Institute of Ecology and Evolution

Bern, Switzerland

Institute of Ecology and Evolution

Bern, Switzerland
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News Article | May 4, 2017
Site: www.newscientist.com

A common parasite that lives in fish eyeballs seems to be a driver behind the fish’s behaviour, pulling the strings from inside its eyes. When the parasite is young, it helps its host stay safe from predators. But once the parasite matures, it does everything it can to get that fish eaten by a bird and so continue its life cycle. The eye fluke Diplostomum pseudospathaceum has a life cycle that takes place in three different types of animal. First, parasites mate in a bird’s digestive tract, shedding their eggs in its faeces. The eggs hatch in the water into larvae that seek out freshwater snails to infect. They grow and multiply inside the snails before being released into the water, ready to track down their next host, fish. The parasites then penetrate the skin of fish, and travel to the lens of the eye to hide out and grow. The fish then get eaten by a bird – and the cycle starts again. Many parasites can change an animal’s behaviour to fit their own needs. Mice infected with the parasite Toxoplasma gondii, for example, lose their fear of cats – the animal the parasite needs to reproduce inside. In a 2015 study, Mikhail Gopko at the Severtsov Institute of Ecology and Evolution in Moscow and his colleagues showed that fish infected with immature fluke larvae swam less actively than usual – making themselves less visible to predators – and were harder to catch with a net than uninfected controls. Now, the same team has tested rainbow trout harbouring mature eye flukes – parasites ready to reproduce inside their bird hosts. The team found that these trout swam more actively than uninfected controls and stayed closer to the water’s surface. Both traits should make fish more conspicuous to birds. When the researchers simulated a bird attack by making a shadow swoop over the tank, the fish froze – but infected fish resumed swimming sooner than uninfected ones. Gopko says both studies show that how eye flukes manipulate their host’s behaviour depends on their age. Immature parasites “are too young and innocent to infect a next host”, he says, so their goal is to protect the fish they are living in. Mature parasites, however, are ready to reproduce – and to do so they need to get inside a bird’s gut. Some earlier studies suggested fluke-infected fish act differently because of impaired vision. But the authors say vision problems wouldn’t explain changes to unfreezing time, or the opposite effects of mature and immature parasites. The researchers also tested how long it took fish to unfreeze after attack when they were infected with both mature and immature parasites at once. Their behaviour matched that of fish carrying only mature parasites. When the parasites’ goals conflict, Gopko says, “mature guys are clear winners”. This fits a pattern of young parasites decreasing their host’s likelihood of being preyed on, while older parasites increase it, says Nina Hafer, a parasitologist at the Max Planck Institute for Evolutionary Biology in Plön, Germany. Few studies have pitted mature and immature parasites against each other in one host, she says. “It contributes to showing how many traits and species can be affected by host manipulation, which should make it an important factor in how parasites alter the ecological interactions of their hosts,” she says. Read more: The cat made me do it: Is your pet messing with your mind?


News Article | November 13, 2015
Site: www.biosciencetechnology.com

University of Oregon scientists have found that strength in numbers doesn't hold true for microbes in the intestines. A minority population of the right type might hold the key to regulating good health. The discovery, based on research using zebrafish raised completely germ free, is reported in a paper published in the Nov. 11 issue of Cell Host & Microbe. The findings provide a path to study the function of each bacterial species in the gut and to eventually, perhaps, predict and prevent disease, says lead author Annah S. Rolig, a postdoctoral researcher in the UO's Institute of Molecular Biology. In the project, researchers watched for immune response as isolates of species of bacteria, normally associated with healthy zebrafish, were introduced one at a time and in combination into previously germ-free intestines of the fish. In a telling sequence, one bacterial species, Vibrio, drew numerous neutrophils, which indicated a rapid inflammatory response in one fish. Another species, Shewanella, inserted into a separate germ-free fish barely attracted an immune response. In a third germ-free fish, both species were introduced together and assembled with a ratio of 90- percent Vibrio to 10-percent Shewanella. The inflammatory response in the third fish was completely controlled by the low-abundance species. "Until now, we've only been able to capture proportional information, like you'd see displayed in a pie graph, of the makeup of various microbiota, in percentages of their abundance," Rolig said. "Biologists in this field have typically assumed an equal contribution based on that makeup." Low counts of a bacterial species generally have been discounted in importance, but slight shifts in the ratios of abundant microbe populations have been thought to have roles in obesity, diabetes and inflammatory bowel diseases such as Crohn's disease. That thinking is now changing, Rolig said. "The contribution of each bacterium is not equal. There is a per-capita effect that needs to be considered." The keystone - an important participant that functions to regulate a healthy microbiota - may reside in low-abundant bacterial species. The research team found through additional scrutiny that these species secreted molecules - for now unidentified - that allowed them to dampen the immune response to the whole community. "Now we've shown that these minor members can have a major impact. If we can identify these keystone species, and find that in a disease state one species may be missing, we might be able to go in with a specific probiotic to restore healthy functioning," said Rolig, who also is a scientist in the National Institutes of Health-funded Microbial Ecology and Theory of Animals Center for Systems Biology, known as the META Center, at the UO. To develop a model to capture per-capita contributions of microbes in a population, Rolig and her co-authors -- biology graduate student Adam R. Burns, microbiologist Brendan Bohannan of the Institute of Ecology and Evolution and biologist Karen Guillemin, director of the META Center -- turned to UO physicist Raghuveer Parthasarathy. His math-driven model, detailed in the paper, provides formulas that predict collective inflammatory responses of combinations of bacteria. "I'm really proud of this paper because it exemplifies an achievement of one of the major goals of the META Center for Systems Biology, namely to provide a predictive model of how host-microbe systems function," Guillemin said. "This experimental and modeling framework could be readily generalized to more complex systems such as humans, for example to predict disease severity in individuals with inflammatory bowel disease based on the pro-inflammatory capacity of their gut microbes as assayed in cell culture."


News Article | December 22, 2016
Site: www.eurekalert.org

Researchers in Bill Cresko's University of Oregon lab and collaborators examined the snakelike fish in detail and published their work as a reference so other labs around the world can follow their lead EUGENE, Ore. -- Dec. 22, 2016 -- University of Oregon biologists have produced a detailed genome of the snakelike gulf pipefish, delivering a new research reference tool to help explore an ancient fish family that includes seahorses and sea dragons and has generated bodies with vastly different features over time through genetic changes. Comparing the genome with other vertebrate organisms may help scientists learn about basic aspects of human biology, such as how skulls develop and change shape and how the genome that people mostly share with other vertebrates can be tweaked to create new structures, said Susan Bassham, a senior research associate in the lab of UO biologist William Cresko where the research was done. While such research connected to human features is an added benefit, a more immediate payoff is that the methods used during the project are laid out so that other small labs can use them as a reference for creating genomes of organisms they are interested in studying. A paper detailing the genome was published Dec. 20 by the journal Genome Biology. The gulf pipefish -- abundant in seagrass beds of the Gulf of Mexico -- has the species name of Syngnathus scovelli. It belongs to the family known as Syngnathidae, which dates back at least 50 million years. "This group of species has novelties that are not well understood from an evolutionary genetic standpoint," said Clay Small, one of the paper's lead authors and a postdoctoral fellow in Cresko's lab in the Institute of Ecology and Evolution. "The family Syngnathidae is a very good model clade for studying these derived structural features because they are so weird looking in terms of their unique body plans. Ultimately, we are interested in identifying genetic changes that are related to the evolution of these novel features in this whole family." Species in the Syngnathid family have long snouts, which help their suction-like feeding behavior. They have bony body armor. They lack pelvic fins, ribs and teeth and have evolved unique placenta-like structures in males for the brooding of developing offspring. The publication of the gulf pipefish genome came less than a week after the genome of another family member, the tiger tail seahorse, was announced in the journal Nature. "Having this pair of papers published almost simultaneously moved genomic analyses of this remarkable group of fish ahead tremendously," said Cresko, a professor of biology. The two genomes show that losses and changes in specific genes or gene functions may be responsible for evolutionary innovations, Small said. Through evolution, the pipefish and seahorse genomes have lost genetic elements compared to distant fish ancestors. These likely explain some changes in body alignment and the loss of pelvic fins, which correspond to legs in the human vertebrate lineage, he said. A big part of Small's efforts focused on the ability of male pipefish to gestate embryos in their brood pouch. The gulf pipefish, Bassham said, provides an example of one of the most elaborated placental structures found in the males of various pipefish species. Some 1,000 genes are expressed differently in the pouch during a male's pregnancy to control developmental processes, nutrient exchange, stability and immunity, the researchers reported. In a comparative analysis between pregnant and non-pregnant male pipefish, Small found a family of genes that behaved unusually. This gene family, patristacins, contains some members that turn on during pregnancy, and others that are suppressed during pregnancy. The group of genes is likely unique to syngnathid fishes, and they behave similarly in seahorses. The UO-led team also found that gulf pipefish have two chromosomes fewer than most ray-finned fish. "By looking at the patterns of where genes lie in the genome, it's very likely this difference resulted simply from the fusion of four of the ancestral chromosomes into two," Bassham said. "Most fish have 24 chromosomes, but the gulf pipefish has 22." The researchers used a genome-sequencer in the UO's Genomics Core Facility, along with a genetics technology developed at the UO called restriction-site associated DNA markers, now known as RAD-sequencing. It allows researchers to sort data and then organize it all back together into a detailed genetic map. The team also used three software packages developed by co-author Julian Catchen, a former UO postdoctoral researcher now at the University of Illinois at Urbana-Champaign. The software was designed to complement RAD-sequencing and genome assembly data. Using fish genomes, Bassham said, should allow research groups to ask a lot of different biological questions. "Fish are vertebrates. We are vertebrates," she said. "We share large swaths of our biology with these fish. We'd like to understand how evolution occurs, and some of the most exciting aspects of evolution happen when novel features appear in an evolutionary lineage. "Novelties can happen multiple ways," Bassham said. "Sometimes it involves a loss of a structure that creates a new way of life. In other cases, it might be an evolution of a new body part that wasn't there before. Where did that tissue come from? How did it come into being? What was modified to make it? Or what developmental gene pathways were changed to allow for it?" Other co-authors with Bassham, Catchen, Cresko and Small were Angel Amores, research associate in the UO Institute of Neuroscience; Allison Fuiten, graduate student in Cresko's lab; former UO student R.S. Brown, who now is at Oregon Health and Science University; and Adam G. Jones of Texas A&M University. The National Institutes of Health and National Science Foundation supported the research. A more-detailed look at the science unveiled by the gulf pipefish genome paper can be seen in a blog posted by the BioMed Central. Sources: Susan Bassham, research associate, Institute of Ecology and Evolution, 541-346-5189, sbassham@uoregon.edu; Clay Small, postdoctoral researcher, Institute of Ecology and Evolution, 541-346-4232, csmall@uoregon.edu Note: The UO is equipped with an on-campus television studio with a point-of-origin Vyvx connection, which provides broadcast-quality video to networks worldwide via fiber optic network. There also is video access to satellite uplink and audio access to an ISDN codec for broadcast-quality radio interviews.


News Article | September 8, 2016
Site: www.biosciencetechnology.com

University of Oregon researchers have found links between the levels of antimicrobial chemicals and antibiotic-resistance genes in the dust of an aging building used for athletics and academics. One of the antimicrobials seen in the study is triclosan, a commonly used antibacterial ingredient in many personal care products. It is among antimicrobials that will be phased out within the next year from hand and bar soaps, according to a ruling Sept. 2 by the U.S. Food and Drug Administration. The findings of the new study reflect relationships in the dust, not that the antimicrobials are the reason for antibacterial genes being present. "We might be tempted to think of the antimicrobial chemicals as being guilty by association," said Erica M. Hartmann, a postdoctoral fellow at the UO's Biology and the Built Environment Center and Institute of Ecology and Evolution who led the study. She joined the faculty at Northwestern University this month. "We don't really know how the genes or the chemicals got there," she said. "They may have arrived by completely different routes and their being found together is a coincidence. However, we know that antimicrobial chemicals can cause an increase in antibiotic resistance in other situations, so I think these results provide a good reason to take a closer look at what's going on in dust." The FDA's ruling, Hartmann noted, does not yet require that antimicrobials be removed from many other products such as paints, baby toys, bedding, and kitchen utensils. "We don't have solid proof that putting antimicrobials in these products makes them any healthier, but we do know that triclosan in the environment can be harmful," she said. The study, published online ahead of print in the journal Environmental Science & Technology, is the first to document the coexistence of the chemicals and genes in indoor dust. In all, the paper reports six significant associations. Levels of triclosan in dust were determined in collaboration with the Biodesign Center for Environmental Security at Arizona State University. Triclosan has been linked with a gene that alters the ribosome -- a complex of RNA and protein in cells that is responsible for RNA translation -- in a way that makes bacteria antibiotic resistant. The research team identified several antibiotic-resistance genes, the most common of which conferred resistance to tetracycline antibiotics. "While present at low abundances, together these genes cover resistance to a wide spectrum of antibiotics," the researchers wrote. The chemicals and genes came from 44 samples from 31 varied-use spaces, using vacuum-fitted collectors. The building, completed in 1921, has window ventilation as well as infiltration of outdoor air through cracks around doors and windows. DNA processing involved the UO Genomics Core Facility, and data were processed with assistance from the lab of co-author Curtis Huttenhower of Harvard University's School of Public Health. Despite the findings, Hartmann said, people don't need to be readily alarmed. Antibiotic-resistance genes in the environment, for example, are 10 to 100 times less abundant than in the human gut, she said. In infants, the genes occur naturally in the absence of antibiotics during initial microbial colonization. "Antibiotic resistance is common in a lot of different places," she said. "Just because we find it in a certain building doesn't mean that everyone who goes into that building is going to get a MRSA infection. The building is still as safe as it was before the study, but now we have a better idea of how many antibiotic-resistance genes there are, and we have reason to believe that the amount of antibiotic resistance genes may be tied to the amount of antimicrobial chemicals." Triclosan and antibiotic resistance have been found in other places and in the environment, Hartmann said, but finding them in indoor dust brings the threat loser to home. Median concentrations of triclosan found in the dust were much less than those found as the active ingredient in toothpaste, where it helps to reduce plaque and gum disease. The new FDA ban does not include toothpaste. "The World Health Organization has said that we're underestimating community-acquired antibiotic-resistant infections," she said. "We know that hospitals and other healthcare settings are burdened by antibiotic-resistant pathogens. Homes and other buildings also can contain antibiotic resistance genes and and the use of antimicrobial chemicals in these buildings may be a contributing factor."


One of the antimicrobials seen in the study is triclosan, a commonly used antibacterial ingredient in many personal care products. It is among antimicrobials that will be phased out within the next year from hand and bar soaps, according to a ruling Sept. 2 by the U.S. Food and Drug Administration. The findings of the new study reflect relationships in the dust, not that the antimicrobials are the reason for antibacterial genes being present. "We might be tempted to think of the antimicrobial chemicals as being guilty by association," said Erica M. Hartmann, a postdoctoral fellow at the UO's Biology and the Built Environment Center and Institute of Ecology and Evolution who led the study. She joined the faculty at Northwestern University this month. "We don't really know how the genes or the chemicals got there," she said. "They may have arrived by completely different routes and their being found together is a coincidence. However, we know that antimicrobial chemicals can cause an increase in antibiotic resistance in other situations, so I think these results provide a good reason to take a closer look at what's going on in dust." The FDA's ruling, Hartmann noted, does not yet require that antimicrobials be removed from many other products such as paints, baby toys, bedding, and kitchen utensils. "We don't have solid proof that putting antimicrobials in these products makes them any healthier, but we do know that triclosan in the environment can be harmful," she said. The study, published online ahead of print in the journal Environmental Science & Technology, is the first to document the coexistence of the chemicals and genes in indoor dust. In all, the paper reports six significant associations. Levels of triclosan in dust were determined in collaboration with the Biodesign Center for Environmental Security at Arizona State University. Triclosan has been linked with a gene that alters the ribosome—a complex of RNA and protein in cells that is responsible for RNA translation—in a way that makes bacteria antibiotic resistant. The research team identified several antibiotic-resistance genes, the most common of which conferred resistance to tetracycline antibiotics. "While present at low abundances, together these genes cover resistance to a wide spectrum of antibiotics," the researchers wrote. The chemicals and genes came from 44 samples from 31 varied-use spaces, using vacuum-fitted collectors. The building, completed in 1921, has window ventilation as well as infiltration of outdoor air through cracks around doors and windows. DNA processing involved the UO Genomics Core Facility, and data were processed with assistance from the lab of co-author Curtis Huttenhower of Harvard University's School of Public Health. Despite the findings, Hartmann said, people don't need to be readily alarmed. Antibiotic-resistance genes in the environment, for example, are 10 to 100 times less abundant than in the human gut, she said. In infants, the genes occur naturally in the absence of antibiotics during initial microbial colonization. "Antibiotic resistance is common in a lot of different places," she said. "Just because we find it in a certain building doesn't mean that everyone who goes into that building is going to get a MRSA infection. The building is still as safe as it was before the study, but now we have a better idea of how many antibiotic-resistance genes there are, and we have reason to believe that the amount of antibiotic resistance genes may be tied to the amount of antimicrobial chemicals." Triclosan and antibiotic resistance have been found in other places and in the environment, Hartmann said, but finding them in indoor dust brings the threat loser to home. Median concentrations of triclosan found in the dust were much less than those found as the active ingredient in toothpaste, where it helps to reduce plaque and gum disease. The new FDA ban does not include toothpaste. "The World Health Organization has said that we're underestimating community-acquired antibiotic-resistant infections," she said. "We know that hospitals and other healthcare settings are burdened by antibiotic-resistant pathogens. Homes and other buildings also can contain antibiotic resistance genes and and the use of antimicrobial chemicals in these buildings may be a contributing factor." More information: "Antimicrobial chemicals are associated with elevated antibiotic resistance genes in the indoor dust microbiome" Environmental Science & Technology, pubs.acs.org/doi/abs/10.1021/acs.est.6b00262


News Article | December 13, 2016
Site: www.eurekalert.org

TALLAHASSEE, Fla. -- Deep stores of carbon in northern peatlands may be safe from rising temperatures, according to a team of researchers from several U.S.-based institutions. And that is good news for now, the researchers said. Florida State University research scientist Rachel Wilson and University of Oregon graduate student Anya Hopple are the first authors on a new study published today in Nature Communications. The study details experiments suggesting that carbon stored in peat -- a highly organic material found in marsh or damp regions -- may not succumb to the Earth's warming as easily as scientists thought. That means if these northern peatlands -- found in the upper half of the northern hemisphere -- remain flooded, a substantial amount of carbon will not be released into the atmosphere. "We do see some breakdown of peat on the surface, but not below 2 feet deep, where the bulk of the carbon is stored," Wilson said. The study is part of a long-term look at how carbon stored in peat will respond to climate and environmental change. The team of researchers, led by Paul Hanson of the Oak Ridge National Laboratory, includes scientists from FSU, University of Oregon, Georgia Institute of Technology, the U.S. Department of Agriculture-Forest Service, Chapman University, Lawrence Livermore National Laboratory, Pacific Northwest National Laboratory and Oak Ridge National Laboratory. Researchers ran four different temperature simulations -- increasing the temperature of the peat by 2.25 degrees Celsius, 4.5 degrees Celsius, 6.25 degrees Celsius and 9 degrees Celsius -- to see how it would respond to increased heat. They found that the surface peat did emit more methane gas when warmed, but the deep peat did not break down and did not start emitting additional methane or carbon dioxide. "If the release of greenhouse gases is not enhanced by temperature of the deep peat, that's great news because that means that if all other things remain as they are, the deep peat carbon remains in the soil," said Joel Kostka, professor of microbiology at Georgia Institute of Technology. The Earth's soils contain 1,550 billion tons of organic carbon, and 500 billion tons of this carbon is stored in northern peatlands around the world. This quantity is roughly the same amount as carbon in the atmosphere. Scientists have been anxious to learn how these northern peatlands will respond to warming because a tremendous amount of carbon could be released into the atmosphere. Researchers worked at the Oak Ridge National Laboratory's experimental site known as SPRUCE in northern Minnesota to examine both surface peat and peat up to 6 feet deep. The majority of the carbon is stored deeper in the ground. Large environmental chambers were constructed by the Oak Ridge team to enclose portions of the peatlands. Within these chambers, scientists simulated climate change effects such as higher temperatures and elevated carbon dioxide levels. They also took some of the deep peat back to their labs to heat in additional studies. While scientists said they were surprised by the results, they also cautioned that this came only after one year of warming. "There are the necessary caveats that this was only for one year, and the experiment is planned to run for a decade, and other ecosystem feedbacks may become important in greenhouse gas emissions," said Scott Bridgham, director of the Institute of Ecology and Evolution at University of Oregon and Hopple's adviser. In the future, scientists also plan to look at how these peatlands respond to heightened carbon dioxide levels combined with the temperature increases. "In the future, we'll be warmer, but we'll also have more carbon dioxide in the atmosphere, so we need to understand how these deep stores of peat, which have all this carbon, respond to these conditions," said Jeff Chanton, professor of oceanography at Florida State University. This work was funded by the U.S. Department of Energy.


News Article | December 14, 2015
Site: phys.org

The fish, seawater-native threespine stickleback, in just decades experienced changes in both their genes and visible external traits such as eyes, shape, color, bone size and body armor when they adapted to survive in fresh water. The earthquake—9.2 on the Richter scale and second highest ever recorded—caused geological uplift that captured marine fish in newly formed freshwater ponds on islands in Prince William Sound and the Gulf of Alaska south of Anchorage. The findings—detailed in a paper available online in the Proceedings of the National Academy of Sciences—are important for understanding the impacts of sudden environmental change on organisms in nature, says UO biologist William Cresko, whose lab led the National Science Foundation-funded research. "We've now moved the timescale of the evolution of stickleback fish to decades, and it may even be sooner than that," said Cresko, who also is the UO's associate vice president for research and a member of the UO Institute of Ecology and Evolution. "In some of the populations that we studied we found evidence of changes in fewer than even 10 years. For the field, it indicates that evolutionary change can happen quickly, and this likely has been happening with other organisms as well." Survival in a new environment is not new for stickleback, a small silver-colored fish found throughout the Northern Hemisphere. A Cresko-led team, using a rapid genome-sequencing technology (RAD-seq) created at the UO with collaborator Eric Johnson, showed in 2010 how stickleback had evolved genetically to survive in fresh water after glaciers receded 13,000 years ago. For the new study, researchers asked how rapidly such adaptation could happen. The newly published research involved stickleback collected by University of Alaska researchers from freshwater ponds on hard-to-reach marine islands that were seismically thrust up several meters in the 1964 quake. RAD-seq technology again was used to study the new samples. Genetic changes were similar to those found in the earlier study, but they had occurred in less than 50 years in multiple, separate stickleback populations. Stickleback, the researchers concluded, have evolved as a species over the long haul with regions of their genomes alternatively honed for either freshwater or marine life. "This research perhaps opens a window on how climate change could affect all kinds of species," said Susan L. Bassham, a Cresko lab senior research associate who also was co-author of the 2010 paper. "What we've shown here is that organisms—even vertebrates, with long generation times—can respond very fast to environmental change. "And this is not just a plastic change, like becoming tan in the sun; the genome itself is being rapidly reshaped," she said. "Stickleback fish can adapt on this time scale because the species as a whole has evolved, over millions of years, a genetic bag of tricks for invading and surviving in new freshwater habitats. This hidden genetic diversity is always waiting for its chance, in the sea." Co-authors with Bassham and Cresko on the PNAS paper were Emily A. Lescak of UA-Anchorage and Fairbanks; Julian Catchen of the University of Illinois at Urbana-Champaign; and Ofer Gelmond, Frank A. von Hippel and Mary L. Sherbick of UA-Anchorage. NSF grants DEB0949053 and IOS102728 to Cresko and DEB 0919234 to von Hippel provided the primary funding for the project. National Institutes of Health grant 1R24GM079486-01A1 and the M. J. Murdock Charitable Trust also supported Cresko. The 2010 study appeared in the PLOS Genetics. Earlier this year the journal named the paper as among its Top 10 articles published in its first decade. The study also was detailed in a UO news release. Explore further: Fitness in a changing world: The genetics and adaptations of the Alaskan stickleback fish More information: Evolution of stickleback in 50 years on earthquake-uplifted islands, PNAS, www.pnas.org/cgi/doi/10.1073/pnas.1512020112


Knop E.,Institute of Ecology and Evolution | Reusser N.,Institute of Ecology and Evolution
Proceedings of the Royal Society B: Biological Sciences | Year: 2012

Invasive alien species might benefit from phenotypic plasticity by being able to (i) maintain fitness in stressful environments ('robust'), (ii) increase fitness in favourable environments ('opportunistic'), or (iii) combine both abilities ('robust and opportunistic'). Here, we applied this framework, for the first time, to an animal, the invasive slug, Arion lusitanicus, and tested (i) whether it has a more adaptive phenotypic plasticity compared with a congeneric native slug, Arion fuscus, and (ii) whether it is robust, opportunistic or both. During one year, we exposed specimens of both species to a range of temperatures along an altitudinal gradient (700-2400 m a.s.l.) and to high and low food levels, and we compared the responsiveness of two fitness traits: survival and egg production. During summer, the invasive species had a more adaptive phenotypic plasticity, and at high temperatures and low food levels, it survived better and produced more eggs than A. fuscus, representing the robust phenotype. During winter, A. lusitanicus displayed a less adaptive phenotype than A. fuscus. We show that the framework developed for plants is also very useful for a better mechanistic understanding of animal invasions. Warmer summers and milder winters might lead to an expansion of this invasive species to higher altitudes and enhance its spread in the lowlands, supporting the concern that global climate change will increase biological invasions. © 2012 The Royal Society.


Sanders D.,Institute of Ecology and Evolution | Sanders D.,University of Exeter | Sutter L.,Institute of Ecology and Evolution | van Veen F.J.F.,University of Exeter
Ecology Letters | Year: 2013

Species extinctions are biased towards higher trophic levels, and primary extinctions are often followed by unexpected secondary extinctions. Currently, predictions on the vulnerability of ecological communities to extinction cascades are based on models that focus on bottom-up effects, which cannot capture the effects of extinctions at higher trophic levels. We show, in experimental insect communities, that harvesting of single carnivorous parasitoid species led to a significant increase in extinction rate of other parasitoid species, separated by four trophic links. Harvesting resulted in the release of prey from top-down control, leading to increased interspecific competition at the herbivore trophic level. This resulted in increased extinction rates of non-harvested parasitoid species when their host had become rare relative to other herbivores. The results demonstrate a mechanism for horizontal extinction cascades, and illustrate that altering the relationship between a predator and its prey can cause wide-ranging ripple effects through ecosystems, including unexpected extinctions. © 2013 Blackwell Publishing Ltd/CNRS.


News Article | December 22, 2016
Site: phys.org

Comparing the genome with other vertebrate organisms may help scientists learn about basic aspects of human biology, such as how skulls develop and change shape and how the genome that people mostly share with other vertebrates can be tweaked to create new structures, said Susan Bassham, a senior research associate in the lab of UO biologist William Cresko where the research was done. While such research connected to human features is an added benefit, a more immediate payoff is that the methods used during the project are laid out so that other small labs can use them as a reference for creating genomes of organisms they are interested in studying. A paper detailing the genome was published Dec. 20 by the journal Genome Biology. The gulf pipefish—abundant in seagrass beds of the Gulf of Mexico—has the species name of Syngnathus scovelli. It belongs to the family known as Syngnathidae, which dates back at least 50 million years. "This group of species has novelties that are not well understood from an evolutionary genetic standpoint," said Clay Small, one of the paper's lead authors and a postdoctoral fellow in Cresko's lab in the Institute of Ecology and Evolution. "The family Syngnathidae is a very good model clade for studying these derived structural features because they are so weird looking in terms of their unique body plans. Ultimately, we are interested in identifying genetic changes that are related to the evolution of these novel features in this whole family." Species in the Syngnathid family have long snouts, which help their suction-like feeding behavior. They have bony body armor. They lack pelvic fins, ribs and teeth and have evolved unique placenta-like structures in males for the brooding of developing offspring. The publication of the gulf pipefish genome came less than a week after the genome of another family member, the tiger tail seahorse, was announced in the journal Nature. "Having this pair of papers published almost simultaneously moved genomic analyses of this remarkable group of fish ahead tremendously," said Cresko, a professor of biology. The two genomes show that losses and changes in specific genes or gene functions may be responsible for evolutionary innovations, Small said. Through evolution, the pipefish and seahorse genomes have lost genetic elements compared to distant fish ancestors. These likely explain some changes in body alignment and the loss of pelvic fins, which correspond to legs in the human vertebrate lineage, he said. A big part of Small's efforts focused on the ability of male pipefish to gestate embryos in their brood pouch. The gulf pipefish, Bassham said, provides an example of one of the most elaborated placental structures found in the males of various pipefish species. Some 1,000 genes are expressed differently in the pouch during a male's pregnancy to control developmental processes, nutrient exchange, stability and immunity, the researchers reported. In a comparative analysis between pregnant and non-pregnant male pipefish, Small found a family of genes that behaved unusually. This gene family, patristacins, contains some members that turn on during pregnancy, and others that are suppressed during pregnancy. The group of genes is likely unique to syngnathid fishes, and they behave similarly in seahorses. The UO-led team also found that gulf pipefish have two chromosomes fewer than most ray-finned fish. "By looking at the patterns of where genes lie in the genome, it's very likely this difference resulted simply from the fusion of four of the ancestral chromosomes into two," Bassham said. "Most fish have 24 chromosomes, but the gulf pipefish has 22." The researchers used a genome-sequencer in the UO's Genomics Core Facility, along with a genetics technology developed at the UO called restriction-site associated DNA markers, now known as RAD-sequencing. It allows researchers to sort data and then organize it all back together into a detailed genetic map. The team also used three software packages developed by co-author Julian Catchen, a former UO postdoctoral researcher now at the University of Illinois at Urbana-Champaign. The software was designed to complement RAD-sequencing and genome assembly data. Using fish genomes, Bassham said, should allow research groups to ask a lot of different biological questions. "Fish are vertebrates. We are vertebrates," she said. "We share large swaths of our biology with these fish. We'd like to understand how evolution occurs, and some of the most exciting aspects of evolution happen when novel features appear in an evolutionary lineage. "Novelties can happen multiple ways," Bassham said. "Sometimes it involves a loss of a structure that creates a new way of life. In other cases, it might be an evolution of a new body part that wasn't there before. Where did that tissue come from? How did it come into being? What was modified to make it? Or what developmental gene pathways were changed to allow for it?" Explore further: Researchers sequence entire genome of seahorse, investigate essential mechanisms of evolution More information: C. M. Small et al, The genome of the Gulf pipefish enables understanding of evolutionary innovations, Genome Biology (2016). DOI: 10.1186/s13059-016-1126-6 Qiang Lin et al. The seahorse genome and the evolution of its specialized morphology, Nature (2016). DOI: 10.1038/nature20595

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