'Biodiversity time machine' provides insights into a century of loss

Scientists have run the first proof of concept of their DNA 'time machine' to shed light on a century of environmental change in a freshwater lake -- including warming temperatures and pollution, leading to the potentially irreversible loss of biodiversity.

Their approach, which uses AI applied to DNA-based biodiversity, climate variables and pollution, could help regulators to protect the planet's existing biodiversity levels, or even improve them.

Researchers from the University of Birmingham, in collaboration with Goethe University in Frankfurt, used sediment from the bottom of a lake in Denmark to reconstruct a 100-year-old library of biodiversity, chemical pollution, and climate change levels. This lake has a history of well-documented shifts in water quality, making it a perfect natural experiment for testing the biodiversity time machine.

Publishing their findings today (7 Nov) in eLife, the experts reveal that the sediment holds a continuous record of biological and environmental signals that have changed over time -- from (semi)pristine environments at the start of the industrial revolution to the present.

The team used environmental DNA -- genetic material left behind by plants, animals, and bacteria -- to build a picture of the entire freshwater community. Assisted by AI, they analysed the information, in conjunction with climate and pollution data, to identify what could explain the historic loss of species that lived in the lake.

Principal investigator Luisa Orsini, Professor of Evolutionary Systems Biology and Environmental Omics at the University of Birmingham and Fellow of the Alan Turing Institute, explained: "We took a sediment core from the bottom of the lake and used biological data within that sediment like a time machine -- looking back in time to build a detailed picture of biodiversity over the last century at yearly resolution. By analysing biological data with climate change data and pollution levels we can identify the factors having the biggest impact on biodiversity.

"Protecting every species without impacting human production is unrealistic, but using AI we can prioritise the conservation of species that deliver ecosystem services. At the same time, we can identify the top pollutants, guiding regulation of chemical compounds with the most adverse effect. These actions can help us not only to preserve the biodiversity we have today, but potentially to improve biodiversity recovery. Biodiversity sustains many ecosystem services that we all benefit from. Protecting biodiversity mean protecting these services."

The researchers found that pollutants such as insecticides and fungicides, alongside increases in minimum temperature (a 1.2-1.5-degree increase) caused the most damage to biodiversity levels.

However, the DNA present in the sediment also showed that over the last 20 years the lake had begun to recover. Water quality improved as agricultural land use declined in the area surrounding the lake. Yet, whereas the overall biodiversity increased, the communities were not the same as in the (semi)pristine phase. This is concerning as different species can deliver different ecosystem services, and therefore their inability to return to a particular site can prevent the reinstatement of specific services.

Niamh Eastwood, lead author and PhD student at the University of Birmingham said: "The biodiversity loss caused by this pollution and the warming water temperature is potentially irreversible. The species found in the lake 100 years ago that have been lost will not all be able to return. It is not possible to restore the lake to its original pristine state, even though the lake is recovering. This research shows that if we fail to protect biodiversity, much of it could be lost forever."

Dr Jiarui Zhou, co-lead author and Assistant Professor in Environmental Bioinformatics at the University of Birmingham, said: "Learning from the past, our holistic models can help us to predict the likely loss of biodiversity under a 'business as usual' and other pollution scenarios. We have demonstrated the value of AI-based approaches for understanding historic drivers of biodiversity loss. As new data becomes available, more sophisticated AI models can be used to further improve our predictions of the causes of biodiversity loss."

Read more at Science Daily

The trilobites' guide to surviving environmental change

Scientists have worked out how one unusual species of trilobite -- an ancient, sea-dwelling relative of spiders and lobsters -- was able to defend itself against predators and survive a bumpy ride as Earth's oxygen levels fluctuated.

The seas were filled with trilobites for nearly 300 million years starting in the Cambrian Period, some 520 million years ago. During their time on Earth, which lasted much longer than the dinosaurs, they survived two major episodes of mass extinctions and dominated ocean floor ecosystems.

Their armored bodies are divided into three sections: a head, a thorax or middle section, and a rigid tail. There are more than 20,000 known trilobite species and, when mature, most of them have a very specific number of segments in their mid-sections. However, in Aulacopleura koninckii, scientists discovered something unusual.

Though each early growth stage showed little variation in size and shape, mature Aulacopleura developed anywhere between 18 and 22 mid-section segments.

"My collaborators and I thought this species was weird. We couldn't understand why Aulacopleura bodies varied and others living at the same time had a constant number," said Nigel Hughes, UC Riverside paleobiologist and corresponding author of a new study about this trilobite.

"Seeing trilobites with variable numbers of segments in the thorax is like seeing humans born with different numbers of vertebrae in their backs," Hughes said.

The researchers had questions about this anomaly, how it affected the animals' ability to protect itself, and why it might have developed in this way. These questions are answered in a new study published in the Proceedings of the Royal Society B: Biological Sciences.

Like modern pillbugs or "rollie pollies," trilobites curled up into a ball shape to protect themselves from large squid-like creatures, fish, and other predators. When rolled up, they could tuck their tails neatly under their heads, so the soft tissues were protected by their hard exterior skeletons. In the case of Aulacopleura, 3D modelling showed that protection during rolling up was restricted to smaller, immature forms with less than 18 segments in the middle.

"As the number of segments increased, the body proportions did not allow them to tuck their posteriors neatly under their heads and still be completely shielded," Hughes said. "So, why did this species keep adding segments anyway, and how could it survive the nasty predators?"

Based on their virtual reconstructions, it seems highly likely that when Aulacopleura with a large number of mid-segments felt threatened, they would roll up like their relatives and simply let their tails extend past their heads, minimizing the exposed gap.

"Other possible defense maneuvers would have left gaps on the sides that exposed critical organs -- highly unlikely," Hughes said.

As to the question of why this trilobite varied in the number of mid-section segments, the researchers turned to their earlier work. "What is underneath these segments? Legs that serve as gills!" Hughes said. "The more segments, the more surface area for respiration."

Growing additional breathing apparati likely gave these animals the ability to tolerate dips in local seafloor oxygen levels that excluded other species, such as those that preyed on larger Aulacopleura. Parts of the sea floor becoming anoxic forced predators to retreat to sites where oxygen remained sufficient. But larger Aulacopleura, with their extra gills, could stay put, predator-free.

Learning how this species adapted to both biological and physical pressures gives researchers a better understanding of how survival strategies evolve. The way trilobites developed holds clues to how the common ancestor to major groups of modern arthropods, including insects and arachnids, first evolved.

Read more at Science Daily

Dune patterns reveal environmental change on Earth and other planets

Dunes, the mounds of sand formed by the wind that vary from ripples on the beach to towering behemoths in the desert, are incarnations of surface processes, climate change, and the surrounding atmosphere. For decades, scientists have puzzled over why they form different patterns.

Now, Stanford researchers have found a way to interpret the meaning of these patterns. Their results, published in Geology Aug. 1, can be used as a new tool for understanding environmental changes on any planetary body that harbors dunes, including Venus, Earth, Mars, Titan, Io, and Pluto.

"When you look at other planets, all you have is pictures taken from hundreds to thousands of kilometers away from the surface. You can see dunes -- but that's it. You don't have access to the surface," said senior study author Mathieu Lapôtre, an assistant professor of Earth and planetary sciences in the Stanford Doerr School of Sustainability. "These findings offer a really exciting new tool to decipher the environmental history of these other planets where we have no data."

The scientists analyzed satellite images of 46 dune fields on Earth and Mars and studied how the dunes interact, or exchange sand. Physically, dune interactions manifest themselves as locations where the crestlines of two dunes get very close to each other. Through such interactions, dunes evolve toward a pattern that is free of defects, reflecting a state of equilibrium with local conditions. Thus, the researchers hypothesized that a high number of interactions, in turn, must signal recent or local changes in those boundary conditions. To test their hypothesis, they used data from Earth and Mars to verify how known changes in environmental conditions, such as wind direction or the amount of sand available, affected dune interactions in the dune fields.

Finding a pattern

In a part of China's Tengger Desert, researchers once flattened a dune field to have a baseline for understanding its subsequent reformation. The study authors analyzed satellite images of the dune field from 2016 to 2022 to see how it grew from a flat bed to large dunes in equilibrium with their environment.

"When the dunes and their patterns were not in equilibrium with their current conditions, the interaction density was high, and through time we could see it decreased consistently, as is expected from our hypothesis," Lapôtre said.

Next, they investigated dunes migrating through a valley in the Namib Desert to see how changes in the wind conditions, triggered by topography, impacted dune patterns. They found that dunes outside the valley displayed few defects in their patterns, but as they migrated through the valley -- which starts very wide, then narrows, then becomes wide again -- dunes interacted more with each other.

"As both sand and winds get funneled into the valley, the dunes feel a change in their boundary conditions, and their pattern needs to adjust," said lead study author Colin Marvin, a PhD student in Earth and planetary sciences. "They move into the portion outside the valley and they again readjust to their unconfined conditions, and we see a drop in the number of interactions. This trend is exactly what we expected to see."

They also found that pattern to be true on Mars, where a big dune field occurs around the north pole. There, the migrating dunes have settled into their current conditions -- they're well spaced, they look the same, they're the same size -- and because of that, they interact very little with one another. But further downwind, the winds become more variable and frost locally makes it harder for grains to be blown away. There, the dunes react to that change until they have migrated far enough into these new conditions for their pattern to have once again matured, decreasing the number of dune interactions.

Testing the tool

"We have an upper bound on the time that it takes for a given dune to adjust to changes in environmental conditions, and that is the time it takes for a dune to migrate by a distance of one dune length," Marvin said. "We can use this to diagnose recent changes in environmental conditions on planetary bodies where we don't have any information other than images taken from orbit or radar for example."

Understanding the recent climate of Mars by analyzing current dune patterns could possibly help scientists better pinpoint, for example, the latitudes and depth where future astronauts might be able to find water ice in the subsurface, Lapôtre added. The study also informs experts about the mechanics of dunes on Earth, which can help them better interpret Earth's rock record, and thus, our planet's distant past. On Saturn's moon Titan, this approach could reveal information about topography around the equator and tropics, which is near where the Dragonfly Mission is going to land in the mid 2030s.

"Topography can tell you about a lot of different things; for example, the geological history of the planet: Does Titan have tectonics? How does the interior of Titan work, and how is it coupled with the surface? Is there significant erosion?" Lapôtre said. "Interpretations of dune patterns could trigger kind of a chain reaction, where you provide a new constraint, and it's going to be useful to a bunch of people to make a bunch of discoveries down the line."

Because other planets have various sizes, gravities, temperatures, and compositions, their geological processes will differ. Compared with a rover that lands on one point of a planet to collect information, the satellite data of entire dune fields can greatly increase scientists' understanding of these extraterrestrial bodies and how they can inform our understanding of Earth.

"If we want to understand what happened in the past, or if we want to predict what will happen in the future, it's hard to do when all you have to create those models is one data point, or just one planet," Lapôtre said. "Ultimately, this kind of information allows us to make much better interpretations of Earth's past and also predictions of Earth's future."

Read more at Science Daily

Ancestral variation guides future environmental adaptations

The speed of environmental change is very challenging for wild organisms. When exposed to a new environment individual plants and animals can potentially adjust their biology to better cope with new pressures they are exposed to -- this is known as phenotypic plasticity.

Plasticity is likely to be important in the early stages of colonising new places or when exposed to toxic substances in the environment. New research published in Nature Ecology & Evolution, shows that early plasticity can influence the ability to subsequently evolve genetic adaptations to conquer new habitats.

Sea campion, a coastal wildflower from the UK and Ireland has adapted to toxic, zinc rich industrial-era mining waste which kills most other plant species. The zinc-tolerant plants have evolved from zinc-sensitive, coastal populations separately in different places, several times.

To understand the role of plasticity in rapid adaptation, a team of researchers lead by Bangor University conducted experiments on sea campion.

As zinc-tolerance has evolved several times, this gave the researchers the opportunity to investigate whether ancestral plasticity made it more likely that the same genes would be used by different populations that were exposed to the same environment.

By exposing the tolerant and sensitive plants to both benign and zinc contaminated environments and measuring changes in the expression of genes in the plant's roots, the researchers were able to see how plasticity in the coastal ancestors has paved the way for adaptation to take place very quickly.

Dr Alex Papadopulos, senior lecturer at Bangor University explained:

"Sea campion usually grow on cliffs and shingle beaches, but mining opened up a new niche for them that other plants weren't able to exploit. Our research has shown that some of the beneficial plasticity in the coastal plants has helped the mine plants to adapt so quickly."

Alex added,

"Remarkably, if a gene responds to the new environment in a beneficial way in the ancestral plants, it is much more likely that that gene will be reused in all of the lineages that are independently adapting to the new environment. Phenotypic plasticity may make it more likely that there would be the same evolutionary outcome if the tape of life were replayed. If we understand the plastic responses that species have to environmental change, we may be better equipped to predict the impacts of climate change on biodiversity."

Read more at Science Daily

Earth might be experiencing 7th mass extinction, not 6th

Earth is currently in the midst of a mass extinction, losing thousands of species each year. New research suggests environmental changes caused the first such event in history, which occurred millions of years earlier than scientists previously realized.

Most dinosaurs famously disappeared 66 million years ago at the end of the Cretaceous period. Prior to that, a majority of Earth's creatures were snuffed out between the Permian and Triassic periods, roughly 252 million years ago.

Thanks to the efforts of researchers at UC Riverside and Virginia Tech, it's now known that a similar extinction occurred 550 million years ago, during the Ediacaran period. This discovery is documented in a Proceedings of the National Academy of Sciences paper.

Although unclear whether this represents a true "mass extinction," the percentage of organisms lost is similar to these other events, including the current, ongoing one.

The researchers believe environmental changes are to blame for the loss of approximately 80% of all Ediacaran creatures, which were the first complex, multicellular life forms on the planet.

"Geological records show that the world's oceans lost a lot of oxygen during that time, and the few species that did survive had bodies adapted for lower oxygen environments," said Chenyi Tu, UCR paleoecologist and study co-author.

Unlike later events, this earliest one was more difficult to document because the creatures that perished were soft bodied and did not preserve well in the fossil record.

"We suspected such an event, but to prove it we had to assemble a massive database of evidence," said Rachel Surprenant, UCR paleoecologist and study co-author. The team documented nearly every known Ediacaran animal's environment, body size, diet, ability to move, and habits.

With this project, the researchers sought to disprove the charge that the major loss of animal life at the end of the Ediacaran period was something other than an extinction. Some previously believed the event could be explained by the right data not being collected, or a change in animal behavior, like the arrival of predators.

"We can see the animals' spatial distribution over time, so we know they didn't just move elsewhere or get eaten -- they died out," said Chenyi. "We've shown a true decrease in the abundance of organisms."

They also tracked creatures' surface area to volume ratios, a measurement that suggests declining oxygen levels were to blame for the deaths. "If an organism has a higher ratio, it can get more nutrients, and the bodies of the animals that did live into the next era were adapted in this way," said UCR paleoecologist Heather McCandless, study co-author.

This project came from a graduate class led by UCR paleoecologist Mary Droser and her former graduate student, now at Virginia Tech, Scott Evans. For the next class, the students will investigate the origin of these animals, rather than their extinction.

Ediacaran creatures would be considered strange by today's standards. Many of the animals could move, but they were unlike anything now living. Among them were Obamus coronatus, a disc-shaped creature named for the former president, and Attenborites janeae, a tiny ovoid resembling a raisin named for English naturalist Sir David Attenborough.

"These animals were the first evolutionary experiment on Earth, but they only lasted about 10 million years. Not long at all, in evolutionary terms," Droser said.

Though it's not clear why oxygen levels declined so precipitously at the end of the era, it is clear that environmental change can destabilize and destroy life on Earth at any time. Such changes have driven all mass extinctions including the one currently occurring.

"There's a strong correlation between the success of organisms and, to quote Carl Sagan, our 'pale blue dot,'" said Phillip Boan, UC Riverside geologist and study co-author.

Read more at Science Daily

Plants use their epigenetic memories to adapt to climate change

Animals can adapt quickly to survive adverse environmental conditions. Evidence is mounting to show that plants can, too. A paper publishing in the journal Trends in Plant Science on November 17 details how plants are rapidly adapting to the adverse effects of climate change, and how they are passing down these adaptations to their offspring.

"One day I thought how the living style and experience of a person can affect his or her gametes transmitting molecular marks of their life into their children," says Federico Martinelli, a plant geneticist at the University of Florence. "Immediately I thought that even more epigenetic marks must be transmitted in plants, being that plants are sessile organisms that are subjected to many more environmental stresses than animals during their life."

Plants are facing more environmental stressors than ever. For example, climate change is making winters shorter and less severe in many locations, and plants are responding. "Many plants require a minimum period of cold in order to set up their environmental clock to define their flowering time," says Martinelli. "As cold seasons shorten, plants have adapted to require less period of cold to delay flowering. These mechanisms allow plants to avoid flowering in periods where they have less chances to reproduce."

Because plants don't have neural networks, their memory is based entirely on cellular, molecular, and biochemical networks. These networks make up what the researchers term somatic memory. "These mechanisms allow plants to recognize the occurrence of a previous environmental condition and to react more promptly in presence of the same consequential condition," says Martinelli.

These somatic memories can then be passed to the plants' progeny via epigenetics. "We have highlighted key genes, proteins, and small oligonucleotides, which previous studies have shown play a key role in the memory of abiotic stresses such as drought, salinity, cold, heat, and heavy metals and pathogen attacks," says Martinelli. "In this peer-reviewed opinion piece, we provide several examples that demonstrate the existence of molecular mechanisms modulating plant memory to environmental stresses and affecting the adaptation of offspring to these stresses."

Read more at Science Daily

Flowers' unseen colors can help ensure pollination, survival

You can't see it, but different substances in the petals of flowers create a "bulls-eye" for pollinating insects, according to a Clemson University scientist whose research sheds light on chemical changes in flowers which helps them respond to environmental changes, including climate change, that might threaten their survival.

Matthew H. Koski, an assistant professor of biological sciences in the Clemson College of Science, led a research team that studied the bright, yellow flowers of Argentina anserina -- a member of the rose family commonly known as silverweed -- to learn how pigments in the petals that are visible only in the ultraviolet spectrum play an integral part in the plant's plasticity; that is, its ability to quickly respond to a changing environment. The team also included Clemson researchers Lindsay M. Finnell, Elizabeth Leonard and Nishanth Tharayil.

The journal Evolution featured the findings on the cover of its March edition.

The researchers studied silverweed growing at different elevations in southwestern Colorado to better understand the roles of the various UV-absorbing chemicals in the plants' petals and how these chemicals work to aid in pollination and, thus, reproduction.

Koski explained that although humans cannot see the UV patterns on the flower's petals, many of its pollinators can.

"I've always been fascinated with how [color variation of flowers] arises and how it evolves and what factors drive the evolution of color variation," Koski said, "so I got interested in thinking about how we perceive color versus how the organisms that interact more frequently with flowers perceive color."

"Insects -- pollinators, for example -- see in the ultraviolet spectrum," he continued. "So, flowers that reflect or absorb ultraviolet wavelengths give (to pollinators) the perception of different colors that we can't see. I've been fascinated with uncovering what these UV signals might be doing functionally with respect to pollination. When I thought about the trait of interest in ultraviolet absorption, it is biochemistry. It's a biochemical trait that leads to different perceptions of UV absorption and reflectance."

Koski said a wide range of plants have concentrations of UV-absorbing chemicals at the base of the flower's petals, while the tips of the petals have more UV-reflecting chemicals. He said this creates an overall "bulls-eye" effect that guides insects in their search for pollen.

The team wanted to uncover more about how the plants adapt to thrive in different environments -- in this case, a difference in altitude of 1,000 meters. They found that flowers at different altitudes adapt to their environments by producing differing amounts of UV-blocking or UV-absorbing chemicals.

"At higher elevations, there are always more UV-absorbing compounds or larger spatial area of UV absorption on the petals, compared to the low-elevation populations," Koski said.

The researchers said this demonstrates the plant's plasticity, which Koski defined as how differing traits arise in the same organisms under different environmental conditions. This is a critical step in understanding how organisms adapt to survive change.

"What's important about plasticity is, when we think about climate change and global change, plasticity is one mechanism by which natural populations can respond really rapidly to changing climates and persist under those climates," he said. "The process of evolution, where you're getting changes in the genetic code over time, is thought to proceed more slowly than just responding plastically to environmental change."

Koski said that one question raised by the research is whether plastic responses to environmental situations are adaptive. Do they offer any advantage to an organism, or are they changes in how a trait develops because of the environment without impacting plant fitness?

"One thing this study found is that the plastic change in UV pigmentation benefited the plant, especially the ones at high elevations because increases in ultraviolet absorption on the petals resulted in increased pollen viability," he explained.

Koski went on to say the research will help scientists better understand how organisms respond to environmental changes and even predict if or how well some organisms would be able to survive rapid environmental change, such as from global climate change. The research could also be important for agriculture, he said, because some of the same UV-sensitive pigments at work in silverweed are also present in commercial crops such as mustard and sunflowers.

"It's interesting to think about if abiotic factors like UV or temperature are shifting the expression of these traits, how is that going to impact how pollinators view the flowers, and how's that going to affect things like yield and seed production in crops, for example," Koski said.

Read more at Science Daily

Male animals are subject to stronger evolutionary pressures than females

Male animals are subject to stronger selection pressures than females, which may allow populations to adapt to environmental change more efficiently, according to a report published in the open-access journal eLife.

The study supports one of the long-standing assumptions underpinning the idea that sexual selection bolsters adaptation: that stronger selection on males allows them to purge the population of genetic mutations that reduce survival fitness.

Sexual selection is selection arising from competition for mating partners and/or their reproductive cells (their eggs or sperm). For almost a century, researchers have thought that sexual selection is the ultimate selective force that generates the differences we see between male and female animals in terms of reproductive fitness and life history. Yet, little is known about how sexual selection combines with other environmental pressures to impact population demography and adaptive ability.

Living organisms accumulate mutations throughout life - some of which help them become fitter for survival, and some of which provide no benefit and may even cause a disadvantage (called deleterious mutations). Sexual selection is thought to promote evolutionary adaptation if it gives rise to stronger net selection - that is, the total purifying selection against deleterious mutations - in males rather than females. This is because a population's productivity relies on females' ability to reproduce, so that stronger net selection on males allows a population to get rid of the deleterious mutations quickly and adapt to their environment with a lower cost to the population, which may eventually reduce the risk of extinction.

"Our knowledge on whether such stronger sexual selection on males translates into stronger net selection to females is still limited," says first author Lennart Winkler, a PhD student at TU Dresden, Germany. "Previous studies have used the phenotypic variance of fitness to measure net selection, but its relevance has been questioned. An alternative measure is the organism's genetic variance of fitness. We used both measures to show whether net selection is generally stronger on males across a broad range of species."

The team ran a systematic literature search and compiled 101 paired estimates of male and female genetic variances across 26 species for two important components of an organism's fitness: reproductive success and lifespan.

They then tested whether the phenotypic variances were aligned to the genetic variances, and whether genetic variances show consistent sex differences. They predicted that males would show larger genetic variance in reproductive success but not in lifespan.

They found that the phenotypic variance of lifespan but not of reproductive success predicted the genetic variance in either males or females. Importantly, however, the phenotypic variance of reproductive success was larger in males than females, and this translated into a male bias in genetic variance. This sex difference could be detected in polygamous but not monogamous species. By contrast, there were no consistent sex differences in phenotypic or genetic variance for lifespan.

Read more at Science Daily