New African genomes: Complicated migrations and strong selection
We finally have more African genomes, revealing over 3 million new variations.

JOHN TIMMER - 10/28/2020

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.

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).

That said, the study still picked up more than approximately 3.4 million genetic variants that hadn't been described previously. These are single sites in the genome with a base (A, T, C, or G) that hadn't been seen there in other populations.

To put that in perspective, most of us carry lots of genetic variations. In the typical individual in the new study, these newly identified variants only account for about 2-5 percent of the total variations in their genomes—all the rest had been seen previously. In addition, a large majority of them (88 percent) were only seen in a single individual and so may only represent a variation that had occurred through a mutation within the last few generations. So, while there might be some new variants here that will help us untangle Africa's population history, most of what we've found is the sort of thing you'd expect from looking at random humans elsewhere.

If we were getting close to having a good grip on the genetic variation present in Africa, then we'd expect to see the number of new variants tail off as we add new genome sequences to the analysis, as each new one would add fewer and fewer undiscovered ones. So, the researchers analyzed the genomes one at a time and found no evidence of this happening—we're still nowhere close to fully cataloging human diversity. They do find, however, that looking beyond West African populations would give us the biggest increase in previously undescribed variation.

Population churn

To try to identify what the genomes tell us about population histories, the researchers turned to principal component analysis, which identifies the major sources of difference in a large set of data. The largest difference separated speakers of Niger-Congo languages from all the rest. The second-largest difference mirrored the geographic distance between Niger-Congo speakers in West Africa and those in Southern Africa. This is likely a product of the Bantu migration, which spread a mix of technology, language, and DNA from a source in West-Central Africa, bringing them to the rest of the continent.

The researchers use this data to argue that the Bantu Migration passed through Zambia on its way to Southern and East Africa, but their data includes a lot of people from Zambia, so it's not clear whether that might have biased their results.


FURTHER READING How the Bantu people surged across two-thirds of Africa

The work also identified a number of ethnolinguistic groups that might be worth looking at in more detail. One looked genetically like East Africans but was located in West Africa. Two other populations were clearly associated with known language groups but weren't part of the tight genetic cluster that most other speakers of that language fell within.

Nearly every population on Earth is a mixture of many sources—Native Americans are largely a mixture of East Asian and ancient Siberian populations, for example. Africans are certainly no different, but the fact that they've stayed on the same continent for so long increases the complexity of these interactions. The new data really drives that home when analyzed for the origins of different segments of DNA.

People from the far west of Africa have a large majority of their DNA from what you could call a West African source. But as you move east into Central Africa, there's an increasing amount of what you'd have to call West-Central African DNA, which is then joined and later displaced by Central African and then a smattering of Southern and East African sources. There's a sudden shift to a majority from East African sources as you exit Central Africa moving east, with an increasing contribution from Southern Africa if you turn south a bit.

While geography seems to drive the majority of the differences, in all populations there are contributions from distant areas of the continent. So, while the Bantu migration may have been the largest event in recent African history, it's layered on top of a long history of population interactions.

What’s changing

Most variations in the human genome are completely silent, as they don't affect genes or other functions and so float through populations at random. A few, however, provide evolutionary advantage, and it can be possible to detect the signal of the selection for or against specific variations.

Searching for these signals, the authors found exactly what you'd expect based on past studies of human populations. The strongest pressure on human evolution is disease, and the genes that are subject to the most pressure are involved in immune functions. After disease comes diet, and again, Africans are quite typical, with strong signs of selection on a handful of genes involved with carbohydrate and lipid metabolism. There were some oddball results, however, such as selection for variants of genes involved in DNA repair, kidney disease, and uterine fibroids. Obviously, those will have to be examined in more detail before we can make any sense out of them or see if it's just spurious.

Immune function isn't the only way to handle diseases, as the sickle cell trait's effects on malaria make clear. And, these being African populations, there's evidence of selection for that in some of them. But hemoglobin isn't the only route to malaria resistance, and some populations show evidence of selection for a different gene (G6PD). In some cases, populations that have high frequency of sickle cell trait have ended up right next to others that have high levels of G6PD selection, likely as a result of migration.

Beyond the cases where there are clear signals of selection, there are a number of cases where genes have been disabled by mutation but are still present in multiple individuals in this data set. That has been something that has been seen a number of times before and has been met with a bit of confusion. In many cases, we have no idea what the gene does and so can't tell whether we should be surprised by its loss or not. In others, the gene actually appears to be essential based on studies of its loss in mice. Over time, we'll probably get closer to understanding what's going on, but each of these genes will have to be studied individually in order to do so. 

The start of a story

While this represents a major effort toward understanding humanity's shared genetic history, it's more of a prologue than a complete story. We've gotten closer to capturing the full diversity of African populations but clearly aren't done yet. And we've been able to piece together more information on some of the migrations within Africa that we know about but aren't at the point where we can infer anything about the migrations we don't know about.

That latter point is rather critical. At this stage, we can examine a piece of DNA and determine that it probably originated in, say, a West African population. But we can't say much about how it ended up in West Africa in the first place. There's evidence that, much as Eurasian populations picked up archaic DNA from Neanderthals, African populations picked up DNA from earlier branches from the human family tree. But, without fossil or DNA-based descriptions of those branches, they remain "ghost lineages" that are invisible to us. It's possible that some small percentage of the sequences we currently assign to an African region belong to one of these branches, and we don't have the tools to identify it yet.

Nature, 2020. DOI: 10.1038/s41586-020-2859-7 (About DOIs).

JOHN TIMMER became Ars Technica's science editor in 2007 after spending 15 years doing biology research at places like Berkeley and Cornell.

Search for Irish chieftain’s skeleton continues in Spain more than 400 years after his death

The hunt for the skeleton of Red Hugh O’Donnell continues

By James Rogers | Fox News

Archaeologists in Spain are continuing their search for the missing bones of “Red Hugh,” a 16th-century Irish chieftain who is said to be buried in the city of Valladolid.

Red Hugh O’Donnell fought English rule in Ireland and died in exile. He was in Valladolid, then the capital of Spain, when he died in 1602.

An excavation began earlier this year to uncover the so-called Chapel of Wonders where O’Donnell was buried. The chapel was once part of a Franciscan monastery that was leveled in the 19th century.

The dig attracted attention when skeletons were discovered at the site, but analysis has revealed they pre-date the century when Red Hugh died, according to Carlos Burgos, a spokesman for the Hispano-Irish Association, which is conducting the excavation. “We are going to try under the bank building that is above the chapel,” he told Fox News on Friday.

THE HUNT FOR RED HUGH: ARCHAEOLOGISTS IN SPAIN SEARCH FOR 16TH-CENTURY IRISH CHIEFTAIN'S BONES

The chapel was also once the burial place of Christopher Columbus.

Picture shows human skeletons found in an archaeological excavation carried out by the Hispano-Irish Association in a ruined chapel in Valladolid, that expects to identify the remains of the Irish rebel lord Red Hugh O'Donnell, on May 28, 2020. (Photo by CESAR MANSO/AFP via Getty Images)

Valladolid mayor Oscar Puente has been documenting the search for Red Hugh on his Twitter account. Earlier this year, the excavation site was also visited by the Irish ambassador to Spain, Síle Maguire.

Born into a noble family, Red Hugh O’Donnell is known as ‘Red Hugh’ as a result of his Irish family name “Ruadh O’Domnhaill” – “Ruadh” is the Irish word for red.

A rebel leader, O’Donnell fought in the Nine Years' War against the English in Ireland, which began in 1593. In 1601 after English forces defeated O’Donnell and allied Spanish troops in the battle of Kinsale, he left Ireland, according to the Ask about Ireland website. The nobleman traveled to Spain to request further help from King Philip III, but, nine months later, he was struck down by illness and died, the website explains. He was 30 years of age.

FACIAL RECONSTRUCTION PROVIDES GLIMPSE OF PRIEST WHO DIED 900 YEARS AGO

A vital clue in identifying the rebel leader is that his skeleton will be missing the big toe on each foot, according to the BBC. O’Donnell lost the toes to frostbite while escaping English forces during the winter of 1591, the Irish Times reports.

Friday marked the 448th anniversary of Red Hugh’s birth, an event marked by a joint Irish and Spanish Zoom press conference.

Oscar Puente

@oscar_puente_

La visita de hoy a la excavaciones en la calle Constitución, junto con la Comisión Territorial de Patrimonio, nos ha mostrado los avances y apuntado las posibilidades de seguir progresando con la indagación.

6:17 AM · May 28, 2020

138

37 people are Tweeting about this

Large, Deep Antarctic Ozone Hole in 2020



September 20, 2020

Persistent cold temperatures and strong circumpolar winds supported the formation of a large and deep Antarctic ozone hole in 2020, and it is likely to persist into November, NOAA and NASA scientists reported.

On September 20, 2020, the annual ozone hole reached its peak area at 24.8 million square kilometers (9.6 million square miles), roughly three times the size of the continental United States. Scientists also detected the near-complete elimination of ozone for several weeks in a 6-kilometer (4-mile) high column of the stratosphere near the geographic South Pole.

The map above shows the size and shape of the ozone hole over the South Pole on September 20, the day of its maximum as calculated by the NASA Ozone Watch team. NASA and NOAA monitor the ozone hole via complementary instrumental methods. NASA’s Aura satellite, the NASA-NOAA Suomi NPP satellite, and NOAA’s JPSS NOAA-20 satellite all measure ozone from space. Aura’s Microwave Limb Sounder also estimates levels of ozone-destroying chlorine.

This year brought the 12th-largest ozone hole (by area) in 40 years of satellite records, with the 14th-lowest ozone readings in 33 years of balloon-borne instrumental measurements. However, scientists noted that ongoing declines in the atmospheric concentration of ozone-depleting chemicals (which are controlled by the Montreal Protocol) prevented the hole from being as large as it might have been under the same weather conditions 20 years ago.

“From the year 2000 peak, Antarctic stratosphere chlorine and bromine levels have fallen about 16 percent towards the natural level,” said Paul Newman, an ozone layer expert and the chief Earth scientist at NASA’s Goddard Space Flight Center. “We have a long way to go, but that improvement made a big difference this year. The hole would have been about a million square miles larger if there was still as much chlorine in the stratosphere as there was in 2000.”

This year represented a dramatic turnabout from 2019, when warm temperatures in the stratosphere and a weak polar vortex hampered the formation of polar stratospheric clouds (PSCs). The particles in PSCs activate forms of chlorine and bromine compounds that destroy ozone. Last year’s ozone hole was the smallest since the early 1980s, growing to 16.4 million square kilometers (6.3 million square miles) in early September.

“This clear contrast between last year and this year shows how meteorology affects the size of the ozone hole,” said Susan Strahan, a scientist with NASA Goddard and Universities Space Research Association. “It also complicates detection of long-term trends.”

Atmospheric levels of ozone-depleting substances increased up to the year 2000. Since then, they have slowly declined but remain high enough to produce significant seasonal ozone losses. During recent years with normal weather conditions, the ozone hole has typically grown to a maximum of 20 million square kilometers (8 million square miles).

In addition to the area of the ozone hole, scientists also track the average amount of ozone depletion—how little is left inside the hole. On October 1, 2020, weather balloons launched from NOAA’s South Pole atmospheric observatory recorded a low value of 104 Dobson units of atmospheric ozone. NASA’s Ozone Watch reported a lowest daily value at 94 Dobson Units on October 6. Prior to the emergence of the Antarctic ozone hole in the 1970s, the average amount of ozone above the South Pole in September and October ranged from 250 to 350 Dobson units.

The amount of ozone between 13 to 21 kilometers (8 to 13 miles) in altitude, as measured over the South Pole, has been close to record lows at several points this year. “It’s about as close to zero as we can measure,” said Bryan Johnson, a scientist with NOAA’s Global Monitoring Laboratory. Still, the rate at which ozone declined in September was slower compared with 20 years ago, which is consistent with there being less chlorine in the atmosphere.

NASA Earth Observatory image by Joshua Stevens, using data courtesy of NASA Ozone Watch and GEOS-5 data from the Global Modeling and Assimilation Office at NASA GSFC. Story by Theo Stein, NOAA, and Ellen Gray, NASA Earth Science News Team, with EO Staff.

First drone mission launched to the North Pole analyses global warming

The data collected will be used to understand how warming temperatures are affecting the Arctic

Laura Millan Lombrana

The data collected will be used to understand how warming temperatures are affecting the Arctic
(Bloomberg)



Roberta Pirazzini set out an Arctic expedition to do something no one had ever tried before: fly a drone near the North Pole.

Sensors on the drone would assess sunlight reflected from the ice. This measurement, known as surface albedo, is key to understanding how much solar radiation is absorbed by the Earth and how much is reflected back into the atmosphere. It's one of the scientific puzzles that can help predict how fast sea ice will melt.

But flying a drone over the planet's northernmost reaches is no simple feat. Ms Pirazzini and a colleague, Henna-Reetta Hannula, spent months learning to fly at the Finnish Meteorological Institute, where both are on staff as scientists. Technicians designed and built a sophisticated navigation system capable of handling extreme weather.

The scientists and their drones then joined the largest Arctic expedition in history aboard the Polarstern, an icebreaker carrying dozens of researchers on a year-long mission. The pair had also brought along a smaller practice drone that could fly inside their tiny cabin, the only chance they'd have to keep their skills sharp in the weeks of sailing before finally stepping onto the ice.

Right away, Ms Pirazzini ran into the same problems that have beset Arctic explorers for two centuries: treacherous navigation conditions and technology that buckles in the deep cold.

Drones and helicopters have trouble near the North Pole because global positioning satellites suffer small uncertainties at extreme northern latitudes. This creates mounting confusion for navigation the closer a pilot gets to the North Pole, and Ms Pirazzini's drones would be operating closer than any before.

The navigation nightmare has claimed another drone earlier in the expedition. The drone took off from the ship, went in a completely uncontrolled direction and crashed. Ms Pirazzini was terrified her albedo-measuring drone would fall victim next, and her fears were confirmed as soon as she stepped onto the ice. The navigation system on the main drone wasn't working, meaning she and Ms Hannula would need to manually calculate distances, direction, altitude and wind speed.

“The freezing conditions were our main enemy, not only for the ice in the blade" of the drone's rotors, “but in our fingers,” Ms Pirazzini says, her voice cracking over a satellite phone during the Polarstern's return voyage earlier this month. “You need very delicate, small motions to operate the drone,” she says. “When your hand is freezing you lose sensitivity, your fingers can't control the features anymore.”

Fog would turn into ice around the drone's blades. Wind gusts stronger than eight meters per hour would ground the drone. Still, the two scientists managed to conduct 18 flights over three weeks. Albedo measurements captured by Ms Pirazzini, 49, and Ms Hannula, 33, will now be analyzed as part of multinational effort to understand how warming temperatures are affecting the Arctic-a scientific race against climate change itself.

Earth's northern icecap is heating about three times faster than the rest of the planet, disrupting a fragile ecosystem. Arctic sea ice, which melts during the summer and freezes back in winter months, shrank to the second-lowest level on record in September, the month when ice cover is usually at its lowest. Only in 2012 was Arctic sea ice cover smaller.

Anomalously warm conditions in the Siberian Arctic, which suffered an unprecedented heatwave during the first half of the year, are now making it harder for the ice to reform. Arctic sea ice is currently at the lowest level for this time of the year since satellite monitoring began in 1979-37% below the historical average.

“By this time in 2012 the ice had started to regrow,” says Samantha Burgess, deputy director at Europe's Copernicus Climate Change Service. “It's a little early to tell what implications this will have for the rest of the season but there are likely to be impacts for the marine food web.”

Back in August when Ms Pirazzini's drone flights started, sea ice in the Arctic had dropped to the lowest level on record for that month. These alarmingly low ice levels made it possible for the Polarstern to reach the North Pole from Norway's Fram Strait in just six days. “There were areas of open water everywhere, it was very easy to go there,” Ms Pirazzini says. “That's not nice if you think about the future of the Arctic. It's a very fragile environment that will change without return.”

Measuring albedo becomes more important as the ice shrinks. The white surfaces of Arctic ice reflect solar radiation back into the atmosphere, while the ocean's blue surfaces absorb it. Not all ice is equally reflective, however, and scientists are trying to figure out just how much solar radiation is being absorbed by ice sitting below shallow melt waters that have been spreading as temperatures stay warmer.

While sea-ice area can be monitored by satellites, other measurements that are crucial to understanding the speed of melting can only be obtained closer to the ground. This more granular data is essential to determining other drivers of climate change, such as how heat transfers through ice and into the atmosphere and water.

Traditionally, scientists have taken albedo readings with airplanes and helicopters. But drones are cheaper, can fly under worse weather conditions and below even low clouds. Ms Pirazzini's flights ranged between five and 30 meters over the ice. “Drone technology is making progress every month, every year,” she says. “We are at the infancy of this business, and I believe it will expand very much because these are unique and needed measurements.”

In the Arctic, operating drones far from other scientists sometimes involved risk. Ms Pirazzini and Ms Hannula had to cross a fracture in the ice using a pontoon as a raft. At one point Pirazzini was kneeling on a raft over icy seawater, holding the carefully-wrapped drone, while Ms Hannula helped her moor to safety using a long stick.

The drones at times proved more resilient to the rough Arctic weather than some of the expedition's other flying objects. Two tethered balloons nicknamed Beluga and Miss Piggy would be sent to take cover from hard conditions in bright orange tent known as Balloon Town. “Sometimes Miss Piggy was misbehaving and flying too low," Ms Pirazzini says laughing. “We would need to make sure the drone wasn't in the area.”

The scientific arsenal on the Polarstern included a helicopter and many weather balloons equipped with a radio system that collected and transmitted data on temperature, humidity, wind direction and speed. A total of 1,574 balloons were launched-up eight per day over 12 months-and scientists often decorated them with names and birthday messages for their families.

Hundreds of researchers from 20 countries took turns on the Polarstern for the MOSAiC mission, an acronym for Multidisciplinary drifting Observatory for the Study of Arctic Climate. Led by Germany's Alfred Wegener Institute for Polar and Marine Research, it was the first expedition in modern history to spend a full winter close to the North Pole. The mission, which had a budget of more than 140 million euros (£126.3m ), ended on October 12 after 389 days at sea.

“Climate change will probably force the organization of more expeditions like this one because there will be an urge to do something, to understand the implications,” Ms Pirazzini says. “This expedition has drawn new paths for research. I feel I have the responsibility to make the most out of it.”

Washington Post

Watch more

North pole 'soon to be ice free in summer', scientists say


Largest ever' hole in ozone layer opens over North Pole


Lightning strikes detected within 300 miles of North Pole


Read more
 

Alarm over huge plumes of methane rising from Arctic seabed

  

We need to get smarter about heating our homes this winter

  

Siberia wildfires ‘engulf area larger than Greece’

There’s no place like the perfectly sized home for the mighty mantis shrimp

Mantis shrimp will fight longer and harder, and often win, for burrows of ideal size.

JENNIFER OUELLETTE - 10/29/2020



"Nice burrow you have there. I want it." Patrick Green of the University of Exeter filmed this fight between mantis shrimp.

Size matters to the small-but-mighty mantis shrimp, which show a marked preference for burrows in coral rubble with volumes that closely match their own body size or are just a bit larger—in other words, large enough to accommodate their body, but small enough that they can defend the entrance. But according to a new paper published in the journal Animal Behavior, sometimes a mantis shrimp will compromise. If a burrow is already occupied and is close to the ideal size, or a bit smaller, the mantis shrimp will fight longer and harder for that burrow—and be more likely to win the contest.

As we previously reported, mantis shrimp come in many different varieties: there are some 450 known species. But they can generally be grouped into two types: those that stab their prey with spear-like appendages ("spearers") and those that smash their prey ("smashers") with large, rounded, and hammer-like claws ("raptorial appendages"). Those strikes are so fast—as much as 23 meters per second, or 51mph—and powerful, they often produce cavitation bubbles in the water, creating a shock wave that can serve as a follow-up strike, stunning and sometimes killing the prey. Sometimes a strike can even produce sonoluminescence, whereby the cavitation bubbles produce a brief flash of light as they collapse.

A 2018 study found that the secret to that powerful punch seems to arise not from bulky muscles but from the spring-loaded anatomical structure of the shrimp's arms, akin to a bow and arrow. The shrimp's muscles pull on a saddle-shaped structure in the arm, causing it to bend and store potential energy, which is released with the swinging of the club-like claw. And earlier this year, scientists discovered that, counterintuitively, the mantis shrimp punches at half the speed in air, suggesting that the animal can precisely control its striking behavior, depending on the surrounding medium.
“Resource value assessment”

Patrick Green of the University of Exeter and J.S. Harrison of Duke University—authors of the new paper in Animal Behavior—were interested in exploring what's known as "resource value assessment" in mantis shrimp of the smashing variety (Neogonodactylus bredini). Both male and female mantis shrimp in this species are known to compete over coral rubble burrows, which provide protection from predators and a safe space to mate and brood eggs. If a preferred burrow is already occupied, it can trigger a fight over who gets the burrow. Those competitions typically involve a ritualized exchange of high-force strikes (mantis shrimp SMASH!), with the defending mantis shrimp also using its armored tailplate to block the burrow entrance from intruders.

These sorts of animal competitions are quite common in nature, and animals seem to be able to assess the value of such "contested resources" and adjust their behavior accordingly. Such encounters are typically described in terms of a linear or categorical value assessment, in which, for example, males will fight more aggressively in the presence of females. Similarly, female parasitoid wasps will compete over the most desirable hosts in which to lay their eggs. The larger the host, the more food will be available for the offspring when they hatch, for example. Past studies have suggested that a female's egg load seems to be a contributing factor (or selective force) in how aggressively they fight over a potential host and how likely they are to win such a competition.

Enlarge / An intruder potentially assessing a burrow.
Roy Caldwell

Past studies have shown that mantis shrimp pick burrows whose sizes (volume) mesh well with their own body size (mass), as do hermit crabs. In the case of hermit crabs, there seems to be a tradeoff at play when it comes to resource assessment: dragging around a larger shell requires more energy but offers more protection from predators, while the reverse is true for smaller shells. Green and Harrison suggest that, when it comes to competing for a desired shell, hermit crabs may prefer shells that are the preferred size or slightly larger, while placing less value on shells that are much larger or smaller.

This would be an example of quadratic resource value assessment, in which resources are valued most highly at a certain peak level. That value decreases in either direction from that peak. In other words, there is an optimal sweet spot, or "Goldilocks zone," where an asset is deemed to be "just right" and the animal will adapt its behavior accordingly—e.g., by fighting more aggressively when such a desirable asset is contested. Green and Harrison thought a similar quadratic resource value assessment might also apply to mantis shrimp—namely, that mantis shrimp would place a higher value on burrows with an ideal volume and would be more aggressive, and more likely to win, when fighting for control of such burrows.

To test their hypothesis, the researchers conducted two sets of experiments: "choice experiments," where mantis shrimp could freely choose unoccupied burrows of varying sizes, and "staged contests," where "defending" and "intruding" mantis shrimp were randomly matched in a competition over a preferred burrow. Green and Harrison predicted that their experiments would show that competitors would fight longer and harder and would be more likely to win when their body length closely matched the volume of the contested burrow—and that these factors would decrease the further that match deviated from the ideal, in either direction.

“This study is an example of maximum effort being reserved for something that’s ‘just right.’”

The researchers built mock burrows out of clear plastic tubing with a single opening, wrapped in black vinyl, with a clear area at the top to enable them to observe what was happening inside. The mantis shrimp were collected from burrows in seagrass beds along the Caribbean coast of Panama. The researchers also videotaped the staged contests (a total of 36) and intervened if it seemed like one of the fighting shrimp was in danger of significant injury or death.

They found that, overall, the occupying mantis shrimps successfully defended their burrows from intruders in 69 percent of the fights. But those odds changed dramatically in cases where the intruding mantis shrimp were competing for burrows slightly smaller than their ideal size; intruders won 67 percent of the fights in those circumstances, typically by striking first and striking more often.

"We know that animals can assess a variety of factors, including the size of the opponent and the value of the prize, when deciding whether to fight and how hard to fight," said Green of the results. "In this case, as a smaller burrow is probably occupied by a smaller opponent, it seems mantis shrimps will compromise on the size of the home if it means an easier fight. It might be assumed that animals fight hardest for the biggest assets, but this study is an example of maximum effort being reserved for something that's 'just right.'"

There were some caveats, most notably sample-size constraints. Green and Harrison also acknowledged that the mock burrows were standardized, with set lengths and diameters, unlike naturally occurring burrows, which usually have more variable dimensions. And the smooth tubing is markedly different from the natural burrows formed in rock and rubble.

"Mantis shrimp are adept modifiers of natural burrows, using appendage strikes to widen too-narrow burrows and using rock and sand to fill in too-large burrows," they wrote. "While the individuals we tested could not widen mock burrows by striking, perhaps with more time in which to establish residency, individuals would have filled in larger mock burrows."

DOI: Animal Behavior, 2020. 10.1016/j.anbehav.2020.09.014 (About DOIs).

Listing image by Roy Caldwell

Dogs were domesticated once from a lost population of wolves
Our history with dogs is complicated, according to a study of ancient dog DNA.

KIONA N. SMITH - 10/29/2020


Genomics researcher Anders Bergstrom and his colleagues recently sequenced the genomes of 27 dogs from archaeological sites scattered around Europe and Asia, ranging from 4,000 to 11,000 years old. Those genomes, along with those of modern dogs and wolves, show how dogs have moved around the world with people since their domestication.

All the dogs in the study descended from the same common ancestor, but that original dog population split into at least five branches as it expanded in different directions. As groups of people split apart, migrated, and met other groups, they brought their dogs along. Dog DNA suggests that their population history mirrors the story of human populations, for the most part.

“Understanding the history of dogs teaches us not just about their history, but also about our history,” said Bergstrom, of the Francis Crick Institute, in a statement.

We still don’t know who let the dogs out

We still don’t know exactly when or where dog domestication first happened; it already had a pretty complex history by 11,000 years ago. But it looks like it only happened once. The ancient genomes suggest that dogs all share a common ancestor, which they don’t share with modern wolves. According to Bergstrom and his colleagues, that probably means that dogs all descend from one group of wolves, and that group is now extinct.

Modern gray wolves don’t appear to be very closely related to any of the ancient or modern dogs in the study. That suggests that since domestication set them apart, wolves haven’t contributed much DNA to dog bloodlines.

The oldest dog in the study lived with Mesolithic hunter-gatherers about 10,900 years ago in what is now Sweden. Its DNA suggests that most of its ancestors were from an eastern branch of the dog family tree—the branch that gave rise to Siberian dogs, indigenous North American dogs, and even New Guinea singing dogs and Australian dingoes.

But some of the dog’s ancestry also came from the branch that had followed humans into the Levant and Southwest Asia. Those bits of DNA were probably picked up as souvenirs when the dog’s ancestors met dogs from another population. In other words, by 11,000 years ago, dogs had had time to become a species, divide into distinct populations as they moved apart, and then meet again and exchange DNA.

Have dogs, will travel

Bergstrom and his colleagues wanted to know how dogs’ population history lined up with that of humans. They compared their ancient dog data to what ancient human DNA tells us about how groups of people migrated and interacted during the last 12,000 years. Not too surprisingly, the timing of splits, mergers, and movements mostly matched up. That suggests that, as groups of people migrated, they brought their dogs with them, and the dogs got up to much the same things the humans got up to when they met new neighbors.

Ancient human DNA tells us that early farmers from what is now Turkey moved north and west into Europe around 8,000 years ago, and it took just a few centuries for them to completely replace the populations of hunter-gatherers who were already there.

“It’s not clear how these movements happened—whether by disease, or by violence, or by some kind of biased intermarriage process—but what the genetics shows unambiguously is that these changes did happen, and much more dramatically than any archaeologists expected,” said Reich back in 2018.

And DNA from ancient European dogs tells us that very similar things were happening between the Neolithic newcomers’ dogs and the ones (like the 11,000-year-old Swedish dog mentioned above) that were already there. In general, dogs found at archaeological sites in north and western Europe have more eastern ancestry, and less Levantine ancestry, than dogs found in the south and east—and vice versa.

Some dogs were on a very long leash

Dogs’ and humans’ stories match up, at least in the broad strokes. But Bergstrom and his colleagues found a few points where the story of dogs seemed “decoupled” from ours. Those differences are probably the result of disease, trading, preferences for particular dog types, or people moving to a new place without taking the dogs (which sounds awful, honestly). These “decoupled” population histories can tell us about how dogs fit into ancient human societies.

A few thousand years after the Neolithic takeover of Europe, another group of people swept westward from Central Asia. They probably brought along dogs like the 3,800-year-old animal recovered from an archaeological site on the Russian Steppes.

But while the pastoralists from the steppes added their DNA to the mix that makes up modern European populations, their dogs didn’t seem to mingle much with local dogs. Meanwhile, in China, the reverse happened. Steppe pastoralists expanded eastward, but modern people in east Asia don’t carry much of their DNA. Modern East-Asian dogs, however, get quite a bit of their ancestry from dogs like the 3,800-year-old Srubnaya dog.

“Perhaps there is sometimes also an element of chance in these processes, such that if we could replay the tape of human history many times, the outcome for dogs might not always be the same,” Bergstrom told Ars.

Old dogs and new genomes

Part of the reason the earliest years of dogs’ domestication are so fuzzy (not sorry) is that ancient dog DNA has been pretty scarce. Until the recent study, scientists had published just six prehistoric dog and wolf genomes. In case you’re keeping score, we had sequenced more Neanderthal genomes than prehistoric dog genomes—until now, that is.

“Ancient DNA is still a young field, and for most animals there have not yet been many studies of whole genomes,” Bergstrom told Ars. For him and his colleagues to add 27 ancient dog genomes to that list, it took an international effort by archaeologists and museum curators. The collaborators found ancient dog remains in museum and university collections and on lists of material excavated at archaeological sites.

According to Bergstrom, more ancient dog genomes, along with more archaeological evidence about how dogs fit into ancient cultures and economies, could help us understand the origin of dogs and the parts of our shared history that don’t seem to line up.

Perhaps someday we’ll even learn the answer to the most pressing question of all: “Who’s a good dog?”

Science, 2020 DOI: 10.1126/science.aba9572 (About DOIs).

KIONA N. SMITH  is a freelance science journalist at Ars Technica.

Trump admin’s pandemic surrender draws impassioned response from WHO
WHO officials were exasperated by Trump admin’s suggestion to give up on pandemic.

BETH MOLE - 10/27/2020, 

Enlarge / World Health Organization (WHO) Health Emergencies Program Director Michael Ryan (L) speaks past Director-General Tedros Adhanom Ghebreyesus during a daily press briefing on COVID-19 virus at the WHO headquarters in Geneva on March 9, 2020.

Top officials at the World Health Organization on Monday appeared at times exasperated, flabbergasted, and wearied as they confronted comments by White House Chief of Staff Mark Meadows suggesting that the United States has given up trying to control the spread of the pandemic coronavirus, SARS-CoV-2.

“We’re not going to control the pandemic,” Meadows said in a CNN interview Sunday. Instead we will focus on “vaccines, therapeutics, and other mitigation areas,” he said. The comments spurred widespread uproar, which Meadows tried to quell Monday. But his clarification only reinforced his earlier comments.

“I mean, when we look at this, we’re going to defeat the virus. We’re not going to control it. We will try to contain it as best we can,” he told reporters outside the White House yesterday. He again emphasized the need for therapeutics and vaccines.
Dangerous

In a WHO press briefing Monday, WHO Director-General Tedros Adhanom Ghebreyesus spoke bluntly: “Giving up on control is dangerous.”

While Tedros agreed on the importance of therapeutics and a vaccine, he noted that so far, they are not yet available. As such, “control should also be part of the strategy,” he said. “The government should do its share and the citizens also should do their share. Otherwise, this virus is dangerous. If it’s let go freely, it can create havoc.”Advertisement

WHO officials made the point repeatedly during the press conference Monday, at times in impassioned and strained pleas given the current state of the pandemic. Last week, the WHO recorded the highest number of COVID-19 cases in the pandemic so far. The world is approaching 44 million cases and has recorded over 1.16 million deaths. Though many countries in the world are currently struggling with surges of new cases, the US stands out as one of the most ravaged, with 8.7 million cases and nearly 226,000 deaths.

The US is currently climbing to its third and highest peak in new cases yet. On Friday, the country logged its highest daily number of new cases in the pandemic, with 83,010, according to The COVID Tracking Project. The current seven-day rolling average is at nearly 70,000. As of Monday, nearly 43,000 people in the country were hospitalized with COVID-19, and the seven-day rolling average of daily deaths was nearly 800.
Protection

WHO officials have acknowledged many times that people generally are tired of efforts to try to control the virus—physical distancing, not visiting family, cancelling events. But, to put it frankly, the virus does not care, and ditching control efforts is a recipe for disaster.

What Meadows was basically suggesting—to not control, but to lessen the impacts of the virus—is to essentially allow the virus to spread among the healthy while trying to shield the most vulnerable. Protecting the most vulnerable is an “honorable objective,” WHO Executive Director Michael Ryan noted. But, “the difficulty arises in trying to actually achieve that goal.” This might work if, for instance, you can identify the most vulnerable people and they’re mostly in nursing homes. You might be able to shield them in that hypothetical situation, he says. But that's not the reality:

The vast majority of vulnerable people live amongst us in multigenerational households—the old, the young, the vulnerable people on chemotherapy, people with underlying conditions, people with diabetes and hypertension. They’re mums, they’re dads, they’re brothers, they’re sisters, they’re sons, they’re daughters. So, the best way to protect those individuals is to do as much as possible to reduce the transmission of this disease at community level.

In other words, the best way to protect the most vulnerable is to protect everyone—and control the virus. “We should not give up on trying to suppress transmission and control transmission,” Ryan added.
Tsunami of cases

He also offered a grim caution of what can happen when countries and governments do not try to control the virus. He noted that in April and March many places in the world, including some in the US, used “mitigation”—he used air quotes for this word—as their strategy and “emergency rooms were overwhelmed and we were rolling freezer trucks up to the back of hospitals,” he said. “That’s the reality of mitigating a disease in the face of a tsunami of cases. You run out of capacity to cope and that is the fear right now.”

The US is currently seeing a surge in hospitalizations, with some area hospitals and intensive care units overwhelmed and forced to open field hospitals.

Ryan’s sweeping response to Meadow’s comments was unusually impassioned for the typically steady WHO press conferences. At times, he was clearly frustrated; at times he was energized. At other points, Ryan seemed stunned and tired, letting out defeated sighs. Perhaps the lowest point in his response came when he acknowledged that convincing some people to follow control efforts appeared hopeless.

Not everyone accepts what we need to do to save lives and stop the pandemic, he acknowledged. “They don’t believe in this disease," Ryan said. "They don’t believe that we have a pandemic on our hands. How can you convince someone to do something if they don’t actually believe that there’s a problem. It’s truly impossible to think about this.”


BETH MOLE is Ars Technica’s health reporter. She’s interested in biomedical research, infectious disease, health policy and law, and has a Ph.D. in microbiology.