Divide and conquer? New insights from the ancients of the microscopic world

UNIVERSITY OF TECHNOLOGY SYDNEY

Research News

 

Australian scientists have unlocked another mystery of the class of microorganisms believed to be among Earth's oldest of life forms, throwing new light on the study of cell division and the evolution of life.

In a newly published paper in Nature Microbiology a research team from the iThree Institute at the University of Technology Sydney describes the cell division process used by the microorganism Haloferax volcanii from the archaea realm of single-celled life, which is distinct from bacteria.

Archaea make up the third major grouping, or domain, of life on the planet, alongside eukaryotes (including all plants and animals) and bacteria, but were only recognised as being distinct from bacteria in the late 1970s.

They can survive in extreme conditions of cold, heat and salinity, exist in the soil, sewage, oceans, and oil wells, and even make up an estimated 10 per cent of the microbial population found within the human gut.

"Our results show that bacteria and archaea divide differently," said Associate Professor Iain Duggin who leads the Microbial Molecular and Cellular Biology research group at the iThree Institute.

"This is a new system to study cell division, and provides a means to compare and contrast with the well-studied bacterial cell division mechanism, based on the protein FtsZ, and related to the microtubules found in human and all other higher organism cells.

"It will help us understand the most important and fundamental aspects of how microbes multiply and the things they all appear to do in common."

A principal author on the study, Dr Yan Liao, said the findings about archaea had unveiled the mystery of a novel "two FtsZs" strategy for cell division, different from bacterial cell division.

"This work opens a door to identifying fundamental activities across the full spectrum of cellular life. We still have so much to discover about the world of archaea, and in doing so gain a better understanding how complex life on Earth evolved.

"Cell division is a central aspect of the biology of all living organisms. For example, abnormal cell division can cause a tumour/cancer to develop. A better understanding of archaea can not only answer basic biological questions but also lead to the development of new biotechnological tools, such as methods for delivering vaccines or drugs that potentially could get around antimicrobial resistance."

Associate Professor Duggin said the study of archaea might also hold solutions to problems beyond human health.

Organisms in the archaea domain are responsible for all biological methane, a major greenhouse gas, as occurs in cattle and other ruminants.

"We've found that the methanogenic archaea responsible for this appear to divide differently from other archaea," Associate Professor Duggin said. "Besides being very interesting in regard to the evolution of the cell wall and its relationship to the division mechanism, it also offers the possibility of vaccinating livestock so they don't produce methane."

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The paper, 'Cell division in the archaeon Haloferax volcanii relies on two FtsZ proteins with distinct functions in division ring assembly and constriction' by Iain G. Duggin, Yan Liao, Solenne Ithurbide and Christian Evenhuis (iThree Institute, UTS) and Jan Löwe (MRC Laboratory of Molecular Biology), has been published in Nature Microbiology, DOI: https://dx.doi.org/10.1038/s41564-021-00894-z.

The study was supported by the Australian Research Council and the UK Medical Research Council.

How do slow anomalies beneath subducting slabs affect giant megathrust earthquakes?

CHINESE ACADEMY OF SCIENCES HEADQUARTERS

Research News

 

IMAGE: ILLUSTRATION OF THE INFLUENCE OF SUBSLAB HETEROGENEITY ON THE GENERATION OF GIANT EARTHQUAKES view more 

CREDIT: IOCAS

Earthquakes and volcanoes in subduction zones may cause great human catastrophe. Previous studies on subduction zone structure and causal mechanisms of giant megathrust earthquakes (M ≥ 9.0) have mainly focused on aspects like subducting plates and plate interfaces.

In contrast, the oceanic asthenosphere structure beneath the subducting slab (at depths of 100-250 km) and its influence on the nucleation of giant megathrust earthquakes have not been well studied.

Recently, Dr. FAN Jianke from the Institute of Oceanology of the Chinese Academy of Sciences (IOCAS) and Prof. ZHAO Dapeng from Tohoku University turned their attention to this problem by investigating the oceanic asthenosphere structure of six subduction zones where giant earthquakes have occurred.

Their findings were published in Nature Geoscience on April 26.

The researchers adopted P-wave tomographic inversions and compiled updated tomographic models. The tomographic images clearly reveal subslab low-velocity (slow) anomalies beneath forearc regions in the six subduction zones.

"The giant earthquake hypocenters are generally located above the edges of the slow anomalies or above the gaps between them. Large coseismic slips of the giant earthquakes mainly occur above gaps between the slow anomalies," said Dr. FAN.

The buoyancy force of a subslab slow anomaly can increase interplate shear stress by enhancing interplate normal stress. Interplate shear stress increases the critical stress threshold for rupture, and the critical shear stress above the slow anomaly gap is slightly smaller than that above the slow anomaly.

However, critical shear stress is still large enough and relatively easier to reach. As such, it can induce a giant megathrust earthquake above the slow anomaly gap, which is primarily controlled by structural heterogeneity on and around the plate interface.

In addition, the buoyancy force of the slow anomaly can cause a morphological response from the subducting slab, thus increasing the shear stress on the plate interface. Thermal conduction or thermo-mechanical erosion from the slow anomaly may result in transformation of the interface rheology from frictional to viscous shear.

This transformation may partly account for the occurrence of slow-slip earthquakes above slow anomalies. The slow-slip area can impede rupture propagation and host afterslip of a giant megathrust earthquake.

"It's necessary to conduct seismic tomography to investigate more detailed asthenospheric structures beneath a subducting slab, which may pinpoint the potential location of a future giant megathrust earthquake," said Dr. FAN.

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This study was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences, the National Natural Science Foundation of China, and the Japan Society for the Promotion of Science.

 

Airports could generate enough solar energy to power a city: Study

Australian airports are ideal hosts for large-scale solar installations

RMIT UNIVERSITY

Research News

IMAGE: MAP SHOWING THE LOCATION OF AUSTRALIA'S LEASED FEDERAL AIRPORTS view more 

CREDIT: RMIT UNIVERSITY

A new study has found Australia's government-owned airports could produce enough electricity to power 136,000 homes, if they had large-scale rooftop solar systems installed.

Researchers at RMIT University compared electricity generated by residential solar panels in a regional Australian city to the potential green energy production of 21 leased federal airports.

They found if large-scale solar panels were installed at the airports, they would generate 10 times more electricity than the city's 17,000 residential panels, while offsetting 151.6 kilotons of greenhouse gasses annually.

Researcher Dr Chayn Sun said the analysis showed the value of focusing renewable energy efforts on large, centralised rooftop solar systems.

"We can't rely on small residential solar panels to get us to a zero-emission economy but installing large panels at locations like airports would get us a lot closer," she said.

"We hope our results will help guide energy policy, while informing future research in solar deployment for large buildings.

"There's so much potential to facilitate national economic development while contributing towards greenhouse gas emission reduction targets."

Sun, a geospatial scientist in RMIT's School of Science, said airports were ideal for solar panels but were not currently being used to their full potential - many Australian airports are without adequate solar systems.

"Airports get good sun exposure because they're not shaded by tall buildings or trees, making them a perfect spot to harness the sun's energy," she said.

"Australia is facing an energy crisis, yet our solar energy resources - such as airport rooftops - are being wasted.

"Harnessing this power source would avoid 63 kilotons of coal being burned in Australia each year, an important step towards a zero-carbon future."

For the study, published in the Journal of Building Engineering, geospatial researchers estimated the solar electricity generated from 17,000 residential solar panels in Bendigo, Victoria, over one year.

Lead author Athenee Teofilo, a Master of Geospatial Science student, then mapped the buildings in every leased federal airport - excluding unsuitable structures like dome and blister-type hangars - and identified 2.61km2 of usable rooftop space.

Researchers determined the optimum tilt angle for the solar arrays for each airport, to maximise efficiency.

Perth Airport had most energy-generating potential; placing solar panels there could produce almost twice the solar output of Bendigo, equal to the combined production from Adelaide, Sydney, Moorabbin and Townsville airports.

Even Melbourne Airport alone would outperform Bendigo's annual solar electricity production by almost 12 gigawatt hours a year.

Airport buildings less suited to solar panels could still be useful for ground-mounted solar systems, the study found.

Sun said the research underlined the necessity for energy policies to include a plan for installing solar panels at airports.

"Based on our solar radiation analysis, we know airports with decent solar systems could not only be self-sufficient but would generate enough electricity to send the excess back into the grid," she said.

"We mapped airports owned by the federal government, but Australia has more than 150 privately-owned airfields, which could also have panels installed.

"Australia receives so much solar radiation, so every airport in the country would benefit from having the right type of solar panels installed.

"The same could be said for many airports and large buildings located around the world."

Sun said reflections from the panels would not be a problem, as modern solar arrays absorb rather than reflect sunlight.

Previous studies have deemed airports as great solar generators but the RMIT research goes further by precisely modelling the use of large-scale systems.

The findings could also be extended to assess the solar potential of other sites, such as large commercial buildings, warehouses or distribution centres.

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'Investigating potential rooftop solar energy generated by Leased Federal Airports in Australia: Framework and implications', with Athenee Teofilo, Dr Chayn Sun, Nenad Radosevic, Yaguang Tao, Jerome Iringan and Chengyang Liu, is published in the Journal of Building Engineering (DOI: 10.1016/j.jobe.2021.102390).

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Comparison of the annual estimated GHG offset, estimated electricity production and solar PV array areas.

CREDIT

RMIT University

 

Researchers solve puzzle of origin and formation of specialized body plan in flatfishes

CHINESE ACADEMY OF SCIENCES HEADQUARTERS

Research News

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IMAGE: THE METAMORPHOSIS PROCESS OF FLATFISHES view more 

CREDIT: IMAGE BY DR. LI YONGXIN

The colonization of the seafloor is one of the most important events in evolutionary history, leading to an explosive radiation and large-scale morphological diversification of marine phyla. Flatfishes are one of the most successful groups of seafloor colonizers and have evolved the most specialized body plan (i.e., flat and asymmetrical) among the teleosts. However, the origin and formation mechanism of the peculiar morphology of flatfishes had long been unclear.

Now, researchers from the Kunming Institute of Zoology of the Chinese Academy of Sciences (CAS), the South China Sea Institute of Oceanology of CAS, the Institute of Hydrobiology of CAS, Zhejiang Ocean University and Northwestern Polytechnical University, have unraveled the evolutionary and genetic origins of the specialized body plan of flatfishes through comparative genomic analysis. The study was published in Nature Genetics.

By analyzing ten de novo-assembled genomes and eight already-published genome sequences from teleost species, the researchers found that Pleuronectoidei and Psettodoidei (the only two suborders of Pleuronectiformes) do not form a monophyletic group, indicating that they each descended independently from their percoid ancestors.

Several genes related to visual perception, immune response, hypoxia tolerance and cardiac function were found to have experienced significant alteration in flatfishes, possibly suggesting a similar remodeling of their visual, immune, respiratory and circulatory systems in benthic adaptation to seafloor colonization.

Genes associated with musculature development and lipid accumulation were also found to have experienced marked changes. Experiments on one fat-related gene showed fast lipid oxidization and decreased fat accumulation in flatfish and thus may correlate with the evolutionary origin and development of flatfishes' flat body plan.

Wnt and retinoic acid (RA) signal pathways have been found to play key roles in normal body axis development. The researchers also found that multiple genes from these pathways have undergone remarkable genetic alteration in flatfishes, suggesting they play a role in the evolution of an asymmetric body plan.

To find gene evolution and expression evidence, the researchers studied Paralichthys olivaceus as a representative species. They found that multiple genes in both RA and Wnt signaling pathways exhibited obvious transient expression fluctuations during metamorphosis, which include marked left-right asymmetrical expression beginning with the pre-metamorphic stage, climbing to an asymmetrical climax during the pro-metamorphic and metamorphic climax stage and then recovering to symmetry in the post-metamorphic stage.

The findings of this study substantially clarify the long-standing controversy (i.e., monophyletic origin vs. non-monophyletic origin) over the phylogeny of flatfishes. At the same time, the genes highlighted in this study offer a blueprint for future functional characterization of the molecular mechanisms underlying the unusual body plan of flatfishes.

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Mysterious ocean-floor trails show Arctic sponges on the move

CELL PRESS

Research News

VIDEO: THIS VIDEO SHOWS SPONGE SPICULE TRAILS ON THE SEAFLOOR. view more 

CREDIT: AWI OFOBS TEAM, PS101

The aquatic animal known as the sponge is often described as entirely sessile: once they've settled in a spot and matured, they aren't generally thought of as moving around. But, according to a new study in the journal Current Biology on April 26--in which researchers describe mysterious trails of light brown sponge spicules (spike-like support elements in sponges) across the Arctic seafloor--that isn't always so.

"We observed trails of densely interwoven spicules connected directly to the underside or lower flanks of sponge individuals, suggesting these trails are traces of motility of the sponges," the researchers, led by Teresa Morganti of the Max Planck Institute of Marine Microbiology and Autun Purser of the Alfred Wegener Helmholtz Centre for Polar and Marine Research, write. "This is the first time abundant sponge trails have been observed in situ and attributed to sponge mobility."

It looked as though the sponges had "crawled" into their current positions. In fact, sponges do have a motile larval stage. But most species are thought to become sessile as adults. Sponges, after all, have no muscles or specialized organs for moving around. They can react to external stimulation and move a little by contracting or expanding their bodies. There also has been some evidence of movement in sponges raised in the lab. In some cases, that movement involved remodeling their whole bodies.

Nevertheless, the new findings took the research team by surprise. The discovery was made by studying video captured in 2016 by the research icebreaker Polarstern as it surveyed the submerged peaks of the permanently ice-covered Langseth Ridge.

A towed marine camera sled and a hybrid remotely operated vehicle (HROV) showed that the peaks of the ridge were covered by one of the densest communities of sponges that's ever been seen. The researchers determined that the impressive sponge populations were primarily comprised of large numbers of Geodia parva, G. hentscheli, and Stelletta rhaphidiophora individuals.

They say it's not clear, given the challenging environment, how the area supports such a vast community of sponges. But, even more intriguing were the numerous trails of sponge spicules. Far from a rarity, the researchers saw trails in nearly 70% of seafloor images that contained living sponges.

Those trails were several centimeters in height and up to many meters long. They often connected directly to living sponges. The trails were seen in areas with lots of sponges, as well as in more sparsely populated areas. The researchers report that they also often seemed to be in areas with smaller, juvenile sponges.

The researchers generated 3D models from the images and video to show the way the trails were interwoven with each other. They say that the findings suggest that the moving sponges sometimes change direction. They don't think the movement is simply a matter of gravity. In fact, the images suggest that the sponges frequently traveled uphill. It may be that the sponges move in order to get food, perhaps driven by the scarce Arctic resources.

"These features are all indicative of feeding and population density behavioral trends previously observed in encrusting sponges," the researchers write. "The extremely low primary productivity, sedimentation, and particle advection rates of the Langseth Ridge region overall result in some of the lowest standing stocks of benthic life; so potentially, this Arctic Geodia community relies on particulate and dissolved fractions from the degradation of old organic debris trapped within the spicule mat as additional food sources. We suggest that the mobility indicated here may be related to sponges searching for and feeding directly on the accumulated detrital matter trapped within the sponge spicule mat underlying the living sponges."

It's also possible that the movement has something to do with reproduction or the dispersal of young sponges. To learn more about how fast and why the sponges make these unexpected moves, they say that further time-lapse imagery and other studies are needed.

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This work was supported by DFG Cluster of Excellence "The Ocean in the Earth System" at the University of Bremen from the ERC Adv Grant ABYSS, the European Union's Horizon 2020 research and innovation program, the Helmholtz Association, the Max Planck Society, and NASA.

Current Biology, Morganti et al.: "In situ observation of sponge trails suggests common sponge locomotion in the deep central Arctic" https://www.cell.com/current-biology/fulltext/S0960-9822(21)00353-5

Current Biology (@CurrentBiology), published by Cell Press, is a bimonthly journal that features papers across all areas of biology. Current Biology strives to foster communication across fields of biology, both by publishing important findings of general interest and through highly accessible front matter for non-specialists. Visit http://www.cell.com/current-biology. To receive Cell Press media alerts, contact press@cell.com.     

CAPTION

This figure shows typical sponge spicule trails.

CREDIT

AWI OFOBS team, PS101; Morganti et al./Current B

CAPTION

This image shows trails left by sponges as they crawl across the seafloor.

CREDIT

AWI OFOBS team, PS101

Surprise in the deep sea

Researchers discover sponge paths on the ocean floor

ALFRED WEGENER INSTITUTE, HELMHOLTZ CENTRE FOR POLAR AND MARINE RESEARCH

Research News

 

Sponges: They are considered to be one of the most primitive forms of animal life, because they have neither locomotion organs nor a nervous system. A team around deep-sea scientist Antje Boetius has now discovered that sponges leave trails on the sea floor in the Arctic deep sea. They conclude that the animals might move actively - even if only a few centimetres per year. They are now publishing these unique findings in the journal Current Biology.

The surprise was great when researchers looked at high-resolution images of the sea floor of the Arctic deep sea in detail: Path-like tracks across the sediments ended where sponges were located. These trails were observed to run in all directions, including uphill. "We conclude from this that the sponges might actively move across the sea floor and leave these traces as a result of their movement," reports Dr Teresa Morganti, sponge expert from the Max Planck Institute for Marine Microbiology in Bremen. This is particularly exciting because science had previously assumed that most sponges are attached to the seafloor or are passively moved by ocean currents and, usually down slopes.

"There are no strong currents in the Arctic deep sea that could explain the structures found on the sea floor," explains expedition leader Prof. Antje Boetius, who works together with deep-sea biologist Dr Autun Purser from the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI) in the HGF-MPG Joint Research Group for Deep-Sea Ecology and Technology. The recently published recordings were made during an expedition at 87 °North at the Karasik Seamount about 350 kilometres away from the North Pole with the research icebreaker Polarstern in 2016 with a towed camera system OFOBS (Ocean Floor Observation and Bathymetry System). "With OFOBS we can create 3D models from the deep sea. The seamount's summit was densely populated with sponges. 69 percent of our images showed trails of sponge spicules, many of which led to live animals," reports Autun Purser.

Many questions arise from these observations: Why do the sponges move? How do they orient themselves? Possible reasons for locomotion could be foraging, avoiding unfavourable environmental conditions, or to distribute offspring. Searching for food in particular plays a major role in nutrient-poor ecosystems such as the Arctic deep sea. Sponges have an important function there anyway. As filter feeders they can utilize particle and dissolved organic matter and are intensively involved in nutrient and matter recycling by means of their bacterial symbionts. Sponges also provide arctic fish and shrimp useful structures to use as a habitat. However, the scientists still have to investigate the mechanisms of locomotion.

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Original publication:

Teresa M. Morganti, Autun Purser, Hans Tore Rapp, Christopher R. German, Michael V. Jakuba, Laura Hehemann, Jonas Blendl, Beate M. Slaby, Antje Boetius: In situ observation of sponge trails suggests common sponge locomotion in the deep central Arctic. Current Biology (2021); DOI: 10.1016/j.cub.2021.03.014

Genome sequencing delivers hope and warning for the survival of the Sumatran rhinoceros

STOCKHOLM UNIVERSITY

Research News

 

IMAGE: PHOTO OF KERTAM, A YOUNG MALE SUMATRAN RHINOCEROS FROM BORNEO WHOSE GENOME WAS SEQUENCED FOR THIS STUDY. view more 

CREDIT: SCUBA ZOO

A study led by researchers at the Centre for Palaeogenetics in Stockholm shows that the last remaining populations of the Sumatran rhinoceros display surprisingly low levels of inbreeding. The researchers sequenced the genomes from 21 modern and historical rhinoceros' specimens, which enabled them to investigate the genetic health in rhinos living today as well as a population that recently became extinct. These findings are published today in the journal Nature Communications.

With less than 100 individuals remaining, the Sumatran rhinoceros is one of the most endangered mammal species in the world. Recent reports of health issues and low fecundity have raised fears that the remaining populations are suffering from inbreeding problems. However, very little has been known about the genetic status of these enigmatic rhinos.

To investigate whether the Sumatran rhinoceros is threatened by genetic factors, the researchers sequenced the genomes from 16 individuals representing the present-day populations on Borneo and Sumatra and the recently extinct population on the Malaysian Peninsula. This enabled them to estimate inbreeding levels, genetic variation, and the frequency of potentially harmful mutations in the populations. Moreover, by also sequencing the genomes from five historical samples, the researchers could investigate the genetic consequences of the severe population decline of the past 100 years.

"To our surprise, we found relatively low inbreeding levels and high genetic diversity in the present-day populations on Borneo and Sumatra", says Johanna von Seth, PhD student at the Centre for Palaeogenetics and co-lead author on the paper.

The researchers think that the comparatively low inbreeding levels in the present-day rhinos is due to the decline in population size having happened very recently. This means that inbreeding hasn't yet caught up with the current small population size. This is good news for the conservation management of the remaining populations, since it implies that there is still time to preserve the species' genetic diversity. However, the researchers also found that there are many potentially harmful mutations hidden in the genomes of these individuals, which could spell bad news for the future.

"Unless the populations start increasing in size, there is a high risk that inbreeding levels will start rising, and consequently that genetic diseases will become more common", cautions Nicolas Dussex, postdoctoral researcher at the Centre for Palaeogenetics who also co-led the study.

The research team's findings from the recently extinct population on the Malaysian Peninsula serve as a stark warning of what might soon happen to the remaining populations in Borneo and Sumatra. A comparison of historical and modern genomes showed that the Malaysian Peninsula population experienced a rapid increase in inbreeding levels before it went extinct. Moreover, the researchers observed changes in the frequency of potentially harmful mutations that are consistent with inbreeding depression, a phenomenon where closely related parents produce offspring that suffer from genetic disease. These results imply that the two remaining populations could suffer a similar fate if their inbreeding levels start to increase.

"The Sumatran rhino is by no means out of the woods. But at least our findings provide a path forward, where we might still be able to rescue a large part of the species' genetic diversity", says Love Dalén, professor of evolutionary genetics at the Centre for Palaeogenetics.

In order to minimize the risk of extinction, the researchers say that it is imperative that the population size increases. They also suggest that actions can be taken to enable the exchange of genes between Borneo and Sumatra, for example by translocating individuals or using artificial insemination. A comparison of genomes from these two islands provided no evidence that such genetic exchange could lead to an introduction of genes that are less well adapted to the local environment. The researchers also point out that genome sequencing could be used as a tool to identify particular individuals with low amounts of potentially harmful mutations, and that such individuals would be especially well-suited for this type of genetic exchange.

In a wider perspective, the study highlights the potential of modern-day genome sequencing technology in guiding conservation efforts for endangered species across the globe. The study was supported by the National Genomics Infrastructure at SciLifeLab in Sweden, and was a collaboration between researchers from several different countries that included geneticists as well as experts on conservation management and reproductive biology.

The Centre for Palaeogenetics is a joint research centre funded by Stockholm University and the Swedish Museum of Natural History.

CAPTION

Photo of Kertam, a young male Sumatran rhinoceros from Borneo whose genome was sequenced for this study.

CREDIT

Scuba Zoo

CAPTION

Photo of Kertam, a young male Sumatran rhinoceros from Borneo whose genome was sequenced for this study.

CREDIT

Scuba Zoo

 NEWS RELEASE 22-APR-2021

Fossils of "giant cloud rats" discovered in Philippine caves

Fluffy rodents twice the size of a gray squirrel survived for tens of thousands of years, and then abruptly disappeared a few thousand years ago--perhaps driven to extinction by humans

FIELD MUSEUM

Research News

 

IMAGE: ILLUSTRATION SHOWING HOW THE THREE NEW SPECIES OF FOSSIL CLOUD RATS MIGHT HAVE LOOKED. view more 

CREDIT: © VELIZAR SIMEONOVSKI, FIELD MUSEUM.

Rats, by and large, aren't terribly popular animals. But while you don't want an infestation of common black rats living in your house, their distant cousins in the Philippines are downright cuddly. These "giant cloud rats" live in the treetops of misty mountain forests, and they fill an ecological role occupied by squirrels in the US. And, it turns out, we have new evidence that they've been living in the Philippines for a long time--scientists have discovered the fossils of three new species of giant cloud rats that lived alongside ancient humans.

"Our previous studies have demonstrated that the Philippines has the greatest concentration of unique species of mammals of any country, most of which are small animals, less than half a pound, that live in the tropical forest," Larry Heaney, the Neguanee Curator of Mammals at Chicago's Field Museum and an author of a study in the Journal of Mammalogy describing the new species. "These recently extinct fossil species not only show that biodiversity was even greater in the very recent past, but that the two that became extinct just a few thousand years ago were giants among rodents, both weighing more than two pounds. Their abrupt disappearance just a few thousand years ago leaves us to wonder if they were big enough that it might have been worthwhile to hunt and eat them."

"We have had evidence of extinct large mammals on the Philippine island of Luzon for a long time, but there has been virtually no information about fossils of smaller-sized mammals. The reason is probably that research had focused on open-air sites where the large fossil mammal faunas were known to have been preserved, rather than the careful sieving of cave deposits that preserve a broader size-range of vertebrates including the teeth and bones of rodents," says Janine Ochoa, an Assistant Professor of Archaeology at the University of the Philippines - Diliman and the study's lead author.

At the outset of the study, Ochoa was examining the fossil assemblages from caves in the Callao limestone formation, where a couple of years ago, scientists discovered the remains of an ancient species of humans, Homo luzonensis. "We were looking at the fossil assemblages associated with that hominin, and we found teeth and fragments of bone that ended up belonging to these new species of cloud rats," says Ochoa.

The fossil fragments discovered by the excavation team in Callao Cave aren't the only traces of the cloud rats, though--they were able to add to them some other fossils in the collections of the National Museum of the Philippines. "Some of these fossils were actually excavated decades ago, in the 1970s and 1980s, and they were in the museum, waiting for someone to have time to do a detailed study. When we began to analyze the fossil material, we were expecting fossil records for known living species. To our surprise, we found that we were dealing with not just one but three buot, or giant cloud rat species that were previously unknown," said Marian Reyes, a zooarcheologist at the National Museum of the Philippines, one of the study's authors.

The researchers didn't have a ton of material to work with, though--just fifty or so fragments. "Normally, when we're looking at fossil assemblages, we're dealing with thousands and thousands of fragments before you find something rare and really nice," says Ochoa. "It's crazy that in these fifty fragments, we found three new species that haven't been recorded before."

The fragments that the researchers found were mostly teeth, which are covered in a hard enamel substance that makes them hardier than bone. From just a few dozen teeth and bits of bone, though, the researchers were able to put together a picture of what these animals were like in life, thanks to, in Heaney's words, "days and days and days staring through a microscope"

By comparing the fossils to the 18 living species of giant cloud rats, the researchers have a decent idea of what these three new fossil species would have looked like.

"The bigger ones would have looked almost like a woodchuck with a squirrel tail," says Heaney. "Cloud rats eat plants, and they've got great big pot bellies that allow them to ferment the plants that they eat, kind of like cows. They have big fluffy or furry tails. They're really quite cute."

The newly recorded fossil species came from Callao Cave, where Homo luzonensis was discovered in 2019, and several adjacent smaller caves in Penablanca, Cagayan Province. Some specimens of all three of the new fossil rodents occurred in the same deep layer in the cave where Homo luzonensis was found, which has been dated at about 67,000 years ago. One of the new fossil rodents is known from only two specimens from that ancient layer, but the other two are represented by specimens from that early date all the way up to about 2000 years ago or later, which means that they were resilient and persistent for at least 60,000 years. "Our records demonstrate that these giant rodents were able to survive the profound climatic changes from the Ice Age to current humid tropics that have impacted the earth over tens of millennia. The question is what might have caused their final extinction?" adds Philip Piper, a coauthor based at the Australian National University.

Two of these giant rodents apparently disappeared about two thousand years ago, or soon after. "That seems significant, because that is roughly the same time that pottery and Neolithic stone tools first appear in the archeological record, and when dogs, domestic pigs, and probably monkeys were introduced to the Philippines, probably from Borneo. While we can't say for certain based on our current information, this implies that humans likely played some role in their extinction," says Armand Mijares, Professor in the Archaeological Studies Program at the University of the Philippines - Diliman, who headed the excavations of Callao Cave.

"Our discoveries suggest that future studies that look specifically for fossils of small mammals may be very productive, and may tell us a great deal about how environmental changes and human activities have impacted the really exceptionally distinctive biodiversity of the Philippines," according to Ochoa. And such studies may also tell us a lot specifically about the impact of human activities, perhaps specifically including over-hunting, on biodiversity, notes Heaney. "This is something we need to understand if we are going to be effective in preventing extinction in the future."

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Photograph of some of the cloud rat fossils.

CREDIT

Lauren Nassef, Field Museum

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Callou Cave site where the fossils were found.

CREDIT

Patricia Cabrera

THEY MUST CHEW WATSON OR THEIR TEET WILL GGROWTH THROLUGH THEIR BRAINS