#CTHULHU STUDIES

First gene knockout in cephalopod achieved 

CRISPR CRITTERS

by Marine Biological Laboratory

Longfin inshore squid (Doryteuthis pealeii) hatchlings. On the left is a control hatchling; note the black and reddish brown chromatophores evenly placed across its mantle, head and tentacles. In contrast, the embryo on the right was injected with CRISPR-Cas9 targeting a pigmentation gene (Tryptophan 2,3 Dioxygenase) before the first cell division ; it has very few pigmented chromatophores and light pink to red eyes. Credit: Karen Crawford

A team at the Marine Biological Laboratory (MBL) has achieved the first gene knockout in a cephalopod using the squid Doryteuthis pealeii, an exceptionally important research organism in biology for nearly a century. The milestone study, led by MBL Senior Scientist Joshua Rosenthal and MBL Whitman Scientist Karen Crawford, is reported in the July 30 issue of Current Biology.


The team used CRISPR-Cas9 genome editing to knock out a pigmentation gene in squid embryos, which eliminated pigmentation in the eye and in skin cells (chromatophores) with high efficiency.

"This is a critical first step toward the ability to knock out—and knock in—genes in cephalopods to address a host of biological questions," Rosenthal says.

Cephalopods (squid, octopus and cuttlefish) have the largest brain of all invertebrates, a distributed nervous system capable of instantaneous camouflage and sophisticated behaviors, a unique body plan, and the ability to extensively recode their own genetic information within messenger RNA, along with other distinctive features. These open many avenues for study and have applications in a wide range of fields, from evolution and development, to medicine, robotics, materials science, and artificial intelligence.

The ability to knock out a gene to test its function is an important step in developing cephalopods as genetically tractable organisms for biological research, augmenting the handful of species that currently dominate genetic studies, such as fruit flies, zebrafish, and mice.
Doryteuthis pealeii, often called the Woods Hole squid. Studies with D. pealeii have led to major advances in neurobiology, including description of the fundamental mechanisms of neurotransmission. The Marine Biological Laboratory collects D. pealeii from local waters for an international community of researchers. Credit: Roger Hanlon

It is also a necessary step toward having the capacity to knock in genes that facilitate research, such as genes that encode fluorescent proteins that can be imaged to track neural activity or other dynamic processes.

"CRISPR-Cas9 worked really well in Doryteuthis; it was surprisingly efficient," Rosenthal says. Much more challenging was delivering the CRISPR-Cas system into the one-celled squid embryo, which is surrounded by an exceedingly tough outer layer, and then raising the embryo through hatching. The team developed micro-scissors to clip the egg's surface and a beveled quartz needle to deliver the CRISPR-Cas9 reagents through the clip.

Studies with Doryteuthis pealeii have led to foundational advances in neurobiology, beginning with description of the action potential (nerve impulse) in the 1950s, a discovery for which Alan Hodgkin and Andrew Huxley became Nobel Prize laureates in 1963. For decades D. pealeii has drawn neurobiologists from all over the world to the MBL, which collects the squid from local waters.

Recently, Rosenthal and colleagues discovered extensive recoding of mRNA in the nervous system of Doryteuthis and other cephalopods. This research is under development for potential biomedical applications, such as pain management therapy.

D. pealeii is not, however, an ideal species to develop as a genetic research organism. It's big and takes up a lot of tank space plus, more importantly, no one has been able to culture it through multiple generations in the lab.

For these reasons, the MBL Cephalopod Program's next goal is to transfer the new knockout technology to a smaller cephalopod species, Euprymna berryi (the hummingbird bobtail squid), which is relatively easy to culture to make genetic strains.


Explore furtherThe mysterious, legendary giant squid's genome is revealed
More information: Current Biology (2020). DOI: 10.1016/j.cub.2020.06.099
Journal information: Current Biology


Provided by Marine Biological Laboratory

Partnerships with bankrupt companies could be double-edged sword for investors
by Indiana University

Credit: Unsplash/CC0 Public Domain

The list of companies that have filed for bankruptcy during the first half of 2020 reads like a "who's who" of major retailers and recognized brands. Consumers may know J.C. Penney, Hertz, Neiman Marcus, J. Crew and Pier 1, but the carnage also includes tech firms previously seen to have much potential.

With the recent rise in bankruptcies, suppliers and partners of these companies are being forced to make a difficult decision: Should they bet on the bankrupt customer or partner to survive by continuing to invest in the relationship? Or should they bet that the bankrupt customer or partner will not survive by cutting off their investments so they can minimize losses and redeploy resources?

New research from the Indiana University Kelley School of Business found that when a company is in bankruptcy, its advertising and research and development investments can cut both ways. They increase the odds of surviving for some bankrupt companies and decrease the odds for others.

"This difference hinges on the influence that the bankrupt company's suppliers have in the bankruptcy process," said Niket Jindal, assistant professor of marketing and the study's author. "Advertising and R&D increase bankruptcy survival when suppliers have high influence, whereas they decrease bankruptcy survival when suppliers have low influence."

His article, "The Impact of Advertising and R&D on Bankruptcy Survival: A Double-Edged Sword," appears in the current issue of the Journal of Marketing.

Jindal studied whether a company's past investments in intangible assets—specifically investments in advertising and R&D—can help suppliers and partners make a decision on whether to bet on the bankrupt company. He analyzed 1,672 bankruptcy cases filed in U.S. bankruptcy courts from 1996 to 2019 and found that managers could substantially improve their odds of correctly predicting whether a bankrupt customer or partner will survive by considering the company's past advertising and R&D investments, in addition to the usual financial predictors.

He found that by considering a bankrupt company's advertising and R&D, managers can increase the accuracy of predicting whether that company will survive by 11 percent.

Specifically, the results show that a bankrupt company's advertising increases the odds of its survival when at least 38 percent of the company's debt has been borrowed from suppliers. For R&D, the cutoff point is when at least 21 percent of the company's debt has been borrowed from suppliers.

"A losing bet can be catastrophic for a supplier or partner," Jindal said. "If the company bets on a bankrupt customer or partner to survive and they do not survive, investments in the relationship will be lost, and the company will have fewer resources and time to try to attract other customers and partners to make up for the lost sales. On the other hand, if the company bets against the bankrupt customer or partner and they do survive, the relationship will be soured and will put future sales from them at risk."

Jindal said that suppliers and partners should be careful when including a bankrupt firm's advertising and R&D investments in their decision-making process.

"The key is to look at the portion of the bankrupt company's debt that is due to suppliers versus banks, because this shows the influence that the bankrupt company's suppliers will have, relative to other creditors, in the bankruptcy process," he said.

Suppliers have greater noncontractual revenue and generally do not require collateral, while banks have less noncontractual revenue and generally do require collateral. The impact of advertising and R&D on the value that is received if the bankrupt firm survives versus gets liquidated differs for suppliers versus banks.

Explore further Hertz allowed to sell $1 bn in shares despite bankruptcy

More information: Niket Jindal, The Impact of Advertising and R&D on Bankruptcy Survival: A Double-Edged Sword, Journal of Marketing (2020). DOI: 10.1177/0022242920936205
Journal information: Journal of Marketing

Provided by Indiana University

Legacies of historical human activities in Medieval forest dynamics of the Italian peninsula

by Gianluca Piovesan, Scott Mensing, University of Tuscia

Springs and wetland vegetation close to the Nature Reserve of Lago Lungo and Ripa Sottile Rieti. Credit: Gianluca Piovesan
When historians and paleoecologists work directly together to study the past (what is called a consilience-driven approach) we are able to develop much more nuanced explanations for the role of people (or climate) as a cause of past abrupt environmental change. The joint histories of socioeconomic change, developed from archival sources, and ecologic change, reconstructed from pollen analysis of lake sediments, has helped clarify the interrelationship between societal factors and climate forcing in shaping land-use legacies along the Italian Peninsula. We found that different communities, guided by different political and economic structures, created entirely different landscapes, even during periods of similar climate, but after the black plague the rewilding landscape is a common trait in the Apennines


Reconstructing landscape history during Medieval times in Italia peninsula

During the period of Medieval Climate, important differences were revealed in the mountain landscape of the Central Apennines in respect to the Pollino massif. Since the ninth century up to the16th century in the Rieti Basin, consolidation of small landholdings under the church led to larger-scale production of agricultural products and forest clearance. Near Pollino massif, under the same climatic regime, a deforested landscape managed using slash and burn agriculture is present up to the Norman conquest, at which point burning stops and preservation of fir forest for extraction of timbers for construction begins.

The fast recolonization of silver fir forest soon after the expansion of early succession maples and alders is a surprising and interesting process that, however, is forecasted by vegetation dynamics in the absence of human disturbance and finds an analog in today's vegetation dynamics. "This unexpected forest rewilding during the Medieval Climate Anomaly led us to suppose that the spread of fir was a consequence of the abandonment of the land and the protection of seedlings and saplings from fires and from grazing, in the same way today observed inside the strict reserves of Pollino, Sila and Aspromonte National parks," says Gianluca Piovesan from the University of Tuscia.

In both locations, following the black plague and depopulation, the forests shifted to a trajectory of secondary succession and rewilding, a trend observed across most of western Europe. However, the individual pathway of each successional pattern was strongly influenced by human activity prior to land abandonment and local environmental conditions.

Forest rewilding in the Apennines: a process that dates back to late Medieval times

This study confirmed that forest expansion in Mediterranean mountain environments is a fast process. However, following land abandonment, the return to an old-growth state takes centuries. "Considering the intense impact of Medieval society on the Apennines, we hypothesize that most old-growth forest remnants are a landscape legacy of the late Medieval rewilding phase that is still moving closer to a more complex forest ecosystem, as in the case of mountain beech forests or subalpine Heldrich's pine stands," says Gianluca Piovesan, who is coordinating Italian Mountain Lab project for Tuscia University.

Written records in the Rieti State Archive dating back to Medieval times, such as this late medieval document, were compared to pollen diagrams – constructed from cores extracted in high sedimentation lakes - to develop a detailed history of landscape change over time. Credit: University of Tuscia
The combination of paleoecologic, paleoclimatologic and archeological/historical data at the local scale provides a much more nuanced interpretation of causality for abrupt environmental change underlying the central role of human pressures in forest degradation. The demographic collapse after the black pest caused a widespread rewilding, particularly evident in the mountain environment of the central and South Apennines. By linking multiple sites across a region, we have the potential to gain a much deeper understanding of human land-use legacies on forest landscapes.


Explore furtherOld pine trees witness the rewilding in Mediterranean mountain forests in consequence of late-medieval pandemics

More information: Mensing, S., Schoolman, E.M., Palli, J. & Piovesan, G. (in press). A consilience-driven approach to land use history in relation to reconstructing forest land use legacies. Landscape Ecol (2020). DOI: 10.1007/s10980-020-01079-5

Provided by University of Tuscia

Are young trees or old forests more important for slowing climate change?
by Tom Pugh, The Conversation

Credit: Jeremy Kieran/Unsplash, CC BY-SA

Forests are thought to be crucial in the fight against climate change—and with good reason. We've known for a long time that the extra CO₂ humans are putting in the atmosphere makes trees grow faster, taking a large portion of that CO₂ back out of the atmosphere and storing it in wood and soils.


But a recent finding that the world's forests are on average getting "shorter and younger" could imply that the opposite is happening. Adding further confusion, another study recently found that young forests take up more CO₂ globally than older forests, perhaps suggesting that new trees planted today could offset our carbon sins more effectively than ancient woodland.

How does a world in which forests are getting younger and shorter fit with one where they are also growing faster and taking up more CO₂? Are old or young forests more important for slowing climate change? We can answer these questions by thinking about the lifecycle of forest patches, the proportion of them of different ages and how they all respond to a changing environment.

The forest carbon budget

Let's start by imagining the world before humans began clearing forests and burning fossil fuels.

In this world, trees that begin growing on open patches of ground grow relatively rapidly for their first several decades. The less successful trees are crowded out and die, but there's much more growth than death overall, so there is a net removal of CO₂ from the atmosphere, locked away in new wood.

As trees get large two things generally happen. One, they become more vulnerable to other causes of death, such as storms, drought or lightning. Two, they may start to run out of nutrients or get too tall to transport water efficiently. As a result, their net uptake of CO₂ slows down and can approach zero.

Eventually, our patch of trees is disturbed by some big event, like a landslide or fire, killing the trees and opening space for the whole process to start again. The carbon in the dead trees is gradually returned to the atmosphere as they decompose.

New trees absorb lots of carbon, old trees store more overall and dead trees shed their carbon to the atmosphere. Credit: Greg Rosenke/Unsplash, CC BY-SA

The vast majority of the carbon is held in the patches of big, old trees. But in this pre-industrial world, the ability of these patches to continue taking up more carbon is weak. Most of the ongoing uptake is concentrated in the younger patches and is balanced by CO₂ losses from disturbed patches. The forest is carbon neutral.


Now enter humans. The world today has a greater area of young patches of forest than we would naturally expect because historically, we have harvested forests for wood, or converted them to farmland, before allowing them to revert back to forest. Those clearances and harvests of old forests released a lot of CO₂, but when they are allowed to regrow, the resulting young and relatively short forest will continue to remove CO₂ from the atmosphere until it regains its neutral state. In effect, we forced the forest to lend some CO₂ to the atmosphere and the atmosphere will eventually repay that debt, but not a molecule more.

But adding extra CO₂ into the atmosphere, as humans have done so recklessly since the dawn of the industrial revolution, changes the total amount of capital in the system.

And the forest has been taking its share of that capital. We know from controlled experiments that higher atmospheric CO₂ levels enable trees to grow faster. The extent to which the full effect is realised in real forests varies. But computer models and observations agree that faster tree growth due to elevated CO₂ in the atmosphere is currently causing a large carbon uptake. So, more CO₂ in the atmosphere is causing both young and old patches of forest to take up CO₂, and this uptake is larger than that caused by previously felled forests regrowing.

The effect of climate change

But the implications of climate change are quite different. All else being equal, warming tends to increase the likelihood of death among trees, from drought, wildfire or insect outbreaks. This will lower the average age of trees as we move into the future. But, in this case, that younger age does not have a loan-like effect on CO₂. Those young patches of trees may take up CO₂ more strongly than the older patches they replace, but this is more than countered by the increased rate of death. The capacity of the forest to store carbon has been reduced. Rather than the forest loaning CO₂ to the atmosphere, it's been forced to make a donation.

So increased tree growth from CO₂ and increased death from warming are in competition. In the tropics at least, increased growth is still outstripping increased mortality, meaning that these forests continue to take up huge amounts of carbon. But the gap is narrowing. If that uptake continues to slow, it would mean more of our CO₂ emissions stay in the atmosphere, accelerating climate change.

Overall, both young and old forests play important roles in slowing climate change. Both are taking up CO₂, primarily because there is more CO₂ about. Young forests take up a bit more, but this is largely an accident of history. The extra carbon uptake we get from having a relatively youthful forest will diminish as that forest ages. We can plant new forests to try to generate further uptake, but space is limited.

But it's important to separate the question of uptake from that of storage. The world's big, old forests store an enormous amount of carbon, keeping it out of the atmosphere, and will continue to do so, even if their net CO₂ uptake decreases. So long as they are not cut down or burned to ashes, that is.


Explore furtherSaving Africa's biggest trees to help Earth breathe

Provided by The Conversation

This article is republished from The Conversation under a Creative Commons license. Read the original article.

One-quarter of native mammals now at risk of extinction in Britain


by University of Sussex

Credit: Mark Evans / The Mammal Society

The first official Red List for British Mammals, led by a University of Sussex professor, shows that 11 of the 47 mammals native to Britain are classified as being at imminent risk of extinction.
A further five species are classified as "near threatened"—meaning that there is a realistic possibility of them becoming threatened with extinction in the near future, and four are "data deficient"—meaning that their conservation status is unknown owing to a lack of information.

The Red List for Great Britain was produced by the Mammal Society for Natural England, Natural Resources Wales, Scottish Natural Heritage (NatureScot) and the Joint Nature Conservation Committee.

Crucially, it has received authorisation on behalf of the International Union for the Conservation of Nature (IUCN) at a regional level. This is significant as it means that the threatened British species have been identified using the same robust, internationally agreed system that is applied to classify threats to species such as elephants and tigers.

Fiona Mathews, Mammal Society Chair and Professor at the University of Sussex, led the report. She says: "The new Red List provides a very clear basis for prioritising funding and conservation efforts for the future. Twenty species—those classed as Threatened, Near Threatened, and Data Deficient—all need urgent attention.

"While we bemoan the demise of wildlife in other parts of the world, here in Britain we are managing to send even rodents towards extinction. Things have to change rapidly if we want our children and grandchildren to enjoy the wildlife we take for granted."

Among those species listed as being at risk of extinction in Britain are the water vole, hedgehog, hazel dormouse, wildcat and the grey long-eared bat. The European wolf is already extinct.

The reasons for the declines vary between species. For some, such as the wildcat, pine marten and beaver (which is doing well in the scattered locations where it has been reintroduced), there has been extensive historical persecution. For bats and the hazel dormouse, habitat loss is the main threat; the water vole, red squirrel and Orkney vole suffer from the combined effects of habitat degradation and the introduction of non-native species.

Natural England Chair Tony Juniper said "This is a wake-up call, but it is not too late to act. We are working with our partners to recover our threatened and widely loved mammals, including licensing the reintroduction of beavers into England, and supporting the recovery of dormice and the grey long-eared bat, but there is so much more to do.

"Central to the recovery of these and other creatures will be the protection and restoration of large areas of suitable habitat, including through the creation of a vibrant and wildlife-rich Nature Recovery Network, enabling populations of rare animals to increase and be reconnected with one another."

Reintroductions can offer hope for some species. For example, local reintroductions of beavers have been successful, with the animals readily breeding in the wild; and translocations of pine martens from Scotland—where over 98% of the British population is found—have boosted populations in Wales. Nevertheless, the animals will cease to be classed as threatened only once their populations are much larger and better connected.

Unfortunately, for most other species, reintroductions are not a solution because the causes of their declines have not been rectified. Instead, fundamental change is needed in the way we manage our landscapes and plan future developments, so that we provide the space and habitat needed for our wildlife to thrive.

Members of the public can get involved with keeping an eye on Britain's mammals using the Mammal Society's free Mammal Mapper app.


Explore further British mammals' fight for survival

Provided by University of Sussex

MURDER MOST FOUL DOWNUNDER
Some crimes have seen drastic decreases during coronavirus, but not homicides in the United States

by Terry Goldsworthy, The Conversation

Credit: Shutterstock

The various restrictions put in place to combat the spread of coronavirus in recent months have disrupted life for everyone—including criminals.

More than six months into the pandemic, it is clear the pandemic has had a major effect on crime rates. Certain crimes, such as robberies and sexual offenses, have declined dramatically, while others, such as online fraud, have been on the rise.

Of course, it is difficult to firmly establish a direct causal relationship between coronavirus restrictions and crime rates, but the statistics reveal some common themes.

Reductions in burglaries and assaults

Lockdown policies in Australia and many other countries around the world have significantly altered the environment in which criminal activity can take place.

The broad view in the early days of the pandemic was some crimes would naturally decrease—those requiring access to public space, for instance, and human contact.

For example, under the routine activity theory in criminology, which focuses on the criteria that must be present for crimes to occur, the lockdown should have led to a significant decline in burglaries of homes. There were fewer suitable targets for burglaries (unoccupied houses) and an increase in capable guardians who could intervene (families staying at home).

The same theory can apply to violent crimes and sexual assaults—if you limit the ability of people to commit these crimes through lockdowns, it's reasonable to expect crime rates would decrease.

The statistics in Australia suggest these theories may be correct.

The NSW Bureau of Crime Statistics and Research found that in April, crime across many categories declined sharply compared to the same month for the past five years: robberies (down 42%), non-domestic assault (down 39%), sexual offenses (down 32%), break and enter of dwellings (down 29%), break and enter of non-dwellings (down 25%), stealing from motor vehicles (down 34%) and car theft (down 24%).

A similar pattern was noticeable in Queensland, comparing crime data for April to the same month in 2019—a 28% decline in unlawful entry of dwellings, 45% reduction in robberies and a 7% drop in sexual offenses.

Increases in crimes committed in private

Conversely, offenses that could be committed in private settings or remotely, such as cybercrimes, rose dramatically during the pandemic.

In Queensland, for instance, computer fraud was up 76% in April compared to the year before, while drug offenses increased by 13%.

There was also great concern that domestic violence would also increase during lockdown periods.

NSW police did not see an increase in domestic violence reports in April, compared to the previous year, and Queensland crime data shows breaches of domestic violence orders have remained stable since the start of the pandemic. The NSW Bureau of Crime Statistics and Research, however, said police could not rule out an increase in unreported domestic violence.

In contrast to this, police data for the Northern Territory showed a 25% spike in domestic violence-related assaults in parts of central Australia during the first months of the COVID-19 lockdown.
Routine activity theory (or the crime triangle). Credit: UN Office on Drugs and Crime

A study by the Australian Institute of Criminology (AIC) surveyed 15,000 Australian women to gage the prevalence of domestic violence during the lockdown period from February to May. It found 4.6% of women experienced physical or sexual violence from a partner and 11.6% reported experiencing emotionally abusive, harassing or controlling behavior.

The report noted more research was needed to understand the problem.

"Given the majority of women experiencing violence and abuse within their relationships do not engage with police or government or non-government agencies—particularly while they remain in a relationship with their abuser—this is a significant gap in knowledge."

Crime also down overseas, but homicides on the rise

Other countries reported similar decreases in crime. In England and Wales, crime dropped consistently by an average of 24% per month over a three-month period from April to June compared to the same period for 2019.

These figures, however, did not include fraud offenses, which increased during the pandemic. In March, reported frauds in the UK increased by 400%.

Scotland also saw an 18% decrease in overall crime in April compared to the same month in 2019. One of the few exceptions to this was a 38% rise in fraud.

In the US, however, the findings have been mixed. One study that looked at crime in 16 large cities from January to May (when lockdowns were coming into force) found reductions in residential burglaries and car thefts in some cities, but little to no change to non-residential burglaries and serious assaults (including homicides).

Another study looking at the effect of social distancing on crime in two cities, Los Angeles and Indianapolis, found it "had a statistically significant impact on a few specific crime types. However, the overall effect is notably less than might be expected given the scale of the disruption to social and economic life."

Finally, a major study by the University of Pennsylvania found overall crime across 25 cities in the US declined by 23% in the first month of the pandemic, compared to the average over five years of data for the same time period.

Notably, the study found crime declined even before stay-at-home orders were issued as people changed their normal routines and spent more time at home. Drug crimes saw the biggest decline of any crime category, while home burglaries, assaults and robberies were also down across the 25 cities.

However, the study found little change to homicide rates or shootings in the first month after stay-at-home orders. One possible reason for this, the authors note, is people committing these types of crime are unlikely to be concerned with stay-at-home orders.

In a separate analysis of crime data conducted by The New York Times, murders were up 21.8% in the 36 US cities it studied through at least May, compared to data for the same time period last year.

Other academics have said it is difficult to draw conclusions on homicide rates during the pandemic due to a lack of long-term data.

Further study of the impact of COVID-19 on crime will be required. In the UK, Leeds University has just been awarded funding to conduct such a study over the next 18 months.

Future challenges

Not only will law enforcement be required to adapt to the effect of COVID-19 responses on criminal behavior, the role of law enforcement is also being expanded to take on non-traditional roles in the pandemic.

And the full economic impact of the pandemic has yet to be seen. Many economies have been insulated to some degree by government assistance programs, but the extent to which a severe economic downturn could affect crime rates is still not known.


Explore furtherStudy shows domestic violence reports on the rise as COVID-19 keeps people at home
Provided by The Conversation

This article is republished from The Conversation under a Creative Commons license. Read the original article.
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Plastics, pathogens and baby formula: What's in your shellfish?

by University of California, Irvine

Joleah Lamb, assistant professor of ecology & evolutionary biology at UCI, collecting data on urban reefs in Myanmar. Credit: Michelangelo Pignani

The first landmark study using next-generation technology to comprehensively examine contaminants in oysters in Myanmar reveals alarming findings: the widespread presence of human bacterial pathogens and human-derived microdebris materials, including plastics, kerosene, paint, talc and milk supplement powders.


The study—led by scientists from the University of California, Irvine, in collaboration with Environmental Defense Fund, Cornell University and the University of Queensland—was conducted in the eastern Andaman Sea through partnerships with local researchers in Myanmar in the densely populated but still rural Tanintharyi region. The study concludes that coastal urbanization and lack of sewage treatment increases contamination in seafood and can cause potential health risks to humans, even large distances from pollution sources.

Study results appear in Science of the Total Environment.

The area covered by the study spanned nine coral reefs off Myanmar's Mergui Archipelago, situated roughly 40 miles from Myeik, a city with a population of over 250,000 people. The study examined contaminants in seawater and in oysters using next-generation DNA sequencing to reveal 5,459 potential human pathogens belonging to 87 species of bacteria. More than half of these pathogens are considered detrimental to human health. In addition, the scientists used infrared spectroscopy to examine individual microdebris particles found in the oysters. Of the 1,225 individual microdebris particles examined, 78 different types of contaminant materials were found.

"While 48 percent of the microparticles were microplastics—a finding representative across numerous ocean ecosystems—many other particles were not plastic and originated from a variety of human-derived materials that are constituents of fuels, paints and cosmetics," said senior author Joleah Lamb, assistant professor of ecology & evolutionary biology at UCI. "We were particularly surprised to find three different brands of milk powder formula, which comprised 14 percent of the microdebris contaminants."

Both types of contaminants—pathogens and microparticles—reflect the pervasive presence of sewage and runoff from human and animal sources. The implications for other coastal regions are significant, since coastal marine environments worldwide are being increasingly subjected to reduced water quality from urbanization that could be leading to the contamination of important fishery species on a global scale.


Implications for human health are also significant. Oysters in this region and elsewhere are part of the local diet and typically consumed raw and whole. The contaminants found in this study indicate that even the Mergui Archipelago in largely rural Myanmar has significant and widespread pollution from runoff of agricultural and human waste that can affect downstream food sources over a wide area far from urban centers.

Today more than half of seafood exports by value originate in developing countries, raising more general concerns about local food safety and food security worldwide.

"It's important to keep in mind that much of our seafood is imported from overseas, from places that may be contaminated, emphasizing the importance of both adequate testing and improvements to coastal water quality worldwide," said lead author Raechel Littman, a postdoctoral scholar in ecology & evolutionary biology at UCI.

Apart from human bacterial pathogens, the predominance of microplastics and other types of microparticles present in seafood could have implications for both the environment and human health.

"Scientists are only beginning to explore the human health consequences from consuming microplastics," said Lamb.

Many plastic particles can carry toxins, such as persistent organic pollutants, or POPs, like dichlorodiphenyltrichloroethane (DDT), polychlorinated biphenyls (PCBs) and bisphenol A (BPA), that subsequently enter the ocean and marine food webs, and can eventually be transferred to people through food. Therefore, the uptake of microplastics in the marine environment could have far-reaching consequences for human consumption of seafood and can be an emerging risk to public health globally.

Also concerning is that over half of the microdebris contaminants detected in the Myanmar oyster tissues were composed of non-polymer materials that can be harmful to human health if ingested, such as kerosene, saponin and talc. Moreover, the prominence of milk supplement detected suggests a direct fecal-oral link between human waste and sewage making its way back into the food chain, thereby elevating the risk of contamination or disease transmission.

"This study in important in its global implications. There is strong evidence of transferability of the findings from Myanmar to other seafood sources around the world," said Douglas Rader, chief scientist for the EDF Oceans program and collaborator on this study. "These findings highlight both the risks of coastal urbanization and the importance of adequate wastewater and stormwater management. It also shows clearly the need for better science related to the potential impacts of these contaminants, and the need for better testing programs so that seafood consumers can rely on its wholesomeness.


Explore further  Research: Crop plants are taking up microplastics

More information: Raechel A. Littman et al, Coastal urbanization influences human pathogens and microdebris contamination in seafood, Science of The Total Environment (2020). DOI: 10.1016/j.scitotenv.2020.139081

Journal information: Science of the Total Environment

Provided by University of California, Irvine

Sharks are thriving at the Kermadec Islands, but not the rest of New Zealand, amid global decline

by Adam Smith, The Conversation

Basking sharks were once common in some coastal areas in New Zealand. Credit: Martin Prochazkacz/Shutterstock

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A recent global assessment of shark populations at 371 coral reefs in 58 countries found no sharks at almost 20% of reefs and alarmingly low numbers at many others.

The study, which involved over 100 scientists under the Global FinPrint project, gave New Zealand a good score card. But because it focused on coral reefs, it included only one region—Rangitāhua (Kermadec Islands), a pristine subtropical archipelago surrounded by New Zealand's largest marine reserve.

It is a different story around the main islands of New Zealand. Many coastal shark species may be in decline, and less than half a percent of territorial waters is protected by marine reserves.

Sharks in Aotearoa

In New Zealand, there are more than a hundred species of sharks, rays, and chimeras. They belong to a group of fishes called chondrichthyans, which have skeletons of cartilage instead of bone.

Some 55% of New Zealand's chondrichthyan species are listed as "not threatened" by the International Union for Conservation of Nature (IUCN). Not so encouraging is the 32% of species listed as "data deficient", meaning we don't know the status of their populations. Most species (77%) live in waters deeper than 200 meters.

Seven species are fully protected under the Wildlife Act 1953. They are mostly large, migratory species such as the giant manta ray. Some are threatened with extinction according to the IUCN, including great white sharks, basking sharks, whale sharks and oceanic white tip sharks.

Historically, basking sharks were caught as bycatch in New Zealand fisheries, and seen in their hundreds in some inshore areas. Sightings of these giant plankton-feeders suddenly dried up over a decade ago. We don't know why.
The first global survey of reef sharks shows they are virtually absent in many areas.

Commercial shark fisheries


Eleven chondrichthyan species are fished commercially in New Zealand under the quota management system. Commercial fisheries for school shark, rig and elephant fish took off from the 1970s and now catch around 8,000 tons per year in total.

Finning of sharks has been illegal throughout New Zealand since 2014.

Most of New Zealand's shark fisheries are considered sustainable. But a sustainable fishery can mean sustained at low levels, and we must tread carefully. School shark was recently added to the critically endangered list after the collapse of fisheries in Australia and elsewhere, and there's a lot we don't know about the New Zealand population.

We do know sharks were much more abundant in pre-European times. In Tīkapa Moana (Hauraki Gulf), sharks have since declined by an estimated 86%. An ongoing planning process provides some hope for the ecosystems of the gulf.

Protecting sharks

Not surprisingly, the global assessment found a ban on shark fishing to be the most effective intervention to protect sharks. Several countries have recently established large shark sanctuaries, sometimes covering entire exclusive economic zones.

These countries tend to have ecotourism industries that provide economic incentives for protection—live sharks can be more valuable than dead ones.

Other effective interventions are restrictions on fishing gear, such as longlines and set nets.
Grey reef, silver tip and hammerhead sharks circle a baited camera station set up near Walpole Island in the Southwest Pacific.

Waters within 12 nautical miles of the Kermadec Islands have been protected by a marine reserve since 1990. In 2015, the Kermadec Ocean Sanctuary was announced but progress has stalled. The sanctuary would extend the boundaries to the exclusive economic zone, some 200 nautical miles offshore, and increase the protected area 83-fold.

A large population of Galapagos sharks, which prefer isolated islands surrounded by deep ocean, thrive around the Kermadec Islands but are found nowhere else in New Zealand. Great white sharks also visit en route to the tropics. Many other species are found only at the Kermadecs, including three sharks and a sex-changing giant limpet as big as a saucer.

New technologies are revealing sharks' secrets

What makes the Global FinPrint project so valuable is that it uses a standard survey method, allowing data to be compared across the globe. The method uses a video camera pointed at a canister of bait. This contraption is put on the seafloor for an hour, then we watch the videos and count the sharks.

Baited cameras have been used in a few places in New Zealand but there are no systematic surveys at a national scale. We lack fundamental knowledge about the distribution and abundance of sharks in our coastal waters, and how they compare to the rest of the world.

Satellite tags are another technological boon for shark research. It is difficult to protect sharks without knowing where they go and what habitats they use. Electronic tags that transmit positional data via satellite can be attached to live sharks, revealing the details of their movements. Some have crossed oceans.

Sharks have patrolled the seas for more than 400 million years. In a few decades, demand for shark meat and fins has reduced their numbers by around 90%.

Sharks are generally more vulnerable to exploitation than other fishes. While a young bony fish can release tens of millions of eggs in a day, mature sharks lay a few eggs or give birth to a few live young. Females take many years to reach sexual maturity and, in some species, only reproduce once every two or three years.

These biological characteristics mean their populations are quick to collapse and slow to rebuild. They need careful management informed by science. It's time New Zealand put more resources into understanding our oldest and most vulnerable fishes, and the far-flung subtropical waters in which they rule.


Explore further Sharks almost gone from many reefs

Provided by The Conversation

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Unwelcome sea change: New research finds coastal flooding may cost up to 20% of global economy by 2100

by Ebru Kirezci, Ian Young, The Conversation

Credit: CC0 Public Domain

Over the past two weeks, storms pummeled the New South Wales coast have left beachfront homes at Wamberal on the verge of collapse. It's stark proof of the risks climate change and sea level rise pose to coastal areas.


Our new research published today puts a potential price on the future destruction. Coastal land affected by flooding—including high tides and extreme seas—could increase by 48% by 2100. Exposed human population and assets are also estimated to increase by about half in that time.

Under a scenario of high greenhouse gas emissions and no flood defenses, the cost of asset damage could equate up to 20% of the global economy in 2100.

Without a dramatic reduction in greenhouse gas emissions, or a huge investment in sea walls and other structures, it's clear coastal erosion will devastate the global economy and much of the world's population.

In Australia, we predict the areas to be worst-affected by flooding are concentrated in the north and northeast of the continent, including around Darwin and Townsville.

Our exposed coasts

Sea levels are rising at an increasing rate for two main reasons. As global temperatures increase, glaciers and ice sheets melt. At the same time, the oceans absorb heat from the atmosphere, causing the water to expand. Seas are rising by about 3-4 millimeters a year and the rate is expected to accelerate.

These higher sea levels, combined with potentially more extreme weather under climate change, will bring damaging flooding to coasts. Our study set out to determine the extent of flooding, how many people this would affect and the economic damage caused.

We combined data on global sea levels during extreme storms with projections of sea level rises under moderate and high-end greenhouse gas emission scenarios. We used the data to model extreme sea levels that may occur by 2100.

We combined this model with topographic data (showing the shape and features of the land surface) to identify areas at risk of coastal flooding. We then estimated the population and assets at risk from flooding, using data on global population distribution and gross domestic product in affected areas.


Alarming findings

So what did we find? One outstanding result is that due to sea level rise, what is now considered a once-a-century extreme sea level event could occur as frequently as every ten years or less for most coastal locations.

Under a scenario of high greenhouse gas emissions and assuming no flood defenses, such as sea walls, we estimate that the land area affected by coastal flooding could increase by 48% by 2100.

This could mean by 2100, the global population exposed to coastal flooding could be up to 287 million (4.1% of the world's population).

Under the same scenario, coastal assets such as buildings, roads and other infrastructure worth up to US$14.2 trillion (A$19.82 trillion) could be threatened by flooding.

This equates to 20% of global gross domestic product (GDP) in 2100. However this worst-case scenario assumes no flood defenses are in place globally. This is unlikely, as sea walls and other structures have already been built in some coastal locations.

In Australia, areas where coastal flooding might be extensive include the Northern Territory, and the northern coasts of Queensland and Western Australia.

Elsewhere, extensive coastal flooding is also projected in Southeast China, Bangladesh, and India's states of West Bengal and Gujurat; U.S. states of North Carolina, Virginia, and Maryland; northwest Europe including the UK, northern France and northern Germany.

Keeping the sea at bay

Our large-scale global analysis has some limitations, and our results at specific locations might differ from local findings. But we believe our analysis provides a basis for more detailed investigations of climate change impacts at the most vulnerable coastal locations.

It's clear the world must ramp up measures to adapt to coastal flooding and offset associated social and economic impacts.

This adaptation will include building and enhancing coastal protection structures such as dykes or sea walls. It will also include coastal retreat—allowing low-lying coastal areas to flood, and moving human development inland to safer ground. It will also require deploying coastal warning systems and increasing flooding preparedness of coastal communities. This will require careful long-term planning.

All this might seem challenging—and it is. But done correctly, coastal adaptation can protect hundreds of millions of people and save the global economy billions of dollars this century.


Explore further  Coastal flooding set to get more frequent, threatening coastal life and global GDP

Provided by The Conversation

Remote islands: Stepping stones to understanding evolution

by Okinawa Institute of Science and Technology

The scientists used Winkler traps to extract the trap-jaw ants out of leaf litter into flasks of ethanol. Credit: OIST

For millions of years, remote islands have been hotbeds of biodiversity, where unique species have flourished. Scientists have proposed different theories to explain how animals and plants colonize and evolve on islands but testing ideas for processes happening over long time scales has always been a challenge.

Recently, cutting-edge techniques in DNA sequencing, 3-D imaging, and computation have opened up opportunities for investigating historical processes. In a new study published in Evolution, researchers from the Okinawa Institute of Science and Technology Graduate University (OIST) and collaborators from the University of the Ryukyus investigated evolutionary and ecological changes in ants in the South Pacific archipelago of Fiji to examine a controversial theory for how evolution occurs on islands.

"Islands like Fiji, which are small and remote, act as perfect natural laboratories to study the interplay between ecological and evolutionary processes," said Dr. Cong Liu, first author and former Ph.D. student from the OIST Biodiversity and Biocomplexity Unit. "But until recently, there haven't been many studies on ants."

The team focused on Strumigenys trap-jaw ants, the genus with the greatest number of ant species in Fiji. They collected many specimens of trap-jaw ants during an expedition to Fiji in 2007.

The researchers set out to examine how well the changes in appearance and distribution observed in trap-jaw ants over time fit with a theory called the taxon cycle hypothesis, which describes how species colonize and evolve on islands. According to this theory, species pass through a predictable "life cycle" of colonization, geographic range expansion, decline, and (sometimes) extinction, with this cycle then restarted by a new colonizer.

Cracking the colonization stage

The scientists extracted and sequenced DNA from Strumigenys species endemic to the Fijian archipelago—in other words, they are only found in these islands. The team also included samples of the trap-jaw ants more regionally and globally distributed relatives. Based on the DNA sequences, the scientists constructed an evolutionary tree, showing how closely related all the species were.

"We discovered that all 14 of the trap-jaw ant species endemic to Fiji were descended from a single original colonizer, rather than from multiple colonizers," Dr. Liu explained.


These results contradict what would be expected by the taxon cycle hypothesis, which predicts that later colonizers arrive and kickstart new taxon cycles of radiation and decline.

"There are a few reasons why repeated colonizations may not have occurred," said Dr. Liu. He explained that the first trap-jaw colonizers could have diversified and occupied all the niches, closing the door to any newcomers. Or perhaps, he added, the Fijian archipelago is so remote that additional colonizers never arrived.

The scientists saw extreme diversification in mandible length, relative to the size of the head, in different species of Fijian trap-jaw ants. (Left) S. oasis has a relatively short mandible. (Right) S. nidifex has a relatively long mandible. Credit: OIST

Revealing the radiation stage

According to the taxon cycle hypothesis, a species first colonizes an island, and then undergoes a huge expansion in range, specializing to the available niches in each habitat.

When the scientists looked at the distribution of the 14 trap-jaw species endemic to Fiji, they found that soon after colonization, the initial lineage split in two, with one giving rise to species living in lowland habitats, and one giving rise to species in upland habitats.

The scientists then measured key morphological features of the ants to determine whether they established their niches through adaptive radiation. "Adaptive radiation often occurs on islands, with the most iconic example being Darwin's finches," said Dr. Liu. "This sudden explosion in abundance, diversity and appearance is often due to a greater number of empty niches that the ants can adapt to, due to a lack of competitors or predators."

The scientists used micro-CT scanners to create 3-D models of each Fijian ant species. They also measured the size of the ants' bodies, jaws (mandibles) and eyes.

"We saw a clear diversification of form that is associated with the niches they are occupying, which was clearly a result of adaptive radiation," said Dr. Liu. In general, the ants in the upland lineage evolved larger bodies, allowing them to catch larger prey. These ants also developed shorter mandibles, defining how they hunt.

Delving into the decline stage

The taxon cycle hypothesis predicts that over time, as species adapt to increasingly specialized niches, their population size and the range of their habitat declines. These predictions only held true for the Fijian trap-jaw ants in the upland habitats.

The team found that the populations of upland species of ants had shrunk in numbers over time and had greater genetic differences between populations, suggesting that they were less able to disperse and breed across the Fijian archipelago.

This loss of competitive ability increases the vulnerability of these older, more specialized ants, which are currently threatened by deforestation—a major environmental issue in Fiji. "Because these endemic species only occupy a small geographical area and only have a limited ability to disperse, deforestation can quickly lead to extinction of these species," said Dr. Liu.

The team now plans to apply their approach, which combines population genomics, phylogenetics and morphological studies, to all ant species on Fiji.

It's still not clear how closely data from the trap jaw ants aligns with the taxon cycle hypothesis, said Dr. Liu. This study, as well as one published last year that examined the Pheidole genus of Fijian ants, "only provided partial support" for the hypothesis, he said. "More data is needed to determine whether evolution on these islands does follow these predictable stages, or whether it is a more random process that differs each time."


Explore furtherLarger than life: Augmented ants

More information: Cong Liu et al, Colonize, radiate, decline: Unraveling the dynamics of island community assembly with Fijian trap‐jaw ants, Evolution (2020). 

DOI: 10.1111/evo.13983

Journal information: Evolution

Provided by Okinawa Institute of Science and Technology

THEM! Gordon Douglas, 1954 - Giant Ants!

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