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How An Icon of Evolution Turned to the Dark Side

A mutation giving rise to the black form of peppered moths has been discovered and is estimated to have occurred around 1820.
A mutation giving rise to the black form of peppered moths has been discovered and is estimated to have occurred around 1820.
Ilik Saccheri

In the early 19th century, coal-fired factories and mills belched a miasma of soot over the English countryside, blackening trees between London and Manchester. The pollution was bad news for the peppered moth. This insect, whose pale speckled body blended perfectly against the barks of normal trees, suddenly became conspicuous—a white beacon against blackened bark, and an easy target for birds.

As the decades ticked by, black peppered moths started appearing. These mutants belonged to the same species, but they had traded in their typical colours for a dark look that once again concealed their bodies against the trees. By the end of the century, almost all the moths in Manchester were black.

As British air became cleaner and trees lighter in colour, the black moths faded back into obscurity. But in their brief reign they became icons of evolution. As geneticist Sewall Wright put it, they are “the clearest case in which a conspicuous evolutionary process has actually been observed.”

The story has endured a fair amount of controversy. Creationists asserted that the blackening of the moth was just a case of shifting gene frequencies rather than an outright change from one organism into another, ignoring that the former is the very definition of evolution. They also seized onto technical disputes between scientists themselves, over whether the moths’ colours really made any difference to their vulnerability to birds. The latter dispute was resolved through some groundbreaking experiments by the late Michael Majerus.

And now, Arjen van’t Hof and Pascal Campagne from the University of Liverpool have strengthened the peppered moth’s iconic status even further by identifying the gene behind its classic adaptation. And in a wonderful twist, the gene turns out to be a jumping gene—a selfish bit of DNA with the power to hop around its native genome.

I’ve written about jumping genes many times before (as has fellow Phenomena blogger Carl Zimmer). These mobile stretches of DNA can cause havoc by disrupting other genes and increasing the risk of cancers or developmental disorders. Or, they can provide opportunities by creating variation that evolution can act upon. Such genes have driven the evolution of mammalian pregnancies and our immune systems. And now, it seems that one of them helped the peppered moth to cope with the Industrial Revolution.

Back in 2011, the Liverpool team, led by Ilik Saccheri, bred and compared dark and light moths to identify the gene or genes responsible for the shadowy look. They narrowed their search down to a small section of the insect’s 17th chromosome—one containing 13 possible genes. Since then, having studied more moths, they’ve homed in on one particular gene called cortex.

Patterns on a Heliconius melpomene butterfly wing are made of tiles of overlapping coloured scales.
Patterns on a Heliconius melpomene butterfly wing are made of tiles of overlapping coloured scales.
Nicola Nadeau

In almost all the dark moths, the cortex gene contains a unique stretch of DNA that’s missing from all the light individuals. It has all the hallmarks of a jumping gene, including the ability to make an enzyme that cuts it out of its original location and pastes it elsewhere. The moth’s genome contains up to 255 copies of this gene, which the team calls carbonaria. It clearly gets around a bit.

And on one particular jump, it landed in the middle of cortex. This fateful event, which nestled one gene (carbonaria) within another (cortex), is what darkened the moth’s body. Van’t Hof and Campagne estimate that it probably happened somewhere around 1819—a couple of decades before entomologists first saw the dark moths in the wild.

The timing fits, but other details are less clear. For example, how exactly did carbonaria cause the dark colours? Genes encode instructions for building proteins—tiny biological machines that perform various jobs around an animal’s cell. You might guess that carbonaria changed the instructions in the cortex gene, leading to the production of a different protein with new capabilities. But not so—the jumping gene actually landed in a part of cortex  that gets discarded, and never contributes to building proteins.

Rather than changing what the cortex gene built, the team suspects that carbonaria changed when and where it is activated. Indeed, with the jumping gene in place, cortex switches on very strongly at the point in the larval moth’s life when it starts producing its adult wings. It’s unclear why that happens, or how it leads to dark wings, but for now, it seems that cortex affects the development of wings and that carbonaria changed how it did its job.

Indeed, in a separate study, Nicole Nadeau and Chris Jiggins from the University of Cambridge showed that cortex controls the patterns of the beautiful Heliconius butterflies, probably by influencing the development of their wing scales. By fiddling with this gene, natural selection has repeatedly tweaked the palettes and patterns of insects.

Paleo Profile: Mexico’s Mystery Dinosaur

Centrosaurine sites in North America. From Rivera-Sylva et al., 2016.
Centrosaurine sites in North America. From Rivera-Sylva et al., 2016.

A few years back, while crashing at my apartment for the night during a long trip west, a friend of mine asked me “Haven’t paleontologists found all the dinosaurs already?” Museums from coast-to-coast seem well-stocked with primordial reptiles, and, really, when dealing with such giants, how many species could there possibly be? I had to chuckle at my friend’s question. Not only were there more dinosaur species than we ever imagined, but we’re still a long way from finding them all.

I can’t think of a place that better exemplifies the dinosaur boom than North America’s southwest. Hell, the fantastic new species coming out of the area from the four corners on south was half the reason I moved to Utah. New explorations in the western deserts have yielded an increasing array of new dinosaur species, and paleontologists already know that there’s more out there than has been formally identified. Take, for example, an animal represented by a smattering of bones found in northern Mexico.

There is no formal name for this dinosaur yet. There’s too little of it to justify a permanent identification. But, as described by paleontologist Héctor Rivera-Sylva and colleagues, the fossils appear to represent a horned dinosaur not seen before.

The bones were found in Coahuila, northern Mexico, between 2007 and 2011. And while paleontologists named another horned dinosaur – Coahuilaceratops – from this area in 2010, the bones described by Rivera-Sylva and coauthors are from something different. That’s because Coahuilaceratops is what experts call a chasmosaurine – the lineage that contains Chasmosaurus and Triceratops – while this new dinosaur belongs to a separate lineage called centrosaurines that includes Centrosaurus, Nasutoceratops, and their relatives. This makes CPC 274 the southernmost occurrence of a centrosaurine dinosaur yet found.

This is how some dinosaurs make their debut. Not as beautiful skeletons with names as awesome as their osteology, but as fragments and pieces that hint at what’s left to find. The recently-named tyrannosaur Timurlengia, for example, first came to paleontologists as a smattering of tantalizing fragments before a braincase tied everything together. Hopefully the Coahuila centrosaurine will follow the same pattern, new finds filling in the identity of what must have been a gnarly herbivore with its own splay of spikes and horns.

I look forward to the day that paleontologists will be able to organize an unveiling for Mexico’s mystery dinosaur, but that’s not the point of this post. I picked this unnamed enigma for my last Paleo Profile here at National Geographic because of what it represents. The unknown is what calls to scientists, both in the lab and in the layers of time laid out in the desert. For every fact or fossil we find, we get a bloom of new questions that itch at the brain and the soles of your boots. That’s the drive to seek out unknown dinosaurs in their remote, ancient tombs, and, truly, we are just getting started.

centrosaurine-squamosal

Fossil Facts

Name: There is no genus and species name yet. For now the dinosaur is designated as specimen CPC 274.

Age: About 80 million years ago.

Where in the world?: Coahuila, Mexico.

What sort of critter?: A horned dinosaur related to Centrosaurus.

Size: Unknown.

How much of the creature’s body is known?: A partial skull and several pieces of the postcrania.

Reference:

Rivera-Sylva, H., Hedrick, B., Dodson, P. 2016. A centrosaurine (Dinosauria: Ceratopsida) from the Aguja Formation (Late Campanian) of northern Coahuila, Mexico. PLOS ONE. doi: 10.1371/journal.pone.0150529

Previous Paleo Profiles:

The Unfortunate Dragon
The Cross Lizard
The South China Lizard
Zhenyuan Sun’s dragon
The Fascinating Scrap
The Sloth Claw
The Hefty Kangaroo
Mathison’s Fox
Scar Face
The Rain-Maker Lizard
“Lightning Claw”
The Ancient Agama
The Hell-Hound
The Cutting Shears of Kimbeto Wash
The False Moose
“Miss Piggy” the Prehistoric Turtle
Mexico’s “Bird Mimic”
The Greatest Auk
Catalonia’s Little Ape
Pakistan’s Butterfly-Faced Beast
The Head of the Devil
Spain’s Megatoothed Croc
The Smoke Hill Bird
The Vereda Hilarco Beast
The North’s Sailback
Amidala’s Strange Horn
The Northern Mantis Shrimp
Spain’s High-Spined Herbviore
Wucaiwan’s Ornamented Horned Face
Alcide d’Orbigny’s Dawn Beast
The Shield Fortress
The Dragon Thief
The Purgatoire River’s Whale Fish
Russia’s Curved Blade
The Dawn Mole
The Oldest Chameleon
The Wandering Spirit
Teyú Yaguá
New Caledonia’s Giant Fowl
The Giant Tarasque Tortoise
The Giant, Bone-Crushing Weasel
The Dawn Rough Tooth

Paleo Profile: The Dawn Rough Tooth

The reconstructed skull of Eotrachodon. From Prieto-Márquez et al., 2016.
The reconstructed skull of Eotrachodon. From Prieto-Márquez et al., 2016.

Eastern dinosaurs are hard to find. Between geologic happenstance, suburban sprawl, and forests that blanket what would otherwise be promising outcrop, we know frustratingly little about the dinosaurs of Appalachia compared to their relatives exposed in the deserts to the west. But every now and then paleontologists are able to pull a prize out of the difficult eastern exposures. The hadrosaur Eotrachodon is one such case.

Paleontologists  Albert Prieto-Márquez, Gregory Erickson, and Jun Ebersole named the dinosaur earlier this year from bones found in Alabama. The remains are pretty scrappy, which is typical for Appalachian finds, but Eotrachodon is nevertheless known from a nearly-complete skull that provides a rich source of osteological comparison for other hadrosaurs. After all, most hadrosaurs are primarily identified by their skulls – different ornamentation on a very conservative chassis.

At about 85 million years old, Eotrachodon lived about 10 million years before the great profusion of its more famous cousins in the west like Parasaurolophus, Lambeosaurus, and their ilk. In fact, Prieto-Márquez and colleagues found, Eotrachodon seems to fall right outside the split between the major crested and crestless hadrosaur lineages, hinting that the eastern half of North America was the place hadrosaurs started to take off before conquering so much of the west.

But there’s another reason I picked Eotrachodon for this week’s Paleo Profile. When I was a kid the hadrosaur Trachodon often made appearances in books and movies, but paleontologists abandoned the name. That’s because the name Trachodon is formally chained to a handful of isolated teeth that can’t be tied back to a body. By coining the name Eotrachodon, however, Prieto-Márquez and coauthors found a workaround to revive the classic title and give poor “Trachodon” a new dawn.

The right maxilla of Eotrachodon. From Prieto-Márquez et al., 2016.
The right maxilla of Eotrachodon. From Prieto-Márquez et al., 2016.

Fossil Facts

Name: Eotrachodon orientalis

Meaning: Eotrachodon means “dawn Trachodon” (or “dawn rough tooth” fully translated), and orientalis is a reference to the fact this dinosaur was found in America’s southeast.

Age: About 85 million years ago.

Where in the world?: Montgomery County, Alabama.

What sort of critter?: A hadrosaur, or “duck-billed” dinosaur.

Size: Comparable to other North American hadrosaurs such as Hadrosaurus and Gryposaurus.

How much of the creature’s body is known?: A nearly-complete skull and fragmentary elements of the postcrania.

References:

Prieto-Márquez, A., Erickson, G., Ebersole, J. 2016. A primitive hadrosaurid from southeastern North America and the origin and early evolution of ‘duck-billed’ dinosaurs. Journal of Vertebrate Paleontology. doi: 10.1080/02724634.2015.1054495

Prieto-Márquez, A., Erickson, G., Ebersole, J. 2016. Anatomy and osteohistology of the basal hadrosaurid dinosaur Eotrachodon from the uppermost Santonian (Cretaceous) of southern Appalachia. PeerJ. doi: 10.7717/peerj.1872

Previous Paleo Profiles:

The Unfortunate Dragon
The Cross Lizard
The South China Lizard
Zhenyuan Sun’s dragon
The Fascinating Scrap
The Sloth Claw
The Hefty Kangaroo
Mathison’s Fox
Scar Face
The Rain-Maker Lizard
“Lightning Claw”
The Ancient Agama
The Hell-Hound
The Cutting Shears of Kimbeto Wash
The False Moose
“Miss Piggy” the Prehistoric Turtle
Mexico’s “Bird Mimic”
The Greatest Auk
Catalonia’s Little Ape
Pakistan’s Butterfly-Faced Beast
The Head of the Devil
Spain’s Megatoothed Croc
The Smoke Hill Bird
The Vereda Hilarco Beast
The North’s Sailback
Amidala’s Strange Horn
The Northern Mantis Shrimp
Spain’s High-Spined Herbviore
Wucaiwan’s Ornamented Horned Face
Alcide d’Orbigny’s Dawn Beast
The Shield Fortress
The Dragon Thief
The Purgatoire River’s Whale Fish
Russia’s Curved Blade
The Dawn Mole
The Oldest Chameleon
The Wandering Spirit
Teyú Yaguá
New Caledonia’s Giant Fowl
The Giant Tarasque Tortoise
The Giant, Bone-Crushing Weasel

Paleo Profile: Teyú Yaguá

Teyujagua-skull
The skull of Teyujagua paradoxa. From Pinheiro et al., 2016.

Do a Google Image search for the word “Triassic” and you’re going to see variations of the same scene over and over again. Svelte little dinosaurs snap and squawk around an ancient lake or river, with the also-rans of their era – such as the armored aetosaurs and superficially-crocodile-like phytosaurs – shuffling through the undergrowth and basking at the water’s edge. Such vignettes are classic Triassic imagery, and yet they’re only a narrow view of one part of the opening chapter in the Age of Reptiles triology. There’s far more to the Triassic story than Coelophysis and its neighbors, with the latest wrinkle to the tale arriving in the form of a beautiful skull found in Brazil.

The fossil, described by paleontologist Felipe Pinheiro and colleagues, was that of an archosauromorph. This was a line of reptiles that first evolved back in the Permian, when the protomammals held sway, and underwent explosive diversification during the Triassic, eventually sprouting branches that would include dinosaurs, pterosaurs, and crocodiles.

Named Teyujagua paradoxa by the researchers, the 251 million year old animal lived just before the great reptilian radiation really took off. So while not necessarily the ancestor of the various lineages that would come later, Pinheiro and coauthors point out that the skull of Teyujagua is a significant part of the story given that it exhibits some characteristics of older forms of reptiles as well as novelties that would come to mark the “ruling reptiles” such as serrated teeth and an opening in the sidewall of the lower jaw. When you look at the skull of Teyujagua, you’re looking at a face that helped set evolutionary trends from the dawn of the Triassic until today.

A close-up of Teyujagua. From Pinheiro et al., 2016.
A close-up of Teyujagua. From Pinheiro et al., 2016.

Fossil Facts

Name:Teyujagua paradoxa

Meaning: The genus was named after Teyú Yaguá, a dog-headed lizard in Guarani mythology, while paradoxa underscored the “unusual” combination of characteristics.

Age: Around 251 million years ago.

Where in the world?: Southern Brazil.

What sort of critter?: An archosauromorph, or an ancient member of the lineage that includes dinosaurs, pterosaurs, crocodiles, and their relatives.

Size: The skull is about four and a half inches long.

How much of the creature’s body is known?: A nearly-complete skull and several neck vertebrae.

Reference:

Pinheiro, F., França, M., Lacerda, M., Butler, R., Schultz, C. 2016. An exceptional fossil skull from South America and the origins of the archosauriform radiation. Scientific Reports. doi: 10.1038/srep22817

Previous Paleo Profiles:

The Unfortunate Dragon
The Cross Lizard
The South China Lizard
Zhenyuan Sun’s dragon
The Fascinating Scrap
The Sloth Claw
The Hefty Kangaroo
Mathison’s Fox
Scar Face
The Rain-Maker Lizard
“Lightning Claw”
The Ancient Agama
The Hell-Hound
The Cutting Shears of Kimbeto Wash
The False Moose
“Miss Piggy” the Prehistoric Turtle
Mexico’s “Bird Mimic”
The Greatest Auk
Catalonia’s Little Ape
Pakistan’s Butterfly-Faced Beast
The Head of the Devil
Spain’s Megatoothed Croc
The Smoke Hill Bird
The Vereda Hilarco Beast
The North’s Sailback
Amidala’s Strange Horn
The Northern Mantis Shrimp
Spain’s High-Spined Herbviore
Wucaiwan’s Ornamented Horned Face
Alcide d’Orbigny’s Dawn Beast
The Shield Fortress
The Dragon Thief
The Purgatoire River’s Whale Fish
Russia’s Curved Blade
The Dawn Mole
The Oldest Chameleon
The Wandering Spirit

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Last-Ditch Antibiotic Resistance: What Is The Role Of Food?

A cattle feedlot in California's Imperial Valley. Photograph by Gerd Ludwig, Nat Geo Creative
A cattle feedlot in California’s Imperial Valley. Photograph by Gerd Ludwig, Nat Geo Creative

As concern for Zika virus ramped up in January, the recent and sudden recognition that last-ditch antibiotic resistance is moving across the globe has all but vanished from the news.

But it’s about to become important again. Two letters published in Lancet Infectious Diseases, the journal that has published all the revelations of the newly identified MCR-1 gene that protects bacteria from the last-resort antibiotic colistin, reveal a worrisome new development. In both humans and animals in China, bacteria have been found that harbor both MCR, and also NDM, the last perilous superbug gene, which confers resistance to a crucial class of drugs called carbapenems.

In the last set of publications about MCR several weeks ago, researchers revealed that bacteria with MCR resistance were doing the equivalent of assembling a winning hand at cards, shuffling the DNA for different resistance factors into shared mobile genetic elements that are capable of transferring among bacteria. With the acquisition of NDM, the hand gets stronger—and the bacteria, closer to lethally untreatable.

Hong Du and colleagues report that, once MCR was identified last November, they went back into the sample banks of a hospital in Suzhou, China. They found four bacteria possessing mcr-1, two E. coli and two Klebsiella, that were collected between January 2013 and November last year. The bacteria came from three patients, two inpatients and one outpatient, and two of the samples, the Klebsiellas, also carried ndm-5, which confers resistance to the carbapenems. The researchers say this is is “of great global public health concern.”

Xu Yao and colleagues, from the team that initially identified MCR, separately report a further discovery of a different MCR-NDM combination, from the initial analysis of human, food and animal samples that first yielded MCR. They found:

…one E. coli strain, THSJ02, recovered from a chicken wing sample purchased at a large supermarket in Guangzhou in July, 2014, was resistant to all antimicrobial drugs tested except doxycycline and tigecycline… This strain carried blaNDM-9, fosA3, rmtB, blaCTX-M-65, and floR, accounting for carbapenem, fosfomycin, aminoglycoside, cephalosporin, and florfenicol resistance, respectively, in addition to mcr-1 accounting for colistin resistance.

Here, they say, is why this is mysterious, and critical:

Recovery of an E. coli strain co-producing MCR-1, NDM-9, and FosA3 from chicken … is concerning since carbapenems and fosfomycin are not approved for use in food animals in China. Given that colistin and carbapenem-resistant E. coli can be found in retail meat, and that the resistance genes for crucial antimicrobials are located on conjugative plasmids, such strains might colonise the human intestinal tract and transfer the resistance plasmids to other Gram-negative pathogens, which might result in untreatable infections.

It’s been clear from the first identification of MCR that the use of last-ditch antibiotics in agriculture is driving its emergence—completely legal use in the case of colistin, as I explained in this analysis of European colistin-use statistics. It’s hard to know, at this point, where the resistance in these newest results comes from, since as the authors say those drugs are not used legally in Chinese livestock. Were they used without authorization? Did the resistance migrate from animals or livestock originating in countries with less oversight than China now applies? Or, since the finding came from an animal part that had been handled several times—at slaughter, while being butchered, while being packaged or displayed—does it represent human contamination, and from whom?

If there is any good news to be found in these reports, it is that MCR and NDM are not moving together. Both sets of researchers say that mcr-1 and the two varieties of the ndm gene are housed on separate plasmids, the mobile genetic elements that can move between organisms. So MCR and NDM resistance have not combined in a single mobile element. Nevertheless, as these dire resistance factors combine and move, it’s going to be crucial to try to identify their sources—possibly healthcare, possibly people in the community, very likely food—and to attempt to slow their march toward an invincible combination.

Previous posts in this series:

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Last-Ditch Resistance: More Countries, More Dire Results

An E. coli bacterium.
An E. coli bacterium.
Photograph by the Public Health Image Library, CDC.gov.

The frantic international hunt triggered by the discovery of genetically mobile resistance to colistin, a last-resort antibiotic, is producing many more findings this evening. The resistance factor is showing up in more countries, but, much more important, it has combined in some bacterial samples with genes conferring resistance to other potent drugs, creating bacteria that look effectively untreatable.

These disclosures are made in letters from research groups in a number of countries that are being published by the journal Lancet Infectious Diseases at 11:30pm London time, which is 6:30pm East Coast time here in the US. They represent evidence that this drug resistance, which was driven by agricultural use of colistin during the years that human medicine did not make use of it, is an imminently serious issue for human health.

“We’re watching our demise in real time,” Lance Price, PhD, a prominent resistance microbiologist and founder of the Antibiotic Resistance Action Center at George Washington University, who not involved in any of the research, told me. “I guess this is one of the advantages of next-generation DNA sequencing, is we can watch ourselves fall apart.”

Here’s a quick way to think about what follows. It’s natural to imagine that antibiotic resistance proceeds step-wise; that in the leapfrog between bug and drug, bacteria gain resistance to one drug, and then the next toughest drug presented to them, and then a last-resort drug after that. But in the wild, the way bacteria accumulate resistance DNA is more like being dealt cards in a hand of poker: one might have a 3, a 5, and a Jack, while another has a King, a Queen and a 10.

In these papers published tonight, researchers are finding bacteria that already possess colistin resistance— call it the Ace—and are accumulating the rest of a winning hand. Only, what looks like winning would be losing, for us. Here are the details:

Laurent Poirel and colleagues in Switzerland have identified an E. coli strain, recovered from an 83-year-old Swiss man who was hospitalized last month, that possesses both colistin resistance and also VIM resistance to the carbapenems, the family of antibiotics that was considered the last and toughest before colistin. The colistin-resistance gene shared a plasmid with genes conferring resistance to chloramphenicol, flofenicol and co-trimoxazole. The authors warn, “Such accumulation of multidrug resistance traits may correspond to an ultimate step toward pandrug resistance.”

Our data suggest that the advent of untreatable infections has already arrived.

Marisa Haenni and collaborators in France and Switzerland queried the Resapath network in France, which conducts surveillance for antibiotic resistance in animals, found that 21 percent of bacterial samples collected from veal calves on French farms between 2005 and 2014 carried the signal of mobile colistin resistance, the gene mcr-1. There were 106 positive samples (out of 517) and they came from 94 different farm properties. On seven of those isolates, the mcr gene lived alongside ones for ESBL resistance—that’s to penicillins and to the first three generations of cephalosporin drugs—and also genes for resistance to sulfa drugs and tetracycline.

Linda Falgenhauer and collaborators in the Reset consortium in Germany examined the sequences of 577 isolates taken from human patients and livestock and from the environment since 2009. They identified four carrying the mcr-1 gene, three from humans and one from a hog. The three from swine also possessed ESBL resistance; the one from the human was also carbapenem-resistant (KPC-2). One of the swine samples dated back to 2010. They say, somberly: “Our data suggest that the advent of untreatable infections has already arrived, as every colistin-resistant isolate described in this study is also resistant to either third-generation cephalosporins or to carbapenems.”

Surbi Malhotra-Kumar and colleagues at the University of Antwerp examined 105 E. coli strains collected from piglets and calves in 2011 in Belgium that had previously been identified as colistin-resistant. They found mcr-1 in 13 of them, and also found that it is being carried on a different plasmid than those identified in China and in Denmark. They descrcibe this as “a marked presence of mcr-1 in animal pathogenic bacteria in Europe, an indication that this is already a truly global phenomenon”— and also note that the 92 resistant strains that did not contain mcr might indicate other transferable colistin resistance that has not yet been identified.

In a separate letter, the same research group and several Vietnamese collaborators report mcr-1 in nine out of 24 E. coli collected from chickens and pigs in two provinces in Vietnam. One isolate contained resistance to eight additional drug families. They also screened 112 ESBL E. coli from three hospitals in Hanoi, but, they report, did not find any mcr.

Nicole Stoesser and colleagues from England and collaborators in Virginia and Bangkok examined sequences from a database of E. coli and Klebsiella collected in North America, Europe and Southeast Asia between 1967 and 2012, and found only a single isolate carrying mcr. It was taken frmo a child hospitalized in Cambodia in 2012, and also possessed ESBL resistance.

In Japan, Satowa Suzuki and collaborators from several institutions say they scoured the sequences of  1,747 plasmid genomes from Gram-negative bacteria, originally taken from human patients and livestock and from the environment, and found five animal isolates carrying mcr, but no human ones. None carried other resistance genes. They also examined a separate database of E. coli from livestock and, out of 9.308, found only two carrying mcr—but 88 others that were colistin-resistant.

And in the eighth letter, Mauro Petrillo and colleagues of the European Union’s Molecular Biology and Genomics Unit present a hypothesis for how the mcr-1 gene is being acquired.

There are some important leads in these reports: that mcr is in more countries,  is appearing on different plasmid backbones, and, apparently, seems more common in animals than in humans in the locations where it has been found. That may suggest, as the CDC said last month, that molecular analysis allowed this to be identified relatively earlier than other dire resistance factors have been in the past.

But the discovery that colistin resistance is combining in the same plasmids with other resistance genes should especially raise alarm bells. That indicates that using any of those drugs—some of which are very common—could amplify this resistance and and increase its spread. It signals that, as serious as mobile colistin resistance appeared at first, it is even more complex and more urgent.

Previous posts in this series:

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Tool-Using Parrots Use Pebbles to Grind Seashells

In the spring of 2013, Megan Lambert noticed the greater vasa parrots of Lincolnshire Wildlife Park doing something odd. They looked like they were licking the cockle shells that lined the floor of their outdoor enclosure. But when Lambert looked closer, she noticed that they were holding a pebble or date pit in their beaks, and rubbing these against the shells.

They were using tools.

Several birds can use tools. Woodpecker finches prise grubs from wood with twigs, New Caledonian crows do the same, Egyptian vultures drop rocks onto eggs to crack them open, and rooks can raise the water level of a pitcher by dropping stones into it, Aesop-style. But among the 300 species of parrot, tool use is relatively rare. Black palm cockatoos use rocks to drum on tree trunks, while hyacinth macaws use sticks to prise open nuts. The kea, a delightfully mischievous New Zealand parrot, can use and make tools in the lab, but no one knows if they do so naturally.

Thanks to Lambert’s observations, the greater vasa parrot joins this exclusive club. Native to Madagascar, the greater vasa is a bit of a goth parrot, eschewing the vibrant hues of its relatives in favour of black and dark grey plumage. They’re sociable and inquisitive, and will often explore and manipulate objects in captivity; while watching them, Lambert saw one thread a twig through the open links of a chain. That seemed like play. By contrast, the thing with the seashells was probably more purposeful.

Seashells are made of calcium carbonate, and birds need calcium to build the shells of their eggs. Lambert thinks that the vasas were using the pebbles and pits to grind down the cockles and liberate the calcium within them. Other egg-laying animals, including sandwich terns and gopher tortoises, have been seen eating seashells, presumably for the same reason. But the vasas are the only ones known to process the shells. “That’s particularly interesting because humans are the only other animals known to use tools for grinding,” says Lambert.

But if that’s the case, why is it that only male parrots ground the seashells? If they’re trying to get at calcium for egg-laying, surely the females should be at it? Possibly, but during courtship and sex, vasa males spend a lot of time feeding females with regurgitated meals. Perhaps the calcium content of those fluids is a signal of the male’s quality as a mate?

Regardless, the behaviour is certainly common. Over a few months, Lambert saw all ten of the park’s greater vasa parrots interacting with the seashells, and at least five of them grinding the shells with pebbles or pits. One particular bird, a male named JD, was an especially prolific tool-user.

He was also a prolific tool-donor. On 16 occasions, Lambert saw one of the female parrots nicking a tool from another—usually JD, who tolerated the “theft”. “It’s quite unique that tools are transferred directly between birds, as this is not commonly observed in the animal kingdom and may provide clues as to how this behaviour came about in the first place,” says Lambert.

So far, Lambert and her colleagues haven’t done any experiments with the parrots, which leaves a lot of unanswered questions. Do the birds learn to use the tools themselves, or do they pick it up from their peers? What’s the purpose of the behaviour, and does it actually influence the birds’ reproductive success? Do the parrots grind seashells, or use other tools, in the wild? And what else are these animals capable of?

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Foetal Cells Hide Out in Mum’s Body, But What Do They Do?

A mother’s children will remain part of her long after they leave her body and enter the world. This isn’t just a saying or a metaphor; it’s biological reality. Every foetus sends some of its own cells into its mother. They cross the placenta, travel through her bloodstream, and lodge in various tissues: brain, thyroid, breast, and more. And then, they stay there. Even after the baby is born, takes its first steps, learns to speak, goes to school, gets a job, and perhaps even becomes a parent itself, some of its cells linger on in its mother.

This phenomenon is called foetal microchimerism, a name that harkens back to the monstrous lion/goat/snake hybrid of Greek mythology. But human chimeras are neither monstrous nor mythical. As fellow Phenom Carl Zimmer wrote in 2013, “scientists are discovering that—to a surprising degree—we contain genetic multitudes”. Twins can pick up cells from their siblings while in the womb. People can end up with several genomes because they arose from two separate fertilised eggs that fused together. And since the 1970s, scientists have found that mothers can harbour their babies’ cells.

These transfers happen during the first trimester of pregnancy, when the placenta hooks up to the mother’s blood supply. The migrant cells are likely to be some type of stem cell: rather than being set in their ways as muscles or skin or neurons, they can transform into many types of tissue. Which type probably depends on where they end up. If they lodge in the breast, for example, they give rise to breast cells. This might explain why the cells are so long-lived. Although many are cleared out of the mother’s body by her immune system, those that infiltrate her tissues could hide out for years, perhaps decades, becoming a genuine part of her body.

But what, if anything, are these cells doing?

In mice, foetal cells accumulate at wounds and injuries, and stimulate the healing process; that might explain why they’ve also been found in healed C-section scars from human mothers. In the breast, thyroid, brain, heart, and skin, they’re sometimes found more frequently in cancerous or diseased tissues, but sometimes more so in healthy, normal tissues. The balance of helpfulness and harmfulness seems to vary from study to study (and since these results are all correlations, it’s possible that the cells have no effect at all).  But this picture, though apparently confused and contradictory, makes sense when viewed through the lens of evolutionary biology.

“Mothers and babies have shared interests, but also the potential for conflict because they don’t have completely shared genomes,” explains Amy Boddy from Arizona State University. “It may be optimal for a mother to invest resources in lots of offspring, while for any offspring, it would be optimal to monopolise those resources.”

Such conflicts aren’t deliberate or calculating. They play out through changes in hormone levels, the composition of milk, cries and smiles and tantrums—and perhaps microchimeric cells. In a new paper, Boddy and three other colleagues argue that such cells could provide a way a baby to inadvertently manipulate its mother’s body in ways that benefit it.

Some of those changes, like faster healing, benefit the mother too. Others may not. For example, foetal cells could stimulate the breast to make more milk, either by releasing certain chemical signals or by transforming into glandular cells themselves. That’s good for the baby but perhaps not for the mother, given that milk takes a lot of energy to make—mothers literally dissolve their own bodies to create it. And if the foetal cells start dividing too rapidly in the breast, they might increase the risk of cancer.

Similarly, the thyroid gland produces hormones that control body temperature. If foetal cells integrate there and start dividing, they could ramp up a mother’s body heat, to a degree that benefits her baby but also drains valuable energy. And again, if they divide uncontrollably, they might increase the risk of cancer. Indeed, thyroid cancer is one of the only types that’s more common in women than men, but is not a reproductive organ like the ovaries or breasts.

These subtle conflicts have played out over hundreds of millions of years, and mothers may have well have developed countermeasures. For example, breast tissues might slightly suppress lactation in anticipation that incoming foetal cells would enhance it. “Maybe in the breast, you’d need a certain amount of microchimeric cells to have a good milk supply,” says Athena Aktipis, another co-author on the paper. “These are all speculations but they emerge from taking this evolutionary framework.”

The point is that you’d expect foetal cells to both help and harm a mother, depending on the circumstances. “It’s a game of moves and counter-moves where the foetal system is trying to do more, and the maternal system is trying not to give in to every whim,” says Boddy.

The team are now thinking of ways of testing their hypotheses. It won’t be easy, especially since the ways in which scientists currently test for foetal microchimerism are pretty crude. The most common method is to look for DNA from the Y chromosome in the body of a pregnant woman. Obviously that doesn’t detect cells from female foetuses. It doesn’t even properly detect cells from male foetuses, since the Y chromosome is the smallest of the chromosomes and the most easily lost.

Most studies have also been fairly unambitious. They’ve simply asked: Are these cells there or not? Are there more of them in healthy tissues, or diseased ones with tumours or other problems? That’s a reasonable start but if they are more abundant in diseased tissues, what does that mean? Are they causing disease? Or are they simply flocking to inflamed or cancerous tissues—or wounds for that matter—because more blood rushes to such places?

“Instead of finding whether they’re there or not there, we should be trying to work out what they’re actually doing,” says Melissa Wilson Sayres, one of the co-authors of the new paper. That means collecting the foetal cells and sequencing them to work out which genes they are activating in different parts of the body. The team can then check if these patterns correspond to traits in the mother, like body temperature, or milk quality. “We’re hoping to have a workshop in the spring where we bring experimentalists and clinicians, brainstorm some testable hypotheses, and work out which of these are the most important from a clinical perspective,” Sayres adds.

And then, there’s the matter of cells that travel in the other direction—from the mother to the foetus. What do they do in their new homes? These paths can get even more complicated. It’s possible that the cells from one foetus can travel into its mother, hide out, and then into a sibling during a later pregnancy. “At one point, we started trying to draw family trees, and trying to work out where all the microchimerc cells could be going,” says Aktipis. “It got really messy.”

Reference: Boddy, Fortunato, Sayres, Aktipis. 2015. Fetal microchimerism and maternal health: A review and evolutionary analysis of cooperation and conflict beyond the womb. BioEssays. Http://dx.doi.org/10.1002/bies.201500059

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A Fossil Snake With Four Legs

Snakes can famously disarticulate their jaws, and open their mouths to extreme widths. David Martill from the University of Portsmouth did his best impression of this trick while walking through the Bürgermeister Müller Museum in Solnhofen, Germany. He was pointing out the museum’s fossils to a group of students. “And then my jaw just dropped,” he recalls.

He saw a little specimen with a long sinuous body, packed with ribs and 15 centimetres from nose to tail. It looked like a snake. But it was stuck in unusual rock, with the distinctive characteristics of the Brazilian Crato Formation, a fossil site that dates to the early Cretaceous period. Snake fossils had been found in that period but never that location, and in South America but never that early. The combination of place and time was unusual.

Tetrapodophis specimen. Credit: Dave Martill.
Tetrapodophis specimen. Credit: Dave Martill.

“And then, if my jaw hadn’t already dropped enough, it dropped right to the floor,” says Martill. The little creature had a pair of hind legs. “I thought: bloody hell! And I looked closer and the little label said: Unknown fossil. Understatement!”

“I looked even closer—and my jaw was already on the floor by now—and I saw that it had tiny little front legs!” he says. Fossil-hunters have found several extinct snakes with stunted hind legs, and modern boas and pythons still have a pair of little spurs. “But no snake has ever been found with four legs. This is a once-in-a-lifetime discovery.”

Tetrapodophis forelimb. Credit: Dave Martill.
Tetrapodophis forelimb. Credit: Dave Martill.
Tetrapodophis hindlimb. Credit: Dave Martill.
Tetrapodophis hindlimb. Credit: Dave Martill.

 

Martill called the creature Tetrapodophis: four-legged snake. “This little animal is the Archaeopteryx of the squamate world,” he says. (Squamates are the snakes and lizards.) Archaeopteryx is the feathered fossil whose mish-mash of features hinted at the evolutionary transition from dinosaurs to birds. In the same way, Martill says, the new snake hints at how these legless, slithering serpents evolved from four-legged, striding lizards.

There are two competing and fiercely contested ideas about this transition. The first says that snakes evolved in the ocean, and only later recolonised the land. This hypothesis hinges on the close relationship between snakes and extinct marine reptiles called mosasaurs (yes, the big swimming one from Jurassic World). The second hypothesis says that snakes evolved from burrowing lizards, which stretched their bodies and lost their limbs to better wheedle their way through the ground. In this version, snakes and mosasaurs both independently evolved from a land-lubbing ancestor—probably something like a monitor lizard.

Tetrapodophis supports the latter idea. It has no adaptations for swimming, like a flattened tail, and plenty of adaptations for burrowing, like a short snout. It swam through earth, not water.

It hunted there, too. Its backward-pointing teeth suggest that it was an active predator. So does the joint in its jaws, which would have given it an extremely large gape and allowed it to swallow large prey. And tellingly, it still contains the remains of its last meal: there are little bones in its gut, probably belonging to some unfortunate frog or lizard. This animal was a bona fide meat eater, and suggests that the first snakes had a similar penchant for flesh.

Martill thinks that Tetrapodophis killed its prey by constriction, like many modern snakes do. “Why else have a really long body?” he says. In particular, why have a long body with an extreme number of vertebrae in your midsection? None of the other legless lizards have that, even burrowing ones. Martill thinks that this feature made early snakes incredibly flexible, allowing them to throw coils around their prey.

Their stumpy legs may even have helped. It’s unlikely that Tetrapodophis used these limbs to move about, and they don’t seem to have any adaptations for burrowing. With tiny “palms” and long “fingers”, they look a little like the prehensile feet of sloths or climbing birds. Martill thinks that the snake may have used these “strange, spoon-shaped feet” to restrain struggling prey—or maybe mates.

Tetrapodophis catching a lizard. Credit: James Brown, University of Portsmouth
Tetrapodophis catching a lizard. Credit: James Brown, University of Portsmouth

But is it even a snake? “I honestly do not think so,” says Michael Caldwell from the University of Alberta, who also studies ancient snakes. He says that Tetrapodophis lacks distinctive features in its spine and skull that would seal the case. “I think the specimen is important, but I do not know what it is,” he adds. “I might be wrong, but that will require me to see the specimen first hand. I’m looking forward to visiting Solnhofen.”

It’s certainly possible that Tetrapodophis could be something else. In the squamates alone, a snake-like body has independently evolved at least 26 times, producing a wide menagerie of legless lizards. These include the slow worm of Europe, and the bizarre worm-lizard Bipes, which has lost its hind legs but has kept the stubby front pair. True snakes represent just one of these many forays into leglessness.

Susan Evans from University College London, who studies reptile evolution, is on the fence. “This happens every time a possible early snake is described,” she says. “Opinions on snake evolution are highly polarised.”  She says that Tetrapodophis has some features you’d expect from an early snake, and doesn’t easily fit into any other known group of squamates. The specimen is also more complete than many other recently alleged snakes, some of which are known only from fragments of vertebrae or jaw. “Unfortunately, the skull is poorly preserved and this complicates interpretation,” says Evans. “The most important thing is that it is now brought to notice and it will be thoroughly scrutinised by other workers.” Above all, she hopes that someone finds one with a better skull.

Martill insists that Tetrapodophis has “got loads of little things that tell you it’s a snake.” There’s the backwards-pointing teeth, the single row of belly scales, the way the 150 or so vertebrae connect to each other, and the unusually short tail. (In lizards and crocodiles, the tail can be as long as the entire body, but a snake’s tail—everything after the hip—is relatively short.) Some of these features are found in other legless lizards, but only snakes have all of them. And Martill adds that you just wouldn’t expect an ancestral snake to have all the features that its descendants picked up over millions of years of evolution.

He also teamed up with Nick Longrich at the University of Bath to compare Tetrapodophis’s features to those of both modern and fossil snakes. Their analysis produced a family tree in which Tetrapodophis came after the earliest known snakes like Eophis, Parviraptor, and Diablophis, but is still very much a snake.

But how could that be? Eophis and the others only have two legs, so how could four-legged Tetrapodophis have come after them? The answer is that evolution doesn’t proceed along simple, straight lines. Even if four-legged lizards gave rise to four-legged snakes, then two-legged snakes, then legless ones, the later stages don’t displace the former ones. For a long time, they would all exist together, in the same way that birds co-existed with the feathered dinosaurs that gave rise to them. (This, incidentally, is also the answer to that tired question: “If we evolved from monkeys, why are there still monkeys?”)

“At any one time in the Cretaceous, chances are you’ve got ten, twenty, maybe thirty species [of early snakes], all going off on their own evolutionary paths,” says Martill. “There would be a whole bunch of very snake-like lizards, all with the potential to become today’s snakes. One of them does. Maybe one of them goes off and loses its front legs and retains its back legs for 20 million years. One maybe loses its back legs and keeps its front legs—and we haven’t found that one yet.”

Reference: Martill, Tischlinger & Longrich. 2015. A four-legged snake from the Early Cretaceous of Gondwana. Science http://dx.doi.org/10.1126/science.aaa9208

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Single-Celled Creature Has Eye Made of Domesticated Microbes

The oceans are full of eyes. Giant squid scan the depths with the world’s largest ones, which are oddly similar to those of the sperm whales that hunt them. Mantis shrimps watch for prey using eyes that work like satellites. Starfish stare through the tips of their arms, chitons look up through lenses made of rock, and scallops peer at the water through dozens of eyes with mirrors inside them. But to see the strangest eyes of all—eyes so weird that we can’t even be sure that they are eyes—you have to squint.

These maybe-eyes belong to a group of rare, free-swimming algae called warnowiids. Each consists of a just one round cell, so small that a few hundred of which could fit in this full stop. Under the microscope, each warnowiid contains a conspicuous dark dot. This is the ocelloid. It consists of a clear sphere sitting in front of a dark red strip, and has components that resemble a lens, an iris, a cornea, and a retina.

Eyes are meant to be animal inventions. They’re supposed to comprise many cells. They are icons of biological complexity. And yet, here’s a non-animal that packs similar components into its single cell. Is the ocelloid actually an eye? Can it sense light? What does a warnowiid use it for? These questions are still mysteries, but in trying to answer them, Gregory Gavelis from the University of British Columbia has discovered something about the ocelloid that’s even weirder. At least two of its components—the “retina” and the “cornea”—seem to be made from domesticated bacteria.Warnowiid

The first scientist to notice the ocelloids was a German zoologist named Oscar Hertwig. In 1884, while working at a research station in Naples, he was distracted by a tiny speck in a Petri dish. It appeared to be jumping up and down in the water as if crying for attention. Hertwig sucked it up with a straw and stuck it in ethanol—which was a mistake. The creature started to disintegrate, and Hertwig speed-drew it as quickly as he could, until it had completely broken down. He then published his observations, describing what looks like an eye.

Karl Vogt, a more senior zoologist, wasn’t having any of it. He accused Hertwig’s of grossly misinterpreting a horribly distorted specimen. A single cell couldn’t possibly have an eye; instead, the creature must have just scavenged an eye from a dead jellyfish—and yes, some jellyfish have eyes. The debate raged back and forth until Hertwig, who never found a second warnowiid to study, moved on to other things (and great acclaim).

No one saw the creatures again until 1921, when Charles Atwood Kofoid and Olive Swezy showed that they live all over the Pacific coast of North America. They were rare, though, and many of the species that Kofoid and Swezy drew have never been seen since. This rarity makes warnowiids extremely hard to study. You can’t culture them. You can barely find them. “You’d be lucky if you ever saw more than five in a single Petri dish,” says Gavelis.

You can, however, study their genes. Sequencing technology has progressed to the point where scientists can parse the DNA of a single cell. Gavelis’s team, led by Brian Leander, used these techniques to study the “eyes” of two warnowiids—Erythropsidinium (the species that Hertwig drew) and Warnowia. In particular, he focused on a curved red structure called the retinal body, so named because it seems analogous to our light-detecting retinas.

Gavelis found evidence to support an old idea that the retinal body is a plastid—a type of compartment found inside the cells of plants and algae. The green chloroplasts that allow these organisms to make their own food, by harnessing the sun’s energy, are a type of plastid. They evolved from a free-living bacterium that was engulfed by an ancient cell and forced into servitude. Over time, this bacterium became an inextricable part of its host, and turned into the plastids we see today.

Cells can acquire plastids by engulfing and taming their own bacteria. Alternatively, they can steal someone else’s. The ancestor of the dinoflagellates—the group of algae that warnowiids belong to—did exactly this. It swallowed another red alga and claimed its plastids for its own.

In warnowiids, Gavelis thinks those pilfered plastids make up the retinal body. He dissected out these structures from the main ocelloids and amplified the DNA within them. Among these sequences, he found several active genes that are involved in photosynthesis and are only used in algal plastids. And when he repeated the same technique on entire cells, including the huge amount of DNA in the warnowiids’ main genomes, he found a far smaller proportion of photosynthesis genes.

 

Down the microscope, the team saw that the retinal body has physical features that are characteristic of plastids. Weirder still, it seems to sit within a network of interconnected plastids that look different, but are enveloped by a single membranous web. There could be just one plastid, or dozens of them. “They’re like drops of oil in a lava lamp,” says Gavelis. “The degree of specialisation in this one structure just boggled my mind.”

Gavelis also showed that the “cornea” of the ocelloid consists of little bean-shaped structures called mitochondria. Mitochondria also descend from free-living bacteria that were domesticated by ancient cells, in an extremely unlikely event that may have given rise to all complex life. For a few billion years, they have provided complex cells with power. In the warnowiids, they also… well, it’s not clear what they do. A continuous layer of them surrounds the “lens”, and seem to send small protrusions into it. They could be helping to collect light in the style of a true cornea, or they could be supplying the lens with energy.

That’s the biggest mystery about the ocelloid: what does it do? It certainly looks like an eye. It has components that would seem to focus light onto the retinal body. But for the retinal body to then respond to that light, it needs some kind of light-sensitive pigment. Chlorophyll is a possibility; the thing’s a plastid, after all. Gavelis’ team are also looking for traces of opsins—the proteins that are universally found in all animal eyes, from starfish to giant squid.

Even if the ocelloid is an eye, what could it possibly see? Fernando Gómez of the University of São Paulo recently told New Scientist that they help warnowiids to aim harpoon-like stings at their prey (he compared them to “snipers”). But Gavelis is sceptical. With just one ocelloid, each warnowiid has at most a one-pixel view of the world. “There were only so many things that it could do with such limiting processing power,” he says. “Even resolving an outline or a shadow is way beyond what anyone has demonstrated that a cell can do.”

Alternatively, the warnowiids could just be using their ocelloids to sense absolute light levels, so they can swim towards bright areas or keep in shade. But Gavelis isn’t happy with that idea either. Other dinoflagellates can sense light levels using much simpler eyespots, which have no lenses. The warnowiids must surely be putting their more complex structures to more complex uses.

Gavelis’ favoured idea is that they are looking for their prey: other dinoflagellates. These creatures reflect a particular kind of light called circularly polarised light, which could betray their presence. Perhaps the warnowiids use the ocelloids to detect this tell-tale signal, and swim towards the creatures that emit it.

Tom Cronin, a vision scientist at the University of Maryland, Baltimore County, is not convinced. “It’s a monstrous stretch,” he says. For a start, many other dinoflagellates eat their own kind and do so without complex ocelloids. Also, complex eyes don’t necessarily imply complex behaviour. The simple box jellyfish has 24 eyes, eight of which are surprisingly similar to our own camera-type peepers. “They have outstanding optics,” says Cronin, “but they’re primarily useful for orienting the animal, or for detecting edges of shadowed areas.”

Finally, he wonders if the ocelloid isn’t really an eye, but more of a “glorified chloroplast”. Maybe its function is to provide its owner with energy, and the “lens” is just a way of focusing more light? Maybe the eye-like elements help the creature to orient itself in the brightest direction?

“That’s inconsistent with the evolutionary history of these critters,” counters Gavelis. The earliest members of the group almost certainly made all of their own food through photosynthesis, but later members are almost totally predatory—and they’re the ones with the most complex ocelloids. Given that, the hunting hypothesis is looking good.

Solving this mystery will be hard, given how hard the warnowiids are to find and study. Cronin says, “In the end, we know more about the structure of the strange eye-like ocelloids, but their function is just as obscure as ever!”

Reference: Gavelis, Hayakawa, White, Gojobori, Suttle, Keeling & Leander. 2015. Eye-like ocelloids are built from different endosymbiotically acquired components. Nature http://dx.doi.org/10.1038/nature14593

 

 

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The Distributed Brainpower of Social Insects

Attenborough-brainsHere’s David Attenborough, chilling out on a rock in the middle of Africa, with four lumps of plasticine. The smallest one on the far left represents the brain of a bushbaby, a small primate that lives on its own. The next one is the brain of a colobus monkey, which lives in groups of 15 or so. The one after that is a guenon, another monkey; group size: 25. And on the far right: a baboon that lives in groups of 50. “Were you to give a skull to a researcher who works on monkeys, even though they didn’t know what kind of monkey it belonged to, they would be able to accurately predict the size of group in which it lived,” says Attenborough.

That sequence, from The Life of Mammals, is a wonderful demonstration of the social brain hypothesis—a bold idea, proposed in the 1980s, which suggests that living in groups drove the evolution of large brains. Social animals face mental challenges that solitary animals do not: they have to recognise the other members of their cliques, cope with fluid and shifting alliances, manage conflicts, and manipulate or deceive their peers. So as social groups get bigger, so should brains. This idea has been repeatedly tested and confirmed in many groups of animals, including hoofed mammals, carnivores, primates, and birds.

What about insects? Ants, termites, bees, and wasps, also live in large societies, and many of them have unusually big brains—at least, for insects. But in 2010, Sarah Farris from West Virginia University and Susanne Schulmeister from the American Museum of Natural History showed that in these groups, large brains evolved some 90 million years before big social groups. If anything, they correlated with parasitic body-snatching rather than group-living.

“That got people thinking,” says Sean O’Donnell from Drexel University. “In recent years, there’s been a growing rumbling, almost subterranean movement arguing that social brain ideas may not apply to the social insects.” His new study is the latest addition to that movement.

O’Donnell’s team studied potter wasps, which lead solitary lives, and the closely related paper wasps, which live in colonies of varying sizes and complexities. They collected queens and workers from 29 species of these wasps, carefully dissected their brains, and measured the size of their mushroom bodies—a pair of structures in insect brains that control higher mental abilities like learning and memory.

And to their surprise, they found that as the wasp colonies got bigger, their mushroom bodies got smaller. Even within the social paper wasps, the team found that species with distinct queens and workers—a sign of a more complex society—have similarly sized mushroom bodies to those with no such castes.

“The pattern is so clear,” says O’Donnell. “Sociality may actually decrease demands on individual cognition rather than increasing it.”

“Here we have the first concerted evidence that costly brains aren’t needed to allow sociality, when you can do it other ways,” says Robin Dunbar, who first proposed the social brain hypothesis. “There are many routes to sociality.”

What other routes? O’Donnell notes that insects and (most) mammals build their societies in fundamentally different ways. Large mammal societies typically include individuals who are distantly related or even unrelated. Insect societies, by contrast, are basically gigantic families, where all the members are either queens (which reproduce) or their descendants (which do not). You could view these colonies less as groups of individuals and more as extensions of the queens.

As such, their members don’t particularly need to keep track of shifting relationships, or manage conflicts, or manipulate their peers, or any of the other social challenges that, say, a baboon or a human faces. They have less of a need for bigger and more sophisticated brains.

Social insects also benefit from swarm intelligence, where individuals can achieve astonishing feats of behaviour by following incredibly simple rules. They can build living buildings, raise crops, vaccinate themselves, and make decisions about where to live. In some cases, they make decisions in a way that’s uncannily similar to neurons—a colony behaves like a giant brain, and in more than a merely metaphorical way. They have a kind of ‘distributed cognition’, where many of the mental feats that other animals carry out using a single brain happen at the level of the colony.

Entomologist Seirian Sumner from Bristol University says that there are mammals, like meerkats and banded mongooses, which live in simple societies where adults cooperatively raise their young. These are often compared to primitively social insects, like paper wasps. “They share very similar family structures, group sizes and plasticity in behavioural roles,” Sumner says. It would be very interesting to see if the brains of these mammals follow the same patterns as those of O’Donnell’s wasps.

O’Donnell is all in favour of more studies. He wants to see if the same patterns hold in other insect groups that include both social and solitary species, including bees and cockroaches. And he’s intrigued by the naked mole rats—colonial mammals that have queen and worker castes, much like ants and wasps. “If our ideas are correct, we’d expect to see mole rats following a similar pattern to insects,” he says.

Reference: O’Donnell, Bulova, DeLeon, Khodak, Miller & Sulger. 2015. Distributed cognition and social brains: reductions in mushroom body investment accompanied the origins of sociality in wasps (Hymenoptera: Vespidae). Proc Roy Soc B. Citation tbc.

PS: The size of brain regions isn’t always the best indicator of intelligence. I asked O’Donnell about this, and he stands by his decision to focus on the mushroom bodies. “It’s definitely a blunt tool for studying brain evolution,” he says. “Brain tissue is metabolically very expensive, and even if it was just filler, tissue weight is a big deal, especially for a flying insect. We expect there to be really strong constrains on the size of the [mushroom bodies].”

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Octopuses, and Maybe Squid, Can Sense Light With Their Skin

Octopuses, squid, and cuttlefish, the animals collectively known as cephalopods, are capable of the most incredible feats of camouflage. At a whim, they can change the colour, pattern, and texture of their skins to blend into the background, baffle their prey, or communicate with each other.

As if that wasn’t amazing enough, Lydia Mäthger and Roger Hanlon recently discovered that the common cuttlefish has light-sensitive proteins called opsins all over its skin. Opsins are the engines of sight. Even though animal eyes come in a wondrous variety of shapes and structures, all of them use opsins of one kind or another. The discovery of these proteins in cuttlefish skin suggested that these creatures might be able to sense light over their entire surface, giving them a kind of distributed “sight”.

It was a tantalising suggestion, but far from a definitive one. Opsins are used in many other contexts, such as sensing the time of day, which still involve detecting light but have nothing to do with seeing images. To work out what exactly opsins are doing in cephalopod skin, the team needed more evidence.

For example, when opsins are struck by light, they change shape. This triggers a Rube Goldberg-esque chain of further changes in other proteins, which culminates in an electrical signal travelling through a nerve towards the brain. That’s the essence of vision. It’s what happens in a cephalopod’s eye. Does it also happen in their skin?

That’s exactly what Alexandra Kingston from the University of Maryland, Baltimore County decided to find out. Working with Hanlon and vision expert Tom Cronin, Kingston studied the skins of the longfin inshore squid, the common cuttlefish, and the broadclub cuttlefish, looking for proteins that act downstream of opsin.

She found them. Several of them are present in the animals’ skin, and only in the chromatophores—the cells that are primarily responsible for their shifting patterns. Each chromatophore is an elastic sac of pigment, surrounded by a starburst of muscles. If the muscles relax, the sac contracts into a small dot that’s hard to see. When the muscles contract, they yank the sac into a wide disc, revealing the colour it contains. Kingston showed that these living pixels contain the same Rube Goldberg set-up that exists in their owners’ eyes.

Her team couldn’t, however, show that the chromatophores actually respond to light. “All the machinery is there for them to be light-sensitive but we can’t prove that. It’s been very frustrating,” says Cronin. The chromatophores might be detecting local light levels to prime them for either expansion or contraction. They could communicate with each other so that small clumps of chromatophores react to light as a unit. Or they could send signals directly to the brain to provide their owners with more information about light levels in their environment. These possibilities could all be right or wrong; no one knows.

“We don’t know if they contribute to camouflage or are just general light sensors for circadian cycling or are driving hormonal changes. They have a job to do but we don’t know what it is,” says Cronin. “That’s biology!” he adds, resignedly.

Cuttlefish. Credit:  Peter Hellberg
Cuttlefish. Credit: Peter Hellberg

Meanwhile, Desmond Ramirez and Todd Oakley from the University of California, Santa Barbara had better luck with a different cephalopod—the California two-spot octopus. When the duo shone bright light onto isolated patches of skin, they found that the chromatophores would dramatically expand. They called this light-activated chromatophore expansion, or LACE.

Ramirez and Oakley showed that the octopus’s skin also contains opsin, but not in the chromatophores. Instead, its opsins reside in small hair-like structures called cilia. People used to think that the octopus used these cilia as organs of touch; they still could be, but they might also detect light too. And echoing Cronin, Oakley says, “We don’t know yet how this is used, or indeed if it is used, in the living animal.”

ColorLACE(1)Neither study is definitive, but they certainly complement each other. They strengthen the case that these animals really are detecting light with their skins, independently of their brains and eyes.

They also serve as useful reminders that cephalopods are a diverse group of very different animals, with different branches separated by over 280 million years of evolution. It shouldn’t be surprising that octopus skin readily responds to light, but squid and cuttlefish skin doesn’t seem to. Or that, in octopus skin, opsins are found in cilia, while in squid and cuttlefish, they live in chromatophores.

They behave differently, too. “Cuttlefish and squid do seem to display to each other more than octopuses,” says Cronin. “Octopuses do pattern dramatically in response to environmental changes, but we don’t know of displays in octopuses designed for other octopuses.” Perhaps each species uses its skin opsins for different tasks.

Reference: Ramirez & Oakley. 2015. Eye-independent, light-activated chromatophore expansion (LACE) and expression of phototransduction genes in the skin of Octopus bimaculoides. Journal of Experimental Biology http://dx.doi.org/10.1242/jeb.110908

Kingston, Kuzirian, Hanlon & Cronin. 2015. Visual phototransduction components in cephalopod

chromatophores suggest dermal photoreception. Journal of Experimental Biology. http://dx.doi.org/10.1242/jeb.117945

One for the Beasts

I like dinosaurs. A lot. Their bones were what first inspired me to start asking questions about the past and, many years later, set me on a path of professionally puzzling over prehistory. But I can’t give all the credit to fantastic saurians.

Mammals have always been part of my ancient education, even when they were shadows of the Cenozoic that I overlooked in favor of Apatosaurus and company. Plastic effigies of Uintatherium were stashed inside plastic bags of scaly monsters I got from the supermarket toy aisle, elephants trussed up as shaggy mammoths tromped through the movies I’d stay up late to watch, and no museum visit was complete without stopping to gaze at the bizarre bones of the giant ground sloths. I feel sorry that I didn’t fully appreciate them earlier. They’re both strange and familiar – animals that are perhaps easier to envision, but difficult to truly understand.

Not that mammals were restricted to the time after the non-avian dinosaurs were ushered off the evolutionary stage. The first mammals evolved over 220 million years ago, back when crocodile cousins were in the limelight and dinosaurs were marginal players. And while mammals stayed small as dinosaurs rose to dominance, the beasts nevertheless took on an array of ecological roles that included swimmers, burrowers, gliders, and more. The catastrophic finale of the Cretaceous is what let the surviving mammals go from understudies to leads, and many of them were as spectacular as any dinosaur.

That’s what makes the present so frustrating. The world is still populated by a wonderful assortment of mammals, but, as paleontologist Jessica Theodor notes in the Dinologue video below, extinction has removed some of the stars. In the deserts and alpine forests around my Utah home, for example, I should still be able to find elephants, camels, ground sloths, sabercats, and more. But I can’t. These communities, which had been evolving for tens of millions of years, were stripped down within the last 8,000 years by natural and human-caused triggers that are still hotly debated by specialists.

We shouldn’t forget these mammals and their forebears. Understanding the mammals of the past, and how they responded to phenomena such as rapid climate change, may help us get at least a rough sketch of what may happen in the future. Their old bones record how life responds to alterations and fluctuations, and what held true for fossil mammals may provide clues about the fate of living species. Fossil beasts aren’t dead history, Theodor reminds us. They’re an essential part of the continuing story of life:

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Could Mothers’ Milk Nourish Mind-Manipulating Microbes?

Breast milk seems like a simple nutritious cocktail for feeding babies, but it is so much more than that. It also contains nutrients that feed the beneficial bacteria in a baby’s gut, and it contains substances that can change a baby’s behaviour. So, when a mother breastfeeds her child, she isn’t just feeding it. She is also building a world inside it and simultaneously manipulating it.

To Katie Hinde, an evolutionary biologist at Harvard University who specialises in milk, these acts are all connected. She suspects that substances in milk, by shaping the community of microbes in a baby’s gut, can affect its behaviour in ways that ultimately benefit the mother.

It’s a thought-provoking and thus far untested hypothesis, but it’s not far-fetched. Together with graduate student Cary Allen-Blevins and David Sela, a food scientist at the University of Massachussetts, Hinde has laid out her ideas in a paper that fuses neuroscience, evolutionary biology, and microbiology.

It begins by talking about the many ingredients in breast milk, including complex sugars called oligosaccharides. All mammals make them but humans have an exceptional variety. More than 200 HMOs (human milk oligosaccharides) have been identified, and they are the third most common part of human milk after lactose and fat.

Babies can’t digest them. Instead, the HMOs are food for bacteria, particularly the Bifidobacteria and Bacteroides groups. One strain in particular—Bifidobacterium longum infantis—can outcompete the others because it wields a unique genetic cutlery set that allows it to digest HMOs with incredible efficiency.

Why would mothers bother producing these sugars? Making milk is a costly process—mums quite literally liquefy their own bodies to churn out this fluid. Obviously, it feeds a growing infant, but why not spend all of one’s energy on filling milk with baby-friendly nutrients? Why feed the microbes too? “To me, it seems incredibly evident that when mums are feeding the microbes, they are investing on a greater return on their energetic investment,” says Hinde. By that, she means that setting up the right communities of microbes provides benefits for the baby above and beyond simple nutrition.

By taking up space and eating all the available food, B.infantis and its peers make it harder for pathogens—microbes that cause disease—to establish themselves. The HMOs deter these invaders more directly. Many pathogens launch their invasions by first recognising sugar molecules on the surface of intestinal cells. HMOs resemble those sugars, and so act like floating decoys that draw pathogens away from the gut itself. So, breast milk selects for beneficial microbes while also warding off harmful ones. It sets babies up with the right pioneers.

It’s important to get these first communities right. They steer the development of the immune system, creating a balanced set of sentries that can detect and respond to pathogens, without also going berserk at innocuous triggers like pollen or dust.

There’s also increasing evidence, at least in mice, that gut microbes can shape the early development of the nervous system. They can communicate with the brain via the vagus nerve—a long phone line that carries messages between the brain and gut. They can also release signalling chemicals like dopamine and serotonin. Through these means, they can affect an animal’s behaviour. Some groups have shown that mice which grow up inside sterile containers behave differently to their normal colonised peers: they tend to be less anxious and take more risks. And some teams have shown that specific microbes can reduce anxiety in normal, healthy rodents.

These mind-manipulating properties might be really useful to mothers. Parenting is costly. It takes time and energy. It’s in a baby’s best interests to monopolise as much of that effort as possible, so they get the strongest start in life. Mums, however, have to divide their effort over many children, both present and future ones. If they expend too much effort on one, they might not be in good enough shape to have more. If they can wean their current infant earlier, they can have another sooner.

These aren’t conscious decisions, mind you. I’m not trying to portray mums as cold and calculating. But it’s important to note that from a cold evolutionary standpoint, mothers and babies have slightly conflicting interests. Simply put, infants will tend to demand more investment than is ideal for a mother to give, and evolution has crafted ways for infants to get that investment—think of smiling, crying, nuzzling, and tantrums. Similarly, mothers should have countermeasures for giving themselves an edge in these inevitable conflicts.

Hinde thinks that the HMOs might act as one such countermeasure. If these sugars can nourish specific microbes, and if certain microbes can change a baby’s behaviour, then mothers could potentially change the HMO content o their milk to influence their babies. The infants might become less demanding. They might be less active, and spend more energy on simple growth rather than on play or exploration. They might be less anxious and more likely to become independent earlier.

Again, this isn’t far-fetched. In her own research, Hinde showed that the milk of younger monkey mothers contains fewer calories but more cortisol—a hormone involved in stress. Babies that drink this cortisol-laden milk tend to be more nervous and less exploratory. They also grow faster. Perhaps these things are connected. The cortisol could be a mother’s way of saying: “Don’t waste the precious calories in my milk; focus on getting bigger.” And perhaps the HMOs might convey similar messages, via microbial messengers.

“I liked the paper,” says John Cryan from University College Cork. “It further emphasises the importance of microbiota-brain interactions  in early life for health and development, and positions HMOs as positive drivers of such interactions. Indeed, this is very plausible.”

Plausible and, more importantly, testable. Scientists could see if different sets of HMOs promote the growth of bacteria that can affect the brain. What kinds of signalling chemicals are those microbes making? Do they affect parts of the brain involved in controlling emotions or motivation? Do these effects lead to noticeable changes in a baby’s behaviour? “Then we can look backwards at what are the HMOs that are really influencing the establishment and maintenance of those particular bacteria,” she says. If you load those specific microbes into germ-free mice, and load them with those specific HMOs, what happens?

“We can also look at the variation and abundance of those HMOs in various settings,” says Hinde. “Winning” the evolutionary conflict between parent and child might matter more to mothers who live in risky environments where food is scarce, or where they spend much of their energy on fighting diseases or evading predators. Likewise, younger mothers who are still growing might also fare better if they reserve more of their energy for themselves.

“This is likely to remain hypothetical for quite some time,” Hinde admits. “In humans, there’s hundreds of bacterial strains and oligosaccharides. Understanding what each one does will take forever, much less their complex interactions.” But as she writes in her paper: “An evolutionary perspective allows us to appreciate the essential tensions within the mother-infant dyad and recognize that the infant’s microbial ecology is a potential landscape for negotiating conflict and maintaining coordination. Among the many, many bacteria in the infant gut, may be lurking mother’s littlest helpers.”

Besides, as Hinde says, “Microbes are so hot right now.”

There will be more about milk, microbes, and mums in my upcoming book, I CONTAIN MULTITUDES, out next year.

Reference: Allen-Blevins, Sela, & Hinde. 2015. Milk Bioactives May Manipulate Microbes to Mediate Parent-Offspring Conflict. Evolution, Medicine, and Public Health. http://dx.doi.org/10.1093/emph/eov007  

More on milk:

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Fish that Walks on Land Swallows With Tongue Made of Water

In the distant past, between 350 and 400 million years ago, a group of our fishy ancestors started crawling up on land. The fins that propelled them through the water gradually evolved into sturdy, weight-bearing limbs. Their hind legs connected directly to their hips, which became bigger. Swimming fish became walking, four-legged tetrapods, such as amphibians, reptiles, and mammals.

Scientists have studied the evolution of tetrapod limbs and skeletons in incredible detail, but other aspects of our invasion of land are less clear. How, for example, did our pioneering ancestors eat?

Many fish feed by sucking. As they open their jaws, a horseshoe-shaped bone called the hyoid pushes down on the floor of the mouth, expanding it, and creating a flow of water that draws prey inside. Even species that take bites and nibbles rely on a similar suction to swallow food once it’s inside their mouths.

This technique works because fish are constantly surrounded by water. It doesn’t work on dry land. Fortunately, tetrapods solve that problem with a muscular tongue, which helps to move food from the mouth to the throat. Once again, the hyoid is involved—it’s the bone that the tongue is attached to. But how did this structure evolve? How did the hyoid go from being a bone that creates suction to one that moves a tongue? How did the first tetrapods swallow?

These questions have been hard to answer because very few fossils of early tetrapods contain decent traces of the hyoid. But Krijn Michel from the University of Antwerp tried a different tactic: he studied a delightful fish called the Atlantic mudskipper. This tiny creature looks like a tiny doorstop with a pair of fins and googly eyes, and it lives throughout the mangrove swamps of eastern Africa, the Indian Ocean, and the western Pacific. It spends a surprising amount of time on land. It hauls itself about on its fins, fighting, mating, and foraging in the open air.

Michel filmed Atlantic mudskippers with high-speed cameras as they sucked up pieces of shrimp that had been placed on dry surfaces. As he reviewed the videos, he noticed something odd. In the moments after a mudskipper leans forward and opens its mouth, a small bubble of water protrudes from its open jaws. The water spreads over the morsel of food, which the mudskipper envelops with its mouth. It then sucks both morsel and water back up.

The water acts like a tongue—a “hydrodynamic tongue”, in Michel’s words. It allows the fish to lap up its food and then swallow it.

Michel showed how important the ‘tongue’ is by placing morsels of shrimp on an absorbent surface and filming the mudskippers with X-ray video cameras. This time, as the mudskippers leant in, their watery tongues were drained away. They could still grab the shrimp in their jaws but they couldn’t swallow. On 70 percent of their strikes, they had to return to water before they could gulp down their mouthfuls.

This explains why mudskippers almost always fill their mouths with water before they come out on land. By keeping that watery tongue, they can swallow several mouthfuls before having to return to the water. By contrast, the eel-catfish, which also ventures onto land but doesn’t use the same trick, must always return to water after it has grabbed its prey.

“These findings suggest that swallowing food in air may have been a substantial problem for the transition from water to land during vertebrate evolution,” says Beth Brainerd from Brown University. “When early tetrapods started feeding on land, they had to evolve a new way to move food to the back of the throat for swallowing.”

Did they use a watery tongue, a la mudskippers? Perhaps, but it’s important to remember that these are modern fish, and not tetrapods-in-the-making. Hundreds of millions of years of evolution separate them from our land-colonising ancestors. At most, they can hint at the kinds of strategies that early tetrapods might have used when they moved onto land.

A watery tongue, for example, could have provided a workable interim solution, allowing the animals to feed successfully while their hyoids changed and they developed muscular tongues. Indeed, when Michel trained his X-ray cameras on a fish and a newt, to watch how their hyoids moved when they ate, he found that the newt’s movements more closely resembled those of the mudskipper. The bone’s making the right sort of movements, even if there’s no muscular organ attached to it.

Reference: Michel, Heiss, Aerts & Van Wassenbergh. 2015. A fish that uses its hydrodynamic tongue to feed on land. Proc Roy Soc B  http://dx.doi.org/10.1098/rspb.2015.0057

PS: Fish do have “tongues” but the term is a loose parallel; unlike our muscular organs, these tongues (usually) can’t stick out of the mouth, and they don’t help with swallowing. They can, however, help with chewing.