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New CU-Boulder study clarifies diversity, distribution of cutthroat trout in Colorado
Sep 24th
Will the real greenback cutthroat trout please stand up?
A novel genetic study led by the University of Colorado Boulder has helped to clarify the native diversity and distribution of cutthroat trout in Colorado, including the past and present haunts of the federally endangered greenback cutthroat trout.
The study, led by CU-Boulder postdoctoral researcher Jessica Metcalf, was based largely on DNA samples taken from cutthroat trout specimens preserved in ethanol in several U.S. museums around the country that were collected from around the state as far back as 150 years ago. The new study, in which Metcalf and her colleagues extracted mitochondrial DNA from fish to sequence genes of the individual specimens and compared them with modern-day cutthroat trout strains, produced some startling results.
The biggest surprise, said Metcalf, was that the cutthroat trout native to the South Platte River drainage appears to survive today only in a single population outside of its native range — in a small stream known as Bear Creek that actually is in the nearby Arkansas River drainage. The strain from Bear Creek is thought to have been collected from the South Platte River drainage in the 1880s by an early hotelier who stocked the fish in a pond at the Bear Creek headwaters to help promote an early tourist route up Pikes Peak.
“We thought one way to get to the question of which cutthroat trout strains are native to particular drainages was to go back to historical samples and use their DNA as a baseline of information,” said Metcalf of the chemistry and biochemistry department and a former postdoctoral researcher at the Australian Centre for Ancient DNA. “Our study indicates the descendants of the fish that were stocked into Bear Creek in the late 1800s are the last remaining representatives of the federally protected greenback cutthroat trout.”
A second, key set of data was all of the Colorado cutthroat trout stocking records over the past 150 years, a task spearheaded by study co-author and fish biologist Chris Kennedy of the U.S. Fish and Wildlife Service. Between 1889 and 1925, for example, the study showed that more than 50 million cutthroat trout from the Gunnison and Yampa river basins were stocked in tributaries of all major drainages in the state, jumbling the picture of native cutthroat strains in Colorado through time and space.
Originating from the Pacific Ocean, cutthroat trout are considered one of the most diverse fish species in North America and evolved into 14 recognized subspecies in western U.S. drainages over thousands of years. In Colorado, four lineages of cutthroats were previously identified: the greenback cutthroat, the Colorado River cutthroat, the Rio Grande cutthroat and the extinct yellowfin cutthroat.
The museum specimens used in the study came from the California Academy of Sciences, the Smithsonian Museum of Natural History in Washington, D.C., the Academy of Natural Sciences in Philadelphia and the Harvard University Museum of Comparative Zoology. Colorado cutthroat trout specimens were collected by a number of early naturalists, including Swiss scientist and former Harvard Professor Louis Agassiz and internationally known fish expert and founding Stanford University President David Starr Jordan.
The new study, published online today in Molecular Ecology, follows up on a 2007 study by Metcalf and her team that indicated there were several places on the Front Range where cutthroat populations thought to be greenbacks by fish biologists were actually a strain of cutthroats transplanted from Colorado’s Western Slope in the early 1900s.
CU graduate researcher, Sierra Stowell (pictured here as a teenager) was a co-author of the study. She spends a lot of time in or near the water where cutthroat trout live.
Other co-authors on the new study included CU-Boulder Professor Andrew Martin and CU-Boulder graduate students Sierra Stowell, Daniel McDonald and Kyle Keepers; Colorado Parks and Wildlife biologist Kevin Rogers; University of Adelaide scientists Alan Cooper and Jeremy Austin; and Janet Epp of Pisces Molecular LLC of Boulder.
“With the insight afforded by the historical data, we now know with a great deal of certainty what cutthroat trout strains were here in Colorado before greenbacks declined in the early 20th century,” said Martin of CU’s ecology and evolutionary biology department. “And we finally know what a greenback cutthroat trout really is.”
Metcalf and her colleagues first collected multiple samples of tissue and bone from each of the ethanol-pickled trout specimens, obtaining fragments of DNA that were amplified and then pieced together like a high-tech jigsaw puzzle to reveal two genes of the individual specimens. The tests were conducted on two different continents under highly sterile conditions and each DNA sequencing effort was repeated several times for many specimens to ensure accuracy in the study, Metcalf said.
Roughly half of the study was conducted at CU-Boulder and half at the Australian Center for Ancient DNA at the University of Adelaide, where Metcalf had worked for two years. “By conducting repeatable research at two very different, state-of-the-art laboratories, we were able to show the Bear Creek trout was the same strain as the cutthroats originally occupying the South Platte River drainage.”
The Bear Creek trout strain is now being propagated in the Colorado Parks and Wildlife hatchery system and at the USFWS Leadville National Fish Hatchery.
In addition to identifying the Bear Creek cutthroat trout, Metcalf and her colleagues discovered a previously unknown cutthroat strain native to the San Juan Basin in southwestern Colorado that has since gone extinct. The study also confirmed that the yellowfin cutthroat, a subspecies from the Arkansas River headwaters that grew to prodigious size in Twin Lakes near Leadville, also had gone extinct.
Fortunately, most fish preserved by naturalists before 1900 were “fixed” in ethanol, which makes it easier for researchers to obtain reliable DNA than from fish preserved in a formaldehyde solution, a practice that later became popular. Prior to the new study — which included DNA from specimens up to about 150 years old — scientists working in ancient DNA labs had only performed similar research on ethanol-preserved museum vertebrate specimens less than 100 years old.
“One of the exciting things to come from this research project is that it opens up the potential for scientists to sequence the genes of other fish, reptiles and amphibian specimens preserved in ethanol further back in time than ever before to answer ecological questions about past diversity and distribution,” said Metcalf, who conducts her research at CU’s BioFrontiers Institute.
Funding for the study was provided by agencies of the Greenback Cutthroat Trout Recovery Team, including the USFWS, the U.S. Forest Service, the Bureau of Land Management, the National Park Service and Trout Unlimited.
“I think in many cases success depends less on the application of a new technology and more on the convergence of people with shared interest and complementary skills necessary for solving difficult problems,” said Martin. “Our greenback story is really one about what can be discovered when dedicated and talented people collaborate with a shared purpose.”
“We’ve known for some time that the trout in Bear Creek were unique,” said Doug Krieger, senior aquatic biologist for Colorado Parks and Wildlife and the Greenback Cutthroat Trout Recovery Team leader. “But we didn’t realize they were the only surviving greenback population.”
The decline of native cutthroats in Colorado occurred because of a combination of pollution, overfishing and stocking of native and non-native species of trout, said Metcalf. “It’s ironic that stocking nearly drove the greenback cutthroat trout to extinction, and a particularly early stocking event actually saved it from extinction,” she said.
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CU study: Global warming increasing heavy metals in streams
Sep 7th
Increase in metal concentrations
in Rocky Mountain watershed
tied to warming temperatures
in Rocky Mountain watershed
tied to warming temperatures
Warmer air temperatures since the 1980s may explain significant increases in zinc and other metal concentrations of ecological concern in a Rocky Mountain watershed, reports a new study led by the U.S. Geological Survey and the University of Colorado Boulder.
Rising concentrations of zinc and other metals in the upper Snake River just west of the Continental Divide near Keystone, Colo., may be the result of falling water tables, melting permafrost and accelerating mineral weathering rates, all driven by warmer air temperatures in the watershed. Researchers 
observed a fourfold increase in dissolved zinc over the last 30 years during the month of September.
Increases in metals were seen in other months as well, with lesser increases seen during the high-flow snowmelt period. During the study period, local mean annual and mean summer air temperatures increased at a rate of 0.5 to 2.2 degrees Fahrenheit per decade.
Generally, high concentrations of dissolved metals in the Snake River watershed are primarily the result of acid rock drainage, or ARD, formed by natural weathering of pyrite and other metal-rich sulfide minerals in the bedrock. Weathering of pyrite forms sulfuric acid through a series of chemical reactions, and pulls metals like zinc from minerals in the rock and carries these metals into streams.
Increased sulfate and calcium concentrations observed over the study period lend weight to the hypothesis that the increased zinc concentrations are due to acceleration of pyrite weathering. The potential for comparable increases in metals in similar Western watersheds is a concern because of impacts on water resources, fisheries and stream ecosystems. Trout populations in the lower Snake River, for example, appear to be limited by the metal concentrations in the water, said USGS research biologist Andrew Todd, lead researcher on the project.
“Acid rock drainage is a significant water quality problem facing much of the Western United States,” Todd said. “It is now clear that we need to better understand the relationship between climate and ARD as we consider the management of these watersheds moving forward.”
Warmer temperatures and earlier snowmelt runoff have been observed throughout mountainous areas of the western United States where ARD is common, but it is not known if these changes have triggered rising acidity and metal concentrations in other “mineralized” watersheds because of lack of comparable monitoring data, according to the research team.
CU-Boulder Professor Diane McKnight, a collaborator on the project, has generated much of the upper Snake River data through research projects conducted with her students since the mid-1990s. McKnight said students in her environmental engineering and environmental studies class like Caitlin Crouch — a study co-author who received her master’s degree under McKnight — are highly motivated to understand ARD problems.
“Student can see that their research will have direct applications to addressing a critical issue for Colorado,” said McKnight, professor in the civil, environmental and architectural engineering department and a fellow in CU’s Institute of Arctic and Alpine Research.
In cases where ARD is linked directly with past and present mining activities it is called acid mine drainage, or AMD. Another Snake River tributary, Peru Creek, is largely devoid of life due to AMD generated from the abandoned Pennsylvania Mine and smaller mines upstream and has become a target for potential remediation efforts.
The Colorado Division of Reclamation Mining and Safety, in conjunction with other local, state and federal partners, is conducting underground exploration work at the mine to investigate the sources of heavy metals-laden water draining from the mine entrance. The new study by Todd and colleagues has important implications in such mine cleanup efforts because it suggests that establishing attainable cleanup objectives could be difficult if natural background metal concentrations are a “moving target.”
A study on the subject was published in the journal Environmental Science and Technology. Other collaborators include Andrew Manning and Philip Verplanck of USGS. The data analyzed for the study came from INSTAAR, the USGS and the U.S. Environmental Protection Agency.
Wrap your mind around this! photo origami CU Boulder
Aug 27th
CU-Boulder ‘photo origami’ proposal
wins $2 million NSF grant
wins $2 million NSF grant
The art of origami has inspired children and artists all over the world because of the amazing objects that can be created by folding a simple piece of paper.
Now an engineering research team at the University of Colorado Boulder has won a $2 million grant from the National Science Foundation to develop a light-controlled approach for “self-assembly” mechanisms in advanced devices based on the same principles.
Known as “photo origami,” the idea is supported by NSF’s Emerging Frontiers in Research and Innovation program, which supports interdisciplinary teams working on rapidly advancing frontiers of fundamental engineering research.
CU-Boulder associate professor of mechanical engineering Jerry Qi will lead the team developing the photo origami technique. Collaborators will include CU faculty Robert McLeod of electrical engineering, Kurt Maute of aerospace engineering sciences and Elisabeth “Beth” Stade of mathematics, along with Patrick Mather of Syracuse University.
The ability to transform a flat polymer sheet into a sophisticated, mechanically robust 3-D structure will enable new approaches to manufacturing and design of devices from the microscopic to centimeter scales, according to the team. Examples include using extremely low-weight, high-strength materials to create micro-electromechanical systems with complicated 3-D architectures that can be used for microscopic sensors such as antennas or microphones, and miniature robotic devices for environmental monitoring.
Present barriers to the development of folding and unfolding mechanisms stem from the lack of understanding of scaling laws that allow researchers to generalize results obtained at various size scales, the inability to easily cause matter to “reorient” itself to achieve the desired folding patterns, and challenges in automated, sequential folding.
To overcome these challenges, the CU team will make use of recent fundamental advances in the control of polymer architecture through light-triggered chemical reactions.
“One has to accurately control how much deformation a material should have in order to obtain a precise folding angle and to determine where to fold or stop folding in order to avoid interference in the folding path and form the desired structure,” said McLeod, who will use the interaction of light with material deformation to develop optical waveguide transistors.
In this new form of logic circuit, light triggers the deformation of a soft polymer, which in turn switches the light on or off. In this way, the optical waveguide transistor will enable a structure to be pre-programmed with a folding pattern through a sequential set of switching events controlled by the shape of an origami sheet.
In recent years, CU researchers and their collaborators have made significant progress in using light to control and alter the structure of a polymer. They are able to both bend and stiffen polymer structures and to develop new, soft, shape-memory composite materials through photo-initiation techniques. Shape-memory composites are “smart” materials that have the ability to return from a temporary, deformed shape to their original shape when induced by a trigger.
In addition, the team will work with the local school district to provide research and educational opportunities for K-12 students and teachers.
