Kirtland’s warblers have also been known as jack pine warblers, as their breeding habitat is limited to young jack-pine forests in Michigan. The species nearly went extinct in the 1970s due to threatened habitat and the population decline was exacerbated by brown-headed cowbirds, who lay their eggs in the nests of other bird species — including warblers — and divert resources away from their chicks. Kirtland’s warblers were classified as endangered under the Endangered Species Act of 1973. Thanks to intensive, targeted management over several decades, Kirtland’s warbler populations have recovered. The species was “delisted” — no longer considered endangered — in 2019, though management efforts remain critical to their survival, according to the researchers.

“When any population goes through a period when few breeding individuals are present, called a ‘bottleneck,’ there is always a chance of inbreeding, which can lead to reduced survival of future generations,” said Anna María Calderón, graduate student in biology in the Penn State Eberly College of Science and first author of the paper. “The 2019 decision to delist Kirtland’s warblers referenced a study that did not find strong evidence of inbreeding, but the tests available at the time were not very high resolution. We used updated sequencing technology to get a clearer picture of the genetic diversity and potential for inbreeding among these songbirds.”

Like other animals, birds receive one copy of their genome from each parent. Some genetic variants can have negative impacts on an animal’s survival or reproductive success. The likelihood of receiving the same potentially damaging variant from both parents increases with inbreeding, when genetically similar individuals mate.

Previous tests of genetic diversity — such as those referenced in the delisting decision — often focus on a small set of specific markers on the genome called microsatellites, which only provide part of the picture. However, advancements in sequencing technology now allow inexpensive analysis of the entire genome from multiple individuals.

“If you think of the genome as a movie of the blueprint of life, then using microsatellites is like trying to get the plot from half a dozen snapshots, while sequencing the entire genome is like watching an entire 4K-resolution film,” said David Toews, Louis Martarano Career Development Professor of Biology at Penn State and co-leader of the research team. “There’s so much more information to be obtained from sequencing the entire genome, and modern technology has made that analysis possible.”

The researchers sequenced the whole genome of Kirtland’s warblers and, as a point of comparison, they also sequenced whole genomes of two closely related species whose populations have remained large and stable, Hooded warblers and American redstarts. The team specifically looked at a measure of inbreeding called “runs of homozygosity.”

A given spot on the genome is called homozygous when the genetic information obtained from an animal’s maternal parent is the same as the information obtained from its paternal parent. Runs of homozygosity (ROH) are long, connected stretches of homozygosity, sometimes millions of letters of the genetic alphabet in length. Particularly long ROH indicate that the individuals who carry them are products of recent inbreeding, when genetically similar individuals mated and were thus more likely to pass on the same genetic information. Fewer and shorter stretches indicate that an individual’s parents are more distantly related.

“Runs of homozygosity give us a unique look into the past and can be an indicator of the genomic health of the population,” said Zachary Szpiech, assistant professor of biology at Penn State and the other co-leader of the research team. “For example, long ROH have been associated with how well other species survive in their first year. ROH can also flag potentially damaging genetic variants, which may be useful when considering the conservation of the bird.”

The researchers found exceptionally long ROH in Kirtland’s warblers, indicating very recent inbreeding that had not previously been identified in this species. Additionally, they found many small to medium-sized ROH in Kirtland’s warblers, while the two closely related species had almost none.

“The contrast between Kirtland’s warblers and their closest related species, which haven’t undergone any population bottlenecks, couldn’t be more stark,” Toews said. “We found no evidence of inbreeding whatsoever in Hooded warblers or American redstarts, and in comparison, the level of inbreeding for the Kirtland’s warblers is almost off the charts. We also found a high frequency of potentially damaging genetic variants. This gives us a clear picture of how the demographic history of songbirds can shape their genetic diversity.”

The researchers noted that the Kirtland’s warblers they sampled did not appear to have any physical deformities. However, they said that inbreeding could manifest during the stages of life they did not observe, for example during development or the energy-intensive task of migration, or impact aspects of their reproductive success, such as how many eggs they lay or how many hatch. According to Toews, continued monitoring of these birds to clarify the impacts of inbreeding will be critical to future conservation efforts.

“An open question in this species has been whether the population of Kirtland’s warblers has always been small, or if it was once large and crashed,” Calderón said. “We can actually use ROH to look into the past, using rates of recombination — one way genomes can swap information around — to estimate when certain combinations of genetic information appeared. From this, we can see that most of the DNA segments within the short ROH in these birds originated between 1874 and 1954, mostly before known bottlenecks. This suggests that Kirtland’s warblers may have always had small population sizes. This makes sense given the high specificity of these birds to young jack-pine forests.”

Comparing these results with information about the distribution and abundance of the species, which has been collected since the 1940s, can provide insight into the events that shaped the genomes of these birds. For example, the researchers dated the origin of many DNA segments within long ROH between 1940 to 1981. This is consistent with a sudden population collapse beginning in the early 1940s, as this bottleneck would result in more, longer ROH. The researchers also plan to sequence the genomes of museum samples, including birds collected as early as the late 1800s, to provide additional context around genetically important events.

“Although Kirtland’s warblers are celebrated as a conservation success story, they are highly inbred and have a high frequency of potentially damaging genetic variants that could impact their ability to persist,” Calderón said. “Our work serves as an important example of how measures of genetic health may tell a different story than simple population numbers. Both need to be considered when assessing a population’s recovery and when making conservation decisions.”

In addition to Calderón, Toews and Szpiech, the research team also includes Andrew Wood, a research technologist in Toews’ lab at the time of the research and now a postdoctoral researcher at the University of Minnesota.

Funding from the U.S. National Science Foundation Division of Environmental Biology, the Penn State Huck Institutes of the Life Sciences and the Penn State Eberly College of Science supported this research.

Unlike the typical quantum chip design that lays the information-processing qubits onto a 2-D grid, the team from the Cleland Lab has designed a modular quantum processor comprising a reconfigurable router as a central hub. This enables any two qubits to connect and entangle, where in the older system, qubits can only talk to the qubits physically nearest to them.

“A quantum computer won’t necessarily compete with a classical computer in things like memory size or CPU size,” said UChicago PME Prof. Andrew Cleland. “Instead, they take advantage of a fundamentally different scaling: Doubling a classical computer’s computational power requires twice as big a CPU, or twice the clock speed. Doubling a quantum computer only requires one additional qubit.”

Taking inspiration from classical computers, the design clusters qubits around a central router, similar to how PCs talk to each other through a central network hub. Quantum “switches” can connect and disconnect any qubit within a few nanoseconds, enabling high-fidelity quantum gates and the generation of quantum entanglement, a fundamental resource for quantum computing and communication.

“In principle there’s no limit to the number of qubits that can connect via the routers,” said UChicago PME PhD candidate Xuntao Wu. “You can connect more qubits if you want more processing power, as long as they fit in a certain footprint.”

Wu is the first author of a new paper published in Physical Review X that describes this new way of connecting superconducting qubits. The researchers’ new quantum chip is flexible, scalable and as modular as the chips in cellphones and laptops.

“Imagine you have a classical computer that has a motherboard integrating lots of different components, like your CPU or GPU, memory and other elements,” said Wu. “Part of our goal is to transfer this concept to the quantum realm.”

Size and Noise

Quantum computers are highly advanced yet delicate devices with the potential to transform fields such as telecommunications, healthcare, clean energy, and cryptography. Two things must happen before quantum computers can tackle these global problems to their fullest potential.

First, they must be scaled to large enough size with flexible operability.

“This scaling can offer solutions to computational problems that a classical computer simply cannot hope to solve, like factoring huge numbers and thereby cracking encryption codes,” Cleland said.

Second, they must be fault-tolerant, able to perform massive calculations with few errors, ideally surpassing the processing power of current state-of-the-art classical computers. The superconducting qubit platform, under development here, is one promising approach to building a quantum computer.

“A typical superconducting processor chip is a square shape with all the quantum bits fabricated on that. It’s a solid-state system on a planar structure,” said co-author Haoxiong Yan, who graduated from UChicago PME in the spring and now works as a quantum engineer for Applied Materials. “If you can imagine a 2-D array, like a square lattice, that’s the topology of typical superconducting quantum processors.”

Limitations in Typical Design

This typical design causes several limitations.

First, putting qubits on a grid means each qubit can only interact with, at most, four other qubits — its immediate neighbors to the north, south, east and west. Greater qubit connectivity usually enables a more powerful processor with respect to both flexibility and component overhead, but the four-neighbor limit is generally considered inherent to the planar design. This means for practical quantum computing applications, scaling the device using brutal force will likely result in unrealistic resource requirements.

Second, the nearest-neighbor connections will in turn limit the classes of quantum dynamics that can be implemented as well as the extent of parallelism the processor is able to execute.

Finally, if all qubits are fabricated on the same planar substrate, then this poses a significant challenge to the fabrication yield, as even a small number of failed devices means the processor won’t work.

“To undertake practical quantum computing, we need millions or even billions of qubits and we need to make everything perfectly,” Yan said.

Rethinking the Chip

To work around these issues, the team retouched the design of the quantum processor. The processor is designed to be modular, in a way that different components can be pre-selected before being mounted onto the processor motherboard.

The team’s next steps are working on ways to scale up the quantum processor to more qubits, find novel protocols for expanding the processor’s capabilities, and, potentially, find ways to link router-connected qubit clusters the way supercomputers link their component processors.

They’re also looking to expand the distance over which they can entangle qubits.

“Right now, the coupling range is sort of medium-range, on the order of millimeters,” Wu said. “So if we’re trying to think of ways to connect remote qubits, then we must explore new ways to integrate other kind of technologies with our current setup.”

Funding: Devices and experiments were supported by the Army Research Office and Laboratory for Physical Sciences (ARO Grant No. W911NF2310077) and by the Air Force Office of Scientific Research (AFOSR Grant No. FA9550-20-1-0270)

“This is the first scientific study to analyze how dogs actually use soundboards,” said lead researcher Federico Rossano, associate professor of cognitive science at UC San Diego and director of the Comparative Cognition Lab. “The findings reveal that dogs are pressing buttons purposefully to express their desires and needs, not just imitating their owners. When dogs combine two buttons, these sequences are not random but instead seem to reflect specific requests.”

The study observed that the buttons most commonly used were related to essential needs, with words such as “outside,” “treat,” “play,” and “potty.” Notably, combinations like “outside” + “potty” or “food” + “water” were used in meaningful ways, occurring more frequently than expected by chance.

For dog owners, this research offers a new way to better understand their pets’ needs. “While dogs already communicate some of these needs,” Rossano said, “soundboards could allow for more precise communication. Instead of barking or scratching at the door, a dog may be able to tell you exactly what it wants, even combining concepts like ‘outside’ and ‘park’ or ‘beach.’ This could improve companionship and strengthen the bond between dogs and their owners.”

Data was collected via the FluentPet mobile app, where owners logged their dogs’ button presses in real time. The research team selected 152 dogs with over 200 logged button presses each to analyze patterns of use. Advanced statistical methods, including computer simulations, were used to determine whether button combinations were random, imitative, or truly intentional. The results showed that multi-button presses occurred in patterns significantly different from random chance, supporting the idea of deliberate communication.

The researchers also compared dogs’ button presses to those of their owners and found that dogs were not simply imitating human behavior. For instance, buttons like “I love you” were far less frequently pressed by dogs than by their people.

While the study provides evidence of intentional two-button combinations, the researchers aim to go further. Future investigations will explore whether dogs can use buttons to refer to the past or future — such as a missing toy — or combine buttons creatively to communicate concepts for which they lack specific words.

“We want to know if dogs can use these soundboards to express ideas beyond their immediate needs, like absent objects, past experiences, or future events,” Rossano said. “If they can, it would drastically change how we think about animal intelligence and communication.”

Rossano’s co-authors on the study are Amalia P. M. Bastos, now at Johns Hopkins University; Zachary N. Houghton, now at UC Davis; and Lucas Naranjo with CleverPet, Inc. Bastos’ work on the study was supported in part by Johns Hopkins’ Provost’s Postdoctoral Fellowship Program. While Bastos and Houghton have previously served as consultants to CleverPet, and Naranjo currently works for the company, which manufactures the FluentPet mobile app and soundboard devices, the research design and analysis were conducted independently.

And researchers from the Case Western Reserve University (CWRU) School of Dental Medicine helped unearth the cave’s secrets over more than a decade of excavation.

Manot Cave was used for thousands of years as a living space for both Neanderthals and humans at different times. In 2015, researchers from Case Western Reserve helped identify a 55,000-year-old skull that provided physical evidence of interbreeding between Neanderthal and homo sapiens, with characteristics of each clearly visible in the skull fragment.

The cave’s living space was near the entrance, but in the deepest, darkest part of the cave, eight stories below, the new paper describes a large cavern with evidence it was used as a gathering space, possibly for rituals that enhanced social cohesion.

The cavern’s touchstone is an engraved rock, deliberately placed in a niche in the cavern, with a turtle-shell design carved into its surface. The three-dimensional turtle is contemporaneous with some of the oldest cave paintings in France.

“It may have represented a totem or spiritual figure,” said Omry Barzilai, Head of Material Culture PaleoLab at the University of Haifa and the Israel Antiquities Authority, who led the team. “Its special location, far from the daily activities near the cave entrance, suggests that it was an object of worship.”

The cavern has natural acoustics favorable for large gatherings, and evidence of wood ash on nearby stalagmites suggests prehistoric humans carried torches to light the chamber.

Manot Cave was discovered in 2008 by workers building condominiums in a mountain resort close to Israel’s border with Lebanon. Case Western Reserve’s School of Dental Medicine got involved in the excavation in 2012. The dean at the time, Jerold Goldberg, committed $20,000 annually for 10 years to CWRU’s Institute for the Science of Origins; the money was used to fund dental students’ summer research in Israel.

“I’m an oral and maxillofacial surgeon by training,” Goldberg said. “I provided the commitment and the money because I wanted people to understand the breadth and intellectual interest that dental schools have.”

And although not trained in archaeology, dental students can quickly identify bone fragments from rock, which makes them invaluable at excavations like Manot Cave.

“Most people would not suspect that a dental school would be involved in an archaeological excavation,” said Mark Hans, professor and chair of orthodontics at the dental school. “But one of the things that are preserved very well in ancient skeletons are teeth, because they are harder than bone. There is a whole field of dental anthropology. As an orthodontist, I am interested in human facial growth and development, which, it turns out, is exactly what is needed to identify anthropological specimens.”

For 10 years, Case Western Reserve sent 10 to 20 dental students every summer to help with the Manot Cave excavation. The summer research became so popular that students from other dental and medical schools began applying to visit Israel with the CWRU team, according to Yvonne McDermott, the project coordinator.

Case Western Reserve also collaborated closely with Linda Spurlock, a physical anthropologist at Kent State University, whose expertise is putting a face on a skull using clay to build out the tissues that would have covered the bone when the person was alive.

“One of the things I liked most about working on this excavation was how much we learned from the other researchers,” Hans said. “Everyone has a narrow focus, like mammals, uranium-dating, hearths; and we all came together and shared our knowledge. We learned a lot over 10 years.”

The Manot Cave project is supported by the Dan David Foundation, the Israel Science Foundation, the United States-Israel Binational Science Foundation, the Irene Levi Sala CARE Archaeological Foundation and the Leakey Foundation. The research also involved experts from the Israel Antiquities Authority, Cleveland State University, the Geological Survey of Israel, the Hebrew University of Jerusalem, the University of Haifa, Tel Aviv University, Ben-Gurion University, the University of Vienna, the University of Barcelona, the University of Siena and Simon Fraser University.

Almost always, battery scientists and engineers have tested the cycle lives of new battery designs in laboratories using a constant rate of discharge followed by recharging. They repeat this cycle rapidly many times to learn quickly if a new design is good or not for life expectancy, among other qualities.

This is not a good way to predict the life expectancy of EV batteries, especially for people who own EVs for everyday commuting, according to the study published Dec. 9 in Nature Energy. While battery prices have plummeted about 90% over the past 15 years, batteries still account for almost a third of the price of a new EV. So, current and future EV commuters may be happy to

“We’ve not been testing EV batteries the right way;’ said Simona Onori, senior author and an associate professor of energy science and engineering in the Stanford Doerr School of Sustainability. “To our surprise, real driving with frequent acceleration, braking that charges the batteries a bit, stopping to pop into a store, and letting the batteries rest for hours at a time, helps batteries last longer than we had thought based on industry standard lab tests.”

A pleasant surprise

The researchers designed four types of EV discharge profiles, from the standard constant discharge to dynamic discharging based on real driving data. The research team tested 92 commercial lithium ion batteries for more than two years across the discharge profiles. In the end, the more realistically the profiles reflected actual driving behavior, the higher EV life expectancy climbed.

Several factors contribute to the unexpected longevity, the study finds. A machine learning algorithm trained on all the data the team collected helped tease out the impacts of dynamic discharge profiles on battery degradation.

For example, the study showed a correlation between sharp, short EV accelerations and slower degradation. This was contrary to long-held assumptions of battery researchers, including this study’s team, that acceleration peaks are bad for EV batteries.

Pressing the pedal with your foot hard does not speed up aging. If anything, it slows it down, explained Alexis Geslin, one of three lead authors of the study and a PhD student in materials science and engineering and in computer science in Stanford’s School of Engineering.

Two ways to age

The research team also looked for differences in battery aging due to many charge-discharge cycles versus battery aging that just comes with time. Your batteries at home that have been sitting unused in a drawer for years will not operate as well as when you bought them, if they work at all.

“We battery engineers have assumed that cycle aging is much more important than time-induced aging. That’s mostly true for commercial EVs like buses and delivery vans that are almost always either in use or being recharged,” said Geslin. “For consumers using their EVs to get to work, pick up their kids, go to the grocery store, but mostly not using them or even charging them, time becomes the predominant cause of aging over cycling.”

The study identifies an average discharge rate sweet spot for balancing time aging and cycle aging, at least for the commercial battery they tested. Luckily, that window is in the range of realistic consumer EV driving. Carmakers could update their EV battery management software to take advantage of the new findings and to maximize battery longevity under real-world conditions.

Looking ahead

“Going forward, evaluating new battery chemistries and designs with realistic demand profiles will be really important,” said energy science and engineering postdoctoral scholar Le Xu. “Researchers can now revisit presumed aging mechanisms at the chemistry, materials, and cell levels to deepen their understanding. This will facilitate the development of advanced control algorithms that optimize the use of existing commercial battery architectures.”

The implications extend beyond batteries, the study suggests. Scientists and engineers could apply the principles to other energy storage applications, as well as to other materials and devices in physical sciences in which aging is crucial, like plastics, glasses, solar cells, and some biomaterials used in implants.

“This work highlights the power of integrating multiple areas of expertise — from materials science, control, and modeling to machine learning- to advance innovation,” Onori said.