Archive for the ‘evolution’ 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)

Cretaceous birds were thought to have small bills—except this one

November 29th, 2020
Precise anatomical profile of a prehistoric bird.

Enlarge / Artist's depiction of Falcatakely forsterae. (credit: Mark Witton)

Given the unusual attention granted to turkeys this week, let’s talk dinosaurs. Today’s birds are, of course, descendants of the only branch of the dino tree that made it through the end-Cretaceous mass extinction. In the dinosaurs’ halcyon days, the early birds were a bit different, still retaining teeth and foreclaws among some subtler anatomical differences with their modern descendant. A new fossil find reveals an unexpected bird from that time—one with a whopping-great, toucan-like beak.

The fossil, named Falcatakely forsterae, comes from late Cretaceous rocks in Madagascar. Many of the early bird fossils we've discovered so far come from older, early-Cretaceous rocks in China, with the timeframe between then and the end-Cretaceous extinction more of a question mark. The new fossil is a nicely preserved head of a crow-sized bird with a strikingly long, tall, and narrow beak.

The early Chinese bird fossils don’t show much diversity in beak shape. That’s a big contrast with modern birds, which have a wild variety of beak shapes befitting their many different ecological niches. Pelicans, woodpeckers, and parrots have very different diets that require a beak adapted to the job. It had been thought that enlarged beaks may not have been possible until some anatomical shifting in the parts of the skull took place, meaning that the early birds were simply limited. But the new find shows that wasn’t entirely true. This species could have inhabited an ecological niche that was empty after the extinction—until a more modern bird drifted back into it much later.

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Posted in birds, evolution, fossils, science | 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)

How the geometry of ancient habitats may have influenced human brain evolution

July 20th, 2020

Hunting in savanna-like landscapes may have helped give rise to planning circuits in the brain. Rife with obstacles and occlusions, terrestrial environments gave prey spaces to hide and predators cover for sneak attacks.

There's a pivotal scene in the 2012 film The Hobbit: An Unexpected Journey when Gandalf, Bilbo Baggins, and a company of dwarves are chased by orcs through a classic New Zealand landscape. For Northwestern University neuroscientist and engineer Malcolm MacIver, the scene is an excellent example of the kind of patchy landscape—dotted with trees, bushes, boxers, and rolling knolls—that may have shaped the evolution of higher intelligence in humans, compared to their aquatic ancestors. Specifically, it falls within a "Goldilocks zone"—not too sparse, and not too dense—that favors strategic thinking and planning ahead, leading to the development of "planning" circuitry in the human brain, according to MacIver's most recent paper, published in Nature Communications.

This latest paper builds on earlier research. Back in 2017, MacIver and several colleagues published a paper advancing an unusual hypothesis: those ancient creatures who first crawled out of the water onto land may have done so because they figured out there was an "informational benefit" from seeing through air, as opposed to water. Eyes can see much farther in air, and that increased visual range could lead them to food sources near the shore. MacIver and his primary co-author, paleontologist Lars Schmitz of the Claremont Colleges, argued that this in turn drove the evolutionary selection of rudimentary limbs, enabling the first animals to move from the water onto land.

That hypothesis grew out of his research on the black ghost knifefish of South America, which is a nocturnal hunter that generates electrical currents in the water to sense its environment. After building a robotic version of the knifefish, with its own electrosensory system, he found that the volume of space in which it could detect prey (in this case, water fleas) was about the same as for a fish that relies on vision to hunt water fleas. The critical factor turned out to be that water absorbs and scatters light, limiting how far that light can travel: typically 10 centimeters to 2 meters, compared to the 25 to 100 kilometers light can travel in air.

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Posted in Biology, computational biology, computer simulation, evolution, neurobiology, science | Comments (0)

SARS-CoV-2 looks like a hybrid of viruses from two different species

June 1st, 2020
Image of a person holding a small bat.

Enlarge / Researchers examine a bat as part of their search for dangerous animal pathogens in the Global Viral Forecasting Initiative Lab in Yaounde, Cameroon. (credit: Brent Stirton/Getty Images)

One of the longest-running questions about this pandemic is a simple one: where did it come from? How did a virus that had seemingly never infected a human before make a sudden appearance in our species, equipped with what it needed to sweep from China through the globe in a matter of months?

Analysis of the virus' genome was ambiguous. Some analyses placed its origin within the local bat population. Others highlighted similarities to pangolins, which might have been brought to the area by the wildlife trade. Less evidence-based ideas included an escape from a research lab or a misplaced bioweapon. Now, a US-based research team has done a detailed analysis of a large collection of viral genomes, and it finds that evolution pieced together the virus from multiple parts—most from bats, but with a key contribution from pangolins.

Recombination

How do pieces of virus from different species end up being mashed together? The underlying biology is a uniquely viral twist on a common biological process: recombination.

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Posted in Biology, coronavirus, evolution, medicine, SARS-CoV-2, 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)

There seems to be no pattern to where humans pick up new viruses

April 22nd, 2020
A colorized transmission electron micrograph (TEM) of an Ebola virus virion.

Enlarge / A colorized transmission electron micrograph (TEM) of an Ebola virus virion. (credit: CDC)

A virus that normally infects animals makes the jump to humans, whose immune systems have never seen it before. It suddenly sweeps across the globe, leaving death and chaos in its wake. We're living with that reality now and have gone through it previously with HIV, SARS, MERS, Ebola, Hanta, and various flu viruses that have threatened humanity in just the past few decades.

While there are many organizations that try to stay on top of threats of emerging diseases, it would be helpful if we could identify major sources of potential threats. If, for example, we knew that certain species were more prone to carrying viruses that could make the jump to humans, we could potentially survey the viruses found in those species, identify major threats, and potentially even develop therapies or vaccines in advance.

But a study published recently in PNAS suggests there's no real pattern to where humans are picking up new viruses. Instead, groups with lots of species tend to have lots of viral species, and those make the jump to humans largely in proportion to the number of species.

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Posted in Biology, evolution, Health, phylogeny, risk, science, viruses, zoonotic | 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)