relatives of the suspect — a critical breakthrough that led to the arrest of Joseph James DeAngelo.

While law enforcement agencies have seen success in using consumer DNA databases to aid with criminal investigations, privacy advocates have long warned of the dangers of these platforms. Not only can these DNA profiles help trace distant ancestors, but the vast troves of genetic data they hold can divulge a person’s propensity for various diseases, predict addiction and drug response, and even be used by companies to create images of what they think a person looks like.

Ancestry and 23andMe have kept their genetic databases closed to law enforcement without a warrant, GEDmatch (which was acquired by a crime scene DNA company in December 2019) and FamilyTreeDNA have previously shared their database with investigators. 

To ensure the genetic privacy of the accused and their relatives, Maryland will, starting October 1, require law enforcement to get a judge’s sign-off before using genetic genealogy, and will limit its use to serious crimes like murder, kidnapping, and human trafficking. It also says that investigators can only use databases that explicitly tell users that their information could be used to investigate crimes. 

In Montana, where the new rules are somewhat narrower, law enforcement would need a warrant before using a DNA database unless the users waived their rights to privacy.

The laws “demonstrate that people across the political spectrum find law enforcement use of consumer genetic data chilling, concerning and privacy-invasive,” said Natalie Ram, a law professor at the University of Maryland. “I hope to see more states embrace robust regulation of this law enforcement technique in the future.”

The introduction of these laws has also been roundly welcomed by privacy advocates, including the Electronic Frontier Foundation. Jennifer Lynch, surveillance litigation director at the EFF, described the restrictions as a “step in the right direction,” but called for more states — and the federal government — to crack down further on FGGS.

“Our genetic data is too sensitive and important to leave it up to the whims of private companies to protect it and the unbridled discretion of law enforcement to search it,” Lynch said.

“Companies like GEDmatch and FamilyTreeDNA have allowed and even encouraged law enforcement searches. Because of this, law enforcement officers are increasingly accessing these databases in criminal investigations across the country.”

A spokesperson for 23andMe told TechCrunch: “We fully support legislation that provides consumers with stronger privacy protections. In fact we are working on legislation in a number of states to increase consumer genetic privacy protections. Customer privacy and transparency are core principles that guide 23andMe’s approach to responding to legal requests and maintaining customer trust. We closely scrutinize all law enforcement and regulatory requests and we will only comply with court orders, subpoenas, search warrants or other requests that we determine are legally valid. To date we have not released any customer information to law enforcement.”

GEDmatch and FamilyTreeDNA, both of which opt users into law enforcement searches by default, told the New York Times that they have no plans to change their existing policies around user consent in response to the new regulation. 

Ancestry did not immediately comment.

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#23andme, #ancestry, #dna, #electronic-frontier-foundation, #federal-government, #gedmatch, #genetics, #health, #judge, #law-enforcement, #maryland, #montana, #privacy, #security, #the-new-york-times, #united-states

Researchers rewire the genetics of E. coli, make it virus-proof

Image of a woman holding bacterial plates.

Enlarge / On the outside, these heavily engineered bacteria look no different from their normal peers. (credit: Raphael Gaillarde / Getty Images)

Many of the fundamental features of life don’t necessarily have to be the way they are. Chance plays a major role in evolution, and there are alternate paths that were never explored, simply because whatever evolved previously happened to be good enough. One instance is the genetic code, which converts the information carried by our DNA into the specific sequence of amino acids that form proteins. There are scores of potential amino acids, many of which can form spontaneously. But most life uses a genetic code that relies on just 20 of them.

Over the past couple of decades, researchers have shown that it doesn’t have to be that way. If you supply bacteria with the right enzyme and an alternative amino acid, they can use it. But bacteria won’t use the enzyme and amino acid very efficiently, as all the existing genetic code slots are already in use.

Now, researchers have managed to edit bacteria’s genetic code to free up a few new slots. They then filled those slots with unnatural amino acids, allowing the bacteria to produce proteins that would never be found in nature. One side effect of the reprogramming? No viruses could replicate in the modified bacteria.

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#amino-acids, #biology, #genetic-code, #genetic-engineering, #genetics, #science, #synthetic-biology

Denisovans may have met us in the Pacific

The highlands of Papua New Guinea.

Enlarge / The highlands of Papua New Guinea. (credit: David Kirkland | Getty Images)

The inhabitants of the Pacific came in waves. Aboriginal Australians were the first to cross the area, and they were followed by separate populations that inhabited New Guinea and nearby island chains. Later still, the Polynesians, descendants of early East Asians, spread through the distant islands of the Pacific.

While modern genetics has made these rough outlines clear, it has also made it clear that these different populations sometimes interacted, sharing DNA along with technology and trade goods. Paleontology finds have made it clear that at least three distinct hominin species had occupied some of these islands before modern humans arrived, including the enigmatic Hobbits of Indonesia and a similarly diminutive species in the Philippines.

A recent study of the genomes of Pacific island populations provides a map of some of the major interactions that took place in the Pacific. And it suggests at least one of these involved the introduction of additional Denisovan DNA.

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#biology, #genetics, #genomics, #human-evolution, #papua-new-guinea, #polynesans, #science

The genetics of relatively healthy obesity

Image of an overweight individual

Enlarge (credit: Matthew Horwood / Getty Images)

In general, obesity is linked with a large range of health problems—for most people, at least. But for a substantial minority of those who are overweight, obesity is accompanied by indications of decent health, with no signs of impending diabetes or cardiovascular disease. These cases have probably received unwarranted attention; who doesn’t want to convince themselves that they’re an exception to an unfortunate rule, after all? But the phenomenon is real, and it’s worth understanding.

To that end, a large international team of researchers has looked into whether some of these cases might be the product of genetic influences. And simply by using existing data, the team found 61 instances where a location in our genomes is associated with both elevated obesity and signs of good health, cardiovascular or otherwise.

Good and bad

The team’s method of searching the genome is remarkably straightforward, and it relies on the fact that many research groups have already done so much work to look for factors associated with obesity, diabetes, and cardiovascular health. This work includes searching for areas of the genome associated with measures of obesity, like body mass index, body fat percentage, and waist-to-hip ratio. Insulin and glucose levels have also been studied genetically, as these numbers give some indication of how the body is responding to weight and food intake. Cardiovascular health measures, including things like cholesterol, triglyceride levels, and blood pressure, have also been explored.

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#biology, #genetics, #genomics, #health, #medicine, #obesity, #science

Coronavirus variants: What they do and how worried you should be


Enlarge / Coronaviruses (credit: Getty | BSIP)

Ever since the novel coronavirus, SARS-CoV-2, began jumping from human to human, it’s been mutating. The molecular machinery the virus uses to read and make copies of its genetic code isn’t great at proofreading; minor typos made in the copying process can go uncorrected. Each time the virus lands in a new human victim, it infects a cell and makes an army of clones, some carrying genetic errors. Those error-bearing clones then continue on, infecting more cells, more people. Each cycle, each infection offers more opportunity for errors. And, over time, those errors, those mutations, accumulate.

Some of these changes are meaningless. Some are lost in the frenetic viral manufacturing. But some become permanent fixtures, passed on from virus to virus, human to human. Maybe it happens by chance; maybe it’s because the change helps the virus survive in some small way. But in aggregate, viral strains carrying one notable mutation can start carrying others. Collections of notable mutations start popping up in viral lineages, and sometimes they seem to have an edge over their relatives. That’s when these distinct viruses—these variants—get concerning.

Scientists around the world have been closely tracking mutations and variants since the pandemic began, watching some rise and fall without much ado. But in recent months, they have become disquieted by at least three variants. These variants of concern, or VOCs, have raised critical questions—and alarm—over whether they can spread more easily than previous viral varieties, whether they can evade therapies and vaccines, or even whether they’re deadlier.

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#covid-19, #features, #genetics, #infectious-disease, #pandemic, #sars-cov-2, #science, #spike-protein, #variants, #who

Sano Genetics, a startup helping with Long Covid research, raises £2.5M in seed funding

Sano Genetics, a startup with a broad mission to support personalised medicine research by increasing participation in clinical trials, has raised £2.5 million in seed funding.

The round is led by Episode1 Ventures, alongside Seedcamp, Cambridge Enterprise, January Ventures, and several Europe and U S.-based angel investors. It adds to £500,000 in pre-seed funding in 2018.

Sano Genetics says part of the new capital will be to fund free at-home DNA testing kits for 3,000 people affected by Long Covid. It will also further invest in the development of its tech platform and grow the team

Founded in 2017 by Charlotte Guzzo, Patrick Short and William Jones after they met at Cambridge University while studying genomics as postgrads, Sano Genetics has built what it describes as a “private-by-design” tech platform to help patients take part in medical research and clinical trials. This includes at-home genetic testing capabilities, and is seeing the company support research into multiple sclerosis, ankylosing spondylitis, NAFLD, and ulcerative colitis2, with a research programme for Parkinson’s disease on the agenda for later in 2021.

“For participants in medical research, the process is not user friendly,” says Sano Genetics CEO Patrick Short. “There is usually little to no benefit for participants beyond altruism, taking part is difficult and time consuming, and people are also concerned about the privacy of their sensitive genetic and medical information.

“[Therefore], for researchers in biotech, pharma, and academia, it is very difficult to attract and retain research participants, which adds substantial costs and time to their research. In particular for research involving genetics and precision therapies, it is doubly challenging to find the ‘right’ patients because genetic testing is not routine in the healthcare system”.

To help solve this, Sano Genetics matches relevant participants to research via its platform. It then makes participation easier by enabling at-home genetic testing and by guiding participants through the process.

“The system is designed so users know exactly what will happen with their data, and we give them straightforward ways to control their data,” explains Short. “We keep our users engaged and involved in the research process by giving them updates on the research they have been a part of, and with free personalised content including genetic reports, and stories from other people like them on our blog”.

A typical end user is someone who has a chronic or rare disease and is using the platform to take part in research that helps them personally (e.g. access to a new therapy via a clinical trial) or to help others like them.

Meanwhile, Sano Genetics generates revenue by charging biotech and pharma companies fees to find the right patients for their studies. “The typical study for us consists of a set-up fee, a per-test fee for our at-home genetic testing and analysis, and a fee for each referral we make of an interested and eligible participant to their research study,” adds the Sano Genetics CEO.

#cambridge-enterprise, #cambridge-university, #ceo, #europe, #fundings-exits, #genetic-testing, #genetics, #genomics, #medicine, #multiple-sclerosis, #parkinsons-disease, #sano-genetics, #seedcamp, #startups, #tc

Dire wolves aren’t wolves at all—they form a distinct lineage with jackals

Two canid skeletons facing each other.

Enlarge (credit: Wikimedia commons)

Dire wolves had a burst of newfound fame with their appearance in Game of Thrones, where they were portrayed as a far larger version of more mundane wolves. Here in the real world, only the largest populations of present-day wolves get as large as the dire wolf, which weighed nearly 70 kilograms. These animals once shared North America—and likely prey—with predators like the smilodon, a saber-toothed cat. Prior to the arrival of humans, dire wolves were far more common than regular wolves, as indicated by the remains found in the La Brea tar seeps, where they outnumber gray wolves by a factor of about 100.

Like the smilodon and many other large North American mammals, the dire wolf vanished during a period of climate change and the arrival of humans to the continent, even as gray wolves and coyotes survived. And with their departure, they left behind a bit of a mystery: what were they?

A new study uses ancient DNA from dire wolf skeletons to determine that they weren’t actually wolves and had been genetically isolated from them for millions of years.

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#dire-wolves, #dogs, #evolution, #genetics, #genomics, #paleontology, #science, #wolves

23andMe raises $82.5 million in new funding

DNA testing technology company 23andMe has raised just shy of $82.5 million in new funding, from an offering of $85 million in total equity shares, according to a new SEC filing. The funding, confirmed by the Wall Street Journal, comes from investors including Sequoia Capital and NewView Capital. It brings the total raised by 23andMe to date to over $850 million.

There’s no specific agenda earmarked for this Series F round, according to a statement from the company to the WSJ, beyond general use to continue to fund and grow the business. 23andMe’s business is based on its distribution of individual home genetic testing kits, which provide customers with insights about their potential health and their family tree based on their DNA.

While the company’s pitch to individuals is improved health, and more knowledge about their ancestry and family tree, the company has also turned its attention to conducting research based on the data it has collected in aggregate, both for its own studies including a recent one that examined how genetic markers could affect a person’s susceptibility to COVID-19, and also for use in supporting the work of third-parties – though it stresses that data is only shared in aggregate, de-identified formats for those purposes.

In January, 23andMe confirmed layoffs affecting roughly 14% of its global workforce. The company’s work this year around COVID-19 has, however, perhaps put the value of its platform in a new light, in the face of this pandemic and the potential of future similar global health issues that may arise.

#23andme, #biology, #biotech, #funding, #genetic-testing, #genetics, #health, #newview-capital, #sequoia-capital, #tc, #technology, #the-wall-street-journal, #u-s-securities-and-exchange-commission, #wall-street-journal

Looking into the genetics of severe COVID-19

A medical worker in protective gear stands beside a bedridden patient hooked into all manner of machines.

Enlarge / Researchers have looked at whether there are genetic influences on who experiences a case of severe COVID-19. (credit: ALBERTO PIZZOLI / Getty Images)

The body’s response to SARS-CoV-2 infection range from imperceptible to death, raising an obvious question: what makes the difference? If we could identify the factors that make COVID-19 so dangerous for some people, we could do our best to address these factors, and provide extra protections for those who are at highest risk. But aside from the obvious—health disparities associated with poverty and race seem to be at play here, too—we’ve had trouble identifying the factors that make a difference.

A recently published study takes a look at one potential influence: genetics. In a large study of UK COVID-19 patients, researchers have found a number of genes that appear to be associated with severe cases, most of them involved in immune function. But the results don’t clarify how immune function is linked to the disease’s progression.

All in the genes

The work took place in the UK, one of the countries involved in the GenOMICC (Genetics Of Mortality In Critical Care) project, which has already been exploring the genetics underlying hospitalization for communicable diseases. For the new study, the researchers worked with over 200 intensive care units in the UK to identify study participants. All told, they managed to get genetic data for over 2,700 critical COVID-19 patients. These were matched with people in the UK’s Biobank who had similar demographics in order to provide a control population. The one weakness of this design is that some people in the Biobank may be susceptible to severe COVID-19 but simply haven’t been infected yet, which would tend to weaken any genetic signals.

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#biology, #covid-19, #genetics, #medicine, #pandemic, #sars-cov-2, #science

The weird genomes of domesticated fish

Image of a goldfish with odd under-eye bubbles.

Enlarge (credit: Jordan Hartig)

Humans have domesticated a large number of animals over their history, some for food, some as companions and protectors. A few species—think animals like rabbits and guinea pigs—have partly shifted between these two categories, currently serving as both food and pets. But one species has left its past as a food source behind entirely. And, in another rarity, it ended up serving not so much as a companion but as a decoration.

We’re talking goldfish here, and we’ve now gotten a look at their genome. And it’s almost as weird as the fish themselves are.

A fine kettle of fish

It’s worth stopping for a moment to consider just how weird they are within the realm of domestication. They started out just as slightly colored variants of a carp that is otherwise used entirely for aquaculture. We’ve completely removed them from the food chain and turned them into pets, but they’re not the sort of pets that we interact with like a dog or cat, or even a guinea pig. Largely, they just sit there and look decorative. And in the process of making them even more decorative, we’ve bred a lot of varieties that are far less functional as fish.

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#biology, #evolution, #fish, #genetics, #genomics, #science

Ancient skull a new window on human migrations, Denisovan meetings

Image of a large, lit trench with people working in it.

Enlarge / These excavations identified Denisovan DNA within the sediment. (credit: Dongju Zhang, Dongju Zhang, Lanzhou University)

The Denisovans occupy a very weird place in humanity’s history. Like the Neanderthals, they are an early branch off the lineage that produced modern humans and later intermingled with modern humans. But we’d known of Neanderthals for roughly 150 years before we got any of their DNA sequence and had identified a set of anatomical features that defined them. In contrast, we had no idea that Denisovans existed until their DNA turned up unexpectedly in a single, tiny piece of finger. And, to this day, we’ve not identified enough remains to really say anything about what they looked like.

But, over time, we’ve gotten increasing ancient DNA samples that are providing a clearer picture of our interactions with this enigmatic lineage. Now, two new reports describe ancient DNA that provides some more details. One paper describes a modern human genome from Asia that dates to closer to the time when interbreeding must have taking place. It provides further evidence that there were at least two instances of interbreeding, and it helps clarify how early human populations moved around Asia. The second confirms that Denisovans were living along the Tibetan Plateau and may have adapted to high altitudes.

The Mongolian skull

Back in 2006, mining in Mongolia’s Salkhit Valley turned up the top of a skull that was clearly old. But, because it didn’t have any definitive features, people argued over whether it might be Neanderthal or Homo erectus. However, preliminary DNA sequencing indicated it belonged to a modern human, with carbon dating placing its age at roughly 34,000 years old.

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#biology, #denisovans, #evolution, #genetics, #genomics, #human-evolution, #science

New African genomes: Complicated migrations and strong selection

A building in a Ndebele village, South Africa. The Ndebele-language speakers, currently about a million strong, arrived in South Africa with the Bantu expansion.

Enlarge / A building in a Ndebele village, South Africa. The Ndebele-language speakers, currently about a million strong, arrived in South Africa with the Bantu expansion. (credit: DEA / S. VANNINI / Getty Images)

Humanity originated in Africa, and it remained there for tens of thousands of years. To understand our shared genetic history, it’s inevitable that we have to look to Africa. Unlike elsewhere on the planet, however, African populations were present throughout our history—they weren’t subject to the same sorts of founder effects seen as populations expanded into unoccupied areas. Instead, those populations were scrambled as groups migrated to new areas within the continent.

Sorting out all of this would be a challenge, but it’s one that has been made harder by the fact that most genome data comes from people in the industrialized world, leaving the vast populations of Africa poorly sampled. That’s starting to change, and a new paper reports on the efforts of a group that has just analyzed over 400 African genomes, many coming from populations that have never participated in genome studies before.

New diversity

New genetic variants arise all the time. As a result, the oldest populations—those in Africa—should have the most novel variations. But identifying these populations can be hard when there are so many; the study mentions that there are over 2,000 ethnolinguistic groups in sub-Saharan Africa, and only a small number of those have been sampled. The new study is a huge step forward, with over 400 complete genome sequences from geographically dispersed populations. But even there, it’s limited, adding only 50 new ethnolinguistic groups and two vast regions of the continent represented by people from a single country (Zambia for Central Africa and Botswana for Southern Africa).

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#africa, #biology, #evolution, #genetics, #genomics, #science

Gedmatch investigating after user DNA data made available to police

Gedmatch, the DNA analysis site that police used to catch the so-called Golden Gate Killer, was pulled briefly offline on Sunday while its parent company investigated how its users’ DNA profile data apparently became available to law enforcement searches.

The site, which lets users upload their DNA profile data to trace their family tree and ancestors, rose to overnight fame in 2018 after law enforcement used the site to match the DNA from a serial murder suspect against the site’s million-plus DNA profiles in the site’s database without first telling the company.

Gedmatch issued a privacy warning to its users and put in new controls to allow users to opt-in for their DNA to be included in police searches.

But users reported Sunday that those settings had changed without their permission, and that their DNA profiles were made available to law enforcement searches.

Users called it a “privacy breach.” But when reached, the company’s owner declined to say if the issue was caused by an error or a security breach, citing an ongoing investigation.

“We are aware of the issue regarding Gedmatch, where user permissions were not set correctly,” said Brett Williams, chief executive of Verogen, which acquired Gedmatch in 2019. “We have resolved that issue; however, as a precaution, we have taken the site down while we are investigating the actual cause of the error. Once we understand the cause, we will be issuing a more formal statement,” he said.

DNA profiling and analysis companies are increasingly popular with users trying to understand their cultural and ethnic backgrounds by discovering new and ancestral family members. But law enforcement are increasingly pushing for access to genetic databases to try to solve crimes from DNA left at crime scenes.

Williams would not say, when asked, if Verogen or Gedmatch have received any law enforcement requests for user data in the past day, or if either company has responded.

Gedmatch does not publish how frequently law enforcement seeks access to the company’s data. Its rivals, like 23andMe and, have already published these so-called transparency reports. Earlier this year revealed that it rejected an out-of-state police warrant, indicating that police continue are still using DNA profiling and analysis sites for information.

“The acknowledgement of an issue is a start, but if a ‘resolution’ means simply correcting the error, there are many questions that remain,” Elizabeth Joh, a professor of law at University of California, Davis School of Law, told TechCrunch.

“For instance, does Gedmatch know whether any law enforcement agencies accessed these improperly tagged users? Will they disclose any further details of the breach? And of course, this isn’t simply Gedmatch’s problem: a privacy breach in a genetic genealogy database underscores the woefully inadequate regulatory safeguards for the most sensitive of information, in a novel arena for civil liberties,” she said. “It’s a mess.”

#ancestry-com, #california, #dna, #gedmatch, #genetics, #health, #law-enforcement, #privacy, #security, #university-of-california

New data indicates that some Polynesians carry Native American DNA

The Tongariki site, built by Polynesians on Rapa Nui. New data suggests that by the time their ancestors arrived on the island, they had already had contact with South America.

Enlarge / The Tongariki site, built by Polynesians on Rapa Nui. New data suggests that by the time their ancestors arrived on the island, they had already had contact with South America. (credit: Andres Moreno-Estrada)

The Polynesians were the greatest explorers of the world. Starting from the vicinity of Taiwan, they sailed across vast stretches of the Pacific, settling—and in some cases, continuing to trade between—astonishingly remote islands from New Zealand to Hawaii. But it’s never been quite clear whether they made the final leap, sailing from Rapa Nui to reach the nearest major land mass: South America.

There are some hints that they have, primarily the presence of South American crops throughout the Pacific. But there has been no clear genetic signature in human populations, and the whole analysis is confused by the redistribution of people and crops after the arrival of European sailors.

Now, a new study finds clear genetic indications that Polynesians and South Americans met—we’ve just been looking at the wrong island—and wrong part of South America—for clear evidence. The researchers also raise a tantalizing prospect: that South Americans were already living on a Polynesian island when the Polynesians got there.

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#anthropology, #genetics, #genomics, #human-evolution, #native-americans, #polynesians, #science

Washington’s COVID-19 outbreak may have begun a month later than we thought

People in protective gear load a stretcher-bound patient into an ambulance.

Enlarge / KIRKLAND, Wash.: A patient is shielded as they are put into an ambulance outside the Life Care Center of Kirkland on March 7, 2020. Several residents have died from COVID-19, and others have tested positive for the novel coronavirus. (credit: Getty | Karen Ducey)

When cases of COVID-19 began popping up in Washington state in late February, researchers were quick to dive into the genetics of the viruses infecting residents. Based on what they knew at the time, they hypothesized that those cases in late February were genetically linked to the very first case found in the state—one in a person who arrived in Washington on January 15 after traveling from Wuhan, China, where the outbreak began. The case was also the first infection identified in the whole of the United States.

If correct, the genetic hypothesis linking the late February cases to that very first case meant that early efforts to contain the pandemic coronavirus—isolating the initial patient, tracing contacts, etc.—had failed spectacularly. It also meant that the virus, SARS-CoV-2, had been cryptically circulating in the state for six weeks. And that would mean that, in addition to those early cases, there were potentially hundreds or thousands of others out there, undetected and possibly spreading the infection further.

The hypothesis played into state officials’ decision to issue some of the country’s earliest social-distancing measures. But now that we know far more about the genetics of circulating SARS-CoV-2 viruses, that hypothesis appears to be wrong.

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#covid-19, #evolution, #genetics, #mutation, #phylogenetics, #public-health, #sars-cov-2, #science, #virology, #virus