Archive for the ‘Genomics’ 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)

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)

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)

Draft study conclusions on SARS-Cov-2 mutation overstep data, grab headlines

May 6th, 2020
Image of gloved hands arranging blood samples.

Enlarge / YOGYAKARTA, INDONESIA - MAY 06: An Indonesian health official wearing protective suit prepare test kits during a mass rapid test for COVID-19 amid the coronavirus pandemic on May 6, 2020 in Yogyakarta, Indonesia. (credit: Ulet Ifansasti | Getty Images)

When SARS-CoV-2 made the jump into humans late last year, it was remarkably well adapted to spread among us. But that doesn't mean things couldn't get worse, as the virus will undoubtedly pick up new mutations as its population expands, some of which might make it more dangerous to humans. In fact, a draft paper recently posted online claimed to have evidence that a more infectious strain of SARS-CoV-2 had already evolved.

But the evidence for this is far from conclusive, and scientists have been taking both the paper and the associated press coverage to task.

The press coverage

The Los Angeles Times had coverage that was typical of the early response to the draft paper, headlining it "Scientists say a now-dominant strain of the coronavirus appears to be more contagious than original." But, by Tuesday, the coverage had been roundly criticized by scientists, and awareness of the problems with the paper was gradually increasing. This ranged from sites dedicated to health news analysis, as well as general circulation newspapers. Yet, even after these criticisms had been published, new articles were still trumpeting an enhanced infectivity.

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Posted in Biology, COVID-19, epidemiology, Genetics, Genomics, SARS-CoV-2, science | Comments (0)

Researchers find an animal without mitochondria

February 26th, 2020
A cartoon image of mitochondria as green, oblong shapes on a black background.

Enlarge / Mitochondria, previously found in all animals, is now in all animals but one. (credit: NIH)

Eukaryotes are the branch of the tree of life with complex cells, containing a separate compartment for DNA, lots of internal compartments, and mitochondria that use oxygen to provide lots of energy. These features were so successful that we can't find any trace of a eukaryotic ancestor that lacks any of them. It has been suggested that the mitochondria's ability to mobilize energy was an essential ingredient for animal life.

That said, there are a small number of single-celled parasites that seem to have lost this energy-producing function over the course of evolution. They typically still have mitochondria-like compartments, but they've lost their DNA and role in aerobic metabolism. Instead, these compartments are involved in specialized chemical functions like producing hydrogen. But these were typically parasites that lived in oxygen-free environments and were only distantly related to animal life.

But now researchers have identified an animal that is also a parasite that lives in oxygen-poor environments. And it, too, has gotten rid of its mitochondria, being the first-known instance of an animal that lacks them.

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Posted in Biology, Genomics, metabolism, mitochondria, science | Comments (0)

Neanderthals may have interbred with a much older human lineage

February 20th, 2020
Image of a collection of ancient skulls.

Enlarge / OK, which one of you is the father? (credit: picture alliance / Getty Images)

Shortly before the publication of the first Neanderthal genome, a number of researchers had seen hints that there might be something strange lurking in the statistics of the human genome. The publication of the genome erased any doubts about these hints and provided a clear identity for the strangeness: a few percent of the bases in European and Asian populations came from our now-extinct relatives.

But what if we didn't have the certainty provided by the Neanderthal genome? That's the situation we find ourselves in now, as several studies have recently identified "ghost lineages"—hints of branches in the human family tree for which we have no DNA sequence but find their imprint on the genomes of populations alive today. The existence of these ghost lineages is based on statistical arguments, so it's very dependent upon statistical methods and underlying assumptions, which are prone to being the subject of disagreement within the community that studies human evolution.

Now, researchers at the University of Utah are arguing that they have evidence of a very old ghost lineage contributing to Neanderthals and Denisovans (and so, indirectly, possibly to us). This is a claim that others in the field will undoubtedly contest, in part because the evidence comes from an analysis that would also revise the dates of many key events in human evolution. But it's interesting to look at in light of how scientists deal with a question that may never be answered by definitive data.

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Posted in anthropology, Biology, denisovan, evolution, Genomics, human evolution, Neanderthal, science | Comments (0)

Ancient African skeletons hint at a “ghost lineage” of humans

January 22nd, 2020
Image of boards surrounding trenches under a rock overhang.

Enlarge / A 1994 photograph of the excavations that yielded the skeletons at Shum Laka. (credit: Pierre de Maret)

Understanding humanity's shared history means understanding what happened in Africa. But figuring out what happened in Africa has been a difficult task. Not every area is well represented in the fossil history, and most African environments aren't conducive to the preservation of ancient DNA. DNA sequencing of modern African populations lags behind other regions, in part because DNA sequencing hardware is more common elsewhere. Finally, as in many other areas, massive migrations within the continent have helped scramble the genetic legacy of the past.

Now, researchers are describing a new window into our collective past: DNA from ancient skeletons found in a rock shelter in West Africa. The skeletons come from a location and time that are both near the origin of the Bantu expansion that spread West African peoples across the entirety of Africa but have little in common with Bantu-speaking populations. Yet, at the same time, they provide hints of what might have happened very early in humanity's history, including the existence of a lineage of archaic humans we've not yet identified.

Right time, right place

The skeletons come from a site called Shum Laka, which is located in a grassland area of Cameroon. For those not up on their African geography, Cameroon is located at the angle where West Africa meets Southern Africa. This is also the region where the Bantu people put together a collection of agricultural and metallurgical technologies that allowed them to sweep across the rest of the continent, leaving their linguistic and genetic mark on many other populations.

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Posted in africa, Biology, evolution, Genetics, Genomics, human evolution, science | Comments (0)

Infectious cancer hasn’t done much over the last 4,000 years

August 3rd, 2019
Image of a dog.

Enlarge / Does this dog look concerned because he realizes he can catch an infectious cancer? (credit: Martin Astley)

Cancer is a horrific disease, with its damage only limited by the fact that it only harms the individual in which it arises—except when it doesn't. In a few extremely rare cases, cancerous cells have evolved the ability to move from host to host, essentially becoming an immortalized parasite. The best known instance of this is in dogs, where a cancer has essentially become a sexually transmitted disease.

While the cancer's been known about for some time, there's been a bit of confusion about its origins. Now, a huge team of researchers has looked at parts of the genome gathered from hundreds of dogs from around the globe, and they've reconstructed the cancer's history and evolution. In the process, the team found that it's not actually doing much evolving anymore.

Dogs can catch cancer while having sex

It's hard to know what to call this thing. Cancer? Parasite? Disease? To an extent, its formal name covers things nicely: canine transmissible venereal tumor, or CTV. As the "venereal" implies, dogs transmit CTV during sex. It results in tumor growth, often on the external genitalia. But, unlike the cancer spreading among Tasmanian devils, the immune system quickly suppresses CTV, and the tumors quickly regress. But it does last long enough to spread throughout dog populations. With fewer working dogs and strays, CTV is rare in Europe and North America, but it remains prevalent elsewhere.

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Posted in Biology, cancer, Dogs, evolution, Genetics, Genomics, science | Comments (0)