Great White Sharks have Races?

ScienceAlert, The DNA of Great White Sharks Defies Explanation. Here's Why.

An animal's genome can be deeply revealing, but ever since researchers started decoding
great white shark (Carcharodon carcharias) DNA more than 20 years ago, their discoveries have raised more questions than answers. In 2024, a study confirmed that, contrary to common thought, this fierce ocean predator does not belong to a single global species. Instead, there appear to be three distinct groups, all descended from a common population that lived 10,000 years ago before the last ice age reduced their numbers. One of the modern groups is in the north Pacific, one in the southern Pacific and Indian Ocean, and one in the north Atlantic and Mediterranean.

No matter how researchers try to explain those groups using evolutionary simulations, they continue to hit dead end after dead end."The honest scientific answer is we have no idea," says study senior author Gavin Naylor, director of the Florida Program for Shark Research at the Florida Museum of Natural History.

Just because they have slightly different genetics doesn't make them separate species. In most animals we would call these subspecies (at best), in humans, races. Fully capable of intermingling, but having enough adaptions to local conditions as to be discernable.

While the nuclear DNA of all three shark groups is mostly the same, their mitochondrial DNA is surprisingly distinct. Nuclear DNA is packaged inside the nucleus of a cell (hence the name), but mitochondrial DNA is packaged inside the mitochondria, which churns out energy for the cell. Unlike nuclear DNA, which is inherited from both parents, mitochondrial DNA (mtDNA) is thought to be inherited from the mother in most multicellular animals – sharks included. Because mtDNA can trace a maternal line, conservation biologists have used it for years to identify population boundaries and migration paths.

When it comes to great white sharks, however, that method isn't working. Even after using one of the largest datasets on great white sharks, globally, researchers came up empty-handed. Previously, scientists suspected the changes in mtDNA were due to female sharks returning to their birthplace to reproduce – a concept known as female philopatry. The hypothesis is even supported by recent observational evidence, which suggests that while both male and female sharks travel vast distances, females return home when it's time to mate.

 

When Naylor and colleagues put that idea to the test, however, it failed to explain the groups of mtDNA. Sequencing the genes of 150 white sharks from around the world, Naylor and his team found no evidence of female philopatry. A small signal would be expected in nuclear DNA if females were only breeding with certain populations. "But that wasn't reflected in the nuclear data at all," says Naylor.

Even when the team ran an evolutionary simulation, showing how sharks might have split off into three groups since their last shared ancestor, the female philopatry hypothesis didn't stand. "I came up with the idea that sex ratios might be different – that just a few females were contributing to the populations from one generation to the next," explains Naylor. That also failed to explain the genetic differences. So did random genetic changes that accumulate over time, called genetic drift.

If the graphic is accurate, the splits between the group happened between 130,000 and 150,000 years ago. 130,000 years ago, the world was near the height of the Eemian Warm period, the previous warm period to our own Holocene. The world was warm, perhaps a bit warmer than our own, but generally similar. White sharks could spread around the globe again. Did the last cold period isolate sharks into three different areas, and encourage the divergence?

The Wombat has Rule 5 Sunday: The Last Champion of Cracker Barrel up at the Other McCain.

Now, About Those "Dire Wolves"

One of Colossal Biosciences’ dire wolves, possibly “Khaleesi.”

There have been lot of articles on the recent announcement that Colossal BioSciences has recreated the long extinct Dire Wolf. One at Reason, Colossal Biosciences Resurrects Long-Extinct Dire Wolf

Dire wolves went extinct around 12,000 years ago, at the end of the last ice age. Weighing around 150 pounds, they were about twice the size of today's gray wolves. Dire wolves roamed both North and South America, preying on ancient horses, camels, sloths, and bison.

Colossal Biosciences, the private company aiming to bring back from extinction the woolly mammoth, announced today that it had produced three dire wolf pups using genetic editing and cloning. The researchers at the company extracted and sequenced the genomes of dire wolves from a 13,000-year-old tooth from Ohio and a 72,000-year-old skull from Idaho. The researchers then made 15 key edits in gray wolf genomes to more closely match the genomes of dire wolves. The nuclei of the edited cells were then inserted into the enucleated dog eggs that were installed in the wombs of surrogate mother dogs. The result was the birth of four dire wolf pups (one died 10 days after birth).

The two six-month-old male pups are named Romulus and Remus, after the founders of Rome who were raised by wolves. The two-month-old female is Khaleesi, a title from Game of Thrones. The new dire wolves have thick white coat and are bigger than gray wolves, with more powerful shoulders, wider heads, larger teeth and jaws, and more muscular legs.

Currently, the wolves are living on a private 2,000-acre facility at an undisclosed location in the northern United States. Some native nations have expressed interest in eventually providing land where dire wolves can once again roam freely.

Colossal Biosciences continues its work to bring woolly mammoths, dodos, and the Tasmanian wolves back from extinction.

Don't get me wrong, this is a major achievement in genetic manipulation, but it is absolutely not the recreation of the infamous dire wolves of the American Ice Ages. Dire wolves, contrary to common opinions, were not just large wolves, they were a totally different branch of the canine family, and a handful of gene edits are not going to change one species into another. What they have produced are GMO wolves, bigger than the original. Wikipedia actually has a pretty thorough (and likely fairly accurate, as the topic in not political and noncontroversial) article on Dire Wolves (there were more than one species), and they actually overlapped in size with the largest American wolves.

All of which reminds me of one of my favorite Grateful Dead songs. 

The Wombat has Rule 5 Sunday: Fresh From The Shower up and garnering clicks at The Other McCain on time and under budget.

Bring Back the Mammoth!

Nathan Stone at Da Fed says Scientists Resurrecting The Woolly Mammoth Are Crazy, Not ‘Cool’. I disagree!

To paraphrase Jeff Goldblum in “Jurassic Park,” just because you can do something doesn’t mean you should — even if that something is “cool.”

Ben Lamm and Eriona Hysolli recently took to Newsweek to announce that they and their team at Colossal Biosciences are bringing the woolly mammoth back to life. This is not a pie-in-the-sky pseudo-sci fi dream that might happen at some undefined future date. “Our first mammoth calves will be born in 2028,” they declare.

The plan is to recreate the genome (the complete set of genes or genetic material of a cell or organism) of the woolly mammoth from preserved mammoth remains. This will be achieved through DNA editing, synthesis technologies, and AI, which will “help us with all the computational analysis of ancient genomes, assembly, comparative genomics, and recommendation systems on what types of tools to use.” These recreated genetic packages will then be implanted into the harvested egg of an Asian elephant (the closest living relation of the mammoth) and — voila! — a baby mammoth (or “a cold-resistant elephant” as Colossal Biosciences’ website says.)

Ask why, exactly, we need to bring mammoths back to life, and the answers become numerous and hideously predictable. Colossal Biosciences’ website lists 10 “core goals” for resurrecting the species that can be boiled down to climate change and saving modern elephants from extinction. Both reasons are bogus.

To take the easiest one — preserving elephants — first, the obvious question is: How will elephants be saved with the reintroduction of mammoths? The Asian elephant’s habitat is India and Southeast Asia. The African forest elephant and the African savannah elephant both live exactly where their names suggest. Making a “cold-resistant elephant” won’t do anything for them.

Lamm and Hysolli give something of an answer when they say that their work could be used to combat elephant endotheliotropic herpesviruses (EEHV), which kill up to 20 percent of elephant calves every year. So why not just direct all of their technology to combat that very concrete threat?

Lamm and Hysolli claim that “there’s no big market from a financing perspective, so not enough technology and resources have gone into that.” At a time when people are literally vowing to not have children to “save the planet,” there’s no market to eradicate an elephant-killing virus, even though elephants are a keystone species? And the elephant in the corner is that Colossal Biosciences already has the technology and equipment. Even if it lost half of its finances (Colossal has an annual revenue of $35.1 million and a total funding of $225 million), there should still be some resources to fight the problem.

 

The arguments about climate change are just as unconvincing. There are the usual, low-hanging objections: If man is the primary causer of climate change, how will bringing mammoths back to life solve the problem? If bringing mammoths back to life is the solution, why does Bill Gates want to dim the sun? Since scientists just now discovered that trees were messing with their climate models, how can we be sure that bringing back an extinct species will actually “fight climate change”?

Then there are more serious problems. It’s a fact that the climate has changed since the last woolly mammoths died 4,000 years ago. This means that if a woolly mammoth were stitched together, brought to life, and plopped into the wilderness, the cold ecosystems would not be the same.

Furthermore, there is the problem of the phenotypes. A phenotype is a set of observable characteristics of an organism that come from the interaction of the organism’s genetic makeup and its environment. Lamm and Hysolli are clear that their genetic engineering must get the phenotypes of their mammoths correct. “We must also be sure the genetic engineering is producing the phenotypes we need to recreate the mammoth and its famous traits,” they say.

But since modern man has never seen a woolly mammoth, how can anyone be sure that the genetic engineering is producing authentic mammoth phenotypes? And if that can’t be guaranteed, how do we know that these assembly-lined lumps of carbon will actually diversify and strengthen the ecosystems they are put into?

The one excuse Lamm and Hysolli give that rings true is that “outside of the benefits to the planet, it’s also just a cool, fun, and inspiring thing to be doing.” Those words become more chilling when you realize that the woolly mammoth is not the only species slated for resurrection. True, most of them are benign. Passenger pigeons and dodos and Carolina parakeets are not exactly going to be threats. But saber-toothed tigers? Cave bears? These animals have been extinct for so many thousands of years and were such ferocious predators that it is doubtful they would have any intrinsic fear of man, similar to polar bears today.

What’s more, what other extinct animals will just be “cool” and “fun” to resurrect? The list will expand as more remains with preserved DNA are found and AI and genetic engineering procedures become more fine-tuned. But we don’t even have to be that melodramatic about it. What sort of diseases will these things bring back with them? What diseases will mutate to infect these new species, and how will these mutations affect humans? How will these newly resurrected species interact with today’s species? How many species will be driven to extinction as resurrected animals fight them for space and resources?

Nope. Don't care. Humans and Mammoths coexisted for hundreds of thousands of years until about 20,000 BC. Then something happened, and it's still not clear what. Did humans become such efficient hunters that they succeeded in eliminating the Mammoth? Possible, but then why did the Mammoth's relatives, the Indian and African Elephants survive? Climate change? Maybe , but they survived multiple excursions and recessions of glacial ice, only to succumb as the climate warmed at the end of the last one? Seems awfully inconvenient.

Bring them back, and create a reservation for them in Alaska, and bribe Canada and Russia to do likewise. Although, I do like the idea of housing a healthy population of them in Central Park, which would have been within their native range.

The Wombat has Rule 5 Sunday: Country Girls ready for your digital pleasure at The Other McCain.

But How Did They Taste?

Live Science, Humans were in South America at least 25,000 years ago, giant sloth bone pendants reveal

The date that humans arrived in South America has been pushed back to at least 25,000 years ago, based on an unlikely source: bones from an extinct giant ground sloth that were crafted into pendants by ancient people.

Discovered in the Santa Elina rock shelter in central Brazil, three sloth osteoderms — bony deposits that form a kind of protective armor over the skin of animals such as armadillos — found near stone tools sported tiny holes that only humans could have made.

The finding is among the earliest evidence for humans in the Americas, according to a paper published Wednesday (July 12) in the journal Proceedings of the Royal Society B.

The Santa Elina rock shelter, located in the Mato Grosso state in central Brazil, has been studied by archaeologists since 1985. Previous research at the site noted the presence of more than 1,000 individual figures and signs drawn on the walls, hundreds of stone tool artifacts, and thousands of sloth osteoderms, with three of the osteoderms showing evidence of human-created drill holes.

Ground Sloth osteoderm with drill hole

The newly published study documents these sloth osteoderms in exquisite detail to show that it is extremely unlikely that the holes in the bones were made naturally, with the implication that these bones push back the date humans settled in Brazil to 25,000 to 27,000 years ago. These dates are significant because of the growing — but still controversial — evidence for very early human occupation in South America, such as a date of 22,000 years ago for the Toca da Tira Peia rock shelter in eastern Brazil.

Using a combination of microscopic and macroscopic visualization techniques, the team discovered that the osteoderms, and even their tiny holes, had been polished, and noted traces of stone tool incisions and scraping marks on the artifacts. Animal-made bite marks on all three osteoderms led them to exclude rodents as the creators of the holes.

"These observations show that these three osteoderms were modified by humans into artefacts, probably personal ornaments," the researchers wrote in their paper.

In an email to Live Science, study co-author Mírian Pacheco, a lecturer in paleontology at the Federal University of São Carlos, Brazil, noted that "it is virtually impossible to define the real meaning these artifacts had for the occupants of Santa Elina." However, the shape and large number of osteoderms "may have influenced the making of a specific type of artifact such as a pendant," she said.

The presence of human-modified sloth bones in association with stone tools from geological layers that date to 25,000 to 27,000 years ago is strong evidence that people arrived in South America far earlier than previously assumed.

"Our evidence reinforces the interpretation that our colleagues working on Santa Elina have been talking about for 30 years," Thaís Pansani, a paleontologist at the Federal University of São Carlos in Brazil, said in an email to Live Science — namely, that "humans were in Central Brazil at least 27,000 years ago."

The Clovis First Hypothesis is well and truly dead. Some of the 1st ice age humans who ventured into Americas came from China, DNA study suggests. Study suggests a migration of people from China to North America from 26 to 19 thousand years ago. If this is correct, they must have rushed right down to Brazil to get in on the Giant Sloth action.

The Wombat has Rule 5 Sunday: Communication Failure up at The Other McCain on time and under budget.

Worm Poop Tells a New Climate Story

Earthworm Calcite Granules

WUWT, of course, Ice Age Temperatures and Precipitation Reconstructed from Earthworm Granules

A new method for determination of past climate data on land applied comparatively for the first time / Ice Age summers in Central Europe were at times warmer than previously known

Scientists from an international research project led by Johannes Gutenberg University Mainz (JGU) have applied a new method to reconstruct past climate. As they report in the current issue of Communications Earth & Environment, they have determined temperatures and precipitation during the last Ice Age, which peaked about 25,000 years ago, by analyzing earthworm granules. “The new method was discovered at Université Paris 1 Panthéon-Sorbonne and further developed at the Max Planck Institute for Chemistry,” said Dr. Peter Fischer of JGU’s Institute of Geography, who was the lead investigator of the TerraClime project funded by the German Research Foundation (DFG) in which the study is embedded. “In cooperation with other scientists, including researchers from the University of Lausanne and Römisch-Germanisches Zentralmuseum, we used the method to reconstruct the climate at Schwalbenberg near Remagen and Nußloch near Heidelberg.” The two sites form well-developed last-glacial dust deposits. The so-called loess contains sequences dating from 45,000 to 22,000 years before present, in which the earthworm granules with up to about only 2.5 millimeters in size can be found throughout. These calcitic granules, technically known as Earthworm Calcite Granules (ECGs), are secreted daily by earthworms. Using the so-called radiocarbon method, which is based on the decay of the naturally occurring radioactive carbon isotope (14C), researchers can precisely determine their age. Additionally, by analyzing the ratios of stable oxygen and carbon isotopes in the ECGs, it is then possible to reconstruct how warm or how humid it was at the time of their formation.

“Analysis of the data obtained from the ECGs shows that from 45,000 to 22,000 years before present it was much drier in Central Europe than it is today, with up to 70 percent less humidity,” said Dr. Charlotte Prud’homme from the University of Lausanne, the study’s lead author. “This allows us for the first time to quantify previous findings about this period.” The novelty in these investigations on ECGs is that summer temperatures at the time were significantly higher than previously thought. “Although summers during the cold maximum of the last glacial were about four to eleven degrees Celsius colder than today, they were only one to four degrees below the values of short milder climatic phases that occurred during the last glacial,” explained Fischer. “Given these summer temperatures, we cannot exclude that Ice Age human populations may have made a seasonal living in Central Europe during the cold maximum, at a time for which it is generally assumed that humans could not survive here,” added Dr. Olaf Jöris of Römisch-Germanisches-Zentralmuseum, who was also involved in the study.

Heidi Klum dressed as an earthworm

OK, that's something I've never heard of before, the ECGs.  Earthworms churn out calcite crystals

“Darwin observed that the crystals formed, but no one has looked closely at their mineralogical composition before,” says Mark Hodson, a geochemist at the University of Reading in England and co-author of a new study published in Geology. “We found the crystals are composed of finely zoned calcite wrapped around a central grain of quartz.”

Hodson and colleagues analyzed scanning-electron-microscope images and found that the calcite starts out in the worm as amorphous calcium carbonate and is then converted into crystalline calcium carbonate, or calcite, before it is excreted. “Amorphous calcium carbonate is thermodynamically unstable,” Hodson says. “So it’s not clear if the earthworm is intentionally converting the amorphous stuff to calcite or whether it’s just thermodynamics taking its toll. It all ties back into why this occurs in the first place, which we don’t yet know.”

“There are a number of theories,” Hodson says. “But each has proved unsatisfactory in one way or another.” Earthworms may use the calcium carbonate to regulate the pH or carbon dioxide levels in their intestines, or perhaps they inadvertently ingest large quantities of calcium carbonate as they move through the soil and the crystals are the most efficient way of getting rid of excess calcium, which can be toxic in high concentrations, he says.

What is known is that calcite granules are produced by most species of earthworms in many different soils. Laboratory studies have shown that an individual worm can produce 2.2 milligrams of calcite per day, or as many as 30,000 granules per year. And soil studies have recorded as much as 56 kilograms of earthworm-produced calcite per hectare of soil. “These worms produce a tremendous amount of calcite. It’s a wonder we’re not knee deep in the stuff,” says Matt Canti, a geoarchaeologist with the English Heritage Commission in England, who has investigated the possibility of using earthworm-derived calcite crystals to radiocarbon date ancient soils. Such techniques are possible, he says, but difficult and very expensive.

So, you get a lot of calcium from eating dirt, and you there's lots of CO2 in most soil, so yes, it make sense to help them to get together and get out of your system. Makes sense. It might even be true. 

Winter is Coming, Maybe

I was first introduced to the Milankovitch theory regarding the timing of glaciations during the Pleistocene back in graduate school in Geological Oceanography, where we were assigned to read the original Milankovitch papers and discuss them in class. It seems clear that issues Milankovitch proposed to be involved in the initiation and end of glacial periods, long term variations in Earth's orbit, precession, obliquity, eccentricity are important, the time scales involved are just too close to be coincidental, but the harder on looks, the less an actual answer seems clear. The problem:

It appears the Earth's climate has been on a wildly variable and generally downward (colder) trend for at least the past 5 million years. Also, the cycle appears to have been approximately 41,000 year during the early period, and then switched to a 100,000 cycle about a million years ago. The Milankovitch theory does not predict the overall decline or the switch from the 41k to the 100k cycle. Lots of people have tried, but a complete explanation continues to elude us. An article at WUWT takes another try at it, and as a bonus, has possible prediction for the end of the current interglacial, What Is Milankovitch Theory, What Is It Not, And What Can We Learn from It?. He believes that obliquity and precession combine to a beat frequency which drives the climate:

Maybe, maybe not. But what was interesting to me was that he had an interesting prediction: 

From the model, the Holocene interglacial will likely terminate within the next 500 years. It’s a low-resolution estimate because the insolation minimum the earth is currently in is very shallow. A very similar interglacial occurred about 787,000 years ago, which terminated in a similar way.

The end of the Holocene interglacial, during which mankind went from a hunter-gatherer living on the bare edge of extinction to a world spanning  civilizations would (will?) have dire consequences for humanity. If we are extremely lucky, our inadvertent interventions in climate may, or may already averted the decline into another glaciation, no thanks to Greta Thunberg. 

Another interesting paper to keep in mind while reading this, The inter-glacial cycle is not a 100,000-year cycle, it is a shorter cycle with missing beats

Abstract:

The "100,000-year problem" refers to an apparent unexplained change in the frequency of inter-glacial periods which occurred about a million years ago. Before that, inter-glacial periods seemed to occur about every 41,000 years, in line with the obliquity Milankovich cycle. But after that, they seemed to occur about every 100,000 years, in line with the orbital inclination Milankovich cycle. Examination of the data shows that there never was a 41,000-year cycle, and that there is no 100,000-year cycle, but that the most influential cycle is the approx 21,000-year precession cycle which is the major factor in the cycles of insolation at higher latitudes. Insolation at 65N is generally regarded as the most significant of these. Inspection of the data shows that every glacial termination (start of an inter-glacial period) began at a time when insolation at 65N increased from a low point in its cycle. That not every such cycle triggered a new inter-glacial period underlines the chaotic non-linear nature of Earth's climate. Until about a million years ago, this cycle occasionally "missed a beat", making the inter-glacial frequency average about 41,000 years. After that, the cycle started missing more "beats", making the inter-glacial frequency average about 100,000 years. There never was an actual 41,000-year or 100,000-year inter-glacial cycle.

It looks to me like the former paper helps to explain the mechanism behind the second. 

Early Americans Waited Out the Last Ice Age in Mexico

Chiquihuite Cave

WUWT Humans inhabited North America in the depths of the last Ice Age, but didn’t thrive until the climate warmed

Lorena Becerra-Valdivia, UNSW

Chiquihuite Cave is an archaeological site more than 2,740 metres above sea level in Zacatecas, Mexico. Ciprian Ardelean of the University of Zacatecas has been leading excavations of the site for more than seven years. Nearly 2,000 stone tools and pieces created through their manufacture have been found.

The tools belongs to a type of material culture never before seen in the Americas, with no evident similarities to any other cultural complexes. Importantly, more than 200 specimens were found below an archaeological layer that corresponds to the peak of the last Ice Age. (Archaeologists call this peak the Last Glacial Maximum.)

During this time, between 26,000 and 19,000 years ago, ice sheets were at their greatest extent. Evidence from Chiquihuite Cave, therefore, strongly suggests that humans were present in North America well before Clovis.

A stone tool found below the Last Glacial Maximum layer

Given the significance of the discovery, myself and a team of international researchers joined in the interdisciplinary study of Chiquihuite Cave. Some of us had the opportunity to visit the site following a four-hour long journey by foot, and see the evidence at first hand. Our aims were to reconstruct the environment humans lived in and define exactly when they occupied the site.

My own research at Chiquihuite Cave focused on the latter. I helped to build a chronology of more than 50 radiocarbon and optical dates.

Combined with the archaeological evidence, the results showed humans inhabited Chiquihuite as early as 33,000 years ago, until the cave was sealed off at the end of the Pleistocene period (around 12,000 years ago).

Clovis first has been dead for quite a while, but this is a pretty amazing finding, more or less continuous occupation of the same site by a succession of  pre-Clovis people and cultures starting at least 33,000 ago.

It's pretty clear that while humans may have reached the Western Hemisphere either early in the last glaciation, or in the Eemian Warm period, they didn't really make much population growth or environmental impact until the planet warmed again, and another wave of population came from Eurasia.

In a second paper, I explore the wider pattern of human occupation across North America and Beringia (the ancient land bridge connecting America to Asia). This involved analysing hundreds of dates obtained from 42 archaeological sites in North America and Beringia, including Chiquihuite Cave, using a statistical tool called Bayesian age modelling.

The analysis showed there were humans in North America before, during and immediately after the peak of the last Ice Age. However, it was not until much later that populations expanded significantly across the continent.

This occurred during a period of climate warming at the end of the Ice Age called Greenland Interstadial 1. The warming began suddenly with a pulse of increased global temperature around 14,700 years ago.

We also observed that the three major stone tool traditions in the wider region started around the same time. This coincides with an increase in archaeological sites and radiocarbon dates from those sites, as well as genetic data pointing to marked population growth.