Some people may be attracted to others over minimal similarities

We are often attracted to others with whom we share an interest, but that attraction may be based on an erroneous belief that such shared interests reflect a deeper and more fundamental similarity — we share an essence — according to research published by the American Psychological Association.

“Our attraction to people who share our attributes is aided by the belief that those shared attributes are driven by something deep within us: one’s essence,” said lead author Charles Chu, PhD, an assistant professor at the Boston University Questrom School of Business. “To put it concretely, we like someone who agrees with us on a political issue, shares our music preferences, or simply laughs at the same thing as us not purely because of those similarities, but because those similarities suggest something more — this person is, in essence, like me, and as such, they share my views of the world at large.”

This thought process is driven by a type of psychological essentialism that is applied specifically to people’s ideas about the self and individual identity, according to Chu, adding that people “essentialize” many things — from biological categories such as animal species to social groups such as race and gender — and do so in virtually all human cultures.

“To essentialize something is to define it by a set of deeply rooted and unchanging properties, or an essence,” said Chu. “For example, the category of ‘wolf’ is defined by a wolf essence, residing in all wolves, from which stems attributes such as their pointy noses, sharp teeth and fluffy tails as well as their pack nature and aggressiveness. It is unchanging in that a wolf raised by sheep is still a wolf and will eventually develop wolf-like attributes.”

Recently, researchers have begun to focus on the category of the self and have found that just as we essentialize other categories, we essentialize the self, according to Chu.

“To essentialize me is to define who I am by a set of entrenched and unchanging properties, and we all, especially in Western societies, do this to some extent. A self-essentialist then would believe that what others can see about us and the way we behave are caused by such an unchanging essence,” he said.

To better understand how self-essentialism drives attraction between individuals, researchers conducted a series of four experiments. The research was published in the Journal of Personality and Social Psychology.

In one experiment, 954 participants were asked their position on one of five randomly assigned social issues (abortion, capital punishment, gun ownership, animal testing, or physician-assisted suicide). Half the participants then read about another individual who agreed with their position, while the other half read about an individual who disagreed with their position. All participants then completed a questionnaire on how much they believed they shared a general view of the world with the fictitious individual, their level of interpersonal attraction to that person and their overall beliefs in self-essentialism.

Researchers found that participants who scored high on self-essentialism were more likely to express an attraction to the fictitious individual who agreed with their position and to report a shared general perception of reality with that individual.

A similar experiment involving 464 participants found the same results for a shared attribute as simple as the participants’ propensity to overestimate or underestimate a number of colored dots on a series of computer slides. In other words, the belief in an essential self led people to assume that just a single dimension of similarity was indicative of seeing the entire world in the same way, which led to more attraction.

In another experiment, 423 participants were shown eight pairs of paintings and asked which in each pair they preferred. Based on their responses, participants were identified as either a fan of the Swiss-German artist Paul Klee or the Russian painter Wassily Kandinsky. Half of each fan group was then told that artistic preference was part of their essence; the other half was told it had no connection. All were then exposed to two hypothetical individuals, one of whom had the same artistic preference and one who differed. Participants who were told that artistic preference was connected to their essence were significantly more likely to express an attraction to a hypothetical person with the same artistic preferences than those who were told artistic preference had nothing to do with their essence.

A final experiment categorized 449 participants as fans of one of the two artists and then presented them with information about whether using one’s own essence was useful or not in perceiving other people. This time, one-third of the participants were told that essentialist thinking could lead to inaccurate impressions of others, one-third were told that essentialist thinking could lead to accurate impressions of others and the final third were given no information.

As expected, researchers found participants who were told that essentialist thinking could lead to accurate impressions of others were more likely to report attraction to and shared reality with hypothetical individuals with similar art preferences.

Chu said he was most surprised to find that something as minimal as a shared preference for an artist would lead people to perceive that another individual would see the world the same way as they do. Self-essentialist thinking, though, could be a mixed blessing, he warned.

“I think any time when we’re making quick judgments or first impressions with very little information, we are likely to be affected by self-essentialist reasoning,” said Chu. “People are so much more complex than we often give them credit for, and we should be wary of the unwarranted assumptions we make based on this type of thinking.”

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New look at climate data shows substantially wetter rain and snow days ahead

A key source of information underpinning the upcoming National Climate Assessment suggests that heavy precipitation days historically experienced once in a century by Americans could in the future be experienced on several occasions in a lifetime.

Scientists at Scripps Institution of Oceanography at UC San Diego and the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) report that extremely intense days of rain or snow will be more frequent by the end of this century than previously thought — as often as once every 30 or 40 years in the Pacific Northwest and southeastern United States.

The conclusions come from analyzing a 30-terabyte data set that models temperature and precipitation at scales roughly the size of urban ZIP codes: six kilometers (3.9 miles). Researchers developed the data set, called Localized Constructed Analogs Version 2 (LOCA2), to provide climate information that is useful for local planners. In contrast, most of the existing advanced climate models look at regions that range from 50 to 250 kilometers (30 to 400 miles).

“With this data set, we’re able to look at the impacts of actual weather pattern changes across the United States at an extremely granular level,” said Dan Feldman, staff scientist at Berkeley Lab and the project’s principal investigator. “We see that there is a lot more extreme weather that is likely to happen in the future — and by looking at actual weather patterns, we show that changes in extreme precipitation will actually be more extreme than previously estimated. Land use managers and planners should expect more extremes, but location matters.”

The LOCA2 data set updates a similar analysis conducted in 2016 in advance of the Fourth National Climate Assessment (NCA), which was released in 2018 by the U.S. Global Change Research Program. The NCA is intended to assist the U.S. government with planning for, mitigating, and adapting to changes in climate that will affect the country. The Fifth NCA is expected to be issued later this year.

LOCA2 projections cover the lower 48 states of the United States, southern Canada, and northern Mexico. The data set draws on more than 70 years of weather data and incorporates 27 updated climate models from the Coupled Model Intercomparison Project (CMIP6), the latest iteration of an international effort to simulate climate that includes the “coupling” of natural systems such as the ocean and atmosphere to understand how they will act in concert as climate changes.

“We’ve spent a lot of effort improving the representation of extreme wet days, which is important for understanding both the likelihood of flooding and the availability of water for agricultural, commercial, and residential use,” said David Pierce, a scientist at Scripps Oceanography and the developer of LOCA and LOCA2.

The LOCA2 climate projections are available through the end of the century down to the daily level, and for three different greenhouse gas emissions scenarios known as SSPs, or Shared Socioeconomic Pathways. The three scenarios are a medium level of emissions that is slightly less than current levels (SSP 245), medium-high (SSP 370), and high, where emissions greatly increase (SSP 585). The data set is freely available for planners and decision makers to use.

The projection reinforces what climate scientists have long predicted: Future weather events will become more extreme in a warming world. LOCA2 finds that the heaviest days of rain and snowfall across much of North America will likely release 20 to 30 percent more moisture than they do now. Much of the increased precipitation will occur in winter, potentially exacerbating flooding in regions such as the upper Midwest and the west coast.

“The big picture is clear: it’s getting warmer and wetter,” Feldman said. “This research translates that bigger picture into more practical data for infrastructure and operations planning. With this more detailed look at local impacts, we can help local officials make better-informed decisions, such as how long to make an airport runway, how much resilience to include for constructing buildings or bridges, or where to put crops or culverts.”

The improved set of LOCA2 data was created by better identifying and preserving extreme weather events in the past, training models to more accurately reflect extremes in simulations of the future.

“We undertook a Herculean effort of personnel and computer time not just to produce a bunch of numbers, but to produce local projections that are relevant and useful,” Feldman said. “We do so by recognizing how heat waves and storms have occurred and will occur at the local level, and projecting those forward.”

Seasonal and regional predictions

While the data varies at the local level, researchers found substantial trends across the area covered by LOCA2 at the end of the century.

Across most seasons, a major part of North America will see roughly the same or fewer number of days with precipitation, roughly the same or fewer number of days with light and medium amounts of precipitation, and a large increase in the number of days with the most extreme precipitation (the top 1 percent and 0.1 percent of storms).

“People will be more affected by the really rare and most extreme events, because those are showing the biggest increase,” said Pierce, who is the lead author of the paper on extreme precipitation published in the Journal of Hydrometeorology. “The wettest day you would expect to see in five years, or 50 years, or 500 years — those extreme events are going to be substantially wetter, and that’s a really big issue, because it has implications for flooding and run-off.”

Southern Canada and most of the United States will see increases in extreme precipitation days that occur primarily in winter. The wettest days of precipitation will increase by 20-30 percent, depending on the emissions scenario and how extreme the storm is.

Arizona, New Mexico, and northern Mexico can expect increases in extreme precipitation days that occur primarily in autumn. The wettest days of precipitation increase by 10-30 percent, depending on which emissions scenarios come to be and how extreme the storms are. While the region becomes drier overall, the number of days with extreme precipitation events still goes up, meaning the precipitation that does come will often do so in larger storms.

“It’s quite interesting that you see the same kind of pattern of fewer low- and medium- precipitation days and more extreme precipitation days across pretty much the entire country,” Pierce said. Knowing the changing character of precipitation and the frequency of extreme events is useful in two ways, Pierce added. “One is for building new infrastructure in the future, and one is for understanding impacts upon existing facilities already there.”

Funding for this research was provided by the Department of Defense and Department of Energy through the Strategic Environmental Research and Development Program (SERDP). The NASA High-End Computing Capability (HECC) Program provided resources supporting this work through the NASA Earth Exchange (NEX), Earth Science Division, and the NASA Advanced Supercomputing (NAS) Division at Ames Research Center.

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M87 in 3D: New view of galaxy helps pin down mass of the black hole at its core

Seen from Earth, the giant elliptical galaxy M87 is just a two-dimensional blob, though one that appears perfectly symmetrical and thus a favored target of amateur astronomers.

Yet, a new, highly detailed analysis of the motion of stars around its central supermassive black hole — the first black hole to be imaged by the Event Horizon Telescope (EHT) in 2019 — reveals that it’s not as perfect as it looks.

In fact, M87 is highly asymmetrical, like a russet potato. The galaxy’s shortest axis is about three-fourths (72.2%) the length of its long axis, while the intermediate axis is about seven-eighths (84.5%) that of the long axis.

Knowing this, University of California, Berkeley, astronomers were able to determine the mass of the supermassive black hole at the galaxy’s core to a high precision, estimating it at 5.37 billion times the mass of the sun. By comparison, our own Milky Way has at its center a massive black hole only 4 million times the mass of the sun.

They also were able to measure the rotation of the galaxy, which is a relatively sedate 25 kilometers per second. Interestingly, it is not rotating around any of the galaxy’s major axes, but instead about an axis that is 40 degrees away from the long axis of its 2D image as observed by the Hubble Space Telescope.

The stereo reconstruction of the M87 galaxy and the more precise figure for the mass of the central black hole could help astrophysicists learn about a characteristic of the black hole they’ve had no way to determine before for any black hole: its spin.

“Now that we know the direction of the net rotation of stars in M87 and have an updated mass of the black hole, we can combine this information with the amazing data from the EHT team to constrain the spin,” said Chung-Pei Ma, a UC Berkeley professor of astronomy and of physics who led the research. “This may point toward a certain direction and range of spin for the black hole, which would be remarkable. We are working on this.”

Further analyses to determine the true shape of giant elliptical galaxies — the galaxies with the largest black holes at their cores — will help astronomers understand better how large galaxies and large black holes form and could help astronomers better interpret gravitational wave signals. Ma leads a long-term study of supermassive black holes that is dubbed MASSIVE.

The results were published online March 15 in The Astrophysical Journal Letters (ApJ Letters).

Determining a galaxy’s 3D shape

While spiral galaxies tend to be small, rotate quickly and have a well-recognized pancake shape, giant elliptical galaxies rotate slowly and have a blobby appearance, their 3D shape difficult to discern. Like M87, the largest galaxy in the massive Virgo Cluster of galaxies, giant elliptical galaxies have grown from the merger of many other galaxies. That’s likely the reason M87’s central black hole is so large — it assimilated the central black holes of all the galaxies it swallowed. In all, the galaxy contains about 100 billion stars, 10 times larger than the Milky Way.

Ma, UC Berkeley graduate student and lead author Emily Liepold, and Jonelle Walsh at Texas A&M University in College Station were able to determine the 3D shape of M87 thanks to a relatively new precision instrument mounted on the Keck II Telescope, one of the twin 10-meter Keck telescopes atop Mauna Kea, a volcano in Hawai’i. Called the Keck Cosmic Web Imager (KCWI), the integral field spectrometer allowed Ma and her team to measure the spectra of stars in the center of the galaxy.

They pointed the telescope at 62 adjacent locations in the galaxy, completely covering a region about 70,000 light-years across, and recorded the spectra of stars within that region. The observations span the central region — about 3,000 light-years across — where gravity is largely dominated by the supermassive black hole, as well as the outer part dominated by dark matter. Though the telescope cannot resolve individual stars — M87 lies about 53 million light- years from Earth — the spectra can reveal the range of velocities within each pixel of each image, enough information to calculate the gravitational mass they’re orbiting.

“It’s sort of like looking at a swarm of 100 billion bees that are going around in their own happy orbits,” said Ma, the Judy Chandler Webb Professor in the Physical Sciences. “Though we are looking at them from a distance and can’t discern individual bees, we are getting very detailed information about their collective velocities. It’s really the superb sensitivity of this spectrograph that allowed us to map out M87 so comprehensively.”

This is the first time KCWI has been used to reconstruct the geometry of a distant galaxy, and M87 is one of only a handful of giant elliptical galaxies whose 3D structure has been determined. Ma’s team had previously determined the 3D structure of two other giant elliptical galaxies, NGC 1453 and NGC 2693, both harboring smaller black holes than M87.

The researchers took the data obtained during four nights of Keck observations between 2020 and 2022, along with earlier photometric data for M87 from NASA’s Hubble Space Telescope, and compared them to computer model predictions of how stars move around the center of a triaxial galaxy. The best fit to the data — axial ratios of 1 to 0.84 to 0.72 — then allowed them to calculate the black hole mass.

“The Keck data are so good that we can measure the intrinsic shape of M87 along with the black hole at the same time,” Ma said. “We made the first measurement of the actual 3D shape of the galaxy. And since we allowed the swarm of bees to have a more general shape than just a sphere or disk, we have a more robust dynamical measurement of the mass of the central black hole that is governing the bees’ orbiting velocities.”

The authors dedicated their manuscript to the late astronomer Wallace “Wal” Sargent, who first suggested that a supermassive black hole lurked at the center of M87 and calculated its mass to be about 5 billion solar masses.

“His number is a twiddle with our error bars, which is very interesting to see after decades of work,” said Ma, who credits Sargent with being a mentor when she was a postdoctoral fellow at the California Institute of Technology.

The previous estimate of the mass of the supermassive black hole in M87, published in 2011, was based on a similar analysis of the dynamical movement of stars around the black hole, though that study assumed the galaxy was axisymmetric. The number, 6.14 billion solar masses, is within error bars of the new, more precise estimate. When imaging the black hole four years ago, the EHT scientists estimated the black hole mass to be 6.5 billion solar masses, 21% higher than the new number.

Interestingly, the dark matter within the volume of the galaxy they analyzed is much higher than that of the black hole — about 388 billion solar masses, or 67% of the entire mass of M87. Though the identity of dark matter is still a mystery, it makes up about 85% of the mass of the universe.

Jonelle Walsh is with the George P. and Cynthia Woods Mitchell Institute for Fundamental Physics and Astronomy at Texas A&M. The work was funded by the National Science Foundation (AST-1817100, AST-2206307), the Heising-Simons Foundation and the Miller Institute for Basic Research in Science.

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Increased droughts are disrupting carbon-capturing soil microbes, concerning ecologists

Soil stores more carbon than plants and the atmosphere combined, and soil microbes are largely responsible for putting it there. However, the increasing frequency and severity of drought, such as those that have been impacting California, could disrupt this delicate ecosystem. In a perspective publishing in the journal Trends in Microbiology on April 12, microbial ecologist Steven Allison warns that soil health and future greenhouse gas levels could be impacted if soil microbes adapt to drought faster than plants do. He argues that we need to better understand how microbes respond to drought so that we can manage the situation in both agricultural and natural settings.

“Soil microbes are beneficial, and we couldn’t live without their cycling of carbon and nutrients, but climate change and drought can tweak that balance, and we have to be aware of how it’s changing,” says Allison of the University of California, Irvine.

Some soil microbes take carbon from decomposing plants and store it in the soil, while others release plant carbon back into the atmosphere. The carbon that ends up in the soil is beneficial in multiple ways. “The carbon in the soil has these reverberating effects out to the rest of the world in terms of the infrastructure in our natural and managed ecosystems,” says Allison. “Carbon-rich soils hold more nutrients, so plants growing in those soils tend to be more productive, and the carbon changes the physical properties of the soil, which prevents erosion.”

“In California now, we have this system where the droughts are more intense, and then the rainfall is more intense,” he says. “So, if you’re losing your soil carbon, when it rains really hard it could carry away your soil and cause erosion, landslides, mudslides, sediments, and all kinds of problems that we’re actually seeing right now.”

The carbon that is released back into the atmosphere is another story. “From a climate mitigation standpoint, what we want is for more carbon to be in plants and soils and less carbon to be in the atmosphere, so the more carbon we can absorb into plants through photosynthesis and the more we can transfer and keep in the soil, the better off we’re going to be in terms of climate change,” says Allison. “That’s why it’s really important to know how the balance of incoming versus outflowing carbon changes with drought, or warming, or any other climate factor.”

Plants and microbes will both be impacted by the increasing frequency of drought, but Allison suspects that microbes will be able to bounce back faster. “Microbes are really adaptable — they can change their physiology, they can change their abundances so that more drought-adapted microbes take over, and they can potentially evolve — so we expect that they are going to resist or bounce back from drought,” says Allison. “All those different processes can happen pretty quickly with microbes, and much more quickly than with plants.”

If more carbon-releasing microbes survive than carbon-sequestering microbes, we could end up with carbon-depleted soils, which would have serious negative implications for plant productivity and future greenhouse gas levels.

We may be able to nudge the balance in the right direction, Allison says, but more research is needed first. “There’s still a lot to be done. Right now, we have data that suggests that when we have drought, something changes that results in carbon loss, but we don’t understand exactly how or why that’s happening, whether drought’s changing the abundance of beneficial plant associated microbes versus the carbon releasing microbes, or if it’s causing the evolution of one of the microbe groups, or if it’s more determined by changes to their immediate physiology,” says Allison.

Some microbes could actually help plants cope with drought. If we knew which microbes were most beneficial to plants, and most likely to retain carbon in soil, we could try to tip the balance in their favor.

“There’s a lot of potential for us to manage or engineer soil microbes,” says Allison. “In agricultural systems, we can look into manipulating the soil or adding beneficial microbes back in. In more natural systems, management would probably be on the plant side: soil microbes are often closely intertwined with plants, so managing the plants can also benefit the microbial part of the ecosystem.”

“We also need more measurements to get a good sense of how drought affects soil carbon change in different ecosystems,” says Allison. “There’s a lot of landscape out there — from the Arctic tundra to the deserts — and we could use more research across those diverse habitats.”

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Wonder material graphene claims yet another superlative

In a paper published in Nature this week (13 Apr 2023), researchers from The University of Manchester report record-high magnetoresistance that appears in graphene under ambient conditions.

Materials that strongly change their resistivity under magnetic fields are highly sought for various applications and, for example, every car and every computer contain many tiny magnetic sensors. Such materials are rare, and most metals and semiconductors change their electrical resistivity only by a tiny fraction of a percent at room temperature and in practically viable magnetic fields (typically, by less than a millionth of 1 %). To observe a strong magnetoresistance response, researchers usually cool materials to liquid-helium temperatures so that electrons inside scatter less and can follow cyclotron trajectories.

Now a research team led by Professor Sir Andre Geim has found that good old graphene that seemed to be studied in every detail over the last two decade exhibits a remarkably strong response, reaching above 100% in magnetic fields of standard permanent magnets (of about 1,000 Gauss). This is a record magnetoresistivity among all the known materials.

Speaking about this latest graphene discovery, Sir Andre Geim said: “People working on graphene like myself always felt that this gold mine of physics should have been exhausted long ago. The material continuously proves us wrong finding yet another incarnation. Today I have to admit again that graphene is dead, long live graphene.”

To achieve this, the researchers used high-quality graphene and tuned it to its intrinsic, virgin state where there were only charge carriers excited by temperature. This created a plasma of fast-moving “Dirac fermions” that exhibited a surprisingly high mobility despite frequent scattering. Both high mobility and neutrality of this Dirac plasma are crucial components for the reported giant magnetoresistance.

“Over the last 10 years, electronic quality of graphene devices has improved dramatically, and everyone seems to focus on finding new phenomena at low, liquid-helium temperatures, ignoring what happens under ambient conditions. This is perhaps not so surprising because the cooler your sample the more interesting its behaviour usually becomes. We decided to turn the heat up and unexpectedly a whole wealth of unexpected phenomena turned up,” says Dr Alexey Berdyugin, the corresponding authors of the paper.

In addition to the record magnetoresistivity, the researchers have also found that, at elevated temperatures, neutral graphene becomes a so-called “strange metal.” This is the name given to materials where electron scattering becomes ultimately fast, being determined only by the Heisenberg uncertainty principle. The behaviour of strange metals is poorly understood and remains a mystery currently under investigation worldwide.

The Manchester work adds some more mystery to the field by showing that graphene exhibits a giant linear magnetoresistance in fields above a few Tesla, which is weakly temperature dependent. This high-field magnetoresistance is again record-breaking.

The phenomenon of linear magnetoresistance has remained an enigma for more than a century since it was first observed. The current Manchester work provides important clues about origins of the strange metal behaviour and of the linear magnetoresistance. Perhaps, the mysteries can now be finally solved thanks to graphene as it represents a clean, well-characterised and relatively simple electronic system.

“Undoped high-quality graphene at room temperature offers an opportunity to explore an entirely new regime that in principle could be discovered even a decade ago but somehow was overlooked by everyone. We plan to study this strange-metal regime and, surely, more of interesting results, phenomena and applications will follow,” adds Dr Leonid Ponomarenko, one of the leading Nature paper authors.

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How skates learned to fly through water

The little skate’s dance on the ocean floor is graceful: its massive frontal fins undulate as it skims beneath a layer of sand. With its mottled sand-colored camouflage, the animal is easy to miss.

Scientists at Max Delbrück Center in Berlin, the Andalusian Center for Developmental Biology (CABD) in Seville and other labs in the United States have discovered how the skate evolved these cape-like fins by peering into their DNA. They found that the key to the evolution of the skate fins lies not in the coding regions of its genome, but rather in the non-coding bits and the three-dimensional complexes that it folds into. These 3D structures are called “topologically associated domains” (TADs).

The international team describes in Nature that genomic changes that alter TADs can drive evolution. Until recently, genome evolution was mostly focused on studying variation at the DNA sequence level, but not in 3D genomic structures. “This is a new way of thinking about how genomes evolve,” says Dr. Darío Lupiáñez, geneticist at the Max Delbrück Center and one of the lead authors of the study.

“Although we found that unique gene-expression patterns establish exceptionally wide skate fins a while ago, the underlying regulatory changes in the genome have previously remained unknown,” says co-author Dr. Tetsuya Nakamura, developmental biologist at Rutgers University.

More than 450 million years ago, the genome of a primitive fish — the ancestor of all vertebrate animals — duplicated twice. The expansion in genetic material drove the rapid evolution of more than 60,000 vertebrates, including humans. One of our most distant vertebrate relativesare little skates (Leucoraja erinacea), which belong to a lineage of cartilaginous fishes that includes sharks and rays. These distant cousins are ideal organisms to learn about the evolution of traits that made us human, such as paired appendages. “Skates are cartilaginous fishes called Chondrichthyans. They are considered more similar to ancestral vertebrates,” says Dr. Christina Paliou, a developmental biologist at the CABD and one of the first authors. “We can compare the characteristics of skates with other species and determine what is novel and what is ancestral.”

An exciting time in evolutionary genomics

In 2017, the late Dr. José Luis Gómez-Skarmeta from the CABD, a founding figure in evolutionary genomics, brought together scientists from around the world to study skate evolution: laboratories with expertise in genome evolution such as the Ferdinand Marlétaz lab at University College London and Daniel Rokhsar lab at the University of California-Berkeley, in skate biology such as the Neil Shubin lab at University of Chicago, where Tetsuya Nakamura was then located (now at Rutgers) and in 3D gene regulation such as the Juan Tena at CABD, Darío Lupiáñez and Gómez-Skarmeta labs, as well as other collaborators. Gómez-Skarmeta was interested in learning how genomes evolve structurally and functionally to promote the appearance of new traits. “To a great extent, evolution is the history of changing the regulation of gene expression during development,” he said in 2018.

It was an exciting time for evolutionary genomics. Genome sequencing technologies had significantly improved and scientists could gain novel insights into how DNA, which stretches a couple of meters end-to-end, is folded into a 0.002-inch-diameter cell nucleus. “The packaging of DNA in the nucleus is far from random,” says Lupiáñez. The DNA folds into 3D structures called TADs, which contain genes and their regulatory sequences. These 3D structures ensure that the appropriate genes are switched on and off at the right time, in the right cells.

Dr. Rafael Acemel, a geneticist at the Max Delbrück Center and one of the first authors, performed experiments using the Hi-C technology, to elucidate the 3D structure of the TADs. But interpreting the results was challenging at first as the scientists needed the complete skate genome as a reference point. “At the time, the reference consisted of thousands of small unordered pieces of DNA sequence, so that did not help,” Acamel says.

To overcome this difficulty, the scientists used long-read sequencing technology, together with Hi-C data, to assemble the pieces of the DNA like a puzzle and assign the unordered sequences to skate chromosomes. With the new reference, assembling the 3D structure of the TADs using Hi-C became trivial.

They compared this improved skate genome with genomes of the closest relatives, sharks, to identify any TADs altered during skate evolution. These altered TADs included genes of the Wnt/PCP pathway, which is important for the development of fins. There was also a skate-specific variation in a non-coding sequence near the Hox genes, which also regulate fin development. “This specific sequence can activate several Hox genes in the front part of the fins, which does not happen in other fish or four-legged animals,” says Paliou. Subsequently, the scientists performed functional experiments that confirmed these molecular changes helped the skates evolve their unique fins.

TADs drive evolution

Earlier research has shown that changes in TADs can affect the expression of genes and cause diseases in humans. In this study, scientists show a role for TADs in driving evolution that has been previously noted for moles, too.

After the primitive fish ancestor duplicated its genome, many unused and redundant parts were subsequently lost. “It was not only the genes that disappeared, but also the associated regulatory elements and the TADs they are contained in,” Lupiáñez says. “I think it’s an exciting finding as it suggests that the 3D structure of the genome has an influence on its evolution.”

TADs are important for gene regulation, 40 percent of them are conserved in all vertebrates, Acemel says. “However, 60 percent of TADs have evolved in some way or another. What were the consequences of these changes for species evolution? I think that we are just scratching the surface of this exciting phenomenon,” Acemel says.

This mechanism of evolution constrained by TADs could be prevalent in nature. “We suspect that these mechanisms might explain many other interesting phenotypes that we observe in nature,” Lupiáñez says. “By adding these new layers of gene expression, gene regulation, and 3D chromatin organization, the field of evolutionary genomics is entering into a new era of discovery.”

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