In the movie Avatar, so many magnificent animals have gone extinct that scientists can only study them virtually. This environmentally ravaged Earth is set in the near future, in the year 2154, but according to University of Florida biologist Todd Palmer and his colleagues, the Earth in 2015 is already undergoing an accelerated mass extinction.

In a study published today in the journal Science Advances, Palmer and his colleagues say there no longer is any doubt: We are entering a mass extinction that threatens humanity’s existence.

“The Earth’s biodiversity plays a really critical role in sustaining the human species, from the pollination of our crops, to the purification of our water supply to the amelioration of climate change. We simply cannot afford to continue losing species at the rate they are currently disappearing,” Palmer said.

There is general agreement among scientists that extinction rates have reached levels unparalleled since the dinosaurs died out 66 million years ago. However, some have challenged the theory, believing earlier estimates rested on assumptions that overestimated the crisis.

The new study shows that even with extremely conservative estimates, species are disappearing up to about 100 times faster than the normal rate between mass extinctions, known as the background rate.

“If it is allowed to continue, life would take many millions of years to recover, and our species itself would likely disappear early on,” said lead author Gerardo Ceballos of the Universidad Autónoma de México.

Conservative approach

Using fossil records and extinction counts from a range of records, the researchers compared a highly conservative estimate of current extinctions with a background rate estimate twice as high as those widely used in previous analyses. This way, they brought the two estimates – current extinction rate and average background or going-on-all-the-time extinction rate – as close to each other as possible.

Focusing on vertebrates, the group for which the most reliable modern and fossil data exist, the researchers asked whether even the lowest estimates of the difference between background and contemporary extinction rates still justify the conclusion that people are precipitating “a global spasm of biodiversity loss.” The answer: a definitive yes.

“We emphasize that our calculations very likely underestimate the severity of the extinction crisis, because our aim was to place a realistic lower bound on humanity’s impact on biodiversity,” the researchers write.

To history’s steady drumbeat, a human population growing in numbers, per capita consumption and economic inequity has altered or destroyed natural habitats. The long list of impacts includes:

  • Land clearing for farming, logging and settlement
  • Introduction of invasive species
  • Carbon emissions that drive climate change and ocean acidification
  • Toxins that alter and poison ecosystems

Now, the specter of extinction hangs over about 41 percent of all amphibian species and 26 percent of all mammals, according to the International Union for Conservation of Nature, which maintains an authoritative list of threatened and extinct species.

“There are currently over 2,400 animal and 2,000 plant species that are critically endangered, and some of those are essentially the walking dead, whose populations have been so drastically reduced that there’s little hope for their recovery,” Palmer said.

As species disappear, so do crucial ecosystem services such as honeybees’ crop pollination and wetlands’ water purification. At the current rate of species loss, people will lose many biodiversity benefits within three generations, the study’s authors write.

“We are responsible for the current extinction crisis. There is no question about it. We simply cannot continue to treat nature like a bottomless checking account,” Palmer said.

Hope for the future

Despite the gloomy outlook, there is a meaningful way forward, according to Palmer and his colleagues. “Avoiding a true sixth mass extinction will require rapid, greatly intensified efforts to conserve already threatened species, and to alleviate pressures on their populations – notably habitat loss, over-exploitation for economic gain and climate change,” the study’s authors write.
In the meantime, the researchers hope their work will inform conservation efforts, the maintenance of ecosystem services and public policy.

Co-authors on the paper include Gerardo Ceballos of Universidad Autónoma de México, Paul R. Ehrlich of Stanford University, Anthony D. Barnosky of the University of California at Berkeley, Andrés García of Universidad Autónoma de México, Robert M. Pringle of Princeton University.
– Gigi Marino and Rob Jordan

Congratulations to Professor William Hager for being named a 2015 Fellow in the Society of Industrial and Applied Mathematics. He is being honored for contributions to optimal control, optimization theory, and numerical optimization algorithms. Hager is a co-director of the Center for Applied Optimization here at UF. His research work focuses on numerical analysis, optimization, optimal control, and lightning.

The Society for Industrial and Applied Mathematics (SIAM), headquartered in Philadelphia, Pennsylvania, is an international society of over 14,000 individual members, including applied and computational mathematicians and computer scientists, as well as other scientists and engineers. Members from 85 countries are researchers, educators, students, and practitioners in industry, government, laboratories, and academia. The Society, which also includes nearly 500 academic and corporate institutional members, serves and advances the disciplines of applied mathematics and computational science by publishing a variety of books and prestigious peer-reviewed research journals, by conducting conferences, and by hosting activity groups in various areas of mathematics. SIAM provides many opportunities for students including regional sections and student chapters. Further information is available here.

Astronomer Charles Telesco is primarily interested in the creation of planets and stars. So, when the University of Florida’s giant telescope was pointed at a star undergoing a magnificent and explosive death, Telesco, a UF professor, didn’t immediately appreciate what a rare and valuable find he had.

He soon learned. The event was about to reveal insights into some of the universe’s most tantalizing mysteries.

A super-bright exploding star is known as a supernova, which can come from the death of a single very massive star or the ignition of a white dwarf – the remains of a low-mass star – as matter overflows onto it from a dying companion. Telesco and his international team, which included UF researchers Dan Li, Peter Barnes, Naibí Mariñas, and Han Zhang, recorded the latter, less-common type on CanariCam, a sophisticated infrared camera developed at UF.

Attached to the largest optical-infrared telescope in the world, the Gran Telescopio Canarias in Spain’s Canary Islands, CanariCam is one of the few astronomical instruments that can record wavelengths in the spectral region 8 to 25 micrometers, well beyond the range of human vision. UF is the nation’s only institution with a stake in the GTC, which has been probing deep into the universe and producing new knowledge of exoplanets, planetary evolution, comets and galaxies for five years.

Supernovae such as 2014J, seen here from the Hubble Space Telescope, are among the most powerful events in the universe, revealing the structure of the universe as a bobbing cork reveals the contours of a lake’s surface.

Supernovae are among the most powerful events in the universe, revealing the structure of the universe as a bobbing cork reveals the contours of a lake’s surface. They are also an essential piece of the puzzle of stellar evolution, but many of their properties remain a mystery.

The observation of supernova 2014J is a first both for Telesco and CanariCam, and, as with many moments in scientific discovery, it wasn’t planned. When Florida State University physicist David Collins visited UF in early 2014, he asked Telesco if he was observing the brand-new supernova that had exploded in the nearby galaxy M82. Telesco jumped at the suggestion and worked with observatory staff in Spain to make it happen. First, they took images of the supernova at two different wavelengths to see if they could detect it.

“We weren’t even sure we would be able to see it at these wavelengths,” says Telesco. “We took pictures and got a weird ratio for the brightnesses of the supernova through the two filters. We thought we’d either screwed up or just made a very interesting finding.” To settle the issue, Telesco’s team took a detailed spectrum of the supernova and were blown away by what they saw.

When a type Ia supernova explodes, carbon and oxygen burn hot and fast, undergoing a series of chain reactions that convert them to a rich soup of other elements, the most prominent being radioactive nickel, which decays into cobalt and finally iron. This nuclear furnace burns at a temperature of hundreds of billions of degrees for just a second as the explosion is ignited. Witnessing this moment and its aftermath gives astronomers a rolling, action-packed picture of unfolding events that scientists use to create accurate models of supernovae and their elusive origins. To the delight and surprise of Telesco and his colleagues, CanariCam recorded a pristine spectral signature of cobalt, a key element in the rapid and powerful alchemy of a supernova.

The CanariCam team observed this elemental probe repeatedly between early and late spring, watching it change shape as the expanding supernova debris revealed more and more of its inner structure. That signature had been seen only once before, in a different, more distant supernova by a NASA space telescope in 2005, but it was only a one-time snapshot. Taking a “movie” of this evolution in 2014J was a big step forward.

“It was like seeing cells divide for the first time,” says Telesco. “Everyone knew that cell division occurred, but no one had actually seen it. Astrophysicists knew that cobalt would be produced, and they had ideas about how its appearance would change in the immediate aftermath of the explosion, but no one had actually seen it happen, which is critical to testing the models that the theorists come up with.”

The spectroscopy of the supernova was so valuable that Telesco and his team used precious telescope time to take a total of four spectra over a four-month period.

“We got to watch it every month in a spectral region no one has ever monitored a type Ia supernova in before,” says Telesco. “We were the only people capable of creating a temporal sequence of the closest type Ia supernova in 300 years.”

According to FSU astronomer Peter Höflich, a key collaborator on this project, these data will be the standard for the study of type Ia supernovae for at least a decade. To Telesco this is an example of a big payoff resulting from a colleague’s offhand comment.

“Sometimes it pays to listen,” he says.

The results of the CanariCam observations are published in the Dec. 20 issue of Astrophysical Journal.

UF geneticist contributes to groundbreaking study of bird evolution

Nature abhors a vacuum, which may explain the findings of a new study showing that bird evolution exploded 65 million years ago when nearly everything else on earth — dinosaurs included — died out.

The study is part of an ambitious project, published in the Dec. 12 issue of the journal Science, in which hundreds of scientists worldwide have decoded the avian genome.

Edward Braun, an evolutionary geneticist at the University of Florida and the UF Genetics Institute, is one of the key scientists who took part in this multi-year project that used nine supercomputers and 400 years of combined computing time to sequence 48 bird genomes representing the 10,500 living species of birds on the planet.

In 2008, Braun worked with scientists at UF and four other institutions to analyze 19 bird genes. This initial study suggested that the diversity of bird evolution occurred very quickly. Now Braun and scientists from Duke University, the Natural History Museum of Denmark, the Beijing Genomics Institute at Shenzhen, the University of Illinois, and many other institutions have built on that effort.

“Six years later, we have whole genomes,” he said. “That’s a major accomplishment. The ornithology books will change.”

The asteroid strike that triggered the Cretaceous–Paleogene extinction was bad news for dinosaurs, but may have created an opening for birds.

“The birds we see today probably diversified into that. That’s probably why it happened so fast,” said Braun. “Can we pick out what the very first split is? The answer is that for the first time, using whole genomes, it appears we can.”

From hummingbirds to herons, 95 percent of avians belong to an order called neoaves (nee-oh-AY-veez). Of this group, 90 percent belong to a group called Passerea and 5 percent called Columbea comprising doves, flamingos and grebes.

“Flamingos and grebes are enough of an odd couple,” said Braun. “Throw in a dove, and that’s a really odd collection.”

The genomic evidence belies common inference that birds of a feather flock together. The Columbea group shows a kinship between water birds and land birds. One might assume the duck to be closely related to other water birds, but it’s on a separate branch of the tree altogether. It was once assumed that grebes and loons belonged together because they’re both foot-propelled divers. Like the 2008 study, this study shows otherwise.

Braun, along with Eric Triplett from the UF Department of Microbiology and Cell Science, also were principal investigators comparing three species of crocodilians — the American alligator, saltwater crocodile and Indian gharial. The inclusion of the crocodilians not only provided a study in contrast but also provided researchers with the ability to reconstruct part of the genome of the common ancestor of archosaurs, the group that includes crocodilians, birds and extinct dinosaurs.

Whereas birds evolved rapidly, crocodilians evolved slowly. The DNA of slowly-evolving organisms is a gold mine for researchers as it allows them to find more things in the genetic structure. Braun looked for evidence of ancient viruses in the genomes in an effort led by Alex Suh from Uppsala University in Sweden.

“We were able to see evidence of viral infections that occurred during the age of the dinosaurs. The oldest we found is 200 million years old,” said Braun. “The fact that you can find ancient viruses in genomes is very cool.”

New research suggests animals prefer human connections

What do animals really want? A new study from the University of Florida suggests it might be human contact, at least in the case of some Galapagos tortoises.

Lindsay Mehrkam, a UF doctoral student in psychology, and psychology professor Nicole Dorey have published a paper in the journal Zoo Biology that examines different types of enrichment preferences in zoo-housed animals.

The findings are particularly important for those who work with animals in captivity every day – zookeepers, trainers and students – and strive to provide the best experience for them.

“Zoos are at the heart of our work, and the welfare of zoo animals is second nature,” Mehrkam said. The team said non-mammalian species have been understudied, and they set out to better understand what makes tortoises happy.

In the experiment, three tortoises at the Santa Fe Teaching Zoo in Gainesville named Larry, Moe and Curly, were given four choices of keeper interaction: playing with a large rubber ball or under a water sprinkler, or having their shells scrubbed or necks rubbed. The zookeepers had used all of these enrichments at least twice a month for several years.

“We wanted to determine if the keeper interactions are just as enriching for the animals as they are for the keepers,” Mehrkam said. “What effect does it have on the animals? Do the animals find it enriching or rewarding?”

The inanimate object and the human were placed on opposite sides of the enclosure. The tortoises were released from the barn and had five minutes to make a choice. Time and time again, they beelined – as much as a lumbering tortoise can beeline – for the human.

“Not only did they prefer keeper interaction overall compared to the traditional forms of enrichment,” Mehrkam said, “but the individual tortoises had preferences for the kind of interaction they wanted. Larry and Curly like having their necks rubbed. Moe liked the shell scrubbing.”

In a follow-up study, Mehrkam and Dorey surveyed zookeepers to see if they could predict which enrichments the animals they work with on a daily basis prefer. They couldn’t.

“The long-term staff who’ve been there for a very long time were the worst at guessing this but were very good at knowing what the animals didn’t like,” Dorey said. “We want to feel like we know our animals, our dog, the animals who live with us and we care for, but in reality [we] don’t. We anthropomorphize how they’re feeling. We really don’t understand their perspective, and that’s what our research shows.”

Both Dorey and Mehrkam use behavior analysis as the foundation of their research. This methodology, used primarily in human study, focuses specifically on behaviors and what factors or situations influence them rather than looking at root causes. The team also is studying aggression in dogs around guarding behaviors in a paper to be submitted for publication soon.

Research shows hunting can have catastrophic effects on tropical forests.

Overhunting has been disastrous for elephants, but their forest habitats have also been caught in the crossfire.

A first-of-its-kind study led by researchers at the University of Florida shows that the dramatic loss of elephants, which disperse seeds after eating vegetation, is leading to the local extinction of a dominant tree species, with likely cascading effects for other forest life.

Their work shows that loss of animal seed dispersers increases the probability of tree extinction by more than tenfold over a 100-year period.

“The entire ecosystem is at risk,” said Trevor Caughlin, a UF postdoctoral student and National Science Foundation fellow. “My hope for this study is that it will provide a boost for those trying to curb overhunting and provide incentives to stop the wildlife trade.”

Caughlin, joined by colleagues from UF, the Conservation Ecology Program in Thailand, Wageningen University in the Netherlands and the Royal Thai Forest Department, published their study in the Proceedings of the Royal Society B showing how vital these animals are to maintaining the biodiversity of tropical forests in Thailand.

The team looked specifically at seed dispersal and how elephants contribute to moving the seeds around the forest.

The elephant has long been an important spiritual, cultural and national symbol in Thailand. At the beginning of the 20th century, their numbers exceeded 100,000. Today, those numbers have plunged to 2,000. Elephants, as well as other animals such as tigers, monkeys and civet cats, are under attack from hunters and poachers, mostly for fabled properties of their organs, teeth and tusks.

Caughlin spent three years gathering tree data in Thailand. He looked at the growth and survival of trees that sprouted from the parent tree and grew up in crowded environs, compared with seeds that were transported and broadcasted widely across the forest by animals. The data were supplemented with a dataset from the Thai Royal Forest Department that contained more than 15 years of data on trees to create a long-term simulation run on UF’s supercomputer, HiPerGator.

The team discovered that trees that grow from seeds transported by those animals being overhunted are hardier and healthier.

“Previously, it’s been unclear what role seed dispersal plays in tree population dynamics,” Caughlin said. “A tree makes millions of seeds during its lifetime, and only one of those seeds needs to survive to replace the parent tree. On the surface, it doesn’t seem like seed dispersal would be that important for tree population. What we found with this study is that seed dispersal has an impact over the whole life of a tree.”

Jeremy Lichstein, an assistant professor of biology at UF and one of the paper’s authors, said, “Our study is the first to quantify the decades-long effects of animal seed dispersal across the entire tree life cycle, from seeds to seedlings to adult trees.”

Richard Corlett, director of the Center for Integrative Conservation at the Xishuangbanna Tropical Botanical Gardens in Yunnan, China, underscored the study’s importance.

“This study fills a major gap in our understanding of how overhunting affects forest trees, particularly in tropical forests,” he said. “We knew hunting was bad, but we were not sure why it was bad, and therefore could not predict the long-term impacts. Now we know it is really, really bad and will get worse. The message that ‘guns kill trees too’ should help put overhunting at the top of the conservation agenda, where it deserves to be.”

The spread of Ebola in West Africa reveals two truths: The disease is swift, and it is devastating. Amid the chaos of deadly outbreak, researchers say another truth may exist: The disease might be quietly inoculating a significant portion of the population who are exposed to the virus but never succumb to it or show symptoms of being infected.

If those individuals have acquired an immunity to Ebola, the strategies for the intervention and treatment of the disease need to be reconsidered, according to a letter published online today in The Lancet, a leading medical journal.

Juliet Pulliam, one of the letter’s authors and an assistant professor of biology at the University of Florida and UF’s Emerging Pathogens Institute, said, “If infection without disease protects people from future Ebola infections and illness, the epidemic should decline sooner than currently predicted and affect a smaller number of people.”

The authors, led by postdoctoral fellow Steve Bellan at The University of Texas at Austin, looked at studies done in the aftermath of an outbreak. One showed that 71 percent of people who had close contact with Ebola patients and tested positive for the virus did not get sick; another showed 46 percent of people who had close contact with Ebola patients and did not get sick had evidence of infection with the virus.

“We want to know whether people who are infected without getting sick become immune,” Pulliam said. “If these people are protected from future infections, this would open up new opportunities for controlling the disease.”

The letter suggests the asymptomatic individuals can help slow the spread of Ebola in two important ways: They can be recruited to work as caregivers in high-risk communities; and their natural immunity may make them prime candidates for donating blood for transfusions.

“If we can take advantage of natural immunity within the affected communities, we may be able impact the course of the epidemic even before a vaccine becomes available,” Pulliam said.

“Even if current projections overestimate how big this epidemic will become, its effects are devastating, and a global effort to control the spread of Ebola within West Africa remains imperative,” she added.