Progress 12/01/14 to 11/30/17
Outputs
Target Audience:The target audience reached during this reporting period includes the general audience of ecologists and scientific community interested in forest dynamics, plant population biology, demographic modeling, exotic/invasive diseases, and ecological restoration, as well as researchers specifically interested in American chestnut and chestnut blight or in responding to similar naturalized exotic pathogens. Undergraduate students interested in biology and forestry were also reached during the current reporting period Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The fellowship supported 1 Postdoctoral Fellow, Nathanael Lichti, and helped support independent research by an undergraduate student at Purdue University (advised by Lichti ) and two undergraduate collaborators at the College of William and Mary. These students gained training and experience in data analysis, demographic modeling, molecular genetic techniques and writing. Several additional undergraduates, a master's student, and a post-baccalaureate intern were trained in ecological methodology through fieldwork associated with the project. Lichti also gained experience teaching and advising graduate students through interactions with graduate students and service on a graduate committee at Purdue, developed expertise in demographic and advanced statistical modeling techniques, and gained experience in molecular genetic techniques through his advising role in the undergraduate project. Professional development opportunities provided by the porject included travel to two conferences, where Lichti developed contacts with other researchers in his field. These networking opportunities have contributed to several professional collaborations during the NCE period, yielding one manuscript in review and a second in the planning stages. How have the results been disseminated to communities of interest?Preliminary results were disseminated to communities of interest through poster and oral presentations. One manuscript was published during the NCE period, a second is in preparation, and at least two more are planned. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
IMPACT The project help support continuing collection of a long-term dataset on demography and seedling dynamics in a naturally regenerating stand of American chestnut (Castanea dentata). The resulting database currently spans a total of 7 years and includes detailed, multiyear observations of >2560 individual trees. It also includes several years of observations prior to the establishment of significant chestnut blight in the population, followed by several years in which blight has invaded the study site from nearby locations, allowing collection ofdata collection on disease spread. Recruitment rates in the population vary from 0.9-5.2 seedlings per flowering tree, which lead to an positiive growth rate prior the introduction of chestnut blight. Herbivory on seedlings by deer and rabbits does suppress individual tree growth, especially in larger seedlings, but adult survival and seed predation appear to be more important long-term regulators of population growth rates. Limited work was conducted during the NCE period. This included collection of a 7th year of field data, as well as development of models for the combined effects of light and herbivore on seedling growth and survival, and identification of strategies to model the effects of management actions. A manuscript submitted in the previous reporting period was revised and published, and a second manuscrip is in draft form. Professional development and traning goals are addressed below.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Elwood, E.C*, N.I. Lichti, S.F. Fitzsimmons, and H.J. Dalgleish. 2017. Scatter-hoarders drive long- and short-term population dynamics of a nut-producing tree, while weevils and herbivores have little effect. Journal of Ecology. Epub ahead of print, DOI:10.1111/1365-2745.12902
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Lichti, N.I. K.F. Kellner, and T.J. Smyser. 2017. Bayesian model-based age classification using small mammal body mass and capture dates. Journal of Mammalogy 98(5): 1379-1388.
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Progress 12/01/15 to 11/30/16
Outputs
Target Audience:The target audience reached during this reporting period includes the general audience of ecologists and scientific community interested in forest dynamics, plant population biology, demographic modeling, exotic/invasive diseases, and ecological restoration, as well as researchers specifically interested in American chestnut and chestnut blight or in responding to similar naturalized exotic pathogens. Undergraduate students interested in biology and forestry were also reached during the current reporting period. Changes/Problems:Progress during the current reporting period was slowed substantially by the technical difficulties encountered in the spore dispersal project and the resulting need to dedicate a much larger than expected portion of time to troubleshooting and undergraduate mentoring. Because this was an undergraduate project and its results are not critical to the project's primary goals, it will not be pursued further. However, we are reviewing the literature and talking with colleagues to determine to potential usefulness and novelty of the new analytical method that was developed (an initial review of the literature indicates that similar approaches have been used in a small number of cancer diagnostic studies, but not in environmental monitoring or ecological genetics). If it appears that the method has value, a small demonstration study may be run and published in the next reporting period, contingent on available time and resources. What opportunities for training and professional development has the project provided?The project has provided numerous opportunities for training and professional development during the reporting period, including both undergraduate training and training/professional development for Lichti. Undergraduate training: 1) Two (2) undergraduate students, 1 post-baccalaureate scholar, and 1 master's student participated in intensive field work in forest ecology and worked closely (8-10 hours/day for 3 weeks) with 2 PhD level researchers (Lichti and Dalgleish) to collect field data. 2) One (1) undergraduate, M. Mount, was trained in general research methodology, molecular genetic techniques, data analysis, and writing. Professional development: In addition to working with undergraduates as listed above, Lichti engaged in the following professional development activities during the reporting period: 1) Independent study to learn advanced statistical techniques such as state space modeling, particle filtering, and population Monte Carlo techniques for inference related to dynamic systems (such systems include, but are not limited to, forest tree growth and demography) and observational data. 2) Informal consultation and training of US Forest Service staff (B. Miranda, USFS Northern Research Station) on Bayesian analysis of forest landscape simulation results. 3) Collaboration with USDA APHIS staff (T. Smyser, USDA APHIS National Wildlife Research Center) on an application of Bayesian demographic modeling to wildlife age determination 4) Independent research on quantitative PCR methodology, including laboratory methods and data analysis. How have the results been disseminated to communities of interest?Preliminary results were disseminated to communities of interest through poster and oral presentations. One manuscript was submitted for publication and others are in preparation. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
IMPACT: The fellowship provided direct salary support to 1 Postdoctoral Fellow, Nathanael Lichti, and supported independent research by an undergraduate student at Purdue University (advised by Lichti ) and an undergraduate collaborator at the College of William and Mary. These students gained experience in data analysis, demographic modeling, molecular genetic techniques and writing. Two additional undergraduates, a master's student, and a post-baccalaureate intern were trained in ecological methodology through fieldwork associated with the project. Lichti also gained experience teaching and advising graduate students through interactions with graduate students and service on a graduate committee at Purdue, developed expertise in demographic and advanced statistical modeling techniques, and gained experience in molecular genetic techniques through his advising role in the undergraduate project. Work during the reporting period continued to make progress toward the project objectives of evaluating the interacting effects of herbivory, understory light availability, and blight resistance on American chestnut population dynamics. One publication was submitted for publication, and preparation of another was begun. OBJECTIVES: Scientific Determine how the blight life cycle, blight-induced mortality, and resistance interact with seed predation/dispersal and seedling establishment, survival, and growth to influence chestnut population trajectories 1) Major activities completed / experiments conducted: Chestnut demography: a fifth year of field data on seedling recruitment, survival, and growth was collected, along with data on blight infection. An initial manuscript, lead authored by William and Mary undergraduate E. Elwood, was submitted and is currently in revision. It describes the pre-blight demography of the main study population and relative importance of herbivory and seed predation to population dynamics. A second manuscript that examines the relative importance of blight, herbivory, and light limitation is in preparation. The demographic modeling work also lead to a collaboration with APHIS staff scientist T. Smyser, and submission of a related manuscript. Blight spore dispersal: Purdue undergraduate, M. Mount (formerly Cooke), continued her work on chestnut blight spore dispersal, assisted by USDA FS Hardwood Tree Improvement and Regeneration Center staff member J. McKenna and postdoc Dr. A. Ibrahimi. Despite promising initial results in year one, all tested primers for Cryphonectria parasitica produced strong dimers that prevented unambiguous quantification via standard qPCR analysis. Several months of efforts to develop alternate primers or alter the reaction mixture failed to resolve the problem. Eventually, we developed an alternative approach to analyzing the data based on the derivatives of the qPCR melt curve. We are currently investigating the novelty and potential general utility of this method, which may allow accurate quantification using standard PCR probes with SYBR green dye. 2) Data collected: As described above, demographic and disease data were collected on a population of > 2560 American chestnut trees ranging in size from 0.14 - 192 cm diameter, along with data on environmental covariates. 3) Summary statistics and discussion of results: Chestnut demography: updated analyses reveal that annual seedling recruitment rates vary from 0.9-5.2 seedlings per flowering tree. Prior to the introduction of chestnut blight, the population was able to maintain a long-term growth rate of l = 1.054, and was therefore expanding. Herbivory on seedlings by deer and rabbits does suppress growth, especially in larger seedlings, and has a dominant effect on the rate of population growth during the initial, transient phase of population establishment and expansion. However, in a healthy population, seed predation and dispersal become much more important as regulators of population growth once the population becomes established and growth rates stabilize. Detailed analyses for the population post-infection are pending. Spore dispersal: The primers that we intended to use for blight spore quantification produced very strong dimers, which prevented spore quantification using standard qPCR methods. A method was developed that allowed accurate quantification of blight spore concentrations in serial dilutions (R2 = 0.976), but when applied to the field samples, the new analysis did not yield interpretable results. In most cases, no spores were detected. 4) Key outcomes or other accomplishments realized: Preliminary analyses and modeling during the previous reporting period showed that simply introducing blight resistance is unlikely to be sufficient to restore American chestnut or to manage remnant populations, and continuing analyses continue to support this finding. Seedling herbivory and seed predation play important roles in regulating population dynamics. A manuscript describing these initial results has been submitted and is in revision (see Products). Evaluate how these relationships change as a function of available light and temperature and moisture effects on fungal growth No work on this topic was carried out in the current reporting period, but analyses of the effects of light on seedling growth and survival were conducted. Model the system's response to specific management actions (e.g., diseased tree removal, overstory thinning). No work on this topic was carried out in the current reporting period. Professional Development and Mentoring Completion of an Individual Development Plan detailing personal objectives, milestones, expectations, and professional development needs. 1) Major activities completed / experiments conducted: An Individual Development Plan was completed in cooperation with co-advisors Jacobs, Dalgleish, and Saunders, and was filed with the Purdue University Department of Forestry and Natural Resources. 2) Data collected: N/A 3) Summary statistics and discussion of results: N/A 4) Key outcomes or other accomplishments realized: Lichti obtained a position as a Visiting Assistant Professor in the Department of Statistics at Purdue University, was invited for 3 phone interviews for tenure-track positions, and has 1 on-site interview currently scheduled for a tenure-track position at the University of Maryland Center for Environmental Science. Delivery of outreach presentations and extension publications through the USFS Hardwood Tree Improvement and Regeneration Center and The American Chestnut Foundation. One presentation was delivered to TACF. c. Delivery of professional presentations and of invited departmental seminars. 1) Major activities completed / experiments conducted: Lichti presented a poster at the annual NIFA Fellowship Program PI meeting. 2) Data collected: N/A 3) Summary statistics and discussion of results: N/A 4) Key outcomes or other accomplishments realized: N/A Participation in the Purdue University Center for Instructional Excellence (CIE) College Teaching Workshops series Major activities completed / experiments conducted: N/A (completed in reporting period 1). 2) Data collected: N/A 3) Summary statistics and discussion of results: N/A 4) Key outcomes or other accomplishments realized: N/A Mentorship of undergraduate independent research 1) Major activities completed / experiments conducted: Lichti advised one undergraduate researcher, served on a doctoral committee, and informally mentored graduate students at Purdue. 2) Data collected: N/A 3) Summary statistics and discussion of results: N/A 4) Key outcomes or other accomplishments realized: N/A Participation in curriculum development. No activities were planned or carried out in the current reporting period.
Publications
- Type:
Other
Status:
Published
Year Published:
2016
Citation:
Mount, M,* A. Ebrahimi, J. McKenna, N. Lichti, and D. F. Jacobs. 2016. Quantifying wind-dispersed chestnut blight spores with qPCR. Purdue University Department of Forestry and Natural Resources Annual Research Symposium. (Honorable Mention for Undergraduate Research)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
Dalgleish, H.J. and N.I. Lichti. The ecology of American chestnut restoration. Spring Meeting of the Maryland Chapter of the American Chestnut Foundation. Frederick, MD. March 12, 2016 (Invited Talk)
- Type:
Journal Articles
Status:
Under Review
Year Published:
2016
Citation:
Elwood, E.C*, N.I. Lichti, S.F. Fitzsimmons, and H.J. Dalgleish. In revision. Scatter-hoarders and herbivores, respectively, drive long- and short-term population dynamics of a nut-producing tree, while weevils have little effect. Journal of Ecology.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2016
Citation:
Lichti, N.I. K.F. Kellner, and T.J. Smyser, in revision. Bayesian model-based age classification using small mammal body mass and capture dates. Journal of Mammalogy.
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Progress 12/01/14 to 11/30/15
Outputs
Target Audience:The target audience reached during this reporting period includes the general audience of ecologists and scientific community interested in forest dynamics, plant population biology, demographic modeling, exotic/invasive diseases, and ecological restoration, as well as researchers specifically interested in American chestnut and chestnut blight or in responding to similar naturalized exotic pathogens. Undergraduate students interested in biology and forestry were also reached during the current reporting period. Changes/Problems:There have been no major changes or problems to report, but progress is approximately 2 months behind schedule relative to the original proposed timeline. There are two reasons for this. First, the original timeline assumed a start date in September, 2014, but project funds did not actually become available until mid-December, 2014. Second, Lichti took paternity leave in April, 2015. What opportunities for training and professional development has the project provided?The project has provided numerous opportunities for training and professional development during the reporting period, including both undergraduate training and training/professional development for Lichti. Undergraduate training: 1) Seven (7) undergraduate students participated in intensive field work in forest ecology and worked closely (8-10 hours/day for 3 weeks) with 2 PhD level researchers (Lichti and Dalgleish) to collect field data. 2) One (1) undergraduate, D. McPherson, was trained in statistical analysis and modeling of plant demographic data 3) One (1) undergraduate, M. Cooke, was trained in general research methodology and molecular genetic techniques. Professional development: In addition to working with undergraduates as listed above, Lichti engaged in the following professional development activities during the reporting period: 1) Participation in a 1-semester, weekly undergraduate seminar on integral projection modeling organized through the NSF-sponsored QUBES (Quantitative Undergraduate Biology Education and Synthesis) network. 2) Independent study to learn basic C++ programming skills and learn how to integrate C++ routines with programs in R through the Rcpp package (C++ integration allows more efficient handling of computationally intensive analysis and simulation tasks). 3) Independent study to learn advanced statistical techniques such as state space modeling, particle filtering, and population Monte Carlo techniques for inference related to dynamic systems (such systems include, but are not limited to, forest tree growth and demography) and observational data. 4) Informal consultation on a project to model the potential spread of sudden oak death in the eastern US (with Dr. F. Tonini, North Carolina State University). How have the results been disseminated to communities of interest?Preliminary results were disseminated to communities of interest through poster and oral presentations at national and international conferences. Manuscripts for publication are currently in preparation. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
IMPACT: During the first year reporting period, the fellowship provided direct salary support to 1 Postdoctoral Fellow, Nathanael Lichti, and supported independent research by 2 undergraduates (1 each at Purdue University [PU] and the College of William and Mary [WM]), and 1 international intern with the USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), advised or co-advised by Lichti. The students gained first-hand experience in field ecology, demographic modeling, forest pathology, and genetic techniques. Four other undergraduates participated project fieldwork. In addition to advising and training undergraduates, Lichti participated in a series of teaching workshops and gained experience in graduate advising through interactions with graduate students and service on a graduate committee at PU. He developed expertise in demographic and statistical modeling techniques, and developed presentation and public speaking skills through attendance to professional conferences and an invited departmental seminar presentation at WM. Work during the first year made progress toward the project objectives of evaluating the interacting effects of herbivory, light, and blight resistance on American chestnut population dynamics, understanding the theoretical thresholds at which populations shift from expansion to collapse, and validating mechanistic models for wind-borne dispersal in chestnut blight. Publication of results is anticipated in the next reporting period. OBJECTIVES: Scientific Determine how the blight life cycle, blight-induced mortality, and resistance interact with seed predation/dispersal and seedling establishment, survival, and growth to influence chestnut population trajectories 1) Major activities completed / experiments conducted: Chestnut demography: field data on American chestnut demography was collected at New England field sites, along with data on blight infection, understory photosynthetically active radiation (PAR) levels, and soil characteristics. A WM undergraduate, D. McPherson, helped analyze the data to estimate models for demographic vital rates and parameterize an integral projection model for American chestnut population dynamics. A manuscript is in preparation. Blight spore dispersal: A PU undergraduate, M. Cooke, was recruited to research the accuracy of physical models for wind-borne spore dispersal in chestnut blight, assisted by HTIRC staff including an intern, M. Valladares (Zamorano University, Honduras) and a post-doctoral scientist (Dr. A. Ibrahimi). An array of spore traps was deployed in a blight-infected American chestnut seed orchard in Indiana to collect data on spore dispersal. Additional spores were collected from Cryphonectria parasitica cultures maintained by J. McKenna (HTIRC) to serve as positive controls for development and testing of DNA extraction techniques, primers, and probes specific to this project. An extraction protocol was developed to recover usable DNA from ascospores trapped in vaseline on microscope slides, and real-time PCR (rtPCR) probes were developed. At the time of this writing, DNA has been extracted from all field-collected samples. 2) Data collected: Demographic and disease data were collected on > 1800 American chestnut trees ranging in size from 0.14 - 192 cm diameter, along with data on environmental covariates. In the spore dispersal project, data include wind speed and direction and spore density as a function of distance/direction from source (pending DNA results). 3) Summary statistics and discussion of results: Chestnut demography: Field data showed that American chestnut seedling growth was significantly affected by both understory light availability and herbivory, and that the probability of being browsed varied unimodally with seedling size. At our main field site, browsing risk peaked at approximately 0.6 cm basal diameter, with a probability of 0.8. Survival increased with seedling size. Although neither light limitation nor browsing directly affected seedling survival after accounting for size effects, they did limit the rate at which seedlings escaped more vulnerable size classes. Blight infection on the site was rare but is spreading rapidly. Larger trees appear to be more vulnerable to infection. Sensitivity analysis for the Chestnut IPM showed that population growth rates are sensitive to both browsing and phenotypic blight resistance (modeled as a reduction in the probability of mortality due to infection), and that in many realistic parameterizations, browsing may be more limiting than disease. In addition, the two factors interact so that the degree of resistance required to achieve positive population growth depends on the level of browsing pressure. Spore dispersal: Preliminary tests using both field and culture-derived samples showed that rtPCR was successful in distinguishing samples with different spore concentrations. 4) Key outcomes or other accomplishments realized: A key goal of this project is to understand how factors that affect chestnut early in its life cycle (seed survival and growth, seedling survival and growth) interact with mortality caused by the chestnut blight fungus. Analyses and modeling efforts thus far show that simply introducing blight resistance is unlikely to be sufficient to restore American chestnut or to manage remnant populations. Phenotypic resistance targets for breeding programs also need to account for the browsing pressure that trees are likely to face in the field. These preliminary lessons were communicated to the target audience through presentations at national and international meetings, and a manuscript describing these results is in preparation. Evaluate how these relationships change as a function of available light and temperature and moisture effects on fungal growth Nothing planned for reporting period. Model the system's response to specific management actions (e.g., diseased tree removal, overstory thinning). Nothing planned for reporting period. Professional Development and Mentoring NOTE: For all activities in this section, Data collected, Summary statistics and discussion of results, and Key outcomes are N/A. Completion of an Individual Development Plan (IDP) detailing personal objectives, milestones, expectations, and professional development needs. 1) Major activities completed / experiments conducted: An IDP was completed with co-advisors Jacobs, Dalgleish, and Saunders and filed with the PU Department of Forestry and Natural Resources. Delivery of outreach presentations and extension publications through the USFS Hardwood Tree Improvement and Regeneration Center and The American Chestnut Foundation. Nothing planned for reporting period. Delivery of professional presentations and of invited departmental seminars. 1) Major activities completed / experiments conducted: Lichti presented 1 invited departmental seminar to the Biology Department at the College of William and Mary and gave 1 presentation at the annual meeting of the Ecological Society of America. He attended the North American Forest Ecology Workshop and was scheduled to give a presentation, but it was canceled due to illness. Participation in the Purdue University Center for Instructional Excellence (CIE) College Teaching Workshops series 1) Major activities completed / experiments conducted: Lichti participated in the semester-long CIE workshop series, attending 8 sessions on topics including active learning, instructional techniques, academic integrity, policy setting, and assessment. Mentorship of undergraduate independent research 1) Major activities completed / experiments conducted: Lichti co-advised an honors thesis student in biology at the WM with Dalgleish, co-advised an international intern with the HTIRC with Jacobs, and advised a PU undergraduate on independent research. He also served on a doctoral committee at PU. Participation in curriculum development. Nothing planned for reporting period.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Lichti, N. D.F. McPherson, and H.J. Dalgeish. American chestnut (Castanea dentata) stand dynamics with natural regeneration and blight-induced mortality. British Ecological Society Annual Symposium: Demography Beyond the Population, Sheffield, U.K.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Swihart, R., K. Kellner, and N. Lichti. Reverend Bayes wants you! Opportunities and obstacles for fish and wildlife professionals to improve statistical fluency. 75th Midwest Fish and Wildlife Conference, Indianapolis, Indiana. (invited talk)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Lichti, N., D.F. McPherson, and H.J. Dalgeish. Interactions between blight resistance and seedling demography limit American chestnut population growth in an integral projection model. Ecological Society of America, Annual Meeting, Baltimore, Maryland
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