Museums Preserve Clues That Can Help Scientists Predict and Analyze Future Pandemics
By Pamela Soltis, Joseph Cook and Richard Yanagihara
In less than 20 years, communities around the globe have been hit by a string of major disease outbreaks: SARS, MERS, Ebola, Zika and now, COVID-19. Nearly all emerging infectious diseases in humans originate from microorganisms that are harbored by wildlife and subsequently "jump," either directly or indirectly – for example, through mosquitoes or ticks – to humans.
One factor driving the increase in zoonotic disease outbreaks is that human activities – including population growth, migration and consumption of wild animals – are leading to increased encounters with wildlife. At the same time, genetic mutations in viruses and other microbes are creating new opportunities for disease emergence.
But humans remain largely ignorant of our planet's biodiversity and its natural ecosystems. Only two million species – about 20% of all the estimated species on Earth – have even been named In our view, this fundamental ignorance of nearly all aspects of biodiversity has resulted in an inefficient, poorly coordinated and minimally science-based response to key aspects of the COVID-19 pandemic.
We have diverse backgrounds in plant and mammal evolution and emerging infectious diseases. In a newly published commentary that we wrote with colleagues from across the U.S. and in six other countries, we identify a largely untapped resource for predicting future pandemics: natural history collections in museums around the world.
These collections preserve specimens of animals, plants and other organisms that illustrate the diversity of life on Earth. They are reservoirs of information and samples that can help scientists identify likely pathogen sources, hosts and transmission pathways. We believe that leveraging collections in this way will require more resources and more collaboration between biodiversity scientists and disease outbreak sleuths.
Archives of Life on Earth
Research shows that zoonotic diseases have increased due to human intrusion into animal habitats. In particular, destruction of tropical rain forests throughout the world has brought us face to face with microbes that occur naturally in wild animals and can cause disease in our own species.
Earth's biodiversity is connected through a family tree. Viruses, bacteria and other microbes have evolved with their hosts for millions of years. As a result, a virus that resides in a wild animal host such as a bat without causing disease can be highly pathogenic when transmitted to humans. This is the case with zoonotic diseases.
Unfortunately, national responses to disease outbreaks are often based on very limited knowledge of the basic biology, or even the identity, of the pathogen and its wild host. As scientists, we believe that harnessing centuries of biological knowledge and resources from natural history collections can provide an informed road map to identify the origin and transmission of disease outbreaks.
These collections of animals, plants and fungi date back centuries and are the richest sources of information available about life on Earth. They are housed in museums ranging from the Smithsonian Institution to small colleges.
Together, the world's natural history collections are estimated to contain more than three billion specimens, including preserved specimens of possible hosts of the coronaviruses that have led to SARS, MERS and COVID-19. They provide a powerful distribution map of our planet's biodiversity over space and through time.
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How can researchers channel these collections toward disease discovery? Each specimen – say, a species of pitcher plant from Florida or a deer mouse from arid New Mexico – is catalogued with a scientific name, a collection date and the place where it was collected, and often with other relevant information. These records underpin scientists' understanding of where host species and their associated pathogens are found and when they occurred there.
Connecting the site of a disease outbreak to potential pathogen hosts that occur in that area can help to pinpoint likely hosts, sources of pathogens, and pathways of transmission from hosts to humans and from one human to another. These natural history collections are connected worldwide through massive online databases, so a researcher anywhere in the world can find information on potential hosts in far-off regions.
But that's just the beginning. A preserved specimen of a rodent, a bat or any other potential host animal in a collection also carries preserved pathogens, such as coronaviruses. This means that researchers can quickly survey microbes using specimens that were collected decades or more before for an entirely different purpose. They can use this information to quickly identify a pathogen, associate it with particular wild hosts, and then reconstruct the past distributions and evolution of disease-causing microbes and hosts across geographic space.
Many collections contain frozen samples of animal specimens stored in special low-temperature freezers. These materials can be quickly surveyed for microbes and possible human pathogens using genetic analysis. Scientists can compare DNA sequences of the pathogens found in animal specimens with the disease-causing agent to identify and track pathways of transmission.
For example, museum specimens of deer mice at the University of New Mexico were key to the rapid identification of a newly discovered species of hantavirus that caused 13 deaths in the southwest United States in 1993. Subsequent studies of preserved specimens have revealed many new species and variants of hantaviruses in other rodents, shrews, moles and, recently, bats worldwide.
Equipping Museums and Connecting Scientists
Natural history collections have the potential to help revolutionize studies of epidemics and pandemics. But to do this, they will need more support.
Even though they play a foundational role in biology, collections are generally underfunded and understaffed. Many of them lack recent specimens or associated frozen tissues for genetic analyses. Many regions of our planet have been poorly sampled, especially the most biodiverse countries near the tropics.
To leverage biodiversity science for biomedical research and public health, museums will need more field sampling; new facilities to house collections, especially in biodiverse countries; and expanded databases for scientists who collect the samples, analyze DNA sequences and track transmission routes. These investments will require increased funding and innovations in biomedical and biodiversity sciences.
Another challenge is that natural history curators and pathobiologists who study the mechanisms of disease work in separate scientific communities and are only vaguely aware of each other's resources, despite clear benefits for both basic and clinical research. We believe now is the time to reflect on how to leverage diverse resources and build stronger ties between natural history museums, pathobiologists and public health institutions. Collaboration will be key to our ability to predict, and perhaps forestall, future pandemics.
Pamela Soltis is a Distinguished Professor and Curator, Florida Museum of Natural History, University of Florida.
Joseph Cook is a Professor of Biology and Curator, Division of Mammals, Museum of Southwestern Biology, University of New Mexico.
Richard Yanagihara is a Professor of Pediatrics and Principal Investigator, Pacific Center for Emerging Infectious Diseases Research, University of Hawaii.
Disclosure statement: Pamela Soltis receives funding from the National Science Foundation. She serves on leadership boards of the American Institute of Biological Sciences and the American Society of Plant Taxonomists. Joseph Cook receives funding from the National Science Foundation. Richard Yanagihara receives funding from the National Institutes of Health. He works at the John A. Burns School of Medicine, of the University of Hawaii at Manoa.
Reposted with permission from The Conversation.
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While the nation overall struggles with rising COVID cases, New York State is seeing the opposite. After peaking in March and April and implementing strict shutdowns of businesses, the state has seen its number of positive cases steadily decline as it slowly reopens. From coast-to-coast, Governor Andrew Cuomo's response to the crisis has been hailed as an exemplar of how to handle a public health crisis.
By Gavin Naylor
Sharks elicit outsized fear, even though the risk of a shark bite is infinitesimally small. As a marine biologist and director of the Florida Program for Shark Research, I oversee the International Shark Attack File – a global record of reported shark bites that has been maintained continuously since 1958.
A Big, Diverse Family<p>Not all sharks are the same. Only a dozen or so of the roughly 520 shark species pose any risk to people. Even the three species that account for almost all shark bite fatalities – the <a href="https://www.floridamuseum.ufl.edu/discover-fish/species-profiles/carcharodon-carcharias/" target="_blank">white shark</a> (<em>Carcharodon carcharias</em>), <a href="https://www.floridamuseum.ufl.edu/discover-fish/species-profiles/galeocerdo-cuvier/" target="_blank">tiger shark</a> (<em>Galeocerdo cuvier</em>) and <a href="https://www.floridamuseum.ufl.edu/discover-fish/species-profiles/carcharhinus-leucas/" target="_blank">bull shark</a> (<em>Carcharhinus leucas</em>) – are behaviorally and evolutionarily very different from one another.</p><p>The tiger shark and bull shark are genetically as different from each other as a dog is from a rabbit. And both of these species are about as different from a white shark as a dog is from a kangaroo. The evolutionary lineages leading to the two groups split 170 million years ago, during the age of dinosaurs and before the origin of birds, and <a href="https://www.ck12.org/book/CK-12-Human-Biology/section/7.2/" target="_blank">110 million years before the origin of primates</a>.</p>
White, tiger and bull sharks are distinct species that diverged genetically tens of millions of years ago. Gavin Naylor / CC BY-ND<p>Yet many people assume all sharks are alike and equally likely to bite humans. Consider the term "shark attack," which is scientifically equivalent to "mammal attack." Nobody would equate dog bites with hamster bites, but this is exactly what we do when it comes to sharks.</p><p>So, when a reporter calls me about a fatality caused by a white shark off Cape Cod and asks my advice for beachgoers in North Carolina, it's essentially like asking, "A man was killed by a dog on Cape Cod. What precautions should people take when dealing with kangaroos in North Carolina?"</p>
Know Your Species<p>Understanding local species' behavior and life habits is one of the best ways to stay safe. For example, almost all shark bites that occur off Cape Cod are by white sharks, which are a large, primarily cold-water species that spend most of their time in isolation feeding on fishes. But they also aggregate near seal colonies that provide a reliable food source at certain times of the year.</p><p>Shark bites in the Carolinas are by warm-water species like bull sharks, tiger sharks and <a href="https://www.floridamuseum.ufl.edu/discover-fish/species-profiles/carcharhinus-limbatus/" target="_blank">blacktips</a> (<em>Carcharhinus limbatus</em>). Each species is associated with particular habitats and dietary preferences.</p><p>Blacktips, which we suspect are responsible for most relatively minor bites on humans in the southeastern United States, feed on schooling bait fishes like menhaden. In contrast, bull sharks are equally at home in fresh water and salt water, and are often found near estuaries. Their bites are more severe than those of blacktips, as they are larger, more powerful, bolder and more tenacious. Several fatalities have been ascribed to bull sharks.</p><p>Tiger sharks are also large, and are responsible for a significant fraction of fatalities, particularly off the coast of volcanic islands like Hawaii and Reunion. They are tropical animals that often venture into shallow water frequented by swimmers and surfers.</p>
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Humans Are Not Targets<p>Sharks do not "hunt" humans. Data from the International Shark Attack File compiled over the past 60 years show a tight association between shark bites and the number of people in the water. In other words, shark bites are a simple function of the probability of encountering a shark.</p><p>This underscores the fact that shark bites are almost always cases of mistaken identity. If sharks actively hunted people, there would be many more bites, since humans make very easy targets when they swim in sharks' natural habitats.</p><p>Local conditions can also affect the risk of an attack. Encounters are more likely when sharks venture closer to shore, into areas where people are swimming. They may do this because they are following bait fishes or seals upon which they prey.</p><p>This means we can use environmental variables such as temperature, tide or weather conditions to better predict movement of bait fish toward the shoreline, which in turn will predict the presence of sharks. Over the next few years, the Florida Program for Shark Research will work with colleagues at other universities to monitor onshore and offshore movements of tagged sharks and their association with environmental variables so that we can improve our understanding of what conditions bring sharks close to shore.</p>
More to Know<p>There still is much to learn about sharks, especially the 500 or so species that have never been implicated in a bite on humans. One example is the tiny <a href="https://www.newsweek.com/one-worlds-rarest-sharks-also-one-most-adorable-325280" target="_blank">deep sea pocket shark</a>, which has a strange pouch behind its pectoral fins.</p><p>Only two specimens of this type of shark have ever been caught – one off the coast of Chile 30 years ago, and another more recently in the Gulf of Mexico. We're not sure about the function of the pouch, but suspect it stores luminous fluid that is released to distract would-be predators – much as its close relative, the <a href="https://sharkdevocean.wordpress.com/2015/04/23/second-ever-pocket-shark-discovered-in-gulf-of-mexico/" target="_blank">tail light shark</a>, releases luminous fluid from a gland on its underside near its vent.</p>
<span style="display:block;position:relative;padding-top:56.25%;" class="rm-shortcode" data-rm-shortcode-id="5783b39d0838d6e410344a852ed0dcc3"><iframe lazy-loadable="true" src="https://www.youtube.com/embed/UTO5debfmsg?rel=0" width="100%" height="auto" frameborder="0" scrolling="no" style="position:absolute;top:0;left:0;width:100%;height:100%;"></iframe></span><p>Sharks range in form from the bizarre <a href="https://www.floridamuseum.ufl.edu/discover-fish/species-profiles/mitsukurina-owstoni/" target="_blank">goblin shark</a> (<em>Mitsukurina owstoni</em>), most commonly encountered in Japan, to the gentle filter-feeding <a href="https://www.floridamuseum.ufl.edu/discover-fish/species-profiles/rhincodon-typus/" target="_blank">whale shark</a> (<em>Rhincodon typus</em>). Although whale sharks are the largest fishes in the world, we have yet to locate their nursery grounds, which are likely teeming with thousands of <a href="https://www.earthtouchnews.com/oceans/sharks/baby-whale-shark-rescued-from-gillnet-in-india-video/" target="_blank">foot-long pups</a>. Some deepwater sharks are primarily known from submersibles, such as the giant <a href="https://twitter.com/gavinnaylor/status/1146144452681113601" target="_blank">sixgill shark</a>, which feeds mainly on carrion but probably also preys on other animals in the deep sea.</p><p>Sharks seem familiar to almost all of us, but we know precious little about them. Our current understanding of their biology barely scratches the surface. The little we do know suggests they are profoundly different from other vertebrate animals. They've had 400 million years of independent evolution to adapt to their environments, and it's reasonable to expect they may be hiding more than a few tricks up their gills.</p>
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Current efforts to curb an infectious disease show the potential we have for collective action. That action and more will be needed if we want to stem the coming wave of heat-related deaths that will surpass the number of people who die from all infectious diseases, according to a new study, as The Guardian reported.
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By Jenny Morber
Caribbean corals sprout off Texas. Pacific salmon tour the Canadian Arctic. Peruvian lowland birds nest at higher elevations.
Known and anticipated changes in species distribution due to climate change around the world have implications for culture, society ecosystems, governance and climate change. Figure used with permission from Gretta T. Pecl, originally published on 31 Mar 2017 in Science 355(6332).<p>How we define species is critical, because these definitions influence perceptions, policy and management. The U.S. National Invasive Species Council (NISC) defines a biological invasion as "the process by which non-native species breach biogeographical barriers and extend their range" and states that "preventing the introduction of potentially harmful organisms is … the first line of defense." But some say excluding newcomers is myopic.</p><p>"If you were trying to maintain the status quo, so every time a new species comes in, you chuck it out," says Camille Parmesan, director of the French National Centre for Scientific Research, you could gradually "lose so many that that ecosystem will lose its coherence." If climate change is driving native species extinct, she says, "you need to allow new ones coming in to take over those same functions."</p><p>As University of Florida conservation ecologist Brett Scheffers and Pecl warned in a <a href="https://www.nature.com/articles/s41558-019-0526-5" target="_blank">2019 paper in <em>Nature Climate Change</em></a>, "past management of redistributed species … has yielded mixed actions and results." They concluded that "we cannot leave the fate of biodiversity critical to human survival to be randomly persecuted, protected or ignored."</p>
Existing Tools<p>One approach to managing these climate-driven habitat shifts, suggested by University of California, Irvine marine ecologist Piper Wallingford and colleagues in <a href="https://www.nature.com/articles/s41558-020-0768-2" target="_blank">a recent issue of Nature Climate Change</a>, is for scientists to adapt existing tools like the <a href="https://www.iucn.org/theme/species/our-work/invasive-species/eicat" target="_blank">Environmental Impact Classification of Alien Taxa (EICAT)</a> to assess potential risks associated with moving species. Because range-shifting species pose impacts to communities similar to those of species introduced by humans, the authors argue, new management strategies are unnecessary, and each new arrival can be evaluated on a case-by-case basis.</p><p>Karen Lips, a professor of biology at University of Maryland who was not associated with the study, echoes the idea that each case is so varied and nuanced that trying to fit climate shifting species into a single category with broad management goals may be impractical. "Things may be fine today, but add a new mosquito vector or add a new tick or a new disease, and all of a sudden things spiral out of control," she says. "The nuance means that the answer to any particular problem might be pretty different."</p>
In recent years, northern flying squirrels in Canada have found themselves in the company of new neighbors — southern flying squirrels expanding their range as the climate warms. Public Domain / USFW<p>Laura Meyerson, a professor in the Department of Natural Resources Science at the University of Rhode Island says scientists should use existing tools to identify and address invasive species to deal with climate-shifting species. "I would like to operate under the precautionary principle and then reevaluate as things shift. You're sort of shifting one piece in this machinery; as you insert a new species into a system, everything is going to respond," she says. "Will some of the species that are expanding their ranges because of climate change become problematic? Perhaps they might."</p><p>The reality is that some climate-shifting species may be harmful to some conservation or economic goals while being helpful to others. While sport fisherman are excited about red snapper moving down the East Coast of Australia, for example, if they eat juvenile lobsters in Tasmania they could harm this environmentally and economically important crustacean. "At the end of the day … you're going to have to look at whether that range expansion has some sort of impact and presumably be more concerned about the negative impacts," says NISC executive director Stas Burgiel. "Many of the [risk assessment] tools we have are set up to look at negative impact." As a result, positive effects may be deemphasized or overlooked. "So that notion of cost versus benefit … I don't think it has played out in this particular context."</p>
Location, Location, Location<p>In a <a href="https://www-nature-com.ezp3.lib.umn.edu/articles/s41558-020-0770-8" target="_blank">companion paper</a> to Wallingford's, University of Connecticut ecology and evolutionary biology associate professor Mark Urban stressed key differences between invasive species, which are both non-native and harmful, and what he calls "climate tracking species." Whereas invasive species originate from places very unlike the communities they overtake, he says, climate tracking species expand from largely similar environments, seeking to follow preferred conditions as these environments move. For example, an American pika may relocate to a higher mountain elevation, or a marbled salamander might expand its New England range northward to seek cooler temperatures, but these new locations are not drastically different than the places they had called home before.</p><p>Climate tracking species may move faster than their competitors at first, Urban says, but competing species will likely catch up. "Applying perspectives from invasion biology to climate-tracking species … arbitrarily chooses local winners over colonizing losers," he writes.</p>
The marbled salamander, a native of the eastern U.S., is among species whose range could expand northward to accommodate rising temperatures. Seánín Óg / Flickr / CC BY-NC-ND 2.0<p>Urban stresses that if people prevent range shifts, some climate-tracking species may have nowhere to go. He suggests that humans should even <a href="https://ensia.com/features/time-for-trees-to-pack-their-trunks/" target="_blank">facilitate movement</a> as the planet warms. "The goal in this crazy warming world is to keep everything alive. But it may not be in the same place," Urban says.</p><p>Parmesan echoes Urban, emphasizing it's the distance that makes the difference. "[Invasives] come from a different continent or a different ocean. You're having these enormous trans-global movements and that's what ends up causing the species that's exotic to be invasive," she says. "Things moving around with climate change is a few hundred miles. Invasive species are moving a few thousand miles."</p><p>In 2019 University of Vienna conservation biology associate professor Franz Essl published a similar argument for species classification beyond the native/non-native dichotomy. Essl uses "neonatives" to refer to species that have expanded outside their native areas and established populations because of climate change but not direct human agency. He argues that these species should be considered as native in their new range.</p>
They Never Come Alone<p>Meyerson calls for caution. "I don't think we should be introducing species" into ecosystems, she says. "I mean, they never come alone. They bring all their friends, their microflora, and maybe parasites and things clinging to their roots or their leaves. … It's like bringing some mattress off the street into your house."</p><p>Burgiel warns that labeling can have unintended consequences. We in the invasive species field … focus on non-native species that cause harm," he says. "Some people think that anything that's not native is invasive, which isn't necessarily the case." Because resources are limited and land management and conservation are publicly funded, Burgiel says, it is critical that the public understands how the decisions are being made.</p><p>Piero Genovesi, chair of the International Union for the Conservation of Nature's Invasive Species Specialist Group, sees the debate about classification — and therefore about management — as a potential distraction from more pressing conservation issues.</p><p>"The real bulk of conservation is that we want to focus on the narrow proportion of alien species that are really harmful," he says. In Hawaii "we don't discuss species that are there [but aren't] causing any problem because we don't even have the energy for dealing with them all. And I can tell you, no one wants to remove [non-native] cypresses from Tuscany. So, I think that some of the discussions are probably not so real in the work that we do in conservation."</p><p>Indigenous frameworks offer another way to look at species searching for a new home in the face of climate change. According to <a href="https://link.springer.com/article/10.1007%2Fs11625-018-0571-4" target="_blank">a study</a> published in Sustainability Science in 2018 by Dartmouth Native American studies and environmental studies associate professor Nicholas Reo, a citizen of the Sault Ste. Marie Tribe of Chippewa Indians, and Dartmouth anthropology associate professor Laura Ogden, some Anishnaabe people view plants as persons and the arrival of new plants as a natural form of migration, which is not inherently good or bad. They may seek to discover the purpose of new species, at times with animals as their teachers. In their paper Reo and Ogden quote Anishnaabe tribal chairman Aaron Payment as saying, "We are an extension of our natural environment; we're not separate from it."</p>
The Need for Collaboration<p>The successful conservation of Earth's species in a way that keeps biodiversity functional and healthy will likely depend on collaboration. Without global agreements, one can envision scenarios in which countries try to impede high-value species from moving beyond their borders, or newly arriving species are quickly overharvested.</p><p>In Nature Climate Change, Sheffers and Pecl call for a Climate Change Redistribution Treaty that would recognize species redistribution beyond political boundaries and establish governance to deal with it. Treaties already in place, such as the Convention on International Trade in Endangered Species of Wild Fauna and Flora, which regulates trade in wild plants and animals; the Migratory Bird Treaty Act; and the Agreed Measures for the Conservation of Antarctic Fauna and Flora, can help guide these new agreements.</p><p>"We are living through the greatest redistribution of life on Earth for … potentially hundreds of thousands of years, so we definitely need to think about how we want to manage that," Pecl says.</p><p>Genovesi agrees that conservationists need a vision for the future. "What we do is more to be reactive [to known threats]. … It's so simple to say that destroying the Amazon is probably not a good idea that you don't need to think of a step ahead of that." But, he adds, "I don't think we have a real answer in terms of okay, this is a threshold of species, or this is the temporal line where we should aim to." Defining a vision for what success would look like, Genovesi says, "is a question that hasn't been addressed enough by science and by decision makers."</p><p>At the heart of these questions are values. "All of these perceptions around what's good and what's bad, all [are based on] some kind of value system," Pecl says. "As a whole society, we haven't talked about what we value and who gets to say what's of value and what isn't."</p><p>This is especially important when it comes to marginalized voices, and Pecl says she is concerned because she doesn't "think we have enough consideration or representation of Indigenous worldviews." Reo and colleagues <a href="https://cpb-us-e1.wpmucdn.com/sites.dartmouth.edu/dist/9/52/files/2012/10/Reo_etal_AIQ_invasive_species_2017.pdf" target="_blank">wrote in American Indian Quarterly in 2017</a> that climate change literature and media coverage tend to portray native people as vulnerable and without agency. Yet, says Pecl, "The regions of the world where [biodiversity and ecosystems] are either not declining or are declining at a much slower rate are Indigenous controlled" — suggesting that Indigenous people have potentially managed species more effectively in the past, and may be able to manage changing species distributions in a way that could be informative to others working on these issues.</p><p>Meanwhile, researchers such as Lips see species classification as native or other as stemming from a perspective that there is a better environmental time and place to return to. "There is no pristine, there's no way to go back," says Lips. "The entire world is always very dynamic and changing. And I think it's a better idea to consider just simply what is it that we do want, and let's work on that."</p>
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