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

Ant queens control insulin to boost lifespan and reproduction

Peer-Reviewed Publication

UNIVERSITY OF FLORIDA

 

IMAGE: A WORKER HARPEGNATHOS SALTATOR ANT. WORKERS CAN BECOME PSEUDO-QUEENS AND EXTEND THEIR LIFESPAN BY YEARS. view more 

CREDIT: HUA YAN

In most of the animal world, there’s a sad trade-off to make: The more babies you have, the shorter you live.

But ants buck the system. The queens — the only individuals in a nest that reproduce — also live five, 10, up to 30 times longer than their genetically identical worker sisters. How do they pull off what the rest of animalkind cannot?

A new study from University of Florida biologist Hua Yan and his colleagues at New York University finds that ant queens implement a dual-control system for insulin, the metabolism-controlling hormone that explains much of the trade-off between reproduction and lifespan. Queens massively boost their insulin production, which promotes egg development. But their ovaries also produce an insulin blocker that slows down the aging process.

“Hopefully this finding allows us to better understand the aging process in many animals,” said Yan, an assistant professor of biology at UF who also studies how ants communicate with pheromones to organize their society.

Whether mammals, including humans, could ever benefit from partially blocking the insulin pathway remains an open question. Calorie restriction, which decreases insulin production, can increase lifespan in mammals but hurts reproduction.

The research team published their work on Sept. 1 in Science. Yan and NYU researchers Comzit Opachaloemphan and Francisco Carmona-Aldana led the study, which was supervised by NYU professors Claude Desplan and Danny Reinberg.

They studied Harpegnathos saltator ants, also known as Indian jumping ants, because of a helpful transformation the ants undergo. When a queen dies, the remaining workers duel to decide which ants will become new pseudo-queens capable of laying eggs. The pseudo-queens acquire longer lifespans, but the process is also reversible if they encounter a true queen. That gave Yan and the research team the perfect system to study how lifespan extension can be switched on and off.

They discovered that pseudo-queens produce much more insulin, which they expected. Insulin helps convert food into energy, and reproduction is an energy-intensive process.

“It’s straightforward, the pseudo-queen is reproductive, so they need insulin. But insulin normally shortens lifespan, yet they have much longer lifespan – why?” Yan pondered. “There must be something in the insulin signaling of the ants that differentially regulates reproduction and longevity.”

The research team found this extra layer of control in the form of an insulin blocker, called Imp-L2, which is produced by the newly active ovaries of the pseudo-queen. This insulin blocker slows down the part of the insulin pathway normally responsible for accelerating the aging process, but leaves the reproduction-boosting side of insulin signaling intact.

In a sense, the ants get to have their cake and eat it too, coupling egg-laying with a long life.

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JOURNAL

Science

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Insulin signaling in the long-lived reproductive caste of ants

ARTICLE PUBLICATION DATE

1-Sep-2022

Altered insulin signaling allows queen ants to live long and reproductively prosper

Peer-Reviewed Publication

AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE (AAAS)

Altered insulin signaling in ant queens may endow them with their characteristic longevity, despite being a colony’s sole reproducers, researchers report. In most living organisms, there exists a trade-off between reproduction and lifespan. This is largely because animals that bear many offspring often allocate important nutritional and metabolic resources for reproduction at the cost of their own longevity. It’s thought that the insulin and the insulin-like growth factor signaling pathway underlies the anti-correlation between reproduction and shortened lifespan. Ants are an exception to this pattern, however. In any colonies, reproductive activity is limited to one or a few queens. Reproductive queens can live for decades – many lifetimes beyond a colony’s non-reproductive female workers – and lay millions of eggs. In some ant species, like Harpegnathos saltator, workers can switch castes and become reproductive pseudo-queens, or gamergates, when a queen dies or is removed. Despite being born as workers, gamergates can live up to five times longer than their previous counterparts. What’s more, gamergates can revert to workers (revertants) when placed in a colony with an established worker caste, returning to a shortened life span. How this reproduction-associated longevity in these animals is regulated, particularly during active reproduction, remains unclear. To evaluate the relationship between reproduction and longevity, Hua Yan and colleagues performed bulk RNA sequencing on tissues important for reproduction and metabolism from worker, gamergate, and revertant H. saltator ants and compared gene expression during caste switching. As expected, Yan et al. found that insulin was upregulated to promote oogenesis in gamergates, however, this did not lead to a shorter lifespan as it does in other animals. The authors propose that part of the insulin signaling pathway (the branch that activates the protein kinase AKT) is inhibited in the fat body of gamergates and that this may be mediated by a protein Imp-L2. According to the authors, decreased activity of AKT may enable H. saltator queens and pseudo-queens to live longer.

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JOURNAL

Science

DOI

10.1126/science.abm8767 

ARTICLE TITLE

Insulin signaling in the long-lived reproductive caste of ants

ARTICLE PUBLICATION DATE

2-Sep-2022

High plant diversity is often found in the smallest of areas

Peer-Reviewed Publication

MARTIN-LUTHER-UNIVERSITÄT HALLE-WITTENBERG

 

IMAGE: THIS MEADOW IN ROMANIA IS ONE OF THE MOST SPECIES-RICH REGIONS ON EARTH - IN 2009, A RESEARCH TEAM FOUND 98 PLANT SPECIES HERE. view more 

CREDIT: JÜRGEN DENGLER

It might sound weird, but it's true: the steppes of Eastern Europe are home to a similar number of plant species as the regions of the Amazon rainforest. However, this is only apparent when species are counted in small sampling areas, rather than hectares of land. An international team of researchers led by the Martin Luther University Halle-Wittenberg (MLU) and the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig has now shown how much estimates of plant diversity change when the sampling area ranges from a few square metres to hectares. Their results have been published in the journal Nature Communications and could be utilised in new, more tailored nature conservation concepts.

In their study, the team analysed a dataset of around 170,000 vegetation plots from all of the Earth’s climate zones. The data included information on all of the plant species found at a location and the coordinates of the respective area under study. The data was taken from the globally unique vegetation database "sPlot", which is located at iDiv.

"Most studies on global biodiversity are conducted on a relatively large scale, for example at a state or provincial scale. We wanted to find out how much results differ when smaller areas are examined," says Professor Helge Bruelheide from MLU. The team used artificial intelligence to investigate, among other things, the relationship between the number of plant species and the size of the area under study. 

Their investigation showed that there are regions on Earth where focusing on large study areas only provide a limited understanding of the distribution of biodiversity: sometimes small areas can have a relatively high biodiversity, for example in the steppes of Eastern Europe, in Siberia and in the Alpine countries of Europe. At fine spatial scales, the large difference in biodiversity between the tropics, like the Amazon, and the temperate climate zones nearly disappears. 

The same applies to the African tropics, which were previously considered an exception in the tropical plant world. "The tropics have always been among the most biodiverse areas in the world. We wondered why this shouldn’t also apply to Western Africa," explains Dr Francesco Maria Sabatini, who led the study at MLU and is now an assistant professor at the University of Bologna. In fact, the distribution of plant species varies greatly in the African tropics, says Sabatini. These species are distributed over very large distances, so that they are not always recorded when a small sampling area is examined. "To correctly recognize the high biodiversity in Western Africa many small areas are required," adds Sabatini. 

The study also shows that the spatial scale at which other very biodiverse areas are examined, such as the Cerrado savanna region in Brazil or regions in Southeast Asia, is irrelevant. These results are also important when it comes to protecting species. "Ecosystems whose high biodiversity is spread out over a large area cannot be protected through the traditional patchwork of nature reserves. In contrast, ecosystems that have a high biodiversity within a small area could benefit well from several distinct protected zones," concludes Bruelheide.  

The study was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation).

Study: Sabatini F. M. et al. Global patterns of vascular plant alpha diversity. Nature Communications (2022). doi: 10.1038/s41467-022-32063-z

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JOURNAL

Nature Communications

DOI

10.1038/s41467-022-32063-z 

ARTICLE TITLE

Global patterns of vascular plant alpha diversity

ARTICLE PUBLICATION DATE

1-Sep-2022

Ferns finally get a genome, revealing a history of DNA hoarding and kleptomania

Peer-Reviewed Publication

FLORIDA MUSEUM OF NATURAL HISTORY

 

IMAGE: ANALYSIS OF THE CERATOPTERIS GENOME PROVIDES HINTS FOR SOLVING THE LONG-STANDING MYSTERY OF WHY FERNS, ON AVERAGE, RETAIN MORE DNA THAN OTHER PLANTS. COMPARISONS TO GENOMES FROM OTHER GROUPS ALSO LED TO THE SURPRISE DISCOVERY THAT FERNS STOLE THE GENES FOR SEVERAL OF THEIR ANTI-HERBIVORY TOXINS FROM BACTERIA. view more 

CREDIT: PHOTO BY DAVID RANDALL, WESTERN SYDNEY UNIVERSITY

Ferns are notorious for containing massive amounts of DNA and an excessively large number of chromosomes. Defying all expectations, a fern no larger than a dinner plate currently holds the title for highest chromosome count, with a whopping 720 pairs crammed into each of its nuclei. This penchant of ferns for hoarding DNA has stumped scientists, and the intractable size of their genomes has made it difficult to sequence, assemble and interpret them.

Now, two papers published in the journal Nature Plants are rewriting history with the first full-length genomes for homosporous ferns, a large group that contains 99% of all modern fern diversity.

“Every genome tells a different story,” said co-author Doug Soltis, a distinguished professor with the Florida Museum of Natural History. "Ferns are the closest living relatives of all seed plants, and they produce chemical deterrents to herbivores that may be useful for agricultural research. Yet until now, they've remained the last major lineage of green life without a genome sequence.” 

Two teams of researchers separately unveiled the genome of Ceratopteris (Ceratopteris richardii) this Thursday and that of the flying spider monkey tree fern (Alsophila spinulosa) last month.

Analysis of the Ceratopteris genome provides hints for solving the long-standing mystery of why ferns, on average, retain more DNA than other plants. Comparisons to genomes from other groups also led to the surprise discovery that ferns stole the genes for several of their anti-herbivory toxins from bacteria.

The Ceratopteris genome bucks a decades-old theory, leaving more questions than answers

Since the 1960s, the most favored explanation for why ferns contain so much DNA invoked rampant whole-genome duplications, in which an extra set of chromosomes is accidentally passed on to an organism’s offspring. This can sometimes be beneficial, as all the extra genes can then be used as raw material for the evolution of new traits. In fact, whole-genome duplication has been implicated in the origin of nearly all crop plants. 

Whole-genome duplication is common in plants and even some animals, but most organisms tend to jettison the extra genetic baggage over time, slimming back down to smaller genomes that are metabolically easier to maintain.

“This has been a major point of discussion for the last half-century and has led to all kinds of conflicting results,” said lead author Blaine Marchant, a postdoctoral scholar at Stanford University and former Florida Museum graduate student. “Trying to figure out the evolutionary process underlying this paradox is incredibly important.”

With the first fully assembled homosporous fern genomes, scientists were finally prepared to address this question, but getting there wasn’t easy. Sequencing the large, complex genome of Ceratopteris took over eight years of work and the combined effort of dozens of researchers from 28 institutions around the world, including the U.S. Department of Energy Joint Genome Institute. The final result was 7.46 gigabases of DNA, more than double the size of the human genome.

If Ceratopteris had bulked up on DNA through repeated genome duplication events, researchers expected large portions of its 39 chromosome pairs would be identical. What they found instead was a mixed bag of repetitive sequences and millions of short snippets called jumping genes, which accounted for 85% of the fern’s DNA. Rather than multiple genome copies, Ceratopteris mostly contains genetic debris accumulated over millions of years. 

“The functional genes are separated by large amounts of repetitive DNA. And although we’re not yet sure how the Ceratopteris and other fern genomes got so big, it’s clear that the prevailing view of repeated episodes of genome duplication is not supported,” said co-author Pam Soltis, a Florida Museum curator and distinguished professor. 

The authors note that it’s too early to make any firm conclusions, especially since this is the first analysis of its scope conducted in this group. Cross comparisons with additional fern genomes down the road will help paint a clearer picture of how these plants evolved.

Still, the results point to a clear difference in the way homosporous ferns manage their genetic content compared to almost all other plants, Marchant said.

“What we seem to be finding is that things like flowering plants, which on average have much smaller genomes than ferns, are just better at getting rid of junk DNA. They’re better at dropping spare chromosomes and even downsizing after small duplications.”

Ferns repeatedly stole toxins from bacteria

A closer look at the billions of DNA base pairs within Ceratopteris revealed multiple defense genes that code for a particularly sinister type of pore-forming toxin. These toxins bind to cells, where they become activated and form small, hollow rings that punch their way into the cellular membrane. Water floods into the cells through the resulting holes, causing them to rupture.

Pore-forming toxins have been intensively studied by scientists for their potential use in nanopore technology, Marchant explained. Most often, however, they’re found in bacteria.

“This is the first concrete evidence of these bacterial toxin-related genes within fern DNA,” Marchant said, noting that the similarity isn’t a coincidence.

Rather than evolving this toxin on its own, Ceratopteris appears to have obtained it directly from bacteria through a process called horizontal gene transfer. And given that there were multiple copies of the gene spread out among three separate chromosomes, it’s likely this happened more than once. 

“What’s fascinating is that the many copies of these genes show up in different parts of the plant,” he said. “Some are highly expressed in the stem and roots, while other copies are expressed solely in the leaves, and others are generally expressed across all tissues. We cannot be sure of the exact function of these genes at this point, but their similarity to the toxin-forming genes in bacteria certainly suggests these genes are defense-related.” 

This wouldn’t be the first time ferns have incorporated foreign DNA into their genomes. A 2014 study indicates ferns may have evolved their characteristic ability to grow in shady environments by borrowing genes from distantly related plants.

However, exactly how organisms separated by millions of years of evolution are able to swap fully functional genes remains unclear. 

“The mechanisms behind horizontal gene transfer remain one of the least investigated areas of land plant evolution,” Doug Soltis explained. “Over evolutionary timescales, it’s a bit like winning the lottery. Any time a plant is wounded, its interior is susceptible to invasion from microbes, but for their DNA to be incorporated into the genome seems amazing.”

The authors say this is merely the first step in a long series of studies with practical applications ranging from the development of novel biopesticides to innovative new conservation strategies. 

Several of the authors are involved in the current effort to sequence the genomes of all known eukaryotic organisms within a 10-year time frame. Called the Earth Biogenome Project, the endeavor will generate untold genomic resources that researchers will have their hands full analyzing for the foreseeable future.  

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JOURNAL

Nature Plants

DOI

10.1038/s41477-022-01226-7 

ARTICLE TITLE

Dynamic genome evolution in a model fern

ARTICLE PUBLICATION DATE

1-Sep-2022

Researchers propose new framework for regulating engineered crops

Peer-Reviewed Publication

NORTH CAROLINA STATE UNIVERSITY

 

IMAGE: SAFETY TESTING WOULD BE RECOMMENDED FOR PRODUCTS WITH NEW CHARACTERISTICS THAT HAVE THE POTENTIAL FOR HEALTH OR ENVIRONMENTAL EFFECTS, OR FOR PRODUCTS WITH DIFFERENCES THAT CANNOT BE INTERPRETED, MOST NEW VARIETIES WOULD NOT TRIGGER A NEED FOR REGULATION. view more 

CREDIT: NC STATE UNIVERSITY

 THURSDAY, SEPT. 1

A Policy Forum article published today in Science calls for a new approach to regulating genetically engineered (GE) crops, arguing that current approaches for triggering safety testing vary dramatically among countries and generally lack scientific merit – particularly as advances in crop breeding have blurred the lines between conventional breeding and genetic engineering.

Rather than focusing on the methods and processes behind the creation of a GE crop to determine if testing is needed, a more effective framework would examine the specific new characteristics of the crop itself by using so-called “-omics” approaches, the article asserts. In the same way that biomedical sciences can use genomic approaches to scan human genomes for problematic mutations, genomics can be used to scan new crop varieties for unexpected DNA changes. 

Additional “-omics” methods such as transcriptomics, proteomics, epigenomics and metabolomics test for other changes to the molecular composition of plants. These measurements of thousands of molecular traits can be used like a fingerprint to determine whether the product from a new variety is “substantially equivalent” to products already being produced by existing varieties – whether, for example, a new peach variety has molecular characteristics that are already found in one or more existing commercial peach varieties. 

If the new product has either no differences or understood differences with no expected health or environmental effects when compared with products of existing varieties, no safety testing would be recommended, the article suggests. If, however, the product has new characteristics that have the potential for health or environmental effects, or if the product has differences that cannot be interpreted, safety testing would be recommended.

“The approaches used right now – which differ among governments – lack scientific rigor,” said Fred Gould, University Distinguished Professor at North Carolina State University, co-director of NC State’s Genetic Engineering and Society Center and the corresponding author of the article. “The size of the change made to a product and the origin of the DNA have little relationship with the results of that change; changing one base pair of DNA in a crop with 2.5 billion base pairs, like corn, can make a substantial difference.”

When dealing with varieties made using the powerful gene editing system known as CRISPR, for example, the European Union regulates all varieties while other governments base decisions on the size of the genetic change and the source of inserted genetic material. Meanwhile, in 2020 the U.S. Department of Agriculture established a rule that exempts from regulation conventionally bred crop varieties and GE crop varieties that could have been developed by methods other than genetic engineering.

The “-omics” approaches, if used appropriately, would not increase the cost of regulation, Gould said, adding that most new varieties would not trigger a need for regulation. 

“The most important question is, ‘Does the new variety have unfamiliar characteristics,’” Gould said. The paper estimates that technological advances could make the laboratory cost for a set of “-omics” tests decrease to about $5,000 within five to 10 years. 

Establishing an international committee composed of crop breeders, chemists and molecular biologists to establish the options and costs of “-omics” approaches for a variety of crops would start the process of developing this new regulatory framework. Workshops with these experts as well as sociologists, policymakers, regulators and representatives of the general public would enable trustworthy deliberations that could avoid some of the problems encountered when GE rolled out in the 1990s. National and international governing bodies should sponsor these committees and workshops as well as innovative research to get the ball rolling and ensure that assessments are accessible and accurate, Gould said.

In 2016, Gould headed a 20-member National Academy of Sciences committee responsible for a report, Genetically Engineered Crops: Experiences and Prospects, which aimed to “assess the evidence for purported negative effects of GE crops and their accompanying technologies” and to “assess the evidence for purported benefits of GE crops and their accompanying technologies.” Most of that committee co-authored the policy article published this week.

- kulikowski -

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JOURNAL

Science

DOI

10.1126/science.abo3034 

METHOD OF RESEARCH

Commentary/editorial

SUBJECT OF RESEARCH

Cells

ARTICLE TITLE

Toward product-based regulation of crops

ARTICLE PUBLICATION DATE

2-Sep-2022

COI STATEMENT

Some of the ideas for this article emerged from discussions during deliberations of the US National Academy of Sciences, Engineering and Medicine “Committee on Genetically Engineered Crops: Past Experiences and Future Prospects”. K.G. is a member of the Sustainable Sourcing Advisory Board of Unilever and of the Scientific Advisory Committee of the African Plant Nutrition Institute. R.D. hold patents in the field of metabolic engineering for improvement of forage crops; received funding for research on the above topic from GrasslaNZ Technologies, New Zealand, and Forage Genetics International, USA; is Chief Scientist, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing, China. 2017-2021; Chair of the Academic Advisory Committee for the Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan; Member of the Departmental Evaluation Board, Flanders Institute of Biotechnology (VIB), Department of Plant Systems Biology, Gent, Belgium. C.N.S.Jr. holds patents in plant biotechnology.