This week’s ASR originally began by looking at an MIT study showing that false stories spread more widely and more rapidly than true stories. Unfortunately, that story outgrew the ASR space, so it got it’s own slot for the day, and instead ASR is opening with this story of pigs gone wild.
Across the country, wild boars are moving in as Japan’s rapidly aging population either moves out or dies out. The boars come for the untended rice paddies and stay for the abandoned shelters.
We tend to think of Japan as a terribly crowded place, and in some places it is. But when you consider that Tokyo has 11 percent of the population tucked into 0.6 percent of the available space, and right behind Tokyo come a dozen other cities with populations over a million, it leaves plenty of room for some places that are pretty rural, if not actually empty. Just as with the United States, Japan’s small towns and villages have been on the decline for decades. Which leaves plenty of semi-wild territory for feral hogs to breed and expand. Not only are these hogs large, topping 200 pounds, and dangerous, they’re fast to adapt and reproduce rapidly. The average female produces 4.5 piglets a year.
Invasive wild pigs are also spreading across many areas of the United States. These pigs carry a mix of characteristics that’s made them tough to eradicate and frightening to encounter on a walk in the woods.
The pigs are the descendants of the domestic swine that were first brought to the United States by Spanish explorers in 1539. Long after their arrival, hunters introduced wild Eurasian boars into some areas where they went on to breed extensively with domestic pigs. The result is a modern invasive species that are known to carry or transmit over 30 diseases and 37 parasites, according to the USDA.
Pigs not only act as disease vectors, they’re highly destructive of habitats. They cause over $1.5 billion in damage each year in the US. Pigs, along with goats, are one of the animals humans have introduced around the globe which have had the most impact in reducing native species. And they’re bringing their damage to new areas — helped along by climate change.
In addition to depopulation, another factor for the boar explosion: The winters are also getting markedly warmer. “We used to have much more snow than this,” Numata said, looking out as snowflakes fell gently on the fields.
When you think about species that are spreading due to less severe winters, don’t just think of insects that harm trees. Think of massive feral hogs that displace native wildlife, uproot whole ecosystems, and are, from personal experience, capable of making you climb a tree to get out of their way.
Okay, let’s go read some science ...
Health and Medicine
A Conference on Retroviruses and Opportunistic Infections this week brought news of possible advances on dealing with AIDS. One presentation showed researchers getting closer to an HIV vaccine, while another looked at what it takes to actually cure an existing infection.
An HIV vaccine may finally be closer, thanks to monkeys
And, of course, thanks to the scientists at Oregon Health & Science University who studied these monkeys. The monkeys in question, rhesus macaques, were injected with HIV’s close relative, SIV (sorry, monkeys). But thanks to a vaccine that involves taking some of the proteins from SIV and introducing them into a harmless virus called cytomegalovirus, 55 percent of the monkeys became infected, but were later able to drive the virus back to undetectable levels.
An earlier study looked at the vaccines’ effectiveness on a smaller group of monkeys. The new study, with minor modifications, upped the test to 200 individuals. But while the 55 percent who shrugged off the SIV infection is exciting, obviously it’s less than what scientists would like to see in an actual HIV vaccine. And there’s a problem: They don’t quite understand how it works.
New research is focusing on looking at the genes of animals where the the vaccine was effective. By doing so, the team is now able to predict which monkeys will develop an effective response. That gives them a better idea of what immune signals are being triggered by the vaccine, and how it might be modified to generate a response across more of the population. The good news here is that the gene sequence that seems to important involves production of interleukin-10, a protein also seen in humans. So it seems likely that if the researchers can find the right key to activate this complex, the vaccine might also “translate” to humans.
Scientists get a better handle on how to cure AIDS, thanks to monkeys
More rhesus macaques, more needles, and more research. This time our 15 pound simian relatives were given an active infection of a virus that hybridized both the human and simian varieties into something called SHIV (sounds extremely unpleasant). But then scientists spent two years administering anti-virals until they drove the infection to undetectable levels. After that the split the monkeys into four groups: A control group which got no more treatment, an HIV antibody, a drug under testing, or a combination of the drug and the antibody.
For the control group … bad news. The disease returned with a vengeance, which is what also happens with humans who stop taking antiviral drugs after an HIV infection. Every single monkey in the control group quickly developed high levels of virus. The reason for that, and for why humans who are infected with HIV redevelop an infection, is that the infection can leave cells in the body carrying the HIV genetic material, but not actively producing virus. Because they’re not making virus, with virus protein coats, they don’t trigger the immune system. These cells, even if they are few in number, can eventually “wake up” and start kicking out HIV again when treatment stops.
But the monkeys getting either the antibody or the drug fared a little better. And those who got both, did the best of all.
Following ART discontinuation, 100% (11 of 11) of sham controls exhibited rapid viral rebound with a median rebound time of 21 days. In contrast, only 55% (6 of 11) of PGT121+GS-9620 treated animals rebounded by day 140 following ART discontinuation and demonstrated a substantial delay in median rebound time of 112 days as well as a 2.64 log reduction of peak viral loads and a 1.52 log reduction of setpoint viral loads as compared with sham controls. All PGT121+GS-9620 treated animals exhibited setpoint viral loads <400 RNA copies/ml. Intermediate outcomes were observed in the animals that received PGT121 alone.
Of the 11 animals that got the drug, TLR7 and the antibody, 6 did not redevelop an infection at all, even after six months. The reason seems to be that TLR7 sounds an alarm clock for those “sleeper cells” that are carrying the vaccine. It may seem perverse that the drug actually causes the body to produce more virus. but by doing so it brings those cells to the attention of the immune system.
Now, like the HIV vaccine folks, the researchers are trying to understand why their treatment worked for 55 percent of the infected, and see how that percentage can be improved.
How much snot does it take to give a ferret the flu?
I realize that this is a serious paper with serious consequences, but I fear it could become the new “shrimp on a treadmill,” or at the very least, the subject of an Ig Nobel award.
Here, we describe and evaluate a transmission chamber that separates virus-laden particles in air by size to study airborne particles that mediate influenza transmission in ferrets. Our results provide direct experimental evidence of influenza transmission via droplets and fine droplet nuclei, albeit at different efficiency. This transmission device can also be applied to elucidate the mode of transmission of other respiratory pathogens.
Coming off a major flu season, it’s critical that we understand how the disease spreads. And the idea that you can get the flu from being in contact with someone who is neither sneezing nor coughing out lungfuls of phlegm is critical knowledge. But this was all done … in ferrets. In fact, the title of the paper is:
Defining the sizes of airborne particles that mediate influenza transmission in ferrets
And that shouldn’t, but does, make me read the rest of the article in Rikki Tikki Tavi voice (and yes, I know mongoose does not equal ferret).
A physical reason why kids are more mentally flexible than adults
If it seems to you that children can both pick up new ideas more quickly, and adapt to radical changes in their living situation more adroitly than adults, there appears to be a good reason. Breaking with previous views, a team led by scientists from UC California has determined that adults are not creating new brain cells in a critical area.
In humans, some studies have suggested that hundreds of new neurons are added to the adult dentate gyrus every day, whereas other studies find many fewer putative new neurons. Despite these discrepancies, it is generally believed that the adult human hippocampus continues to generate new neurons. Here we show that a defined population of progenitor cells does not coalesce in the subgranular zone during human fetal or postnatal development. We also find that the number of proliferating progenitors and young neurons in the dentate gyrus declines sharply during the first year of life and only a few isolated young neurons are observed by 7 and 13 years of age. In adult patients with epilepsy and healthy adults, young neurons were not detected in the dentate gyrus.
The dentate gyrus plays an important (though, like most things about the brain, not well understood) role in forming new memories, in dealing with stress, and in handling “novel situations.” Damage to this area can not only result in a loss of the ability to create new memories, but problems in dealing with a new environment, and panic or depression when facing change.
It’s long been thought that the dentate gyrus was one of those areas in the brain where new cells were constantly being added, even in adults. But looking at both monkeys and humans, this doesn’t appear to be the case.
We conclude that recruitment of young neurons to the primate hippocampus decreases rapidly during the first years of life, and that neurogenesis in the dentate gyrus does not continue, or is extremely rare, in adult humans.
Clearly, humans — even adults — do make new memories, and do adapt to new environments, but they apparently do it using some other mechanism, or through the rewiring of existing cells. And that old idea that kids “land on their feet,” pick up new ideas more quickly, and in general respond better to change, apparently has a very physical basis.
Wildlife Biology
This bat copter is piloted by bat men, for the good of bats
Scientists at Saint Mary's College in Indiana have developed a drone with a purpose. Using both physical modifications and active sound-dampening to mask the noise of their UAV, they built a small device that can be introduced into the midst of flying bats. This let them record the sounds and actions of bats on the wing from a unique perspective.
Their big test came just outside a New Mexico cave where 800,000 free-tailed bats spew out at dusk and stream back before dawn. They were able to hover their tiny drone inside the column of bats without collisions, while recording echolocation sounds. The hope is that by better understanding what bats look for to avoid smacking into trees, each other, or tiny UAVs, the team will learn something that will help in creating bat-safe architecture, windmills, and other structures.
Bats everywhere are under threat from a disease that first appeared in the Eastern United States. Millions of bats in 31 states and Canada have died from “white nose syndrome,” a fungal infection that thrives in damp, cool environments and tends to infect bats as they hibernate. Considering their vital role in the control of insect populations, we want to save every bat we can.
Predicting invasive species
A team from flippin’ everywhere (seriously, go check out that crew) worked on a project to see if it was possible to predict the next wild boar raging across Japan, zebra mussel clogging waterways, or Chestnut blight felling forests. What they found was a rising tide of threats ...
Our ability to predict the identity of future invasive alien species is largely based upon knowledge of prior invasion history. Emerging alien species—those never before encountered as aliens—therefore pose a significant challenge to biosecurity interventions worldwide. Using a global database of the first regional records of alien species covering the years 1500–2005 we detected a surprisingly high proportion of species in recent records that have never been recorded as alien before.
Despite centuries of trade that has spread species around the globe, there are still fresh invasions going on that are every bit as disruptive as those in the past. These invasions are helped, again, by climate change, which is making tropical and subtropical creatures viable in areas that were previously too cold. This can have effects at both ends. Even areas that have traded for decades might find that insects have moved into their areas from warmer adjoining regions, creating new potential to cause harm to partners in a trading network.
The conclusion is that the potential for new invasions, and for disasters like the ones that destroyed American chestnut and elm forests, remains high.
Cartography
Making better visualizations through cartograms
This is something that everyone in politics struggles with. Donald Trump loves to show maps that paint the country red, indicating that he got the votes of a huge percentage of America — if empty land could vote. But creating visualizations that actually represent populations, while maintaining physical relationships, is a challenge. The Daily Kos election team has tackled this ably using several different approaches, but some quants from Yale and Kyoto University have a new mathematical approach.
Densely populated cities should be given more prominence than large, but sparsely populated territories. Cartograms solve this problem by rescaling map regions in proportion to, for example, population or gross domestic products. Until now, it has generally been cumbersome or slow to calculate map projections for contiguous cartograms. Here we describe and benchmark a fast flow-based algorithm that computes cartograms in a matter of seconds, yet maintains the strengths of previous methods—a development which may lead to a more widespread adoption of cartograms.
The C code for their fast approach is out on Github. Visit the article to see some examples of the output.
Paleontology
Putting the first land plants on a timeline
When thinking of paleontology, it’s the animals who get all the glory. But then, the same is true of most nature shows. All those glitzy, fast-moving, photogenic critters get the narrative while poor plants are the background players. But a team from the University of Bristol in the UK has stopped to give early land plants their moment in the spotlight, as they’ve worked out a timeline of plant development. Which turns out to be a less than straightforward task.
The sparseness of early land plant megafossils and stratigraphic controls on their distribution make the fossil record an unreliable guide, leaving only the molecular clock. However, the application of molecular clock methodology is challenged by the current impasse in attempts to resolve the evolutionary relationships among the living bryophytes and tracheophytes. Here, we establish a timescale for early land plant evolution that integrates over topological uncertainty by exploring the impact of competing hypotheses on bryophyte−tracheophyte relationships, among other variables, on divergence time estimation. We codify 37 fossil calibrations for Viridiplantae following best practice. We apply these calibrations in a Bayesian relaxed molecular clock analysis of a phylogenomic dataset encompassing the diversity of Embryophyta and their relatives within Viridiplantae.
If you didn’t get that, don’t worry. Basically, the relationship between mosses and everything else you probably think of a plant (“vascular plants”) isn’t all that well understood. So they went back to genetic markers present in green algae, and played things forward from there, looking at how divergent the groups were from 37 markers on a group that’s understood as the parent for all land plants. The big conclusion out of all this is that land plants probably got a foothold earlier than expected — mosses and liverworts likely got their start around the middle Cambrian, around 520 million years ago, while all four major groups of plants were represented by the late Silurian, about 425 million years ago. So when you’re looking at recreations of some ancient shoreline, remember that it might have actually been more green, and more diverse in its greenery, than previously thought.
Archeology
Ancestors of the Caribbean ‘Taino’
Consider this a week off from the recent spate of Neanderthal news. Instead, another large team of geneticists from the US, Europe, and South America (seriously, what’s up with the papers that have twenty-plus authors?) looked at the ‘Taino’ people who were widespread across the Caribbean right up until Columbus arrived to kill them with disease, enslave those who survived, and crucify a few just for the hell of it.
The results of the genetic research show that the Taino didn’t get to the islands by stepping out from Florida. Instead, they made their way up from the south.
We demonstrate that the ancestors of the so-called “Taino” who inhabited large parts of the Caribbean in pre-Columbian times originated in northern South America, and we find evidence that they had a comparatively large effective population size.
One of the lessons of recent studies has been that the slaughter of Native Americans was greater than previously thought, and that’s also true for the Taino.
As it happens, I once spent six weeks on San Salvador Island, where among other things I helped researchers looking at former sites of the Lucayan people. The Lucayan, a branch of the Taino, were the first people Columbus met when he reached the New World and San Salvador was the first land he sighted. As Columbus’ ships lay offshore, the Lucayan brought out to them fresh water. Columbus said the people were handsome, graceful, gentle, generous and peaceful. So he killed some, seized others, and carried off several to take back to Spain as examples — and slaves. Amerigo Vespucci grabbed 230 more Lucayans as slaves in 1500, but by then San Salvador Island was already deserted. In 1520, a Spanish search through the Bahamas found only 11 Lucayans remaining on all the islands. In less than a generation, the Lucayans went from tens of thousands of people — and perhaps much more — spread over hundreds of islands, to a handful of slaves shipped off to work new Spanish plantations on Hispaniola. Except for the occasional pirate or castaway, no one lived on the Bahamas for the next 130 years.
It’s only now that we’re starting to understand something of their story.
We report the genome sequence of a 1,000-year-old Lucayan Taino individual recovered from the site of Preacher’s Cave in the Bahamas. We sequenced her genome to 12.4-fold coverage and show that she is genetically most closely related to present-day Arawakan speakers from northern South America, suggesting that the ancestors of the Lucayans originated there. Further, we find no evidence for recent inbreeding or isolation in the ancient genome, suggesting that the Lucayans had a relatively large effective population size. Finally, we show that the native American components in some present-day Caribbean genomes are closely related to the ancient Taino, demonstrating an element of continuity between precontact populations and present-day Latino populations in the Caribbean.
Think of it as the danger of invasive species, human variety.
As usual, today’s infographic was produced by Andy Brunning at Compound Interest. You’ll want to read all of this one, so head over to his site for an expanded version.