Archive for the ‘Genetics’ Category

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

January 13th, 2021
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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Posted in dire wolves, Dogs, evolution, Genetics, Genomics, paleontology, science, wolves | Comments (0)

Looking into the genetics of severe COVID-19

December 17th, 2020
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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Posted in Biology, COVID-19, Genetics, medicine, pandemic, SARS-CoV-2, science | Comments (0)

Cops Are Getting a New Tool For Family-Tree Sleuthing

December 16th, 2020
Verogen’s push into public crime labs with genetic genealogy may help solve more cold cases, but it raises concerns about DNA data collection.

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The Genome of Your Pet Fish Is Extremely Weird

November 8th, 2020
Unlike most domestic animals, the goldfish is purely decorative.

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The weird genomes of domesticated fish

November 6th, 2020
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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Posted in Biology, evolution, fish, Genetics, Genomics, science | Comments (0)

Ancient skull a new window on human migrations, Denisovan meetings

October 29th, 2020
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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Posted in Biology, Denisovans, evolution, Genetics, Genomics, human evolution, science | Comments (0)

New African genomes: Complicated migrations and strong selection

October 28th, 2020
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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Posted in africa, Biology, evolution, Genetics, Genomics, science | Comments (0)

Your ‘Ethnicity Estimate’ Doesn’t Mean What You Think It Does

October 2nd, 2020
DNA testing companies are rolling out algorithm updates, spotlighting the fickleness of ethnicity results, and perhaps reinforcing some troubling beliefs.

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New data indicates that some Polynesians carry Native American DNA

July 8th, 2020
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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Posted in anthropology, Genetics, Genomics, human evolution, Native Americans, Polynesians, science | Comments (0)

Flawed COVID hypothesis may have saved Washington from being NYC

May 29th, 2020
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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Posted in COVID-19, evolution, Genetics, mutation, phylogenetics, public health, SARS-CoV-2, science, virology, virus | Comments (0)