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S48. Developing quantitative models for ecological transport processes in rivers


Closing Date: April 15, 2020

This Research Opportunity will be filled depending on the availability of funds. All application materials must be submitted through USAJobs by 11:59 pm, US Eastern Standard Time, on the closing date.


The hydraulics of material transport are fundamental to physical, chemical, and ecological conditions of rivers. In the ecological sphere, transport of eggs and larvae is a key determinant of dispersal, survival, and recruitment in both endangered and invasive fishes (Braaten and others, 2012; Erwin and Jacobson, 2014; Garcia and others, 2015; Murphy and others, 2016; Erwin and others, 2018; Prada and others, 2019). In larval dispersal, variability of biomechanics associated with larval fish development (from passive transport to development of swimming capabilities) presents substantive challenges to prediction and requires a strong interdisciplinary approach to inquiry. The transport of environmental DNA (eDNA) has emerged as another important research topic in ecological transport because of the potential for using eDNA to detect and quantify populations of aquatic organisms, including invasive species like Asian carps (Klymus and others, 2015; Song and others, 2017) and endangered mussels (Sansom and Sassoubre, 2017; Currier and others, 2018). Dispersal transport processes share many factors in common with eDNA transport including the need to quantify hydrology, hydraulics, dispersion, mixing, decay (mortality), and advection. Both include the methodological challenges of generalizing understanding through computational models at scales relevant to decision making and the practicalities of measuring and sampling in the field.

The River Studies Branch, Columbia Environmental Research Center (CERC), has an ongoing, interdisciplinary research program to inform management and restoration of rivers. This program is funded through partnerships with the USGS Ecosystems Mission Area, US Army Corps of Engineers, and the Department of Defense Strategic Environmental Research and Development Program. We have a new opportunity to develop fundamental research in ecological transport phenomena related to two projects: 1) prediction of larval dispersal of the endangered pallid sturgeon (Scaphirhynchus albus) and 2) development of transport models related to using quantitative eDNA for monitoring freshwater mussel abundance. We seek a post-doctoral fellow with a strong background in hydraulics, turbulence, hydrodynamic modeling, and aquatic ecology; substantial flexibility exists for determining the scope and approach of each project.

Larval dispersal: This project builds on a foundation of extensive field sampling, computational hydrodynamic modeling, and early-life-stage development research on the dispersal of pallid sturgeon larvae in the Missouri River. Key unknowns relate to the biomechanics of larval transport. Two specific issues are how passively drifting larvae are distributed vertically in the water column (which has an important influence on advection and dispersion) and how and when developing larvae transition to holding themselves in the current (settling). While field sampling has provided critical information about these factors, advances in answering these fundamental questions requires a more controlled, experimental approach.  Accordingly, we are in the process of building a 11 m x 5 m racetrack flume (“eco-flume”) capable of 1-m depth and current velocities up to 1 m/s. The opportunity involves working with the final design stages and implementation of the flume (and associated instrumentation), design and implementation of experiments, and application of results to computational particle-tracking models.

eDNA transport: This project builds on previous work on eDNA shedding and decay to address how eDNA may be applied to monitoring freshwater mussel abundance in two river systems (Clinch River, Virginia and Big Piney River, Missouri). The Fellow will work with molecular biologists developing eDNA assays and sampling protocols to develop an appropriate hydrodynamic transport model to evaluate mixing, dilution, decay, and biogeochemical interactions as eDNA is advected downstream from mussel beds. The project is based on selected reaches of the two rivers but is open-ended as to the complexity of the modeling approach needed. The incumbent will develop the modeling approach and implement the model for the selected field sites, using field-sampled eDNA to evaluate model performance.

At CERC, the fellow will have broad opportunities for collaboration with existing interdisciplinary teams of biologists, chemists, and physical scientists with extensive experience in studying riverine ecological processes. Extramural collaborations are in place with the Saint Anthony Falls Hydraulics Laboratory (University of Minnesota), University of Missouri, Missouri State University, U.S. Fish and Wildlife Service, and the U.S. Army Corps of Engineers. The Fellow can build their research using the River Studies Branch robust cadre of technicians to support field work and development of laboratory instrumentation, and can access existing experience in hydroacoustic surveying, GPS and conventional surveying, and computational modeling (including high-performance computing applications). To support biological aspects of the research, CERC has captive pallid sturgeon, Asian carp, and native mussels for breeding and propagation of experimental subjects. The post-doctoral fellowship will allow for additional collaborative interactions related to large-river ecological processes, sediment transport, hydroacoustics, and habitat assessments, in field and laboratory contexts.

Interested applicants are strongly encouraged to contact the Research Advisor early in the application process to discuss project ideas.


Braaten, P.J., Fuller, D.B., Lott, R.D., Ruggles, M.P., Brandt, T.F., Legare, R.G., and Holm, R.J., 2012, An experimental test and models of drift and dispersal processes of pallid sturgeon (Scaphirhynchus albus) free embryos in the Missouri River: Environmental Biology of Fishes, v. 93, no. 3, p. 377–392, 10.1007/s10641-011-9925-9.

Currier, C.A., Morris, T.J., Wilson, C.C., and Freeland, J.R., 2018, Validation of environmental DNA (eDNA) as a detection tool for at-risk freshwater pearly mussel species (Bivalvia: Unionidae): Aquatic Conservation: Marine and Freshwater Ecosystems, v. 28, no. 3, p. 545-558, 10.1002/aqc.2869.

Erwin, S.O., Bulliner, E.A., Fischenich, J.C., Jacobson, R.B., Braaten, P.J., and DeLonay, A.J., 2018, Evaluating flow management as a strategy to recover an endangered sturgeon species in the Upper Missouri River, USA: River Research and Applications, 10.1002/rra.3371.

Erwin, S.O., and Jacobson, R.B., 2014, Influence of channel morphology and flow regime on larval drift of pallid sturgeon on the Lower Missouri River: River Research and Applications, v. 31, no. 5, p. 538-551, 10.1002/rra.2752.

Garcia, T., Murphy, E.A., Jackson, P.R., and Garcia, M.H., 2015, Application of the FluEgg model to predict transport of Asian carp eggs in the Saint Joseph River (Great Lakes tributary): Journal of Great Lakes Research, v. 41, no. 2, p. 374-386,

Klymus, K.E., Richter, C.A., Chapman, D.C., and Paukert, C., 2015, Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix: Biological Conservation, v. 183, p. 77-84,

Murphy, E.A., Garcia, T., Jackson, P.R., and Duncker, J.J., 2016, Simulation of hypothetical Asian carp egg and larvae development and transport in the Lockport, Brandon Road, Dresden Island, and Marseilles Pools of the Illinois Waterway by use of the Fluvial Egg Drift Simulator (FluEgg) model: 2016-1011, 31 p., 10.3133/ofr20161011.

Prada, A.F., George, A.E., Stahlschmidt, B.H., Jackson, P.R., Chapman, D.C., and Tinoco, R.O., 2019, Influence of turbulence and in-stream structures on the transport and survival of grass carp eggs and larvae at various developmental stages: Aquatic Sciences, v. 82, no. 1, p. 16, 10.1007/s00027-019-0689-1.

Sansom, B.J., and Sassoubre, L.M., 2017, Environmental DNA (eDNA) Shedding and Decay Rates to Model Freshwater Mussel eDNA Transport in a River: Environmental Science & Technology, v. 51, no. 24, p. 14244-14253, 10.1021/acs.est.7b05199.

Song, J.W., Small, M.J., and Casman, E.A., 2017, Making sense of the noise: The effect of hydrology on silver carp eDNA detection in the Chicago area waterway system: Science of The Total Environment, v. 605-606, p. 713-720,

Proposed Duty Station: Columbia, MO

Areas of PhD: Hydraulics, turbulence, ecohydraulics, aquatic ecology or related fields (candidates holding a Ph.D. in other disciplines, but with extensive knowledge and skills relevant to the Research Opportunity may be considered).

Qualifications: Applicants must meet the qualifications for: Research Hydrologist, Research Physical Scientist

(This type of research is performed by those who have backgrounds for the occupations stated above.  However, other titles may be applicable depending on the applicant's background, education, and research proposal. The final classification of the position will be made by the Human Resources specialist.)

Human Resources Office Contact: Audrey Tsujita, 916-278-9395,