Comprehensive Sturgeon Research Project Blog - 2022
The USGS Comprehensive Sturgeon Research Project is a multi-year, interdisciplinary research study to determine factors leading to spawning and survival of the endangered pallid sturgeon and the closely related shovelnose sturgeon.
Thousands of New Genetic Markers Resolve Differences Between Sturgeons
By: Kimberly Chojnacki, Killian Kelly, Parker Golliglee, and Aaron DeLonay
December 12, 2022
Researchers from U.S. Geological Survey, Columbia Environmental Research Center — in collaboration with Southern Illinois University Carbondale, Texas A&M University Corpus Christi, and the U.S. Fish and Wildlife Service — recently published the scientific article, “Haploid gynogens facilitate disomic marker development in paleotetraploid sturgeons” in the journal, Molecular Ecology Resources. Sturgeons and paddlefish are polyploids, which means that understanding their genetics is particularly challenging. In this study, principally authored by Dr. Richard Flamio Jr. at the Department of Zoology, Southern Illinois University Carbondale, the team of researchers developed 11,082 new genetic markers for the endangered pallid sturgeon. Dr. Flamio and the team of researchers successfully overcame complications of the complex genetic structure and developed new markers using a novel technique involving genetically altered shovelnose sturgeon with DNA contributed from only the maternal parent (see previous blog, New Foundation for Genetic Identification of Scaphirhynchus Sturgeon). The expanded set of new genetic markers demonstrates differences between pallid sturgeon and the closely related shovelnose sturgeon with far greater resolution than previous methods.
Prior to this study, genetic markers at only 19 locations were used to differentiate between the two species and their hybrids. These few markers lacked the ability to separate multiple generations of hybrids from the parental species. The inability to detect multi-generational hybrids poses a risk to pallid sturgeon conservation efforts that rely on capturing pure pallid sturgeon from the Missouri River and breeding them in hatcheries to restore populations. Breeding and releasing possible hybrid pallid sturgeon would erode the genetic integrity of the species and jeopardize recovery efforts. This newly expanded set of thousands of genetic markers will help protect the integrity of restoration stocking efforts and provide the toolset necessary to examine large numbers of pallid sturgeon throughout their range to determine the extent and trajectory of hybridization.
Larval Pallid Sturgeon and Shovelnose Sturgeon Diets Overlap, But Are Different
By: Patrick Braaten and Killian Kelly
November 1, 2022
Researchers from the US Geological Survey, Fort Peck Project Office and Columbia Environmental Research Center (CERC), Southern Illinois University (Carbondale), and Montana Fish, Wildlife, and Parks recently published the scientific article, “Diet composition and overlap of larval pallid sturgeon and shovelnose sturgeon from the upper Missouri River, USA” in the journal, Endangered Species Research. Information on the feeding ecology of larval pallid sturgeon (Scaphirhynchus albus) in their native rivers is limited because wild-produced larvae are rarely collected.
In this study authored by Colt Holley and others, researchers identified stomach contents from 75 larval pallid sturgeon (Scaphirhynchus albus) and 148 shovelnose sturgeon (Scaphirhynchus platorynchus) collected in the Upper Missouri River upstream and downstream from the Yellowstone River confluence. The larval pallid sturgeon collected in the study originated from free embryos that were released far upstream (see previous blog Unprecedented Pallid Sturgeon Larval Drift Experiment), dispersed, then settled as feeding larvae prior to trawl capture (see previous blog A Nine Week Search for Baby Pallid Sturgeon). The larval shovelnose sturgeon originated from natural spawning events. Food items from sturgeon stomachs were identified to order, family, and genus. Diet similarity was compared between the two sturgeon species at each level of taxonomic identification. Both species consumed mostly Diptera larvae, and diet similarity was high between the two sturgeon species at the order level of taxonomic identification. Diet similarity diminished when analyzed at the genus level of taxonomic identification. In total, pallid sturgeon consumed 11 unique taxa of aquatic macroinvertebrates, whereas shovelnose sturgeon consumed 6 unique taxa. Lack of specific information on larval pallid sturgeon diets in riverine environments has often resulted in the use of the more common shovelnose sturgeon as a surrogate in the development of models and evaluation of management actions. These results indicate that caution should be taken when considering larval and young-of-year shovelnose sturgeon as a feeding surrogate for young pallid sturgeon in the Upper Missouri River Basin.
Remote Sensing Advances Study of Sturgeon Habitat
By: Brandon Sansom and Robert Jacobson
October 18, 2022
Researchers from the U.S. Geological Survey, Columbia Environmental Research Center, in collaboration with scientists at the Geomorphology and Sediment Transport Laboratory (GSTL)—Integrated Modeling and Prediction Division, U.S. Geological Survey in Golden, Colorado, recently published analyses of innovative methods to measure dispersion patterns of dye tracers in large, turbid rivers using remote sensing.
The scientific journal article, “Remote Sensing of Visible Dye Concentrations During a Tracer Experiment on a Large, Turbid River” authored by Carl Legleiter, Brandon Samson and Robert Jacobson was published in the journal, Water Resources Research. The journal article examines data collected from the large dye tracer study conducted in the Lower Missouri River, near Huntsdale, Missouri in 2021 (see previous blog, Missouri River Dye Trace Experiment at Searcy’s Bend, Missouri). The study demonstrates that visible, dye tracers released into large, turbid rivers can be accurately measured using remote sensors from watercraft, fixed-winged aircraft, and sUAS (small unoccupied aircraft systems). For example, applying an optimal band ratio analysis (OBRA) algorithm revealed strong correlations between a spectrally based quantity and in-situ concentration measurements. OBRA also performed well for broadband images extracted from the sUAS-based videos, allowing for dye concentration maps and animations to capture the movement of the dye pulse. Previously these studies were limited to relatively clear rivers and relied on point measurements of dye tracers taken from watercraft, or recorded from a few stationary devices, called fluorometers, anchored at strategic locations in the river. This approach provides new opportunities to understand interception and retention processes for early life-stage pallid sturgeon transitioning from drifting free embryos to feeding larval sturgeon that settle on the river bottom. Dye tracer studies, combined with directed sampling approaches (see previous blog post, Areas of Enhanced Catch), are important emerging approaches to identify, assess, and model habitats that support interception, retention, and survival of early life-stage pallid sturgeon in the Missouri River and its tributaries.
USGS Researchers Describe Early Sturgeon Development
By: Kimberly Chojnacki, Killian Kelly, and Aaron DeLonay
October 12, 2022
Researchers from the U.S. Geological Survey, Columbia Environmental Research Center (CERC) recently published the scientific article, “Ontogenetic development of pallid sturgeon (Scaphirhynchus albus) and shovelnose sturgeon (Scaphirhynchus platorynchus) from hatch through yolk absorption” in the journal, Ecology of Freshwater Fish. Sturgeons undergo a rapid sequence of changes during the free-embryo period beginning at hatch and extending through yolk plug expulsion and the initiation of exogenous feeding. This series of developmental changes has been described for other sturgeon species, but not for the sturgeons from the genus Scaphirhynchus. In this study authored by Kimberly Chojnacki and others, CSRP researchers identified changes that occur during discrete stages of development in both pallid sturgeon (Scaphirhynchus albus) and shovelnose sturgeon (Scaphirhynchus platorynchus) and compared them to other sturgeon species. While Scaphirhynchus sturgeons developed similarly to other sturgeon species, there were notable differences. Between species, both pallid sturgeon and shovelnose sturgeon exhibited similar rates of growth and development at the same temperature. Description of the sequence of developmental stages of Scaphirhynchus free embryos and the timing of transitions from one stage to the next provides a crucial template for incorporating behavior into studies of downstream dispersal and interception and retention into supportive habitats for feeding. Understanding the relationship between growth and development may provide improved estimates of the age of free embryos collected in the river and assist in calculating the timing and location of upstream spawning events.
USGS Hosts “High Resolution Rivers” Workshop
By: Caroline Elliott and Robert Jacobson
September 23, 2022
Scientists from the U.S. Geological Survey, Columbia Environmental Research Center (CERC) hosted a workshop for hydrologists and geomorphologists who study detailed features and processes of rivers and other shallow, freshwater habitats. The 5th Biennial High Resolution Rivers Workshop drew 35 participants, including researchers from academia and government institutions, private consultants, industry representatives, and non-governmental organizations. The three-day workshop included two days of presentations and discussions, and a day of demonstrations on the Missouri River. Scientists shared information and experience in cutting-edge applications of technologies such as multibeam sonars, laser imaging, photogrammetry, acoustic Doppler current profiling, sediment transport, and substrate classification. The River Studies Branch at CERC has long been among the leaders in the application of technologies to survey shallow water rivers and characterize the dynamic nature of these habitats. The Comprehensive Sturgeon Research Project relies heavily on these technologies to understand the habitat requirements of the endangered pallid sturgeon and to assess their response to changes in the river around them (See previous blog post, Equipment Testing 1, 2, Spring!).
Growth and Survival Rates of Free Embryos Revealed
By Patrick Braaten and Aaron DeLonay
September 5, 2022
Researchers from the U.S. Geological Survey, Columbia Environmental Research Center recently published the results of a study conducted in collaboration with scientists at the U.S. Fish and Wildlife Service, Southern Illinois University Carbondale, and Montana Fish, Wildlife, and Parks. The scientific journal article, “Growth and survival rates of dispersing free embryos and settled larvae of pallid sturgeon (Scaphirhynchus albus) in the Missouri River, Montana and North Dakota”, authored by Patrick Braaten and others was published in the journal Environmental Biology of Fishes. The article presents findings from the large-scale free-embryo release experiment conducted in the Upper Missouri River below Fort Peck Dam in 2019. Nearly 1 million 1-day post-hatch and 5-day post-hatch pallid sturgeon were released into the river and studied as they dispersed downstream (see previous blog, Unprecedented Pallid Sturgeon Larval Drift Experiment). This study is the first to report daily growth and survival rates of pallid sturgeon free embryos as they dispersed downstream prior to settling in supportive benthic habitats. Results indicated that free embryos grew at a rate of about 0.75 mm per day at 16.8 °C, and survival rates tended to be higher for the older than younger released free embryos. About 4% of dispersing free embryos may survive to initiate feeding as benthic larvae at the end of downstream dispersal. Accurate estimates of growth and survival rates of the earliest life stages of pallid sturgeon are critical to develop population models to predict population responses to river management actions.
Ecoflume Arrives at CERC
By Brandon Sansom, Ty Helmuth, Kim Chojnacki, and Robert Jacobson
August 22, 2022
The Ecoflume has arrived! During the week of August 15th, engineers from the University of Minnesota, Saint Anthony Falls Laboratory (SAFL) installed the Ecoflume at the U.S. Geological Survey – Columbia Environmental Research Center (see previous blog, Ecoflume Construction and Testing Nears Completion). The delivery of the flume occurred in two shipments: large flume sections were delivered on a flat-bed trailer while the propulsion systems (jet pumps and paddlewheels) and remaining components were delivered in a second enclosed trailer.
Engineers from SAFL and staff from CERC spent the week unloading and installing the flume in the designated flume laboratory. One turning end and the two straight flume sections were moved into place first, followed by the paddlewheel stands, and finally the second turning end. All four flume sections were placed on blocking, bolted and glued together, and carefully lowered onto rubber skirtboard that was used to level the flume.
The remaining components (jet pumps, sump tanks, plumbing and electrical supplies) were then moved into place and staged for the next round of installment. SAFL engineers will return in late September 2022 for a second phase of installation that will include plumbing and electrical connections as well as installation and testing of the paddlewheel propulsion system. SAFL engineers will return for a third visit in winter 2022 to finalize the installation of the jet arrays, complete testing, and train CERC scientists on flume controls and operation.
Potential Wooden Shipwreck Discovered in Missouri River
By Caroline Elliott and Tyrell Helmuth
August 4, 2022
Columbia Environmental Research Center (CERC) scientists and United States Army Corps of Engineers (USACE) biologists collaborated this summer to research Areas of Enhanced Catch (AECs) as part of the ongoing Comprehensive Sturgeon Research Project (CSRP) (see previous blog post, Areas of Enhanced Catch. While conducting a sidescan sonar survey for this study, CERC scientists found a possible wooden shipwreck between Boonville, MO and Rocheport, MO.
This find has been reported to the USACE archeologist in the Kansas City District office as well as the State Historical Preservation Office in Jefferson City, MO. As can be seen in the Chittenden (1897) map above, several shipwrecks were historically thought to be located between Boonville and Rocheport, MO.
Areas of Enhanced Catch
By Caroline Elliott and Tyrell Helmuth
August 4, 2022
The Interception of drifting larval pallid sturgeon (Scaphirhynchus albus) into off-channel habitats from the main channel of the Missouri River is hypothesized to be important for recruitment and survival of this endangered fish. Scientists from the Columbia Environmental Research Center (CERC) spent the month of June mapping sections of the Missouri River to better understand why biologists catch more larval sturgeon in some areas than others. As part of the Comprehensive Surgeon Research Project, scientists from CERC coordinated with biologists from the U.S. Army Corps of Engineers (USACE) to provide habitat data to match the biological data collected from larval trawling behind wing-dikes.
In years past, effort was made to repeatedly map and characterize “hotspots”, now known as Areas of Enhanced Catch (AEC). These AECs are areas of the Missouri River where biologists consistently catch high numbers of larval sturgeon, often just downstream of wing-dikes (See previous blog post, Using “Hotspots” to Guide Habitat Assessments). With the lessons learned from datasets collected on the Missouri River over the past few years, scientists are now trying to determine what the physical and hydraulic characteristics may be that create an AEC.
This year, a statistical model was developed based on dike and channel characteristics hypothesized to influence interception. Larval catch was predicted based on past data for 788 wing dikes between the Kansas River and Osage River on the Missouri River. A random selection of 58 dikes within 5 miles of eight boat ramps was chosen for sampling and habitat measurements.
The day following larval sampling, CERC scientists surveyed each wing-dike with single beam sonar, an acoustic Doppler current profiler (ADCP), and sidescan sonar. An ADCP was utilized to measure water velocity along transects both parallel and perpendicular to the USACE trawl lines. Single beam sonar was operated at the same time as the ADCP, collecting depth data and giving an indication of the bedforms present in the trawl location. Finally, sidescan sonar was operated to further document bedforms thought to indicate habitat quality.
Left: Sidescan sonar image collected parallel to the USACE trawl lines. The end of the wing-dike can be seen on the left side of this image.
The data collected by the USACE biologists and CERC scientists will be compiled in the coming months and compared to the predicted score for each site surveyed. This data will help to refine the framework for predicting the presence of AECs and will help to identify the physical and hydraulic characteristics that create an AEC, furthering the understanding of downstream larval sturgeon dispersal on the Missouri River and contributing to restoration designs.
Ecoflume Construction and Testing Nears Completion
By Brandon Sansom, Kim Chojnacki, and Robert Jacobson
Date: July 28, 2022
Since 2019, scientists and engineers at University of Minnesota, Saint Anthony Falls Laboratory (SAFL) have been designing and constructing a continuous-loop, racetrack Ecoflume (see previous blog post, Ecoflume Design Takes Shape) for the Comprehensive Sturgeon Research Project (CSRP) led by scientists at the U.S. Geological Survey – Columbia Environmental Research Center (CERC). As the construction and assembly of the new EcoFlume is nearing completion, researchers from CERC made a trip to Minneapolis for a final review before it is delivered. The EcoFlume was designed primarily to study the early life-stages of the endangered pallid sturgeon (Scaphirhynchus albus) but will also be used for biomechanical studies of other sturgeon species, invasive carps, and native mussels. The EcoFlume will be housed in a new 1,350 square-foot laboratory at CERC and be used to study transport phenomena in river environments. The new flume has an overall length of 11.4 meters and width of 4.3 meters, with depths up to 1.0 meter and a total capacity of 34 cubic meters (~9,000 gallons). Each straight ‘test’ section is 7 meters long and 1.5 meters wide. Two propulsion systems will be used to move water within the flume, depending on experimental needs. A novel paddlewheel system specifically developed by SAFL to be safe for sturgeon free embryos will move the water up to 0.5 meters per second. A pump system with jet arrays will be used to move water up to 1.0 meter per second for other studies with later life stages having greater swimming capacity. Internal heat exchangers were fabricated into the turning vanes in each end of the flume in order to precisely maintain water temperatures during experiments. The Ecoflume will also be equipped with state-of-the-art instrumentation, such as digital imaging systems, acoustic Doppler velocimeters, and particle imaging velocimetry, to study the response of aquatic species under controlled fluvial conditions. Installation of the Ecoflume at CERC is expected to be completed in August of 2022, with initial demonstration experiments taking place through the fall of 2022.
Research Ecologist Joins Sturgeon Research Project
By: Aaron DeLonay
May 24, 2022
The USGS Comprehensive Sturgeon Research Project (CSRP) recently added a new research scientist to the team. Dr. Mike Colvin joined the River Studies Branch at the Columbia Environmental Research Center in May 2022. Mike is a Research Ecologist with extensive experience in fisheries science, fisheries management, and natural resources decision making.
His academic background includes a master’s degree in Fisheries Biology from the University of Idaho and a doctorate degree in Fisheries Resources from Iowa State University. Dr. Colvin also pursued research at Oregon State University as a postdoctoral scholar. Most recently, Mike was an Associate Professor in the Department of Wildlife, Fisheries, and Aquaculture at Mississippi State University where his research applied decision analyses to natural resource monitoring and management. In addition to teaching and research at Mississippi State, he provided expert support to the U.S. Army Corps of Engineers, Missouri River Recovery Program—Pallid Sturgeon Population Assessment Program and the Science and Adaptive Management Program. Within the CSRP, Mike’s focus will be on supporting science components and decision analysis for the endangered pallid sturgeon. He will also apply his expertise in structured decision-making and adaptive management in a broader research program to control invasive carps, the status assessment of southeastern aquatic species, and natural resource management issues throughout the United States.
Selected Recent Publications:
Norris, D.M., M.E. Colvin, L.E. Miranda, and M.A. Lashley. 2022. Supplemental habitat is reservoir dependent: Identifying optimal planting decision using Bayesian Decision Networks. Journal of Environmental Management: v. 304: Article 114139.
Schumann, D.A., Colvin, M.E., Campbell, R.L., Wagner, M.D., and Schwarz, D.E., 2021, Suitability of passive integrated transponder tags and a new monitoring technique for at-risk madtoms (Noturus spp.): Endangered Species Research, v. 44, p. 1-10.
Richardson, B.M., Griffin, M.J., Colvin, M.E., Wise, D.J., Ware, C., Mischke, C.C., Greenway, T.E., Byars, T.S., Hanson, L.A., and Lawrence, M.L., 2021, Using quantitative polymerase chain reaction (qPCR) and occupancy models to estimate atypical Aeromonas hydrophila (aAh) prevalence in catfish: Aquaculture, v. 530, p. 735687.
Colvin, M.E., Peterson, J.T., Sharpe, C., Kent, M.L., and Schreck, C.B., 2018, Identifying optimal hauling densities for adult Chinook salmon trap and haul operations: River Research and Applications, v. 34, no. 9, p. 1158-1167.
USFWS and USGS Host Multi-Agency Ultrasound Training Workshop
By Colt Holley and Aaron DeLonay
April 7, 2022
Fish Biologists from the Upper Missouri River Basin gathered at the U.S. Fish and Wildlife Service (USFWS) Gavins Point National Fish Hatchery (GPNFH) in Yankton, South Dakota for a hands-on training workshop in the use of ultrasound to determine sex and reproductive readiness of endangered pallid sturgeon. More than a dozen biologists from the U.S. Geological Survey Fork Peck Project Office, USFWS Missouri River Fish and Wildlife Conservation Office, U.S. Bureau of Reclamation, and Montana Fish, Wildlife and Parks travelled to the Gavins Point hatchery for the April 6th workshop. The hatchery is home to a large captive broodstock facility where approximately 1600 hatchery-origin pallid sturgeon (HOPS) are maintained. The April workshop was a unique opportunity to practice ultrasound techniques on more of the rare, adult fish in a single day than many biologists would capture over the course of several years working on the river.
Trained ultrasound sonographers from the GPNFH and the USGS Columbia Environmental Research Center instructed the attendees on the proper use of portable ultrasound imaging systems. New ultrasound probes connect to hand-held devices and tablets, an innovation that makes the technology extremely portable and useful in boats and on the riverbank. Biologists were trained to identify structural characteristics used in the determination of the sex of pallid sturgeon and its stage of sexual maturity. The trainees were split into three groups and performed ultrasound on several hundred of the large sturgeon over eight hours. Pallid sturgeon of varying ages and stages of sexual maturity were assessed as part of the comprehensive training. Expertise gained in ultrasound will be used by biologists in the coming months in monitoring and research studies in the Missouri and Yellowstone Rivers of Montana and North Dakota.
The transfer of low-cost, portable ultrasound technology from the clinical setting into the hands of biologists on boats has made real-time assessment of pallid sturgeon sex and reproductive status possible (see previous blog post “Mobile Ultrasound Technology Empowers Biologists”). Previously, ultrasound units were much more expensive and not widely accessible to biologists working on the river. With field biologists throughout the Upper Missouri River Basin equipped and trained in ultrasound techniques, reproductive assessments can be routinely performed on endangered sturgeon with much less stress and handling than in the past. As management actions to benefit pallid sturgeon migration and spawning are implemented, and as more HOPS become sexually mature, access to cost-effective, portable ultrasound technology will allow field crews to provide better monitoring data to managers and stakeholders to make informed decisions.
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