Graduate Projects

 Title: Comparison of Methods for Sampling and Analyzing Spatial Structures in Landscape Genetics
Student Name: Niko Balkenhol
Department: Fish & Wildlife Resources

Project Summary:
Landscape genetics is a new and interdisciplinary research area that aims at detecting landscape influences on genetic diversity and structure. The number of landscape genetics studies is increasing rapidly, but most of the methods used for analyzing landscape genetic data have not been compared or evaluated.
In our project, we are evaluating the different analytical approaches using simulated data, and develop guidelines for optimal sampling and analysis. We are also analyzing various empirical data sets from Mongolian gazelles & wolves, cougars, etc.
In addition, we are collaborating with faculty members from other departments and colleges in interdisciplinary teaching efforts, and have given several landscape genetics workshops at international conferences.

For more information, email the Principle Investigator (PI): Dr. Lisette Waits

Title:  Invasiveness of Hawkweeds in the Pacific Northwest: The Role of Their AMF, Mycorrhizal Partners.
Student: Melissa Baynes [PhD Student]
Summer Intern: Shantel Tank
Collaborators: Dr. Timothy Prather & Dr. Linda Wilson
Department: Forest Resources

Meadow Hawkweed infestation near Santa, Idaho.

Project Summary:
We have discovered that the ability of meadow hawkweed, Hieracium caespitosum, to outcompete Idaho fescue, Festuca idahoensis, depends on feedback with mycorrhizal fungi.

For more information, email the PI: Dr. George Newcombe

Title: The Invasive Species Project: Spotted Knapweed (Centaurea stoebe)
Department: Plant, Soil & Entomological Sciences (PSES), and Forest Resources

Larinus Minutus knapweed eating weevil

Project Summary:
Spotted knapweed is one of Idaho’s most environmentally invasive and aggressive non-native plants. In previous greenhouse experiments we have shown that knapweed and its competitors are affected by endophytes in the absence of mycorrhizae. In addition, we have found that certain endophyte isolates differ in their susceptibility to attack by aphids and by the flower-feeding weevil Larinus minutes. This weevil has been released in North America for management of the biologically invasive Centaurea spp. The goal of this long-term project is to improve the management of invasive spotted knapweed; in this phase of the project, the REU student will test the relationship between C. stoebe and Larinus minutes, a weevil used for biological control of invasive plants.

For more information, email the PI: Dr. Sanford Eigenbrode

 Title: Exploring Feasibility of Proposed Control Strategies for New Zealand Mud Snails at Fish Hatcheries
Student Name: Rolita Louise Bruce and Jordan Nielson
Department: Fish & Wildlife Resources

New Zealand Mudsnail.                    New Zealand Mudsnails at hatchery.
                                                    Photo courtesy of Christine Moffitt.

Project summary:
The New Zealand mud snail is an invasive species that affects rivers and streams throughout the United States. Fish movement through stocking regimes have been documented as likely vectors of spread through the gut of trout. R. Louse Bruce’s studies indicate that a portion of the New Zealand mud snail could survive transit in the intestinal track of rainbow trout. She found in several sizes of fish that 8-12% of the snails in the fish fecal material were alive and over time the snail survival decreased in the trout gastrointestinal tract.

For more information, email the PI: Dr. Christine Moffitt

Title: Knapweed Project
Students: Alexey Shipunov [Postdoctoral Research Associate now at the Woods Hole Oceanographic Institution], Anil Raghavendra [PhD candidate]
Summer Intern: Maryse Crawford
Collaborators: Dr. Cort Anderson, Dr. Timothey Prather, Dr. Sanford Eigenbrode, Dr. Mark Schwarzlaender, Dr. Ray Callaway
Department: Forest Resources

Spotted knapweed (Centaurea stoebe)
east of Missoula, Montana. Photo courtesy of
Norman E. Rees, USDA
Agricultural Research Service, Bugwood.org
 

Project summary:
Invasiveness may be the result of ‘novel weapons’ that aid an introduced plant to outcompete evolutionarily naïve neighbours in its new range. Roots of Eurasian species of Centaurea are thought to produce allelochemicals that function as novel weapons in North America. However, a series of three experiments suggested that fungal endophytes that naturally established in seedling roots could have been confounded with novel weapons. In the first two experiments, endophtyes in roots of C. stoebe significantly reduced the biomass of naïve neighbours (i.e., Festuca idahoensis plants), compared to the effect of endophyte-free C. stoebe on F. idahoensis. For the third experiment, relative abundances of endophytes of C. stoebe in both its native and invaded ranges were determined so that representatives of the six most common haplotypes, three from each range, could be employed as root inoculants. In general, each of these endophytes again reduced the growth of naïve neighbours (i.e., Festuca idahoensis); remarkably, each also increased the growth of adapted neighbours (i.e., Festuca ovina) that were tested for the first time. Four of the six endophytes caused C. stoebe to gain a competitive advantage over its naïve neighbour that was significantly greater than the competitive advantage of endophyte-free C. stoebe over that same neighbour. Endophyte-free C. stoebe had no greater competitive advantage over F. idahoensis than it had over F. ovina. By aiding an invasive plant against F. idahoensis in a cryptic manner, endophytes could be confounded with novel weapons. However, without evidence that these endophytes are themselves native to Eurasia, it is premature to assert that they are themselves novel weapons.

For more information, email the PI: Dr. George Newcombe

Title: Cheatgrass Project
Student Name: Melissa Baynes [PhD student], and Joyce Sun [MS student]
Collaborators: Dr. Timothy Prather
Department: Forest Resources

Cheatgrass colonizing the edge of a burn near the Weiser River in Idaho.

Project Summary: We have discovered fungi that can reduce the growth of cheatgrass.

For more information, email the PI: Dr. George Newcombe

Left: Giant Palouse Earthworm in comparison to the invasive A. trapezoides (the most common earthworm within the Palouse region). Right: Yaniria Sanchez-de Leon sampling in a native Palouse prairie remnant.
 

Project Summary:
Driloleirus americanus is the only known native earthworm in the Palouse region. The main habitat of this earthworm is Palouse Prairie which has largely been converted to agricultural lands. Before the earthworm was found by a CRISSP-funded graduate student (Yaniria Sanchez-de Leon) working in our lab in 2005, it was thought to be extinct. Currently we are focusing on determining the range of this rare earthworm and testing methods to identify habitat using less destructive sampling methods.  

For more information, email the PI: Dr. Jodi Johnson-Maynard

Title: North American Burbot Project
Student Name: Nathan Jensen
Department: Fish & Wildlife Resources

left:Developing burbot eggs and first feeding larvae (increments = 1mm)
right: Captive adult burbot
 

Project Summary:
Burbot (Lota lota maculosa) are the only freshwater member of the Cod family Gadidae and native to the Kootenai River in Idaho and Montana USA and BC Canada. In the past, KR burbot sustained recreational, commercial, and sustenance fisheries. Over the last half century populations declined due to anthropogenic influences that changed the KR ecosystems. The most recent population estimates of KR burbot total less than 50. In 2003 KR burbot were denied federal listing as an endangered species. They are currently considered a species of concern in Idaho and Montana and red listed in BC. Although KR burbot were not listed, a multi-agency team of stakeholders; consisting of international, tribal, state, and local governments and non-government entities, developed a multifaceted conservation recovery plan with the goal to revitalize the KR burbot population. Development of aquaculture techniques was included in this plan. In 2004, a UI graduate student (MS) project was funded by the Kootenai Tribe of Idaho and focused on developing fundamental aquaculture techniques that could be used as a basis for developing a future conservation breeding program. This primary research successfully developed spawning, semen cryopreservation, egg incubation and larval feeding methods. Following the successful developments, additional funding support was awarded by the KTOI and the US Fish and Wildlife Service to continue aquaculture technique development. Currently, two graduate student (MS) projects are being funded; one with support by KTOI and the other supported by the USFWS. Ongoing research includes improving egg survival during incubation by controlling fungus using fungicides, evaluating the susceptibility of burbot juveniles to specific viral and bacterial pathogens and development and evaluation of extensive larval and juvenile rearing techniques and systems.
 
For more information, email the PI: Dr. Kenneth Cain

Title: Connections across a fragmented landscape: dispersal and gene flow among pygmy rabbit (Brachylagus idahoensis) populations
Student: Wendy Estes-Zumpf
Department: Fish & Wildlife Resources

Pygmy rabbit in winter. Photo courtesy of J. Witham.

Project Summary: Pygmy rabbits are habitat specialist living in the sagebrush steppe of the Great Basin. A disjunct population in Washington is federally listed as a distinct population segment, and a petition for range-wide federal listing has raised concern about the status of this species. Many questions remain regarding the dynamics of their populations. For example, it is not known if populations cycle or fluctuate like other lagomorphs, however, rapid declines and local extirpations have been documented. We have noted heavy ectoparasite infestations in some populations, but the effect of parasite prevalence, the potential for pathogen transmission, and potential impacts on dynamics of pygmy rabbit populations have not been explored. Research conducted by an undergraduate at UI provided the first information on this topic. The student used PCR assays to survey pygmy rabbit ectoparasites for pathogens and documented the first evidence of both plague (Yersinia pestis) and tularemia (Francisella tularensis ) in this species. Results of that research are currently in preparation for publication. We propose to expand on that initial survey. The goal of this work is to quantify parasite prevalence and diversity across populations and to survey for pathogens.

For more information, email the PI: Dr. Janet Rachlow

Rachel Winston monitoring for biocontrol insects in Hell's Canyon.

Project Summary: The study aimed to determine the effects of several variables on the survival and reproduction of a Crepis bakeri Greene ssp. idahoensis Babc. & Stebb., an Asteraceae listed as “sensitive” by the BLM. The ultimate goal of the project was to be one of the few studies to empirically document the effects of an invasive species on a native plant. The study variables included: the effects of YST, the effects of exotic plant species not including YST, the effects of insect herbivores, the effects of ungulate herbivores, and the effects of YST impacted by high levels of introduced insect biological control agents. Because this species is a perennial and the study sought to answer questions at a population level, the study was designed to be conducted over multiple years. During the growing season of 2007, the Hell’s Canyon study site was consumed by the Chimney Complex wildfire. In 2008, the fourth year of the study, the extra variable of fire was added to the study of C. bakeri. Results of this study will strengthen as the project continues and will be presented to CRISSP as they are produced.

For more information, email the PI: Dr. Mark Schwarzlaender

Former CRISSP graduate student, Chandalin Bennett,
as shown in February 2007 at Lake Tahoe where she worked
 for the University of Nevada at Reno before becoming
the Monitoring Specialist in the State Forests Program
for the Oregon Department of Forestry.

Project Summary: Exotic plant pathogens have been the cause of many devastating disease epidemics in America’s forests and agriculture. Famous examples include chestnut blight and white pine blister rust, both cases of native plants showing catastrophic susceptibility to the pathogen of a congener. This project tries to understand this phenomenon of resistance and susceptibility to pathogens of congeners by performing host-range inoculation experiments using a speciose plant genus and multiple isolates of its most common pathogen.

The plant genus Salix (willows) was chosen as an ideal group for inoculation experiments because in North America there are over one hundred native species and are commonly host to a rust fungus in the genus Melampsora.  Twenty-six different Salix species were inoculated in three separate experiments with isolates from different hosts of this pathogen. Results from these experiments show that in each case greater than 80% of the plants were resistant to the pathogen of a congener. Extreme susceptibility of congener species occurred in less than 5% of plants in each experiment. This susceptibility occurred at the greatest frequency in small Southwestern populations of Salix and to a lesser extent a few isolated Pacific Northwest populations. One of the Salix species that showed this extreme susceptibility was Salix arizonica, which just recently was taken off the endangered species list.

For more information, email the PI: Dr. George Newcombe
 

Project Summary: Flavobacterium psychrophilum is the etiological agent of coldwater disease (CWD) and rainbow trout fry syndrome (RTFS) and has emerged as one of the most significant bacterial pathogens in salmonid aquaculture in the Pacific Northwest and worldwide. This bacterium is especially problematic for restoration programs of native steelhead (Oncorhynchus mykiss), coho salmon (O. kisutch), chinook salmon (O. tshawytscha), and sockeye salmon (O. nerka) that are endangered and/or threatened species. Much research is being devoted to the development of an efficacious vaccine, since current disease prevention options are inconsistent and many times ineffective. Previous studies in our laboratory and others have suggested that the O-polysaccharide (O-PS) component of the lipopolysaccharide (LPS) of F. psychrophilum is highly immunogenic and may have been involved in eliciting a protective immune response following challenge with F. psychrophilum. We proposed to test the protective efficacy of the O-PS of LPS conjugated to a carrier protein, however, recent findings in our laboratory suggest that the carbohydrate antigens referred to as high molecular mass LPS with O-PS are likely the repeating carbohydrate antigens of the glycocalyx of F. psychrophilum and not LPS. Therefore, we will re-direct our research to further characterize and determine the protective ability of the glycocalyx. Initial studies will involve sodium dodecyl sulfate-polyacrylamide gel electrophoresis of LPS preparations and western blotting to demonstrate the presence of and distinct differences between the LPS and glycocalyx. Passive immunization experiments will also be conducted using a monoclonal antibody specific for the glycocalyx to determine if antibodies specific for this antigen are protective in rainbow trout. If these antibodies provide protection against F. psychrophilum challenge, then methods to purify the glycocalyx will be examined in order to test the glycocalyx as a vaccine candidate antigen for the prevention of CWD and RTFS.

For more information, email the PI: Dr. Kenneth Cain
 

 
Idaho Ground Squirrel.

Project summary:
Both the northern Idaho ground squirrel (NIDGS) and southern Idaho ground squirrel (SIDGS) are considered species of great conservation need. The northern Idaho ground squirrel is listed as an endangered subspecies while the southern Idaho ground squirrel is a candidate for listing under the Endangered Species Act. Both species have undergone population declines due to habitat loss and fragmentation.
An important aspect of Idaho ground squirrel ecology and conservation is evaluating gene flow between isolated populations by identifying how habitat features influence these species movement patterns. We investigated the effects of different landscape features on gene flow for both the NIDGS and SIDGS using several genetic analyses.
We found that landscape features such as elevation, vegetation types, rivers, and slopes did not limit gene flow for NIDGS, however the SIDGS had gene flow limited by the Weiser River suggesting that this landscape feature was an effective barrier to ground squirrel movement. Overall, our results suggest that there is greater connectivity among Idaho ground squirrel populations than indicated in previous studies.

For more information, email the PI: Dr. Lisette Waits

Photo by George Grail.
 

Project Summary: The most common diagnostic approach for identifying white sturgeon iridovirus (WSIV) infection in white sturgeon involves lethal sampling to obtain tissue sections from the head for histological examination. In the present study, non-lethal sampling of fin tissue by histology and PCR was compared to the lethal sampling method for the ability to detect viral infection in sturgeon undergoing an experimental 80-day co-habitation challenge with WSIV isolated from the Columbia River as well as in asymptomatic sturgeon from the Kootenai River. Lethal and non-lethal sampling of each fish involved sagittally cut half heads and left pectoral fin-punch tissue to obtain stained sections for histological examination as well as the removal of a portion of the right pectoral fin for PCR testing. An increase in mortality started to occur after 40 days in the cohabitation groups and by 80 days reached 94%. All three sampling methods were equally capable of identifying infection following 28 days post challenge. However, non-lethal fin histology did not identify infection earlier than this time point and non-lethal PCR of fin tissue was more likely to detect infection compared to the standard lethal sampling method. Both lethal and non-lethal histology identified the same asymptomatic individuals from the Kootenai River population but no fish were positive by PCR, suggesting genomic differences exist between isolates. Results from this study suggest that WSIV infection requires at least 4 weeks of incubation before it can be identified histologically in fin tissue. Results also suggest that combining PCR and histological examination of fin tissue by non-lethal sampling could provide an alternative approach for detecting infected individuals in small populations where lethal sampling would be detrimental.    

For more information, email the PI: Dr. Kenneth Cain
 

Title: Development and optimization of an Enzyme-Linked Immunosorbent Assay (ELISA) to detect Flavobacterium psychrophilum, etiologic agent of bacterial coldwater disease and rainbow trout fry syndrome in salmonids
Student Name: Nicole M. Lindstrom
Department: Fish & Wildlife Resources

Project summary:  There is strong evidence that Flavobacterium psychrophilum, the etiologic agent of coldwater disease (CWD), is transmitted vertically and it has been hypothesized that disease management at hatchery facilities may be improved through broodstock screening and implementation of culling programs. This study describes the development of two assays to screen broodstock tissues (kidney and ovarian fluid) for the presence of F. psychrophilum. Four monoclonal antibodies were generated against F. psychrophilum (CSF 259-93) outer membrane preparations. Of these, FL43 was selected for assay development and shown to react with 67 F. psychrophilum isolates tested, but did not react with two strains of Flavobacterium columnare or one strain each of F. pectinovorum, F. aquatile, F. branchiophilum, and F. saccharophilum. An ELISA was developed using FL43 as the capture antibody and FL43 conjugated to horseradish peroxidase as the secondary detection antibody. The ELISA had a lower detection boundary of approximately 1.6 x 103 cfu/mL of F. psychrophilum in kidney tissue homogenates spiked with known bacterial concentrations. Asymptomatic coho salmon broodstock (n=50 samples) were sampled and showed 100% infection by ELISA analysis of kidney tissue and had an estimated bacterial load of 2.0 x 103 – 9.4 x 103 cfu/mL. Ovarian fluid was also collected from these same coho as well as rainbow trout broodstock; however, the ELISA proved unsuitable for ovarian fluid. A filtration based florescent antibody test (FAT) was subsequently developed by conjugating FL43 to Alexa Fluor®-488. This FAT was able to detect F. psychrophilum in 74% of ovarian fluid samples collected from coho salmon and 42% from rainbow trout. Interestingly, yellow-pigmented bacteria were isolated on culture plates from 100% of kidney and ovarian fluid samples. All yellow-pigmented colonies were tested by PCR and 100% of the coho and rainbow trout were confirmed positive for F. psychrophilum infection.

For more information, email the PI: Dr. Kenneth Cain