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Researchers find genetic stability in a long-term Panamanian hybrid zone of manakin birds

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Researchers find genetic stability in a long-term Panamanian hybrid zone of manakin birds


We often think of species as separate and distinct, but sometimes they can interbreed and create hybrids. When this happens consistently in a specific area, it forms what’s known as a hybrid zone. These zones can be highly dynamic or remarkably stable, and studying them can reveal key insights into how species boundaries evolve — or sometimes blur. In a new study published in Evolution, researchers at the University of Illinois Urbana-Champaign describe a hybrid zone between two manakin species in Panama that has overall remained relatively stable over the past 30 years.

Hybrids resulting from mixed-species breeding are not uncommon; consider, for example, the mule (horse-donkey) or the liger (lion-tiger). However, many of these classic examples of hybrids are typically infertile and exist only as first-generation crosses. In contrast, along the western edge of Panama, against the Caribbean Sea, a long-term hybrid zone exists between two species of birds, the golden-collared manakin and the white-collared manakin.

Previous research conducted nearly 30 years ago on this hybrid zone found that the genomic center — where the population’s genome is nearly 50% white-collared DNA and 50% golden-collared DNA — did not overlap with the phenotypic transition zone, the area where the population visually transitions from more golden-collared plumage to more white-collared. The previous study found these two areas were about 60 km apart, and until recently, it was unclear whether there had been any changes over the years.

Kira Long, a former graduate student in Jeff Brawn’s lab, now a postdoctoral researcher at the University of Idaho, and her team decided to compare the current population of manakins in the hybrid zone to those from the previous study ~30 years ago. Doing so would allow the researchers to see whether the genomic center or the phenotypic transition zone has moved over time, and how stable the genomic and phenotypic traits are across the population.

“Currently, hybrids at the genomic center look phenotypically almost identical to the golden-collared manakins,” explained Long. “They have the golden yellow collar and dark green belly of golden-collared manakins. What’s crazy is that these hybrids are the most genetically mixed between white and golden-collared manakins, yet they look almost identical to the golden-collared parents. Whereas the birds that visually look the most mixed have genetically a majority of white-collared DNA.”

Long’s team includes Illinois researchers Jeff Brawn, a professor emeritus of natural resources and environmental sciences, Julian Catchen (CIS/GNDP), an associate professor of integrative biology, and his former graduate student Angel Rivera-Colón, as well as collaborators from the University of Maryland College Park and the Smithsonian Institution.

Over four years, the team captured and took blood samples from over 600 manakins across different areas of the hybrid zone. The blood samples were sequenced using RADseq to examine thousands of genomic markers across the genome. These were then compared to samples taken from museum specimens housed at the Smithsonian Institution that were used in the original, older study. The team also measured phenotypic traits of the wild-caught and historical birds, known to differ between golden-collared and white-collared manakins, including feather coloration and length.

After comparing the historical and wild-caught bird genomes, the researchers found that the genomic center of the population had not moved in approximately 30 years. Less than 3% of the genomic markers tested had changed over time. Furthermore, the phenotypic transition zone had also remained stable, with only one trait — belly color — having shifted in location over time by about 10 km.

“What this means is that if you went to the same location in the phenotypic transition of the hybrid zone 30 years ago, you would see birds with more yellow bellies, whereas if you went to that same spot now you would see birds with more olive-colored bellies,” said Long. “The hybrid bellies are essentially getting darker over time. This may mean that there is some sort of selection for the green bellies in these populations where it is spreading.”

Hybrids have varying success in the animal kingdom depending on the species that are mixed. There is a hybrid zone of cottonwood trees, for example, that is extremely stable, only moving slowly during interglacial periods, according to Long. Hybrids of many species often have less fitness than the parental species because they are too intermediate in their traits, but sometimes hybrids are able to capitalize on this and find success, by making use of environmental niches that are between the optimums for the parental species.

According to Long, the population of hybrid manakins seem to be doing just fine, which may explain why the hybrid zone is so stable. While there is evidence of decreased hatching success in the hybrids — which Long says will be published soon in her next article — she notes that this is essentially nature filtering out the genetic combinations between the white-collared and golden-collared manakins that do not work. Once they hatch, the hybrids’ survival appears similar to the parental species, and they do not seem to have issues finding mates, according to Long.

The next big steps for this system is to determine if female choice is affecting selection for specific hybrid phenotypes and determine the underlying genomic architecture of these traits, Long said. This may provide insight into why hybrids typically resemble the golden-collared species and why the transition zone for belly color is shifting while other phenotypic traits remain relatively stable among hybrids.

“It’s thought the females prefer golden-collared colors, and that might be why the more olive belly color, which is a trait of golden-collared manakins, is spreading in the hybrids,” said Long. “We have indirect evidence for this, but it’s never been formally tested, so it would be great to get that last piece of the puzzle.”

The study was funded by the NSF, USDA, the Smithsonian Institution and the National Museum of Natural History.



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Waste Styrofoam can now be converted into polymers for electronics

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Researchers find genetic stability in a long-term Panamanian hybrid zone of manakin birds


University of Delaware and Argonne National Laboratory have come up with a chemical reaction that can convert Styrofoam into a high-value conducting polymer known as PEDOT:PSS. In a new paper published in JACS Au, the study demonstrates how upgraded plastic waste can be successfully incorporated into functional electronic devices, including silicon-based hybrid solar cells and organic electrochemical transistors.

The research group of corresponding author Laure Kayser, assistant professor in the Department of Materials Science and Engineering in UD’s College of Engineering with a joint appointment in the Department of Chemistry and Biochemistry in the College of Arts and Sciences, regularly works with PEDOT:PSS, a polymer that has both electronic and ionic conductivity, and was interested in finding ways to synthesize this material from plastic waste.

After connecting with Argonne chemist David Kaphan during an event hosted by UD’s research office, the research teams at UD and Argonne began evaluating the hypothesis that PEDOT:PSS could be made by sulfonating polystyrene, a synthetic plastic found in many types of disposable containers and packing materials.

Sulfonation is a common chemical reaction where a hydrogen atom is replaced by sulfonic acid; the process is used to create a variety of products such as dyes, drugs and ion exchange resins. These reactions can either be “hard” (with higher conversion efficiency but that require caustic reagents) or “soft” (a less efficient method but one that uses milder materials).

In this paper, the researchers wanted to find something in the middle: “A reagent that is efficient enough to get really high degrees of functionalization but that doesn’t mess up your polymer chain,” Kayser explained.

The researchers first turned to a method described in a previous study for sulfonating small molecules, one that showed promising results in terms of efficiency and yield, using 1,3-Disulfonic acid imidazolium chloride ([Dsim]Cl). But adding functional groups onto a polymer is more challenging than for a small molecule, the researchers explained, because not only are unwanted byproducts harder to separate, any small errors in the polymer chain can change its overall properties.

To address this challenge, the researchers embarked on many months of trial and error to find the optimal conditions that minimized side reactions, said Kelsey Koutsoukos, a materials science doctoral candidate and second author of this paper.

“We screened different organic solvents, different molar ratios of the sulfonating agent, and evaluated different temperatures and times to see which conditions were the best for achieving high degrees of sulfonation,” he said.

The researchers were able to find reaction conditions that resulted in high polymer sulfonation, minimal defects and high efficiency, all while using a mild sulfonating agent. And because the researchers were able to use polystyrene, specifically waste Styrofoam, as a starting material, their method also represents an efficient way to convert plastic waste into PEDOT:PSS.

Once the researchers had PEDOT:PSS in hand, they were able to compare how their waste-derived polymer performed compared to commercially available PEDOT:PSS.

“In this paper, we looked at two devices — an organic electronic transistor and a solar cell,” said Chun-Yuan Lo, a chemistry doctoral candidate and the paper’s first author. “The performance of both types of conductive polymers was comparable, and shows that our method is a very eco-friendly approach for converting polystyrene waste into high-value electronic materials.”

Specific analyses conducted at UD included X-ray photoelectron spectroscopy (XPS) at the surface analysis facility, film thickness analysis at the UD Nanofabrication Facility, and solar cell evaluation at the Institute of Energy Conversion. Argonne’s advanced spectroscopy equipment, such as carbon NMR, was used for detailed polymer characterization. Additional support was provided by materials science and engineering professor Robert Opila for solar cell analysis and by David C. Martin, the Karl W. and Renate Böer Chaired Professor of Materials Science and Engineering, for the electronic device performance analyses.

One unexpected finding related to the chemistry, the researchers added, is the ability to use stoichiometric ratios during the reaction.

“Typically, for sulfonation of polystyrene, you have to use an excess of really harsh reagents. Here, being able to use a stoichiometric ratio means that we can minimize the amount of waste being generated,” Koutsoukos said.

This finding is something the Kayser group will be looking into further as a way to “fine-tune” the degree of sulfonation. So far, they’ve found that by varying the ratio of starting materials, they can change the degree of sulfonation on the polymer. Along with studying how this degree of sulfonation impacts the electrical properties of PEDOT:PSS, the team is interested in seeing how this fine-tuning capability can be used for other applications, such as fuel cells or water filtration devices, where the degree of sulfonation greatly impacts a material’s properties.

“For the electronic devices community, the key takeaway is that you can make electronic materials from trash, and they perform just as well as what you would purchase commercially,” Kayser said. “For the more traditional polymer scientists, the fact that you can very efficiently and precisely control the degree of sulfonation is going to be of interest to a lot of different communities and applications.”

The researchers also see great potential for how this research can contribute to ongoing global sustainability efforts by providing a new way to convert waste products into value-added materials.

“Many scientists and researchers are working hard on upcycling and recycling efforts, either by chemical or mechanical means, and our study provides another example of how we can address this challenge,” Lo said.

The complete list of co-authors includes Chun-Yuan Lo, Kelsey Koutsoukos, Dan My Nguyen, Yuhang Wu, David Angel Trujillo, Tulaja Shrestha, Ethan Mackey, Vidhika Damani, Robert Opila, David Martin, and Laure Kayser from the University of Delaware and Tabitha Miller, Uddhav Kanbur, and David Kaphan from Argonne National Laboratory.



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New snake discovery rewrites history, points to North America’s role in snake evolution

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Researchers find genetic stability in a long-term Panamanian hybrid zone of manakin birds


A new species of fossil snake unearthed in Wyoming is rewriting our understanding of snake evolution. The discovery, based on four remarkably well-preserved specimens found curled together in a burrow, reveals a new species named Hibernophis breithaupti. This snake lived in North America 34 million years ago and sheds light on the origin and diversification of boas and pythons.

Hibernophis breithaupti has unique anatomical features, in part because the specimens are articulated — meaning they were found all in one piece with the bones still arranged in the proper order — which is unusual for fossil snakes. Researchers believe it may be an early member of Booidea, a group that includes modern boas and pythons. Modern boas are widespread in the Americas, but their early evolution is not well understood.These new and very complete fossils add important new information, in particular, on the evolution of small, burrowing boas known as rubber boas.

Traditionally, there has been much debate on the evolution of small burrowing boas. Hibernophis breithaupti shows that northern and more central parts of North America might have been a key hub for their development. The discovery of these snakes curled together also hints at the oldest potential evidence for a behavior familiar to us today — hibernation in groups.

“Modern garter snakes are famous for gathering by the thousands to hibernate together in dens and burrows,” says Michael Caldwell, a U of A paleontologist who co-led the research along with his former graduate student Jasmine Croghan, and collaborators from Australia and Brazil. “They do this to conserve heat through the effect created by the ball of hibernating animals. It’s fascinating to see possible evidence of such social behavior or hibernation dating back 34 million years.”



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Good timing: Study unravels how our brains track time

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Researchers find genetic stability in a long-term Panamanian hybrid zone of manakin birds


Ever hear the old adage that time flies when you’re having fun? A new study by a team of UNLV researchers suggests that there’s a lot of truth to the trope.

Many people think of their brains as being intrinsically synced to the human-made clocks on their electronic devices, counting time in very specific, minute-by-minute increments. But the study, published this month in the latest issue of the peer-reviewed Cell Press journal Current Biology, showed that our brains don’t work that way.

By analyzing changes in brain activity patterns, the research team found that we perceive the passage of time based on the number of experiences we have — not some kind of internal clock. What’s more, increasing speed or output during an activity appears to affect how our brains perceive time.

“We tell time in our own experience by things we do, things that happen to us,” said James Hyman, a UNLV associate professor of psychology and the study’s senior author. “When we’re still and we’re bored, time goes very slowly because we’re not doing anything or nothing is happening. On the contrary, when a lot of events happen, each one of those activities is advancing our brains forward. And if this is how our brains objectively tell time, then the more that we do and the more that happens to us, the faster time goes.”

Methodology and Findings

The findings are based on analysis of activity in the anterior cingulate cortex (ACC), a portion of the brain important for monitoring activity and tracking experiences. To do this, rodents were tasked with using their noses to respond to a prompt 200 times.

Scientists already knew that brain patterns are similar, but slightly different, each time you do a repetitive motion, so they set out to answer: Is it possible to detect whether these slight differences in brain pattern changes correspond with doing the first versus 200th motion in series? And does the amount of time it takes to complete a series of motions impact brain wave activity?

By comparing pattern changes throughout the course of the task, researchers observed that there are indeed detectable changes in brain activity that occur as one moves from the beginning to middle to end of carrying out a task. And regardless of how slowly or quickly the animals moved, the brain patterns followed the same path. The patterns were consistent when researchers applied a machine learning-based mathematical model to predict the flow of brain activity, bolstering evidence that it’s experiences — not time, or a prescribed number of minutes, as you would measure it on a clock — that produce changes in our neurons’ activity patterns.

Hyman drove home the crux of the findings by sharing an anecdote of two factory workers tasked with making 100 widgets during their shift, with one worker completing the task in 30 minutes and the other in 90 minutes.

“The length of time it took to complete the task didn’t impact the brain patterns. The brain is not a clock; it acts like a counter,” Hyman explained. “Our brains register a vibe, a feeling about time. …And what that means for our workers making widgets is that you can tell the difference between making widget No. 85 and widget No. 60, but not necessarily between No. 85 and No. 88.”

But exactly “how” does the brain count? Researchers discovered that as the brain progresses through a task involving a series of motions, various small groups of firing cells begin to collaborate — essentially passing off the task to a different group of neurons every few repetitions, similar to runners passing the baton in a relay race.

“So, the cells are working together and over time randomly align to get the job done: one cell will take a few tasks and then another takes a few tasks,” Hyman said. “The cells are tracking motions and, thus, chunks of activities and time over the course of the task.”

And the study’s findings about our brains’ perception of time applies to activities-based actions other than physical motions too.

“This is the part of the brain we use for tracking something like a conversation through dinner,” Hyman said. “Think of the flow of conversation and you can recall things earlier and later in the dinner. But to pick apart one sentence from the next in your memory, it’s impossible. But you know you talked about one topic at the start, another topic during dessert, and another at the end.”

By observing the rodents who worked quickly, scientists also concluded that keeping up a good pace helps influence time perception: “The more we do, the faster time moves. They say that time flies when you’re having fun. As opposed to having fun, maybe it should be ‘time flies when you’re doing a lot’.”

Takeaways

While there’s already a wealth of information on brain processes over very short time scales of less than a second, Hyman said that the UNLV study is groundbreaking in its examination of brain patterns and perception of time over a span of just a few minutes to hours — “which is how we live much of our life: one hour at a time. ”

“This is among the first studies looking at behavioral time scales in this particular part of the brain called the ACC, which we know is so important for our behavior and our emotions,” Hyman said.

The ACC is implicated in most psychiatric and neurodegenerative disorders, and is a concentration area for mood disorders, PTSD, addiction, and anxiety. ACC function is also central to various dementias including Alzheimer’s disease, which is characterized by distortions in time. The ACC has long been linked to helping humans with sequencing events or tasks such as following recipes, and the research team speculates that their findings about time perception might fall within this realm.

While the findings are a breakthrough, more research is needed. Still, Hyman said, the preliminary findings posit some potentially helpful tidbits about time perception and its likely connection to memory processes for everyday citizens’ daily lives. For example, researchers speculate that it could lend insights for navigating things like school assignments or even breakups.

“If we want to remember something, we may want to slow down by studying in short bouts and take time before engaging in the next activity. Give yourself quiet times to not move,” Hyman said. “Conversely, if you want to move on from something quickly, get involved in an activity right away.”

Hyman said there’s also a huge relationship between the ACC, emotion, and cognition. Thinking of the brain as a physical entity that one can take ownership over might help us control our subjective experiences.

“When things move faster, we tend to think it’s more fun — or sometimes overwhelming. But we don’t need to think of it as being a purely psychological experience, as fun or overwhelming; rather, if you view it as a physical process, it can be helpful,” he said. “If it’s overwhelming, slow down or if you’re bored, add activities. People already do this, but it’s empowering to know it’s a way to work your own mental health, since our brains are working like this already.”



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