Shell ring villages were coastal communities built around fishing, as indicated by their sitting next to shellfish estuaries, and their large mounds of mollusk shells which remain to this day. Shell rings formed some of the earliest human village settlements along the U.S. South Atlantic coast but were abandoned at the end of the Late Archaic around 4,000 years ago. While scholars have proposed socio-ecological explanations, there has been limited examination of the physical evidence for these.

Garland, Thompson and colleagues analyzed the biochemistry and paleobiology of mollusk shells found at three abandoned shell rings on Sapelo Island in Georgia, U.S. For example, they measured the size of oyster shells as an indicator of the health of the environment and compared oxygen isotope values to determine salinity conditions. They integrated their findings with chronological data — such as tree ring analyses — using a Bayesian chronological model, to determine environmental fluctuations over time.

The researchers found that the three Sapelo shell rings, known as Ring I, Ring II and Ring III, were occupied in the Late Archaic for varying, sometimes overlapping, periods. Ring II appeared to be the oldest and longest-lasting, founded around 4290 years ago and being occupied until 3950 years ago, with Ring I lasting around 150 years in the middle of this period. Ring III was the newest and outlasted the others, before abandonment around 3845 years ago. While Rings I and II featured large oyster shells, those at Ring III were significantly smaller, indicating a decrease in oyster shell size over time. Smaller oysters tend to be less healthy or younger, so this may indicate a depletion in oyster stocks and/or oyster health. Oxygen isotopes also indicated significantly lower salinity conditions by the time of Ring III as compared to Rings I and II.

The analysis suggests that the inhabitants of the shell ring villages experienced environmental fluctuations, especially around the occupation of Ring III. Coastal settlement may have initially been an adaptation to climate change as a way to effectively manage fisheries — which are highly sensitive to such changes. However, by the time of occupation of Ring III, fishing may have become unsustainable, leading to dispersals to other settlements and other forms of subsistence.

The authors believe that their work provides “comprehensive evidence for correlations between large-scale environmental change and societal transformations on the Georgia coast during the Late Archaic period.”

The authors add: “The emergence of village life and adaptation to coastal environments are significant transitions in human history that have occurred at various times and places across the globe. Our research shows that Indigenous peoples who established North America’s first coastal shell ring villages some 4200 years ago were resilient and, through cooperation and collective action, were able to adapt to environmental instability and resource shortfalls.”

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“We were surprised by this fascinating phenomenon that mitochondria appear to have a dual purpose: their well-established metabolic role producing energy, as well as this optical effect,” said the study’s lead investigator, Wei Li, Ph.D./B.M., who leads the NEI Retinal Neurophysiology Section.

The findings also address a long-standing mystery about the mammalian retina. Despite evolutionary pressure for light to be translated into signals and pass instantly from the retina to the brain, the trip is hardly direct. Once light reaches the retina, it must pass through multiple neural layers before reaching the outer segment of photoreceptors, where phototransduction (the conversion of light’s physical energy into cellular signals) occurs. Photoreceptors are long, tube-like structures divided into inner and outer segments. The last obstacle a photon must traverse before moving from the inner to the outer segment is an unusually dense bundle of mitochondria.

Those bundles of mitochondria would seem to work against the process of vision either by scattering light or absorbing it. So, Li’s team set out to investigate their purpose by studying cone photoreceptors from the 13-lined ground squirrel.

Unlike other animal models used for vision research, the 13-lined ground squirrel’s retina comprises mostly cones, which see color, as opposed to rods that enable night vision. Li’s team studies the 13-lined ground squirrel to better understand the causes of human eye diseases that primarily affect cone photoreceptors.

The researchers used a modified confocal microscope to observe the optical properties of living cone mitochondria exposed to light. Far from scattering light, the tightly packed mitochondria concentrated light along a thin, pencil-like trajectory onto the outer segment. Computational modeling using high-resolution mitochondrial reconstructions corroborated the live-imaging findings.

“The lens-like function of mitochondria also may explain the phenomenon known as the Stiles Crawford effect,” said first author of the paper, John Ball, Ph.D., a staff scientist in the Retinal Neurophysiology Section.

Scientists measuring retinal responses to light have long observed that when light enters the eye near the center of the pupil, it appears brighter compared to light of equal intensity entering the eye near the edge of the pupil.

In this study, Li found that the lens-like effect of mitochondria followed a similar directional light intensity profile. That is, depending on light source location, the mitochondria focused light into the outer segment of the cell along trajectories that mirrored those observed from the Stiles-Crawford effect.

Linking mitochondria’s lens-like function to the Stiles-Crawford effect has potential clinical implications. The long-observed effect may now be used as the basis for non-invasively detecting retinal diseases, many of which are thought to involve mitochondrial dysfunction at their origin. For example, patients with retinitis pigmentosa have been reported to have abnormal Stiles-Crawford effect even when they have good visual acuity. More research is needed to explore the structural and functional changes in cone mitochondria and their manifestations in detectable optic features.

Finally, the findings provide new insights into how our eyes may have evolved.

Like the mitochondria in Li’s study, within the photoreceptors of birds and reptiles, tiny oil droplets are located in the portion of the inner segment closest to the outer segment, and they are thought to serve an optical role. Furthermore, the mitochondrial “microlens” in mammalian cone photoreceptors confers a functionality reminiscent of that achieved by the compound eye of arthropods like flies and bumblebees.

“This insight conceptually bridges compound eyes in arthropods with the camera eyes of vertebrates, two independently evolved image-forming systems, demonstrating the power of convergent evolution,” Li said.

The study was funded by the NEI Intramural Research Program.

Video: https://youtu.be/BPWXpam_mcU

The study also found that, at a time when mental health problems soared due to financial woes, supply shortages and nonstop news coverage of the virus, people sought solace in the great outdoors, with one-third spending more time there than they did pre-COVID.

“This research shows how critical it is to keep parks and green spaces open in times of crisis,” said senior author Colleen Reid, an assistant professor of geography in the Institute for Behavioral Science. “It also shows that, as a public health measure, more effort should be made to put in green spaces and make them accessible.”

For the study, the authors presented about 1,200 Denver-area residents with a 30-minute survey gauging their mental health and their perceptions of green space near their home, including: how much there was, whether they could see it, whether it was accessible, how much they used it and its quality. They also collected aerial satellite imagery to objectively quantify greenery in respondents’ neighborhoods.

The survey ran from November 2019 to January 2021.

Once COVID-19 emerged and lockdowns ensued, Reid added additional questions, providing a rare opportunity to also look at how the pandemic influenced mental health over time and what was most stressful about it.

“Not surprisingly, we found that the pandemic impacted mental health negatively,” said co-author Emma Rieves, a master’s student in the Department of Geography. “But we also found that green space could have a powerful protective effect, even at a time of such extraordinary stressors.”

Supply shortages and job losses stressed people out

Surprisingly, the study found no association between being diagnosed with COVID and having poor mental health. But respondents reported that having symptoms, no diagnosis and no way to test was distressing.

Those who lost income or felt they were working in an unsafe environment were also more likely to be stressed or depressed, while the strongest source of mental health problems was a fear of supply shortages (including toilet paper and food).

People who spent a lot of time scrolling the internet looking at the news reported poorer mental health. In contrast, merely having abundant green space nearby, as measured by satellite images, was associated with lower depression scores.

To get the most benefit out of nearby green space, the study found, people had to get out and use it. Those who used green space most had significantly lower anxiety and depression.

“There are many dimensions of green space, and our study looked closely at how these dimensions impact mental health,” said Rieves, noting that policymakers often rely solely on objective measures, like satellite images or proximity to parks when assessing whether to invest in more greenery in a community.

On a satellite image, Rieves points out, a large patch of greenery could actually be a weed-filled lot. A ‘nearby park’ could be on the other side of a busy highway.

“It’s not just about being able to see trees from your home. The amount, quality and accessibility of that green space matters,” said Rieves.

Many public agencies closed public green spaces, including neighborhood playgrounds and national parks, at the onset of the pandemic for fear that the virus could be easily spread via surfaces. Once parks reopened, with places like gyms, bars and churches still closed, Coloradans flocked to the outdoors: 33% of respondents reported spending more time in parks or on trails than the year before.

The ‘biophilia hypothesis’

The study adds to a growing body of evidence suggesting that green space can have a measurable impact on health.

According to one theory, known as the ‘biophilia hypothesis,’ humans innately tend to seek connections with green spaces, where the calming environment influences stress hormones in a way that promotes healing and fends off disease.

“The idea is that we have evolved with nature, and only in the recent past have we been living in the concrete jungle,” said Reid.

One famous 1984 study even found that when hospital patients had rooms with a window looking out on green space, their wounds healed faster and they required less pain medication than those looking out on a brick wall.

Reid cautioned that correlations between green space and health have been scrutinized, in part because people with higher incomes and, thus, better access to healthy food and health care may also be more able to afford to live near green spaces.

To address that, Reid’s study took sociodemographic factors into account, along with the many unique circumstances that have emerged during COVID.

After controlling for all the factors, the benefits still remained clear: “Spend more time outside,” Rieves said. “Pandemic or no pandemic, it’s good for your mental health.”

Ongoing observations of that 2017 merger by the Chandra X-ray Observatory, an orbiting telescope, suggests the latter: that the merged object stuck around, likely for a mere second, before undergoing ultimate collapse.

The evidence is in the form of an X-ray afterglow from the merger, dubbed GW170817, that would not be expected if the merged neutron stars collapsed immediately to a black hole. The afterglow can be explained as a rebound of material off the merged neutron stars, which plowed through and heated the material around the binary neutron stars. This hot material has now kept the remnant glowing steadily more than four years after the merger threw material outward in what’s referred to as a kilonova. X-ray emissions from a jet of material that was detected by Chandra shortly after the merger would otherwise be dimming by now.

While the excess X-ray emissions observed by Chandra could come from debris in an accretion disk swirling around and eventually falling into the black hole, astrophysicist Raffaella Margutti of the University of California, Berkeley, favors the delayed collapse hypothesis, which is predicted theoretically.

“If the merged neutron stars were to collapse directly to a black hole with no intermediate stage, it would be very hard to explain this X-ray excess that we see right now, because there would be no hard surface for stuff to bounce off and fly out at high velocities to create this afterglow,” said Margutti, UC Berkeley associate professor of astronomy and of physics. “It would just fall in. Done. The true reason why I’m excited scientifically is the possibility that we are seeing something more than the jet. We might finally get some information about the new compact object.”

Margutti and her colleagues, including first author Aprajita Hajela, who was Margutti’s graduate student when she was at Northwestern University before moving to UC Berkeley, report their analysis of the X-ray afterglow in a paper recently accepted for publication in The Astrophysical Journal Letters.

The radioactive glow of a kilonova

Gravitational waves from the merger were first detected on Aug. 17, 2017, by the Advanced Laser Interferometer Gravitational-wave Observatory (LIGO) and the Virgo collaboration. Satellite- and ground-based telescopes quickly followed up to record a burst of gamma rays and visible and infrared emissions that together confirmed the theory that many heavy elements are produced in the aftermath of such mergers inside hot ejecta that produces a bright kilonova. The kilonova glows because of light emitted during the decay of radioactive elements, like platinum and gold, that are produced in the merger debris.

Chandra, too, pivoted to observe GW170817, but saw no X-rays until nine days later, suggesting that the merger also produced a narrow jet of material that, upon colliding with the material around the neutron stars, emitted a cone of X-rays that initially missed Earth. Only later did the head of the jet expand and begin emitting X-rays in a broader jet visible from Earth.

The X-ray emissions from the jet increased for 160 days after the merger, after which they steadily grew fainter as the jet slowed down and expanded. But Hajela and her team noticed that from March 2020 — about 900 days after the merger — until the end of 2020, the decline stopped, and the X-ray emissions remained approximately constant in brightness.

“The fact that the X-rays stopped fading quickly was our best evidence yet that something in addition to a jet is being detected in X-rays in this source,” Margutti said. “A completely different source of X-rays appears to be needed to explain what we’re seeing.”

The researchers suggest that the excess X-rays are produced by a shock wave distinct from the jets produced by the merger. This shock was a result of the delayed collapse of the merged neutron stars, likely because its rapid spin very briefly counteracted the gravitational collapse. By sticking around for an extra second, the material around the neutron stars got an extra bounce that produced a very fast tail of kilonova ejecta that created the shock.

“We think the kilonova afterglow emission is produced by shocked material in the circumbinary medium,” Margutti said. “It is material that was in the environment of the two neutron stars that was shocked and heated up by the fastest edge of the kilonova ejecta, which is driving the shock wave.”

The radiation is reaching us only now because it took time for the heavy kilonova ejecta to be decelerated in the low-density environment and for the kinetic energy of the ejecta to be converted into heat by shocks, she said. This is the same process that produces radio and X-rays for the jet, but because the jet is much, much lighter, it is immediately decelerated by the environment and shines in the X-ray and radio from the very earliest times.

An alternative explanation, the researchers note, is that the X-rays come from material falling towards the black hole that formed after the neutron stars merged.

“This would either be the first time we’ve seen a kilonova afterglow or the first time we’ve seen material falling onto a black hole after a neutron star merger,” said co-author Joe Bright, a UC Berkeley postdoctoral researcher. “Either outcome would be extremely exciting.”

Chandra is now the only observatory still able to detect light from this cosmic collision. Follow-up observations by Chandra and radio telescopes could distinguish between the alternative explanations, however. If it is a kilonova afterglow, radio emission is expected to be detected again in the next few months or years. If the X-rays are being produced by matter falling onto a newly formed black hole, then the X-ray output should stay steady or decline rapidly, and no radio emission will be detected over time.

Margutti hopes that LIGO, Virgo and other telescopes will capture gravitational waves and electromagnetic waves from more neutron star mergers so that the series of events preceding and following the merger can be pinned down more precisely and help reveal the physics of black hole formation. Until then, GW170817 is the only example available for study.

“Further study of GW170817 could have far-reaching implications,” said co-author Kate Alexander, a postdoctoral researcher who also is from Northwestern University. “The detection of a kilonova afterglow would imply that the merger did not immediately produce a black hole. Alternatively, this object may offer astronomers a chance to study how matter falls onto a black hole a few years after its birth.”

Margutti and her team recently announced that the Chandra telescope had detected X-rays in observations of GW170817 performed in December 2021. Analysis of that data is ongoing. No radio detection associated with the X-rays has been reported.

In a new report, researchers from the University of Pennsylvania’s School of Veterinary Medicine and Perelman School of Medicine find that, for at least one example of apparent interspecies transmission, this crossing the species boundary did not cause the virus to gain a significant number of mutations.

Writing in the journal Viruses, the scientists identified a domestic house cat, treated at Penn Vet’s Ryan Hospital, that was infected with the delta variant of SARS-CoV-2 subsequent to an exposure from its owner. The full genome sequence of the virus was a close match to viral sequences circulating in people in the Philadelphia region at the time.

“SARS-CoV-2 has a really incredibly wide host range,” says Elizabeth Lennon, senior author on the work, a veterinarian, and assistant professor at Penn Vet. “What this means to me is that, as SARS-CoV-2 continues to be prevalent in the human population, we need to watch what’s happening in other animal species as well.”

The find is the first published example of the delta variant occurring in a domestic cat in the United States. Notably, the cat’s infection was only identified by testing its fecal matter. A nasal swab did not result in a positive test.

“This did highlight the importance of sampling at multiple body sites,” says Lennon. “We wouldn’t have detected this if we had just done a nasal swab.”

Lennon and colleagues have been sampling dogs and cats for SARS-CoV-2 since early in the pandemic. This particular pet cat, an 11-year-old female, was brought to Ryan Hospital in September with gastrointestinal symptoms. It had been exposed to an owner who had COVID-19 — though that owner had been isolating from the cat for 11 days prior to its hospitalization, another household member doing the cat care in the interim.

Working through the Penn Center for Research on Coronaviruses and Other Emerging Pathogens and Perelman School of Medicine microbiologist Frederic Bushman’s laboratory, the team obtained a whole genome sequence of the cat’s virus.

Sequencing revealed the delta variant, more specifically, the AY.3 lineage. The researchers did not have a sample from the infected owner. Comparing the sequence to the database kept by the Bushman laboratory, however, the cat’s virus was nothing out of the ordinary in terms of the sequences of SARS-CoV-2 circulating in the Delaware Valley region at the time.

“When we looked at a random sampling of human sequences from our geographic area, there wasn’t anything dramatically different about our cat’s sample,” Lennon says. “So, our takeaway was that the cat was not infected by a virus that was somehow highly different.”

Not all variants of SARS-CoV-2 have been equally able to infect a wide range of hosts. For example, the original Wuhan strain could not naturally infect mice; later variants gained that ability. Scientists began seeing infections in cats and dogs from the early days of the pandemic, presumably infected through close contact with their owners.

“A main takeaway here is that as different variants of SARS-CoV-2 emerge, they seem to be retaining the ability to infect a wide range of species,” Lennon says.

While this particular case does not raise alarms for the virus acquiring significant numbers of mutations as it moved between species, Lennon and colleagues, including Bushman and Susan Weiss of Penn’s medical school, hope to continue studying other examples to see how SARS-CoV-2 evolves. Penn Vet’s Institute for Infectious and Zoonotic Disease will facilitate this look at human-animal interactions when it comes to pathogen transmission.

“We know that the SARS-CoV-2 is undergoing changes as it passes between to become more and more transmissible over time,” says Lennon. “We saw that with the omicron variant. It’s host-adapting to people. We also want to know, when other animal species get infected, does the virus start to adapt to those species? And for those viruses that may adapt to a different species, do they still infect humans?”

Elizabeth Lennon is the Pamela Cole Assistant Professor of Internal Medicine at the University of Pennsylvania School of Veterinary Medicine.

Lennon’s coauthors on the study were Penn Vet’s Oliva C. Lenz and Stephen D. Cole and the Perelman School of Medicine’s Andrew D. Marques, Brendan J. Kelly, Kyle G. Rodino, Ranawaka A. P. M. Perera, Susan R. Weiss, and Frederic D. Bushman.

Lenz and Marques were co-first authors and Lennon is the corresponding author.

Support for the study came from the Penn Vet COVID-19 Research Fund, the Centers for Disease Control and Prevention (grants BAA 200-2021-10986 and 75D30121C11102/000HCVL1-2021-55232), philanthropic donations to the Penn Center for Research on Coronaviruses and Other Emerging Pathogens, and the National Institutes of Health (grants HL137063, AI140442, and AI121485).

Called environmental DNA or eDNA, the technique searches for trace amounts of genetic material left behind by wildlife.

The scientists, from California State University, CUNY, Wildlife Conservation Society (WCS), and Columbia University, published their results in the journal Frontiers.

The scientists say that eDNA can be used to complement other methods to locate whales and dolphins such as visual observations and acoustic monitoring, and their eDNA detections are some of the most promising to date for detecting whales and dolphins from seawater in the open ocean.

Said the study’s lead author Dr. Elizabeth Alter of California State University: “Determining how cetaceans and other threatened marine animals use coastal habitats is critical to their effective conservation. By generating eDNA data in parallel with survey data, it will be possible to gain a clearer understanding of how this tool can be used in management and conservation contexts to monitor species of conservation concern over large marine ecosystems.”

In addition to finding whales and dolphins, the technique detected baitfish present in the area preyed on by whales and dolphins. The authors say the technique could eventually be used to identify individual animals.

Said Dr. Howard C. Rosenbaum, Director of WCS’s Ocean Giants Program/Senior Scientist NY Aquarium and a co-author of the study: “Innovation and application of new techniques, such as the possibility of using eDNA, that leads to having better information about distribution of whales, dolphins and their prey is so important today, especially where potential impacts in these habitats may be increasing human activities.”

The authors say that eDNA drops to lower levels over time and that additional research is needed to better understand how factors such as behavior and oceanographic conditions contribute to the longevity of eDNA signals.

Though there are some signs of promising recovery for many whale species and populations, whales continue to face a range of modern day threats ranging from ship strikes, to entanglement with nets, to ocean noise.

The Biden-Harris administration, New York State and other states on the eastern seaboard are scaling up massive renewable energy projects to meet energy demands and help address climate change, including a wind energy auction for more than 488,000 acres in the New York Bight. There are many potential impacts from these developments to whales that the environmental community, industry, and state/federal authorities are aiming to address. WCS has been involved at state and national level dialogues as well as developing best practice guidance through the IUCN.

The use of emerging and novel techniques such as eDNA as demonstrated by the results of the current study in the NY Bight and other approaches can offer new insights as to whale presence and their prey in and around lease areas as offshore wind scales up along the eastern seaboard. More broadly, WCS increasingly uses eDNA in its conservation work, detecting critically endangered wildlife such as Swinhoe’s softshell turtle, in the Bolivian Amazon, and in some of the most rugged areas on the planet including Mt. Everest.

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