Monday, September 22, 2025

 

Snapdragon secrets



ISTA scientists collect snapdragon flowers in the Pyrenees to trace their ancestry



Institute of Science and Technology Austria

A hybrid snapdragon. 

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A hybrid snapdragon. Snapdragons are usually magenta or yellow. In the valley of Planoles in Spain, these two types come together, forming hybrid plants in a variety of colors. 

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Credit: © Daria Shipilina / ISTA






Every season, scientists from the Institute of Science and Technology Austria (ISTA) go on field trips to the Pyrenees. Their mission: gather snapdragon flowers to understand their genetic makeup. In a recently published study in Molecular Ecology, they show how nature uses color genes to keep two varieties of snapdragons distinct, even when they share the same habitat. 

On the border between France and Spain lies a mountain range that spans from the Bay of Biscay to the Mediterranean Sea. The lush valleys and high peaks attract many tourists to the Pyrenees, known as “Pireneus” in Catalan.

Arka Pal, a biologist and PhD student from the Barton group at the Institute of Science and Technology Austria (ISTA), visits the region for a different reason. He comes to collect snapdragons or Antirrhinum—a vibrant plant that, when squeezed, resembles the jaws of a dragon. Together with an international team of scientists, Pal’s newest publication highlights the importance of flower color genes that keep two snapdragon varieties separated in several valleys across the Pyrenees, although they hybridize and occupy the same space.

Collecting snapdragons

For the past 17 years, scientists from the Barton group have been travelling to Planoles—a Spanish village situated 1,135 meters above sea level, near the Río Rigat and the French border—looking for snapdragons. Each field season, around 20 researchers reside in a small hut, venture into the picturesque surroundings and collect over 5,000 samples.

“You could romanticize it and say we are hiking,” Pal jokes. “But Antirrhinum likes to grow in human-disturbed habitats, often alongside mountain roads. So, we walk these beautiful roads in the Pyrenees, sporadically climbing steep slopes through brambles and nettles to collect snapdragons.”

When in bloom, snapdragons are easy to spot with their striking yellow or magenta petals. When they are not, the scientists rely on identifying their leaves. Pal and his colleagues keep records of the plants’ growth and their GPS locations, and collect both flowers and leaves for processing back in the hut. There they assess the color of their samples, score how much magenta or yellow they have, and take pictures of the flowers from different angles. Additionally, they dry the leaves in silica gel and put them in envelopes to bring them back to ISTA to genetically analyze them.

What drives the Barton group to invest such effort in studying these plants? What deeper insights into evolution does the color of a snapdragon reveal?

Hybrid zones – nature’s laboratory

Pal is interested in how speciation happens—how different varieties emerge from a common ancestor and separate over time. In the valley of Planoles, two varieties of Antirrhinum—distinguished by their vibrant yellow (A. majus striatum) and magenta flowers (A. majus pseudomajus)—come together and hybridize naturally. During the last ice age, the two Antirrhinum varieties were geographically isolated in different parts of the Pyrenees. As the ice melted, they likely gradually spread along the valley from opposite directions, forming a so-called ‘hybrid zone.’

“Hybrid zones are essentially ‘natural laboratories’ where you can study the process of speciation and evolution in nature, letting nature conduct the experiments for us instead of crossing them in greenhouses,” says Pal. The magenta and yellow snapdragons form a narrow strip, roughly 1 km in length, where they hybridize to produce a kaleidoscope of colors.

The genetic encyclopedia

Planoles is not the only hybrid zone in the Pyrenees. A very similar one also exists 100 km to the west, near the town of Avellanet. The Barton group collected samples there, too. In his latest study, Pal compared both hybrid zones to understand how evolution has shaped them. Back at ISTA, Pal analyzed the two sets of samples to see whether their genomes look the same.

“You can think of the genome as an ‘encyclopedia of words.’ Within this encyclopedia, there are billions of letters which make up thousands of words—our genes. Yet, only a few key ‘words’ are important to keep species or varieties separated,” says Pal.

“The same bee species pollinates both the yellow and the magenta species. Bees learn where to go to find nectar. On the magenta side, they visit magenta flowers, while on the yellow side, they frequent yellow ones,” Pal says. Hybrids do not attract as many bees due to their lack of distinct color contrast required for bees to learn, resulting in reduced fitness and fewer offspring.

For snapdragons, the key trait is the flower color, which attracts pollinators and is essential for survival and passing genes onto the next generation. Despite sharing most genetic ‘words,’ only a few critical genes—seven to be specific—determine flower color and remain unique to each species. These genes, with names as alluring as those of Pokémon, include RoseaElutaRubiaSulfureaFlaviaAurina, and Cremosa.

Color genes eclipse proximity

To tackle this data set, Pal made use of whole-genomic sequencing—a tool commonly used to map the DNA of humans and other animals. In this case, he and his team employed a novel sequencing technique that had previously been untested for Antirrhinum. Unlike well-studied organisms such as mice or Arabidopsis thaliana plants, where more genomic data exists, this large-scale sequencing of snapdragon genomes involved a process that resembled piecing together a vast puzzle.

“When we compared the Planoles and Avallenet hybrid zones, we found their genomes were quite different—they all had different mixtures of ‘words.’ But the seven genes that control the flower color were the same in both zones,” explains Pal. Those genes, act like keywords that stay consistent.

In hybrid zones, one would expect nearby plants to be closely related to each other. But when the researchers traced the plants’ genetic ancestry, they discovered that the flower color genes did not follow that pattern. The seven genes in the yellow snapdragons from the Planoles zone were more closely related to those in the yellow plants in the Avellanet zone. The same was true for magenta plants too.   

Pal’s new study reveals that, although there is a lot of genetic variation between the zones, the genes responsible for flower color have a shared evolutionary history. This finding is important—it suggests these color genes help snapdragons remain distinct and recognizable, even when they grow in the same environment, and share other genes across their extensive genome.

Beneath 300 kilometers: Natural evidence for nickel-rich alloys in the mantle






The Hebrew University of Jerusalem

Slice of South African diamond with inclusion-rich zones and laser ablation pits from microanalysis 

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A diamond slice of a South African diamond showing various inclusion-rich zones and laser ablation pits from microanalytical sampling.

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Credit: Yaakov Weiss






Diamonds from South Africa’s Voorspoed mine have revealed the first natural evidence of nickel-rich metallic alloys forming deep in Earth’s mantle, between 280–470 km. A new study reveals that these inclusions coexist with nickel-rich carbonates, capturing a rare snapshot of a “redox-freezing” reaction whereby oxidized melts infiltrate reduced mantle rock. The growing diamond trapped both reactants and products of a diamond-forming reaction. This finding not only confirms long-standing predictions about mantle redox conditions but also highlights how such processes may fuel diamond formation of volatile-rich magmas that erupt from hundreds of kilometers and bring the diamond to the surface.

Link to pictureshttps://drive.google.com/drive/folders/1k3N3VldHzvpJ38LFIuPG4xjG-igObO5y?usp=sharing

[Hebrew University of Jerusalem]– The Earth’s mantle is a restless, enigmatic engine that powers volcanism, recycles crust, and regulates the long-term evolution of the planet. But one of its most elusive characteristics—the redox state, or the balance of oxidized and reduced chemical species—remains difficult to measure directly. A new study led by Yael Kempe and Yaakov Weiss, from the Hebrew University’s Institute of Earth Sciences, offers a rare glimpse into these deep processes, captured within nano- and micro-inclusions in diamonds from South Africa’s Voorspoed mine.

A Rare Discovery in the Depths

For decades, models and high-pressure experiments have suggested that nickel-rich metallic alloys should stabilize in the mantle at depths of roughly 250–300 km. Yet, natural samples confirming these predictions have been vanishingly scarce.

Working with colleagues from the University of Nevada, the University of Cambridge, and the Nanocenter at the Hebrew University, Weiss’s team has now identified nickel-iron metallic nanoinclusions and nickel-rich carbonate microinclusions preserved inside diamonds that formed between 280–470 km below Earth’s surface. These inclusions represent the first direct evidence of nickel-rich alloys at their predicted depth—a long-sought validation of mantle redox models.

The diamonds’ mineral cargo also includes coesite, K-rich aluminous phases, and molecular solid nitrogen inclusions, providing multiple pressure markers that firmly constrain their origin to the deep upper mantle and shallow transition zone.

Redox Snapshots Frozen in Carbon

The significance of the find goes beyond simple confirmation of theoretical models. The coexistence of nickel-iron alloy and nickel-rich carbonate points to a metasomatic redox-freezing reaction—a dynamic interaction in which an oxidized carbonatitic-silicic melt infiltrated reduced, metal-bearing peridotite. It joins earlier evidence from shallower depths that this is the main mode of formation of natural diamonds.

In this environment, preferential oxidation of iron relative to nickel drove enrichment of the residual alloy in nickel. At the same time, nickel-rich carbonates and diamonds crystallized from the melt. In effect, the diamonds froze a fleeting geochemical moment: the conversion of a reduced mantle rock into a more oxidized, volatile-rich domain and the reduction of carbonates to form diamonds.

“This is a rare snapshot of mantle chemistry in action,” says Weiss. “The diamonds act as tiny time capsules, preserving a reaction that would otherwise vanish as minerals re-equilibrate with their surroundings.”

Implications for Mantle Dynamics and Magmatism

These findings carry broad implications. If localized metasomatic reactions periodically oxidize small portions of the mantle, they may help explain why some inclusions in other superdeep diamonds record unexpectedly high oxidized conditions.

Such processes also shed light on the origins of volatile-rich magmas. The enrichment of mantle peridotite in carbonate, potassium, and incompatible elements during these redox events could prime the mantle for the later formation of kimberlites, lamprophyres, and even some ocean island basalts. In other words, the tiny inclusions in Voorspoed diamonds hint at large-scale links between subduction, mantle redox dynamics, and the generation of magmas that shape continents and bring diamonds to the surface.

Diamonds as Mantle Witnesses

The study underscores the scientific value of diamonds as more than just gemstones. Their inclusions—whether nanometer-scale alloys or high-pressure minerals—offer one of the only natural records of conditions hundreds of kilometers beneath our feet.

Kempe and Weiss’s work marks a milestone: the first natural confirmation of nickel-rich alloys at mantle depths predicted by theory, and a vivid illustration of how the deep Earth’s redox landscape evolves through melt-rock interaction.

As researchers continue to probe these mineral time capsules, we may find that diamonds, once symbols of permanence, are also storytellers of change—bearing witness to the mantle’s hidden chemistry and the processes that continue to shape our dynamic planet.

 

New tool makes generative AI models more likely to create breakthrough materials



With SCIGEN, researchers can steer AI models to create materials with exotic properties for applications like quantum computing.



Massachusetts Institute of Technology







The artificial intelligence models that turn text into images are also useful for generating new materials. Over the last few years, generative materials models from companies like Google, Microsoft, and Meta have drawn on their training data to help researchers design tens of millions of new materials.

But when it comes to designing materials with exotic quantum properties like superconductivity or unique magnetic states, those models struggle. That’s too bad, because humans could use the help. For example, after a decade of research into a class of materials that could revolutionize quantum computing, called quantum spin liquids, only a dozen material candidates have been identified. The bottleneck means there are fewer materials to serve as the basis for technological breakthroughs.

Now, MIT researchers have developed a technique that lets popular generative materials models create promising quantum materials by following specific design rules. The rules, or constraints, steer models to create materials with unique structures that give rise to quantum properties.

“The models from these large companies generate materials optimized for stability,” says Mingda Li, MIT’s Class of 1947 Career Development Professor. “Our perspective is that’s not usually how materials science advances. We don’t need 10 million new materials to change the world, we just need one really good material.”

The approach is described in a paper that will be published by Nature Materials. The researchers applied their technique to generate millions of candidate materials consisting of geometric lattice structures associated with quantum properties. From that pool, they synthesized two actual materials with exotic magnetic traits.

“People in the quantum community really care about these geometric constraints, like the Kagome lattices that are two overlapping, upside-down triangles. We created materials with Kagome lattices because those materials can mimic the behavior of rare earth elements, so they are of high technical importance.” Li says. 

Li is the senior author of the paper. His MIT co-authors include PhD students Ryotaro Okabe, Mouyang Cheng, Abhijatmedhi Chotrattanapituk, and Denisse Cordova Carrizales; postdoc Manasi Mandal; undergraduate researchers Kiran Mak and Bowen Yu; visiting scholar Nguyen Tuan Hung; Xiang Fu ’22, PhD ’24; and professor of electrical engineering and computer science Tommi Jaakkola, who is an affiliate of the Computer Science and Artificial Intelligence Laboratory (CSAIL) and Institute for Data, Systems, and Society. Additional co-authors include Yao Wang of Emory University, Weiwei Xie of Michigan State University, YQ Cheng of Oak Ridge National Laboratory, and Robert Cava of Princeton University.

Steering models toward impact

A material’s properties are determined by its structure, and quantum materials are no different. Certain atomic structures are more likely to give rise to exotic quantum properties than others. For instance, square lattices can serve as a platform for high-temperature superconductors, while other shapes known as Kagome and Lieb lattices can support the creation of materials that could be useful for quantum computing.

To help a popular class of generative models known as a diffusion models produce materials that conform to particular geometric patterns, the researchers created SCIGEN (short for Structural Constraint Integration in GENerative model). SCIGEN is a computer code that ensures diffusion models adhere to user-defined constraints at each iterative generation step. With SCIGEN, users can give any generative AI diffusion model geometric structural rules to follow as it generates materials.

AI diffusion models work by sampling from their training dataset to generate structures that reflect the distribution of structures found in the dataset. SCIGEN blocks generations that don’t align with the structural rules.

To test SCIGEN, the researchers applied it to a popular AI materials generation model known as DiffCSP. They had the SCIGEN-equipped model generate materials with unique geometric patterns known as Archimedean lattices, which are collections of 2D lattice tilings of different polygons. Archimedean lattices can lead to a range of quantum phenomena and have been the focus of much research.

“Archimedean lattices give rise to quantum spin liquids and so-called flat bands, which can mimic the properties of rare earths without rare earth elements, so they are extremely important,” says Cheng, a co-corresponding author of the work. “Other Archimedean lattice materials have large pores that could be used for carbon capture and other applications, so it’s a collection of special materials. In some cases, there are no known materials with that lattice, so I think it will be really interesting to find the first material that fits in that lattice.”

The model generated over 10 million material candidates with Archimedean lattices. One million of those materials survived a screening for stability. Using the supercomputers in Oak Ridge National Laboratory, the researchers then took a smaller sample of 26,000 materials and ran detailed simulations to understand how the materials’ underlying atoms behaved. The researchers found magnetism in 41 percent of those structures.

From that subset, the researchers synthesized two previously undiscovered compounds, TiPdBi and TiPbSb, at Xie and Cava’s labs. Subsequent experiments showed the AI model’s predictions largely aligned with the actual material’s properties.

“We wanted to discover new materials that could have a huge potential impact by incorporating these structures that have been known to give rise to quantum properties,” says Okabe, the paper’s first author. “We already know that these materials with specific geometric patterns are interesting, so it’s natural to start with them.”

Accelerating material breakthroughs

Quantum spin liquids could unlock quantum computing by enabling stable, error-resistant qubits that serve as the basis of quantum operations. But no quantum spin liquid materials have been confirmed. Xie and Cava believe SCIGEN could accelerate the search for these materials.

“There’s a big search for quantum computer materials and topological superconductors, and these are all related to the geometric patterns of materials,” Xie says. “But experimental progress has been very, very slow,” Cava adds. “Many of these quantum spin liquid materials are subject to constraints: They have to be in a triangular lattice or a Kagome lattice. If the materials satisfy those constraints, the quantum researchers get excited; it’s a necessary but not sufficient condition. So, by generating many, many materials like that, it immediately gives experimentalists hundreds or thousands more candidates to play with to accelerate quantum computer materials research.”

The researchers stress that experimentation is still critical to assess whether AI-generated materials can be synthesized and how their actual properties compare with model predictions. Future work on SCIGEN could incorporate additional design rules into generative models, including chemical and functional constraints.

“People who want to change the world care about material properties more than the stability and structure of materials,” Okabe says. “With our approach, the ratio of stable materials goes down, but it opens the door to generate a whole bunch of promising materials.”

The work was supported, in part, by the U.S. Department of Energy, the National Energy Research Scientific Computing Center, the National Science Foundation, and Oak Ridge National Laboratory.

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Written by Zach Winn, MIT News

Study identifies hotspots of disease-carrying ticks in Illinois




University of Illinois at Urbana-Champaign, News Bureau
Map of Illinois Tick Incidence, 2018-2022 

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Scientists mapped deer tick, dog tick and lone star tick abundance in Illinois and reported on tick-borne diseases across the state from 2018-2022. 

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Credit: Graphic by Julie McMahon





CHAMPAIGN, Ill. — Scientists analyzed the distribution of three potentially harmful tick species in Illinois, identifying regions of the state with higher numbers of these ticks and, therefore, at greater risk of infection with multiple tick-borne diseases.

The study found that, of the three species tracked, the lone star tick, Amblyomma americanum, is most prevalent in southern Illinois; the black-legged tick or deer tick, Ixodes scapularis, is more common in northern and central Illinois; and the dog tick, Dermacentor variabilis, dominates the central and southern parts of the state. The findings, reported in the journal Ticks and Tick-borne Diseases, include clusters of counties with the highest number of ticks of each species.

All three tick species are likely present in every Illinois county, said Rebecca Smith, a pathobiology professor at the University of Illinois Urbana-Champaign who led the new research with graduate student Abrar Hussain.

“There are some counties where we’ve looked and we haven’t found them, but most counties that have looked for ticks have found all three species,” Smith said. “It’s just that some ticks are more common in the south, some are more common in the north, and the dog tick does better in central Illinois, where there is a lot of grassland and open habitat.”

Each of these ticks can be infected with one or more of several pathogens, and a tick bite can pass along those infections to humans or other animals. Many of these tick-borne diseases undermine human health and some, like the Heartland virus, can be life-threatening.

The lone star tick is a disease vector for ehrlichiosis, tularemia and the Heartland virus, the latter “a condition with low incidence, thankfully, but high mortality,” Smith said. Its bite also can trigger Alpha-gal syndrome, an allergy to consuming mammalian meat.

“It’s not a pathogen at all. It’s just a reaction to a sugar molecule present in the saliva of the tick,” Smith said. “The response can be anything from discomfort to anaphylactic shock.”

Dog ticks can transmit ehrlichiosis, Rocky Mountain spotted fever, tularemia and Powassan virus disease, which in rare cases causes encephalitis. The deer tick can transmit Lyme disease, anaplasmosis, babesiosis and POWV.

For the new study, the researchers gathered tick-occurrence and tick-borne-disease data from several sources, including the Illinois Department of Public Health, the Illinois Natural History Survey Insect Collection, the Global Biodiversity Information Facility, several museum and academy collections, and iNaturalist, a platform that records citizen-scientist field observations. The team focused on five years of recorded observations ending in 2023.

“We knew that tick-borne diseases from the most common, medically important tick species are here in Illinois, so we wanted to see if the hotspots for ticks match with the incidence of diseases transmitted by those ticks,” Hussain said.

 Analyzing the data was tricky, however. Only 80 of 102 Illinois counties collected tick occurrence data during the study timeframe, and some counties had more aggressive tick-sampling initiatives than others, the researchers said.

The data included 1,414 ticks collected through active surveillance in 80 Illinois counties from 2018-2022. The team built spatial statistical models to identify county-level clusters with higher-than-expected tick distributions.

“Hamilton, Pope and Macon counties had the highest tick-collection numbers, each reporting 100 or more ticks,” the researchers wrote. Hamilton, Jackson and Williamson had the highest numbers of lone star ticks. Hamilton, Macon and Pope counties in southern and central Illinois had the most dog ticks; and Macon, Piatt and Kane counties in central and northern Illinois had the highest numbers of deer ticks.

The scientists used two spatial analyses to identify multicounty clusters with high numbers of ticks of a particular species.

The lone star tick was the most prevalent tick species in southern Illinois.

“Ten counties — Union, Johnson, Hardin, Jackson, Williamson, Saline, Franklin, Hamilton, Jefferson and Perry — were identified as spatial clusters” for the lone star tick, they report. “The Illinois Department of Public Health has also classified all ten of these counties as having a high incidence of Ehrlichia chaffeensis,” a pathogen transmitted by this tick. There were 219 reported human cases of ehrlichiosis in Illinois from 2018-2022.

Illinois also “ranks among the top 13 states with increasing incidence of Alpha-gal syndrome,” caused by the bite of the lone star tick, they wrote.

“With 350 cases, southern Illinois has a high incidence of Rocky Mountain spotted fever group rickettsiosis,” which is transmitted by the dog tick, the team reports. Pope and Hardin counties in southern Illinois, and Piatt and Moultrie in central Illinois were identified as hotspots for the dog tick.

Macon, Piatt, Champaign and Douglas counties in central Illinois, and Cook, DuPage and Kendall in northeastern Illinois were identified as clusters for the deer tick.

Between 2018 and 2022, the state recorded “1,728 cases of Lyme disease, 81 cases of anaplasmosis, and 23 cases of babesiosis,” all of which are transmitted by the deer tick, the researchers report.

Illinoisans who don’t live near regional hotspots of ticks are still at risk of tick bites from each of these species, Smith said.

“Just because there isn’t a county-level hotspot near you doesn’t mean that there’s no ticks,” she said. “You can have tick hotspots within counties, too. We just don’t have that level of specification for where the ticks are within a county.”

Smith urges people to protect themselves from ticks whenever they venture out into wild areas, road edges, parks, woodlands or prairies. This includes wearing long pants and light-colored clothing, tucking pants into socks, wearing close-toed shoes, spraying clothes with insecticides and scouring one’s body for ticks at the end of a hike. The insecticide permethrin can be applied to clothing or individuals can buy permethrin-treated clothing, she said.

The new analysis offers insight into some of the areas that are most at risk of tick-borne disease, Smith said, and will allow health and safety officials to concentrate their resources accordingly. The lack of data from 22 Illinois counties may undermine these public health efforts in those parts of the state, however.

Smith also is a professor in the Carl R. Woese Institute for Genomic Biology and the National Center for Supercomputing Applications at the U. of I.

Abrar Hussain, left, Rebecca Smith and their colleagues mapped the distribution of three tick species across the state of Illinois. They compared this distribution to the incidence of tick-borne diseases in the state. 

Credit

Photo by Fred Zwicky



sis incidence has remained low across the state, with most cases reported in counties lacking active tick surveillance.

 
^Illinois ranks among the top 13 states with increasing incidences of Alpha-Gal Syndrome. AGS is not a reportable condition at present.
 
*Heartland virus was diagnosed in two individuals in 2018: one in Kankakee County and one in Williamson County, 272 miles away. A third person residing in Jackson County was diagnosed with HV in 2023.

 

Credit

Graphic by Julie McMahon

The paper “Spatial distribution and clustering of medically important tick species in Illinois: Implications for tick-borne disease” is available online.

DOI: 10.1016/j.ttbdis.2025.102533