COVID radar: Genetic sequencing can help predict severity of next variant

Drexel University computer model could help project severity of next COVID variant.

Peer-Reviewed Publication

DREXEL UNIVERSITY

As public health officials around the world contend with the latest surge of the COVID-19 pandemic, researchers at Drexel University have created a computer model that could help them be better prepared for the next one. Using machine learning algorithms, trained to identify correlations between changes in the genetic sequence of the COVID-19 virus and upticks in transmission, hospitalizations and deaths, the model can provide an early warning about the severity of new variants.

More than two years into the pandemic, scientists and public health officials are doing their best to predict how mutations of the SARS-CoV-2 virus are likely to make it more transmissible, evasive to the immune system and likely to cause severe infections. But collecting and analyzing the genetic data to identify new variants — and linking it to the specific patients who have been sickened by it — is still an arduous process.

Because of this, most public health projections about new “variants of concern” — as the World Health Organization categorizes them — are based on surveillance testing and observation of the regions where they are already spreading.

“The speed with which new variants, like Omicron have made their way around the globe means that by the time public health officials have a good handle on how vulnerable their population might be, the virus has already arrived,” said Bahrad A. Sokhansanj, PhD, an assistant research professor in Drexel’s College of Engineering who led development of the computer model. “We’re trying to give them an early warning system – like advanced weather modeling for meteorologists – so they can quickly predict how dangerous a new variant is likely to be — and prepare accordingly.”

The Drexel model, which was recently published in the journal Computers in Biology and Medicine, is driven by a targeted analysis of the genetic sequence of the virus’s spike protein — the part of the virus that allows it to evade the immune system and infect healthy cells, it is also the part known to have mutated most frequently throughout the pandemic — combined with a mixed effects machine learning analysis of factors such as age, sex and geographic location of COVID patients.

Learning to Find Patterns

The research team used a newly developed machine learning algorithm, called GPBoost, based on methods commonly used by large companies to analyze sales data. Via a textual analysis, the program can quickly home in on the areas of the genetic sequence that are most likely to be linked to changes in the severity of the variant.

It layers these patterns with those that it gleans from a separate perusal of patient metadata (age and sex) and medical outcomes (mild cases, hospitalizations, deaths). The algorithm also accounts for, and attempts to remove, biases due to how different countries collect data. This training process not only allows the program to validate the predictions it has already made about existing variant, but it also prepares the model to make projections when it comes across new mutations in the spike protein. It shows these projections as a range of severity – from mild cases to hospitalizations and deaths – depending on the age, or sex of a patient.

“When we get a sequence, we can make a prediction about risk of severe disease from a variant before labs run experiments with animal models or cell culture, or before enough people get sick that you can collect epidemiological data. In other words, our model is more like an early warning system for emerging variants” Sokhansanj said.

Genetic and patient data from the GISAID database – the largest compendium of information on people who have been infected with the coronavirus – were used to train the algorithm. Once the algorithms were primed the team used them to make projections about the Omicron subvariants post-BA.1 and BA.2.

“We show that future Omicron subvariants are likelier to cause more severe disease,” Sokhansanj said. “Of course, in the real world, that increased disease severity will be mitigated by prior infection by the previous Omicron variants – this factor is also reflected in the modeling.”

Keeping up with Covid

Drexel’s targeted approach to predictive modeling of COVID-19 is a crucial development because the massive amount of genetic sequencing data being collected has strained standard analysis methods to extract useful information quickly enough to keep up with the virus’s new mutations.

“The amount of spike protein mutations has already been quite substantial and it will likely continue because the virus is encountering hosts that have never been infected before,” said Gail Rosen, PhD, a professor in the College of Engineering, who heads Drexel’s Ecological and Evolutionary Signal-processing and Informatics Laboratory.

“Some estimates suggest that SARS-CoV-2 has only ‘explored’ as little as 30-40% of the potential space for spike mutations,” she said. “When you consider that each mutation could impact key virus properties, like virulence and immune evasion, it seems vital to be able to quickly identify these variations and understand what they mean for those who are vulnerable to infection.”

Rosen’s lab has been at the forefront of using algorithms to cut though the noise of genetic sequencing data and identify patterns that are likely to be significant. Early in the pandemic the group was able to track the geographic evolution of new SARS-CoV-2 variants by developing a method for quickly identify and labeling its mutations. Her team has continued to leverage this process to better understand the patterns of the pandemic.

Vision Among Variables

Up until now, scientists have predominantly used genetic sequencing to better identify mutations alongside lab experiments and epidemiological studies. There has been little success in linking specific genetic sequence variations to virality of new variants. The Drexel researchers believe this is due to progressive changes in vaccination and immunity over time, as well as variations in how data is reported in different countries.

“We know that each successive COVID-19 variant thus far has resulted in slightly milder infections because of increases in vaccination, immunity and health care providers having a better understanding of how to treat infections. But what we have discovered through our mixed effects analysis is that this trend does not necessarily hold for each country. This is why our model considers geographic location as one of the variables taken into consideration by the machine learning algorithm,” Sokhansanj said.

While disparities and inconsistencies in patient and public health data have been a challenge for public health officials throughout the pandemic, the Drexel model is able to account for this and explain how it affected the algorithm’s projections.

“One of our key goals was making sure that the model is explainable, that is, we can tell why it's making the predictions that it's making,” Sokhansanj said. “You really want a model that allows you to look under the hood to see, for example, the reasons why its predictions may or may not agree with what biologists understand from lab experiments — to ensure the predictions are built on the right structure.”

A Better View

The team notes that advances like this underscore the need to provide more public health resources to vulnerable areas of the world — not only for treatment and vaccination, but also for collecting public health data, including sequencing emerging variants.

The researchers are currently using the model to more rigorously analyze the current group of emerging variants that will become dominant after Omicron BA.4 and BA.5.

“The virus can and will continue to surprise us,” Sokhansanj said. “We urgently need to expand our global capacity to sequence variants, so that we can analyze the sequences of potentially dangerous variants as soon as they show up — before they become a worldwide problem.”

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JOURNAL

Computers in Biology and Medicine

DOI

10.1016/j.compbiomed.2022.105969 

METHOD OF RESEARCH

Computational simulation/modeling

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Predicting COVID-19 disease severity from SARS-CoV-2 spike protein sequence by mixed effects machine learning

ARTICLE PUBLICATION DATE

27-Aug-2022

Three COVID-19 vaccines may provide greater protection from COVID-19 infections than two

Peer-Reviewed Publication

PLOS

 

IMAGE: RESEARCHERS FIND A THIRD COVID-19 VACCINE DOSE OFFERS BETTER PROTECTION THAN TWO. view more 

CREDIT: HAKAN NURAL, UNSPLASH (CC0, HTTPS://CREATIVECOMMONS.ORG/PUBLICDOMAIN/ZERO/1.0/)

Two vaccine doses provide only limited and short-lived protection against SARS-CoV-2 infection with the Omicron variant. A study publishing September 1st in the open-access journal PLOS Medicine by Mie Agermose Gram at Statens Serum Institut, Copenhagen, Denmark and colleagues suggests that a third COVID-19 vaccine dose increased the level and duration of protection against Omicron infection and hospitalization.

Emergence of new SARS-CoV-2 variants may decrease long-term vaccine durability, increasing the risk of infection and hospitalization. However, evidence is limited regarding the vaccine effectiveness of three vaccines over time. In order to estimate the effectiveness of two or three vaccine doses against COVID-19 infection and hospitalization, researchers conducted a nationwide cohort study of all previously uninfected Danish residents aged 12 and older by accessing individual-level data stored in the national Danish Civil Registration System and Danish Vaccination Registry. The researchers then estimated vaccine effectiveness using vaccination status as a time-varying exposure, adjusting for age, sex, geographic location, and comorbidities, before comparing infection and hospitalization rates to unvaccinated individuals.

The researchers found that a third vaccine dose provided greater protection against infection and hospitalization from the Omicron variant than with two vaccines and also that there was less evidence of waning protection. Future studies are needed to better understand the durability of a third vaccine dose after 120 days and evaluate the need for subsequent boosters. One limitation of the study was that the data was non-randomized, so there could be unmeasured differences between the vaccinated and unvaccinated groups.

According to the authors, “Our findings indicate that a third dose is necessary to maintain protection against infection for a longer time and to ensure a high level of protection against COVID-19 hospitalization with the Omicron variant. Continued emergence of new variants and waning vaccine durability require ongoing evaluation of vaccine effectiveness against infection and hospitalization to inform future vaccination strategies”.

Gram adds, “Despite being less effective against infection with Omicron than previous variants, a third mRNA COVID-19 vaccine dose offers better protection against Omicron infection than two doses and protects well against COVID-19 hospitalization.”

#####

In your coverage, please use this URL to provide access to the freely available paper in PLOS Medicine:

http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1003992

Citation: Gram MA, Emborg H-D, Schelde AB, Friis NU, Nielsen KF, Moustsen-Helms IR, et al. (2022) Vaccine effectiveness against SARS-CoV-2 infection or COVID-19 hospitalization with the Alpha, Delta, or Omicron SARS-CoV-2 variant: A nationwide Danish cohort study. PLoS Med 19(9): e1003992. https://doi.org/10.1371/journal.pmed.1003992

Author Countries: Denmark, United Kingdom

Funding: The author(s) received no specific funding for this work.

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JOURNAL

PLoS Medicine

DOI

10.1371/journal.pmed.1003992 

METHOD OF RESEARCH

Observational study

SUBJECT OF RESEARCH

People

Second Chance for Science Conference with researchers from Ukraine

Prof. Dr. Carmen Bachmann organizes virtual meetings between German and Ukrainian researchers

Meeting Announcement

UNIVERSITÄT LEIPZIG

“We have 160 presentations on the programme. I’m now looking for partners throughout Germany who fit in thematically with the lectures from Ukraine and will ask if they would like to participate,” said Carmen Bachmann. As the chair of business taxation in the Faculty of Economics and Management Science at Leipzig University, she launched the Chance for Science initiative during the Syrian refugee crisis in 2015 and is now using the volunteer platform and her network to support Ukrainian researchers. The conference will cover a range of topics – from artificial intelligence and veterinary medicine to water research and special tax and legal issues in wartime. This year, for the first time, the initiators and financial supporters of the conference will present Chance for Science awards to nine of the presenters, who will each receive €500. Representatives from the sponsoring companies will also be present at the conference and will explore opportunities to partner with researchers from Ukraine.

Given the enthusiastic response to the first Chance for Science conference in April of this year, Bachmann decided to organise a second one. “Even at the beginning of the war, Ukrainian researchers approached me with the request to help them network with German colleagues. In the beginning, I tried to establish contacts one by one. But at some point, the large number of requests made this no longer feasible, and so the idea for the conference was born,” said Bachmann. This first conference resulted in several successful partnerships being established. She reports, for example, on Professor Anastasiya Babintseva from western Ukraine, who has formed a strong scientific partnership with Professor Mario Rüdiger from the University Hospital Dresden. Since the conference, Babintseva has been in close contact with Rüdiger, who is a neonatologist and paediatric intensivist. Rüdiger and the charity fund German Foundation for Sick Newborns (DSKN) have delivered equipment for the treatment of newborns to Ukraine. Joint webinars and training to help Ukrainian doctors and nurses improve their theoretical knowledge and practical skills are also planned.

The conference on 8 and 9 September will provide another networking opportunity, from which new contacts can be established afterwards. In addition, networking via the existing platform is still possible online. And Bachmann does not rule out organising a third Chance for Science conference. But for now, she said, she has her hands full with the September meeting.

IOP Publishing’s open access Environmental Research journal series expands with the opening of the first issue of Environmental Research: Ecology

Business Announcement

IOP PUBLISHING

 

IMAGE: ENVIRONMENTAL RESEARCH: ECOLOGY view more 

CREDIT: IOP PUBLISHING

IOP Publishing (IOPP) has published the first articles in the open access journal, Environmental Research: Ecology featuring research from a number of world-renowned ecologists. The journal represents one of three new interdisciplinary titles opening in 2022 that will extend IOPP’s Environmental Research series to six open access journals. The full suite of environmental journals provide universally accessible publishing options covering the most critical areas of environmental science and sustainability in support of the United Nations Sustainability Development Goals. 

Environmental Research: Ecology is devoted to addressing the interface of environmental science, large-scale ecology, biodiversity and conservation. The journal publishes full-length research papers, without word restriction, alongside other content including authoritative reviews, perspectives and opinion pieces. It builds on the established reputation of Environmental Research Letters and shares the same modern publishing principles as part of IOPP’s expanding Environmental Research series.  

IOPP’s Environmental Research series of journals combine outstanding levels of author service, inclusive editorial policies, strict quality assurance and have open science principles at their core. In the spirit of transparency and reproducibility, authors publishing in the journal are encouraged to share data and code where appropriate for the benefit of the research community. Authors also have the option to submit their papers for double anonymous and transparent peer review.  

In support of the community and the journal’s first authors, the open access Article Publication Charges (APCs) are being covered by IOPP for all articles submitted to Environmental Research: Ecology through to the end of 2023. 

Environmental Research: Ecology Editor-in-Chief Professor Scott Goetz, Northern Arizona University, USA says: “Ecosystems across the globe are undergoing enormous changes brought about by alteration of the climate system and related transformations associated with human activity. The need to both mitigate and adapt to these changes has been recognised by international policy agreements, yet policies need to be better informed by ecological research. Environmental Research: Ecology provides a platform for incorporating fundamental and applied ecological research using a diverse range of approaches to address realistic science-based policy solutions.” 

Published in the first issue is an impactful study that examines the effects of past and current climate variability on global forest productivity. The work highlights sensitive regions where forests may be most at risk as the planet warms and temperatures become more extreme. Dr Winslow Hansen, from the Cary Institute of Ecosystem Studies, New York, lead author of the study comments: “Forests influence a number of ecological factors. Trees sequester carbon emissions that would otherwise cause climate warming, support much of the planet’s biodiversity, and provide essential services such as fuel, food, and clean water and air. Human-caused shifts in mean climate and climate variability could fundamentally alter 21st-century forests with profound consequences for our planet and its ecosystem. The new Environmental Research: Ecology journal provides a platform for climate scientists to further develop, explore, and discover new policies to protect our ecosystem and combat climate change.” 

Dr Tim Smith, Associate Director at IOPP says: “This further expansion of our Environmental Research series builds upon the established reputation and publishing values of Environmental Research Letters and enhances the role we want IOP Publishing to have in serving a multidisciplinary field of great importance. The first articles in Environmental Research: Ecology as the latest addition to the portfolio provide an early glimpse of the quality and breadth of science that the ecology community can expect from a journal aimed at delivering a combination of outstanding publishing services and content for researchers worldwide.” 

Protein that could prevent chemical warfare attack created at Rutgers

Peer-Reviewed Publication

RUTGERS UNIVERSITY

A team that includes Rutgers scientists has designed a synthetic protein that quickly detects molecules of a deadly nerve agent that has been classified by the United Nations as a weapon of mass destruction and could be used in a chemical warfare attack.

This development could pave the way for a new generation of tailor-made biosensors and treatments that could be deployed against the chemical warfare agent, VX, scientists said.

As described in Science Advances, the team created the protein through a special design on high-speed computers in Rutgers laboratories.

“We’ve made an artificial protein that binds a chemical target – in this case, the VX nerve agent,” said Vikas Nanda, an author on the study and a scientist at Rutgers’ Center for Advanced Biotechnology and Medicine (CABM). “We wanted to design it to generate a signal that could be coupled to a device, making a biosensor for chemical weapons. And we’ve been able to achieve that.”

VX is an odorless, tasteless, human-made chemical compound that is the most toxic and rapidly acting of any of the known chemical warfare agents. It works by attacking the nervous system, causing muscle paralysis and death via asphyxiation within minutes. Because VX is classified as a weapon of mass destruction, countries are banned from stockpiling it. However, nations are permitted to store small amounts for research.

The Rutgers team designed the protein to have a cavity at its center that matched the precise shape and chemical composition of VX. Collaborators at the City College of New York took the Rutgers design and produced a real version of the protein, purified it and shipped the sample on ice overnight to an approved chemical weapon testing facility, MRIGlobal in Kansas City, Mo. There, the protein was tested against VX within 24 hours.

“The protein underwent a dramatic shape change, burying VX in the cavity we designed,” said Nanda, who also is a professor in the department of biochemistry and molecular biology at Rutgers Robert Wood Johnson Medical School. “This shape change is the signal which could be coupled to a sensor device.”

The protein, Nanda said, can detect VX at levels a thousand times more sensitive than current technologies. In addition, the protein doesn’t produce false positives that occur when present-day sensors accidentally detect non-nerve agent chemicals which are similar, like some pesticides.

According to the website of the U.S. Centers for Disease Control and Prevention, VX or other nerve agents were possibly used in chemical warfare during the Iran-Iraq War in the 1980s. Chemical weapons experts have alleged it also has been used more recently in warfare and, in one case, an assassination. While antidotes are available for VX, they are most useful if given as soon as possible after exposure.

“The design method presented here should enable the development of a new generation of biosensors, therapeutics and diagnostics,” Nanda said.

Douglas Pike, a graduate student at CABM, was involved in the study. In addition, James McCann, Mia Brown, and Ronald Koder of the Department of Physics, City College of New York, and David Crouse of the Department of Electrical and Computer Engineering, Clarkson University, were on the study.

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JOURNAL

Science Advances

DOI

10.1126/sciadv.abh3421 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Computational design of a sensitive, selective phase-changing sensor protein for the VX nerve agent

Better metal oxides to boost the green credentials of many energy applications

Peer-Reviewed Publication

IMPERIAL COLLEGE LONDON

Metal oxides are compounds that play a crucial role in processes that reduce carbon dioxide (CO2) emissions. These processes include carbon capture, utilisation and storage (CCUS), purifying and recycling inert gases in solar panel manufacturing, thermochemical energy storage, and producing hydrogen for energy. 

These processes are based on reactions where metal oxides gain and lose electrons, known as redox reactions. However, the performance of metal oxides suffers under redox reactions at the high temperatures required for chemical manufacturing. 

Now, a team led by Imperial College London has developed a new materials design strategy that produces copper-based metal oxides that perform better under high temperatures. The technology is already having a global impact on argon recycling in solar panel manufacturing and is expected to help unleash even more power from existing energy technologies that fight the climate crisis. 

Senior author Dr Qilei Song, of Imperial’s Department of Chemical Engineering, said: “As the world transitions to net zero, we need more innovative industrial processes for decarbonisation. To enhance energy security, we must diversify the electricity supply, from renewable energy generation and storage to clean use of fossil fuels with CCUS technologies. Our improved metal oxides hold great potential for use in the energy processes that are helping us reach net zero.” 

The paper is published in Nature Communications. 

Unpicking a process 

Metal oxides are key players in a relatively new process called chemical looping combustion (CLC).  

CLC is an alternative way of burning fossil fuels that uses metal oxides, such as copper oxides, to transport oxygen from the air to react with the fuel. The reaction produces CO2 and steam, which is condensed to allow the efficient capture of CO2 to prevent it entering the atmosphere 

By capturing the CO2 that is produced, CLC can help people to use fossil fuels in a cleaner way, and is already used in the EU, USA, and China.  

However, a key issue that has held back CLC from use on a larger scale is metal oxides’ inability to maintain good oxygen-releasing performance over multiple redox cycles at high temperatures.  

To solve the problem, the researchers examined the fundamental structures of the metal oxides used in CLC, reasoning that the precursor chemistry to metal oxides was poorly understood, which limited their rational design. 

Co-lead author Michael High, PhD candidate at Imperial’s Department of Chemical Engineering, said: “To solve the question of how metal oxides maintain their performance, we looked to the basics of the chemical processes involved in CLC. This is a key example of combining fundamental research and smart design to produce a strategy that’s applicable to a wide range of engineering processes.” 

They used an alternative way to engineer the metal oxide structure from a well-known precursor composed of copper-magnesium-aluminium layered double hydroxides (LDHs). By tailoring the chemistry of LDH precursors, researchers found they could produce metal oxides that could still perform well under remarkably high temperatures. They demonstrated this by putting the oxides through 100 chemical cycles in a widely used type of reactor, known as a fluidised bed reactor, for 65 hours. 

Their greater ability to withstand heat means that metal oxides produced in this way can be used to unleash more power from purifying and recycling inert gases like argon in manufacturing solar panels, capturing and storing carbon, chemical energy storage, and producing clean hydrogen. To show this, the researchers scaled up the production of metal oxides for use in fluidised bed reactors. They found that creating these materials is simple and readily suitable for upscaling using existing industrial manufacturing methods. 

Senior author Professor Paul Fennell, also of the Department of Chemical Engineering, said: “The world must reach net zero carbon emissions by 2050. Renewable energies are developing rapidly, but in the short term we need to develop cost-effective carbon capture technologies that can be applied to decarbonise the industry. Our work will help solve this global challenge.” 

Next, the researchers will study the long-term stability of the materials during the combustion of different types of fuels, explore new applications for thermochemical energy storage, and extend the approach to other metal oxide systems for producing clean hydrogen via thermochemical redox cycles.

This research was funded by Engineering and Physical Sciences Research Council (EPSRC), part of the UKRI, European Research Council, China Scholarship Council, and the National Science Foundation for Distinguished Young Scholars of China. 

Recycling greenhouse gases

CO2 and methane can be turned into valuable products. But until now the catalysts required for such reactions quickly lose their effectiveness. TU Wien has now developed more stable alternatives

Peer-Reviewed Publication

VIENNA UNIVERSITY OF TECHNOLOGY

 

IMAGE: FLORIAN SCHRENK (LEFT) AND CHRISTOPH RAMESHAN view more 

CREDIT: TU WIEN

Wherever the production of harmful greenhouse gases cannot be prevented, they should be converted into something useful: this approach is called "carbon capture and utilisation". Special catalysts are needed for this. Until now, however, the problem has been that a layer of carbon quickly forms on these catalysts - this is called "coking" - and the catalyst loses its effect. At TU Wien, a new approach was taken: tiny metallic nanoparticles were produced on perovskite crystals through special pre-treatment. The interaction between the crystal surface and the nanoparticles then ensures that the desired chemical reaction takes place without the dreaded coking effect.

Dry reforming: Greenhouse gases become synthesis gas

Carbon dioxide (CO2) and methane are the two human-made greenhouse gases that contribute most to climate change. Both gases often occur in combination, for example in biogas plants. "So-called methane dry reforming is a method that can be used to convert both gases into useful synthesis gas at the same time," says Prof. Christoph Rameshan from the Institute of Materials Chemistry at TU Wien. "Methane and carbon dioxide are turned into hydrogen and carbon monoxide - and it is then relatively easy to produce other hydrocarbons from them, right up to biofuels."

The big problem here is the stability of the catalysts: "The metal catalysts that have been used for this process so far tend to produce tiny carbon nanotubes," explains Florian Schrenk, who is currently working on his dissertation in Rameshan's team. These nanotubes deposit as a black film on the surface of the catalyst and block it.

Perovskite crystals as the key to success

The TU Wien team has now created a catalyst with fundamentally different properties: "We use perovskites, which are crystals containing oxygen, which can be doped with various metal atoms," says Christoph Rameshan. "You can insert nickel or cobalt, for example, into the perovskite – metals that have also been used in catalysis before."

A special pre-treatment of the crystal with hydrogen at around 600 °C allows the nickel or cobalt atoms to migrate to the surface and form nanoparticles there. The size of the nanoparticles is crucial: Success has been achieved with nanoparticles with a diameter of 30 to 50 nanometres. The desired chemical reaction then takes place on these tiny grains, but at the same time the oxygen contained in the perovskite prevents the formation of carbon nanotubes.

"We were able to show in our experiments: If you choose the right size of nanoparticles, no carbon film is created – coking is no longer a danger," says Florian Schrenk. "Moreover, the nanoparticles are stable, the structure of the catalyst does not change, it can be used permanently."

Important building block for tomorrow's bio-refinery

The novel perovskite catalysts could be used wherever methane and carbon dioxide are produced simultaneously - this is often the case when dealing with biological substances, for example in biogas plants. Depending on the selected reaction temperature, one can influence the composition of the resulting synthesis gas. In this way, the further processing of climate-damaging greenhouse gases into valuable products could become an important building block for a sustainable circular economy.

 

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JOURNAL

Applied Catalysis

DOI

10.1016/j.apcatb.2022.121886 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Impact of nanoparticle exsolution on dry reforming of methane: Improving catalytic activity by reductive pre-treatment of perovskite-type catalysts

Eight new species of tiny geckos tumbling out of Madagascar’s rainforests

An international team has discovered and named eight new day gecko species from Madagascar, and each of them is no longer than your pointer finger

Peer-Reviewed Publication

UNIVERSITY OF COPENHAGEN - FACULTY OF SCIENCE

 

IMAGE: LYGODACTYLUS TANTSAHA IS LESS THAN 7 CM (LESS THAN 3 INCHES) FROM NOSE TO TAIL TIP, SHORTER THAN A CRAYON. view more 

CREDIT: DR MARK D. SCHERZ, PHD (DR RER. NAT.)

An international team has discovered and named eight new day gecko species from Madagascar, and each of them is no longer than your pointer finger.

Researchers working in the rainforests of Madagascar have been studying the tiny brown Lygodactylus geckos in the subgenus Domerguella for decades. All this time they have been trying to understand their distribution and evolution, thinking that there were just five species. Now, based on analysis of their DNA and careful examination of their scales and proportions, an international team has discovered that there may be as many as seventeen! They have named eight new species in the journal Zootaxa.

In some places, the team found there were three or four different species found in the same place. ‘This was a remarkable discovery’ says Professor Miguel Vences of the Technische Universität Braunschweig, Germany, first author on the study, ‘On Montagne d’Ambre in the north of Madagascar we thought we were collecting just one species, but now we find there are four. Four different, closely related species that are almost indistinguishable to us, occurring together in the same place, apparently without interbreeding—this is exceptional, even for Madagascar.’

Indeed, Madagascar has remarkably high levels of reptile diversity and endemism, and over 150 new species have been discovered and named in the last thirty years. ‘These results highlight how important it is that we continue to collect samples across Madagascar, even of species we think we understand,’ says Dr Frank Glaw, Curator of Herpetology at the Zoologische Staatssammlung München in Munich, Germany, ‘There is still very much more to discover.’

Many of the new reptile and amphibian species described from Madagascar in recent years have been tiny, and the new species are no exception. ‘Domerguella are tiny, at just five to seven centimetres (or roughly two inches) from the nose to the tip of the tail. We think that their small size may play a role in the way they speciate,’ says Dr Mark D. Scherz, Curator of Herpetology at the Natural History Museum of Denmark and last author on the study, ‘because small animals are generally less able to move from one area to another, and are more likely to get isolated by barriers like rivers cropping up between populations. This could explain why we have seen these kinds of patterns in the tiny frogs, chameleons, and now also geckos that we have been studying in Madagascar.’

The new results also reveal how threatened some Domerguella species have been, even without having had scientific names before. ‘The five species we knew before were mostly thought to be unthreatened, but the eight new species are all either probably endangered or critically endangered’ says Dr Fanomezana Ratsoavina, manager of the Unit for Zoology and Animal Biodiversity at the University of Antananarivo in Madagascar. ‘This shows how important it is to continue to work to discover, describe, and assess the conservation status of the wildlife of Madagascar.’

Citation: Vences, M., Multzsch, M., Gippner, S., Miralles, A., Crottini, A., Gehring, P.-S., Rakotoarison, A., Ratsoavina, F.M., Glaw, F. & Scherz, M.D. (2022) Integrative revision of the Lygodactylus madagascariensis group reveals an unexpected diversity of little brown geckos in Madagascar’s rainforest. Zootaxa, In press.

PRESS MATERIALS, INCLUDING ADDITIONAL PHOTOS, AVAILABLE AT www.markscherz.com/LygoPress

CAPTION

Caption: Seven of the new species of dwarf geckos described from Madagascar. Photos: P.-S. Gehring, H.-P. Berghof, M. Vences & M.D. Sc

CREDIT

Photos: P.-S. Gehring, H.-P. Berghof, M. Vences & M.D. Sc

 

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JOURNAL

Zootaxa

DOI

10.11646/zootaxa.5179.1.1 

SUBJECT OF RESEARCH

Animals

ARTICLE PUBLICATION DATE

1-Sep-2022

Global fish stocks can’t rebuild if nothing done to halt climate change and overfishing, new study suggests

Peer-Reviewed Publication

UNIVERSITY OF BRITISH COLUMBIA

Global fish stocks will not be able to recover to sustainable levels without strong actions to mitigate climate change, a new study has projected.

Researchers at UBC, the Stanford Center for Ocean Solutions and University of Bern projected the impact that different global temperature increases and ranges of fishing activity would have on biomass, or the amount of fish by weight in a given area, from 1950 to 2100. Their simulations suggest that climate change has reduced fish stocks in 103 of 226 marine regions studied, including Canada, from their historical levels. These stocks will struggle to rebuild their numbers under projected global warming levels in the 21st century.

“More conservation-oriented fisheries management is essential to rebuild over-exploited fish stocks under climate change. However, that alone is not enough,” says lead author Dr. William Cheung, professor in the Institute for the Oceans and Fisheries (IOF). “Climate mitigation is important for our fish stock rebuilding plans to be effective” 

The research team, including co- author Dr. Colette Wabnitz of Stanford Centre for Ocean Solutions, used computer models to find out the climate change levels at which over-exploited fish stocks cannot rebuild. Currently, the world is on track to exceed 1.5 degrees of warming relative to preindustrial levels and approach two degrees in the next few decades, says Dr. Cheung.

The study projected that, on average, when fisheries management focuses on the highest sustainable catch per year, the additional climate impacts on fish at 1.8 degrees Celsius warming would see fish stocks unable to rebuild themselves.

If people around the world fished only three quarters of the annual highest sustainable catch, fish stocks would be unable to rebuild at a higher degree of warming, 4.5 degrees.

“Tropical ecoregions in Asia, the Pacific, South America and Africa are experiencing declining fish populations as species both move further north to cooler waters and are also unable to recover due to fishing demands,” said Dr. Cheung. “These regions are the ones that feel the effects of global warming first and our study shows that even a slight increase of 1.5 degrees Celsius could have a catastrophic effect on tropical nations that are dependent on fisheries for food and nutrition security, revenue, and employment.”

In a worst-case scenario, where nothing is done to mitigate global warming, including meeting internationally agreed targets, and where overfishing beyond sustainable targets occurs, fish stocks globally would drop to 36 per cent of current levels, the study projects.

“To rebuild fish stocks, climate change must be fully considered,” said co-author Dr. Juliano Palacios-Abrantes, IOF postdoctoral fellow. “We live in a globalized world, where situations are interconnected. We are seeing this most significantly in tropical regions, but also in the Arctic, where many exploited species are slow to mature, or Ireland, Canada and the USA, with high fishing mortality rates. These climate effects, even when we looked at conservation-focused scenarios, are making it too difficult for fish stocks to bounce back.”

Dr. Cheung says that due to climate change, the world is unlikely to return to historical levels of fish stocks. “We are at a turning point. What we need is a coordinated global effort to develop practical and equitable marine conservation measures to support effective biomass rebuilding under climate change,” he added. “These need to recognize the ways that marine biodiversity contributes to livelihood and economies, particularly in tropical marine ecoregions, as well as requiring more stringent limits on fishing activities to achieve greater biomass rebuilding potential.”

The paper 'Rebuilding fish biomass for the world's marine ecoregions under climate change' was published today in Global Change Biology.

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JOURNAL

Global Change Biology

DOI

10.1111/gcb.16368 

ARTICLE TITLE

Rebuilding fish biomass for the world's marine ecoregions under climate change

Scientists discover new ant species

International research team uses micro-computed tomography to scan 20-million-year-old amber

Peer-Reviewed Publication

FRIEDRICH-SCHILLER-UNIVERSITAET JENA

 

IMAGE: THREE-DIMENSIONAL IMAGE OF THE PREVIOUSLY UNKNOWN EXTINCT ANT SPECIES. view more 

CREDIT: HAMMEL/LAUSTRÖER

The name given to the new species and genus is †Desyopone hereon gen. et sp. nov. In this way, the scientists are honouring the two research institutions involved – DESY and Hereon – which contributed significantly to this find with the help of modern imaging techniques. Ultimately, it was only possible to identify the new species and genus through the combination of extensive phenotype data from scans and recent findings from genome analyses of living ants.

Ponerinae instead of Aneuretinae

Initial anatomical comparisons led the scientists to hypothesize that the animals were a species of Aneuretinae, an almost extinct subfamily of ants known so far only through fossils and through a single living species from Sri Lanka. But they revised this identification thanks to the high-resolution images obtained by synchrotron micro-computed tomography.

“The complex waist segment and the large but rudimentary mandibles – the mouthparts – are more familiar to us from the Ponerinae, a dominant group of predatory ants,” says Brendon Boudinot, who is currently working at the University of Jena on a Humboldt Research Fellowship. “For this reason, we’ve assigned the new species and genus to this subfamily, even though it has a unique appearance, as the long waist and otherwise unconstricted abdomen are more reminiscent of the Aneuretinae.”

The present research results also contribute to putting male ants more under the spotlight of evolutionary research. “Because they have such a different body shape compared to the worker ants, all of whom are female, research has neglected them for a long time. This is because males are simply too often overlooked because they cannot be properly classified,” says ant expert Boudinot. “Our results not only update the literature on identifying male ants, but also show that by understanding male-specific features, such as the sex-specific shape of the mandible, we can learn more about the evolutionary patterns of female ants.” This is because in the present study, the researchers have identified a fundamental pattern that occurs in all ants, namely that male and female mandibles follow the same developmental pattern in most species, even if they look very different.

Unique amber

Dating the find also presented the scientists with some challenges, as the amber itself is as unique as the organisms inside it. “The piece with these ants is from the only amber deposit in Africa so far that has featured fossil organisms in inclusions. Altogether, there are only a few fossil insects from this continent. Although amber has long been used as jewellery by locals in the region, its scientific significance has only become clear to researchers in the last 10 years or so,” explains Vincent Perrichot from the University of Rennes. “The specimen therefore offers what is currently a unique insight into an ancient forest ecosystem in Africa.” It dates from the early Miocene and is 16 to 23 million years old, says Perrichot. Its complicated dating was only possible indirectly, by determining the age of the fossil palynomorphs – the spores and pollen – enclosed in the amber. 

Modern methods for looking into the distant past

Research results such as these are only possible through the use of state-of-the-art technology. As the genetic material of fossils cannot be analysed, precise data and observations on the morphology of animals are particularly important. Comprehensive data can be obtained using high-resolution imaging techniques, such as micro-computed tomography (CT), in which X-rays are used to look through all layers of the sample.

“Since the ants enclosed in amber that are to be examined are very small and only show a very weak contrast in classical CT, we carried out the CT at our measuring station, which specialises in such micro-tomography,” explains Jörg Hammel from the Helmholtz-Zentrum Hereon. “This provided the researchers with a stack of images that basically showed the sample that was being studied slice by slice.”

Put together, these produced detailed three-dimensional images of the internal structure of the animals, which the researchers could use to reconstruct the anatomy with precision. This was the only way to exactly identify the details that ultimately led to the new species and genus being determined.

  

CAPTION

Dr Brendon E. Boudinot is working at the Institute of Zoology and Evolutionary Research at Friedrich Schiller University Jena. In the foreground a 3D image of the newly discovered ant species can be seen. On the screen in the background an several million year old amber find with enclosed ants is shown.

CREDIT

Jens Meyer/University Jena

Original Publication:

Brendon E. Boudinot, Adrian K. Richter, Jörg U. Hammel, Jacek Szwedo, Błażej Bojarski, Vincent Perrichot: “Genomic-phenomic reciprocal illumination: †Desyopone hereon gen. et sp. nov., an exceptional aneuretine-like fossil ant from Ethiopian amber (Hymenoptera: Formicidae: Ponerinae), Insects 2022, 13(9), 796; https://doi.org/10.3390/insects13090796

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JOURNAL

Insects

DOI

10.3390/insects13090796 

ARTICLE TITLE

Genomic-Phenomic Reciprocal Illumination: Desyopone hereon gen. et sp. nov., an Exceptional Aneuretine-Like Fossil Ant from Ethiopian Amber (Hymenoptera: Formicidae: Ponerinae) †

ARTICLE PUBLICATION DATE

1-Sep-2022