HHMI Faculty Research Award (FRA)
Cover Sheet
Title
Modeling Rainforest Pioneer Plant Populations in Treefall Gaps of
the Monteverde, Costa Rica Cloud Forest
Name of PI
Brian Yurk
Department of PI
Mathematics
Name(s) of collaborators K. Greg Murray
Undergraduates
2 undergraduate students in summer 2014
Associated with Project:
(Give names if known or
simply numbers if
students are not yet
identified)
Projected start date
Projected end date
Total Budget
Requested
May 19, 2014
July 25, 2014
$15,000
ABSTRACT
Tropical rainforests are biologically diverse and ecologically complex terrestrial ecosystems.
Understanding the factors that drive the ecological dynamics is a difficult problem but an
important one to address if we are to understand how these ecosystems will likely respond to
climate change and land-use changes. Rainforest pioneer plants are specialists that colonize
trefall gaps that arise primarily through windthrow. These gaps are rare and heal quickly,
presenting conditions suitable for pioneer plant growth and maturation for only very short
periods of time. It is our goal to develop stochastic mathematical models of landscape-scale
pioneer plant population dynamics. These models will be parameterized using data on
rainforest canopy gaps collected over the last 30 years and demography data collected over the
last 13 years in the Monteverde, Costa Rica Cloud Forest. We will also continue to add to this
data set, which is possibly unique in its extent. Using these mathematical models we will
determine the vital rates (reproduction and growth) that the plant populations are particularly
sensitive to, and we will simulate possible future environmental scenarios (e.g., increased
storm frequency).
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1.1
Project Description
Significance of Work
Tropical rainforests are the most biologically diverse terrestrial ecosystems on earth, and the
interactions between organisms and between organisms and the physical environment make them
the most complex ecosystems as well. As a result, understanding how these systems work, and
how they are likely to respond to altered conditions like climate change or land-use changes,
presents a daunting but important challenge. Like most forests, tropical rainforests are highly
dynamic, with small-scale physical disturbances (e.g., deaths of one to a few trees at a time,
primarily by windthrow) driving both tree-by-tree replacement patterns and the generation of
short-lived patches of early successional species. Physical disturbance generates much of the
structural complexity of forests that in turn maintains highly diverse animal communities.
“Pioneer” plants comprise a guild that specializes on colonizing patches disturbed by treefalls.
Compared with plants that characterize mature forest patches, pioneers grow and mature rapidly,
produce small seeds with adaptations for effective seed dispersal, and are intolerant of deep
shade (Murray and Mauricio Garcia-C. 2002; Veldman et al. 2007). Trefall gaps are rare
(making up 1-1.5% of the forest land area [Murray 1988]), ephemeral, and unpredictable, and
canopy closure following a treefall is rapid. Consequently, tree fall gaps can be considered a
limiting resource for rainforest pioneer plants. In particular, young treefall gaps are crucial for
pioneer plant recruitment, as many species fail to germinate in gaps as young as 4 months old
(Murray 1988).
1.2
Objectives
Our objective is to combine our respective areas of expertise in ecology and mathematical
modeling with long-term data sets on forest dynamics and pioneer plant demography to
accomplish what neither of us could do alone – to develop comprehensive, patch-specific models
of pioneer plant population dynamics. In addition to elucidating processes that maintain plant
species diversity and thus support unique assemblages of animals, the models we develop can be
used to predict community responses to altered disturbance regimes driven by climate change.
Of course, one of the most important benefits derives from the engagement of students with
authentic interdisciplinary research that highlights the importance of both a deep understanding
of the natural history of real organisms and the ways in which mathematics can transform that
understanding into general principles that apply in other places with different species.
1.3
Methods
A landscape-scale mathematical model of pioneer plant population dynamics must consist of two
parts: a model of canopy gap formation and regrowth and patch-specific models of pioneer plant
dynamics. Parameterizing such a model requires many years of data on both gap dynamics and
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pioneer plant populations due to the long time scales of the forest processes. Working in the
Monteverde Cloud Forest in Costa Rica, Murray, his collaborators, and students have been
conducting yearly gap censuses along 2.5 km of transects (5 transects total) since 1983.
Censuses of 6 focal pioneer plant species have also been conducted along these transects since
2000. This gives us the (possibly unique) opportunity to construct data-driven models for this
system. We will continue to collect yearly data on canopy gaps and pioneer plant populations
along the five transects. In summer 2014, Murray and Yurk and two Hope research students will
travel to Costa Rica to collect these data.
Our model of canopy gap formation and regrowth will be based on a preliminary model
developed by Kristen Bosch, an HHMI Science Education Scholar. Bosch developed a
preliminary classification system for treefall gaps based on gap age and area. Gaps in different
classes present different growth environments to colonizing pioneer plants. A treefall gap
transitions from one class to another as the canopy closes and the patch ages or as new adjacent
treefalls occur. New gaps also form as trees fall within the mature forest. Our preliminary model
is a transition matrix model (Caswell 2001) that is based on estimated average transition
probabilities between gap classes and on new gap formation frequencies along the five
Monteverde transects. Given a distribution of gap classes for a particular year, the model
predicts the distribution of gap classes for consecutive years. Model projections of gap
distributions using this approach for one transect are shown in Fig. 1 along with observed
distributions for the same time period. These results demonstrate that gross trajectories of gap
distributions can be predicted with reasonable accuracy with this simple approach. On the other
hand, this approach does not account for the stochastic nature of gap formation and maturation.
Consequently, the model predictions do not exhibit the random fluctuations apparent in the
measured gap distributions (Fig. 1).
Trefall gap formation and growth are
random processes that are influenced
by random environmental factors. We
will develop a gap transition model
that extends the preliminary model by
incorporating these stochastic effects to
predict possible future gap
Fig. 1. Predicted and observed treefall gap
distributions. The model will be
distributions along Monteverde Transect C.
implemented using the statistical software
R (R Core Development Team 2013), and simulations will be used to construct probability
distributions for future gap dynamics and to simulate potential environmental conditions for the
plant populations.
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Since vital rates (e.g., growth and reproduction) of pioneer plants vary between gap classes, we
will develop pioneer plant demography models for each of the six focal pioneer species within
each gap class. Using the Monteverde plant demography data, we will estimate reproduction
rates and transition probabilities between plant size classes within gaps of different classes. By
combining the stochastic model of gap dynamics with patch-specific models of plant population
dynamics, we will be able to predict how pioneer plants populations within the forest will change
over time as gaps develop and evolve. These models will also allow investigations of the
impacts of possible future scenarios (e.g., increased frequency of strong wind events) on pioneer
plant populations and, by extension, rainforest plant species diversity.
1.4
Expected Outcomes
Ultimately, the proposed research will generate modeling tools and insights into rainforest
pioneer plant population dynamics. The preliminary results from this work will be used to write
a NSF-REU proposal to support continued plant demography research at Hope. Our results will
also be disseminated via conference presentations and peer-reviewed papers jointly authored by
Murray, Yurk, and undergraduate researchers.
The proposed research is the beginning of a multi-year research program that will involve
numerous undergraduate researchers, including 2 research students in summer 2014. These
students will be involved in data collection and analysis and model development. There is less
mathematical background required to understand the basic demography models than is required
for most other mathematics research projects at Hope. Consequently, this project is particularly
well-suited for novice researchers. We intend to recruit first year students that we hope will
continue to work on the project the following summer. This will encourage students to assume a
leadership role, particularly in their second summer of work. At the same time, this provides
continuity from year to year, which benefits the research program itself. Summer research
students will also be asked to work as teaching assistants in the Research-Based Statistics/FYS
course, which will also incorporate plant demography research.
1.5
Potential Difficulties
It is possible that even with 13 years of plant demography data, vital rate parameter values will
be difficult or impossible to estimate for some species. The research will be successful if we
develop a model for at least one of them in summer 2014. The process of model development
may point out the need to collect additional field data, which we will begin to pursue in summer
2014. As we continue to collect data in future years, parameter estimates will also improve.
1.6
Connection to other HHMI Programs
The proposed research will be part of a larger program that involves undergraduate students in
plant demography modeling through summer and course-based research. The broader program
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will also involve investigation of Pitcher’s thistle, a threatened pioneer plant that inhabits local
sand dune complexes. In addition to undergraduate researches working during the summer and
academic year, students will conduct research related to one of the two plant systems in the
Research-Based Statistics/FYS and in the Mathematical Biology course. The former, first
offered fall 2013, was funded through the HHMI CRE program (PIs Yurk and Airat Bekmetjev).
It involves a Bridge component in which first year students are invited to come to campus for
three days before the beginning of the fall semester. In the future, this period will be largely
devoted to working on elements of the plant demography research program, including collecting
population data on Pitcher’s thistle each year. One or two students involved in summer
demography research will be asked to serve as teaching assistants for this course during the
three-day research experience. We hope that some of the students involved in the summer
research will be supported by the HHMI program, just as Kristen Bosch was in the past.
1.7
Plans for External Funding To Continue Work
We plan to submit an NSF-REU proposal in August 2014 to fund the plant demography
program. It is likely that we will also submit an NSF-RUI proposal to fund continued work on
the rainforest system.
1.8
Timeline
Travel arrangements for the field work in Costa Rica will be made during spring 2014. Some
initial modeling work, including developing R scripts to import and process demography and
treefall gap data, will occur during that period. Two research students will work for 10 weeks
during summer 2014 from May 19 – July 25, the last two weeks of which will be spent collecting
data in Costa Rica. During the first 8 weeks, we will work to simultaneously develop stochastic
gap dynamics models and patch-specific pioneer plant demography models. Throughout spring
and summer 2014, Murray and Yurk will work to write an NSF-REU proposal incorporating
some of the modeling results. This proposal will be submitted on or before the deadline of
August 27.
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Bibliography/References
Caswell, H. 2001. Matrix Population Models: Consttruction, Analysis, and Interpretation.
Sundarland: Sinauer.
Murray, K.G. 1988. Avian seed dispersal of three neotropical gap-dependent plants. Ecological
Monographs 58: 271-298.
Murray, K.G., and J. Mauricio Garcia-C. 2002. Contributions of seed dispersal and demography
to recruitment limitation in a Costa Rican cloud forest. Pp. 323-338, in: Levey, D. J., W. R.
Silva, and M. Galetti. (eds) Seed dispersal and frugivory: Ecology, evolution, and conservation.
CABI Publishing, Wallingford, UK.
R Development Core Team 2013. R: A language and environment for statistical computing.
Vienna, Austria: R Foundation for Statistical Computing, http://www.R project.org.
Veldman, J.W., K.G. Murray, A.L. Hull, J.M. Garcia-C., W.S. Mungall, G.B. Rotman, M.P.
Plosz, and L.K. McNamara. 2007. Chemical Defense and the Persistence of Pioneer Plant Seeds
in the Soil of a Tropical Cloud Forest. Biotropica 39: 87-93.
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4
Biographical Sketches
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Brian P. Yurk
Department of Mathematics
Hope College
Holland, MI 49423
(616) 395-7526
yurk@hope.edu
Professional Preparation
Institution
Hope College
Utah State University
Major
Mathematics/Geology
Mathematics
Degree & Year
B.S., 2003
Ph.D., 2009
Appointments
Assistant Professor, Hope College, Department of Mathematics, 2009-present.
Graduate Instructor, Utah State University, Department of Mathematics, 2006-2009
Most closely related publications
B. Yurk, E. Hansen, and D. Hazel. “A deadtime model for the calibration of impact sensors with
an application to a modified miniphone sensor,” Aeolian Research 11: 43-54. 2013.
B. Yurk and J. Powell. “Modeling the effects of developmental variation on insect Phenology,”
Bulletin of Mathematical Biology. 72(6): 1334-1360, 2010.
B. Yurk and J. Powell. “Modeling the evolution of insect phenology,” Bulletin of Mathematical
Biology. 71(4): 952-979, 2009.
E. Hansen, S. DeVries-Zimmerman, D. van Dijk, and B. Yurk. “Patterns of wind flow and aeolian
deposition on a parabolic dune on the southeastern shore of Lake Michigan,” Geomorphology.
105:147-157, 2009.
B. Yurk. “Modeling the evolution of insect phenology with particular reference to mountain pine
beetle,” Graduate Theses and Dissertations. Paper 385.
http://digitalcommons.usu.edu/etd/385, 2009.
Other significant publications
B. Yurk, S. DeVries-Zimmerman, E. Hansen, B. Bodenbender, Z. Kilibarda, T. Fisher, D. van
Dijk. “Dune complexes along the southeastern shore of Lake Michigan,” Insights into Michigan
Basin: Salt Deposits, Impact Structures, Youngest Basin Bedrock, Glacial Geomorphology,
Dune Complexes, and Coastal Bluff Stability. Ed. R. Gillespie. Pp. 57-102, 2013.
B. Yurk, B. Bodenbender, Z. Kilibarda, D. van Dijk, and E. Hansen. “The role of storm winds in
shaping dunes along southern and southeastern Lake Michigan,” Abstracts with Programs 2011
G.S.A. Annual Meeting.
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L. Labarge, C. Mulcahy, B. Yurk, and E.C. Hansen. “Mathematical model of dune grass
(Ammophila breviligulata) population dynamics: testing a possible mechanism for blowout
initiation,” Abstracts with Programs 2011 G.S.A. Annual Meeting.
A. Arbogast, E.C. Hansen, and B. Yurk. “The history of dune growth and migration along the
southeastern shore of Lake Michigan: a perspective from Green Mountain Beach,”
Michigan Academician. 35(4): 455-478, 2004.
E. Hansen, A. Arbogast, D. van Dijk, and B. Yurk. “Growth and migration of parabolic dunes
along the southeastern coast of Lake Michigan,” Journal of Coastal Research SI 36
(Proceedings of the 8th International Coastal Symposium): 209-214, 2006.
Synergistic Activities
Mentored students as part of the Mathematics Department REU and the REACH
(Research Experience Across Cultures at Hope) on projects in mathematical biology and
mathematical geology for the past three years. This includes 22 undergraduate students
(two from underrepresented groups in the STEM fields), three high school students (one
from an underrepresented group in the STEM fields), and two high school teachers.
Developed guided inquiry laboratory exercises for college and high school biology
courses in association with the NSF-funded Bean Beetle Curriculum Network.
Reviewed for the journals Mathematical and Computer Modeling, Environmental
Entomology, Natural Resource Modeling, and Journal of Theoretical Biology.
Have given research talks to Tulip City Gem and Mineral Club and Holland Area Senior
Professionals, both Holland, MI area community groups. Have led several dune field
trips for local community groups.
Collaborators & Other Affiliations
Full Name
Bentz, Barbara
Bekmetjev, Airat
Bodenbender, Brian
Cobbold, Christina
Cusack, Charles
DeVries-Zimmerman, S.
DeYoung, Paul
Fisher, Timothy
Hansen, Edward C.
Kilibarda, Zoran
Murray, Kelvin G.
Pearson, Paul
Pennings, Timothy
Powell, James A.
Putzke, Aaron
van Dijk, Deanna
Institution
USDA Forest Service
Hope College
Hope College
University of Glasgow
Hope College
Hope College
Hope College
University of Toledo
Hope College
Indiana University Northwest
Hope College
Hope College
Davenport University
Utah State University
Hope College
Calvin College
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Relationship
Collaborator
Collaborator
Co-author
Collaborator
Collaborator
Co-author
Collaborator
Co-author
Co-author
Co-author
Collaborator
Collaborator
Co-author
Ph.D. advisor
Collaborator
Co-author
K. Greg Murray
(a) Professional Preparation:
California State University, Northridge
California State University, Northridge
University of Florida
Biology
Biology
Zoology
B.A., 1977
M.S., 1980
Ph.D., 1986
(b) Appointments:
Professor of Biology, Hope College, 2001-Present
Associate Professor of Biology, Hope College, 1992-2001
Assistant Professor of Biology, Hope College, 1986-92
(c) Products – * denotes undergraduate student
i. five most closely related to the proposed project:
1. Veldman, J.W.*, K.G. Murray, A.L. Hull*, J.M. Garcia-C., W.S. Mungall, G.B. Rotman*, M.P.
Plosz*, and L.K. McNamara*. 2007. Chemical Defense and the Persistence of Pioneer
Plant Seeds in the Soil of a Tropical Cloud Forest. Biotropica 39: 87-93.
2. Murray, K.G., and J. Mauricio Garcia-C. 2002. Contributions of seed dispersal and
demography to recruitment limitation in a Costa Rican cloud forest. Pp. 323-338, in: Levey,
D. J., W. R. Silva, and M. Galetti. (eds) Seed dispersal and frugivory: Ecology, evolution,
and conservation. CABI Publishing, Wallingford, UK.
3. Murray, K.G. 2000. Fruiting phenologies of pioneer plants: constraints imposed by flowering
phenology, disturbance regime, and disperser migration patterns. Pp. 283-286 in: N.M.
Nadkarni and N.T. Wheelwright [eds]. Monteverde: Ecology and Conservation of a Tropical
Cloud Forest. Oxford University Press, New York.
4. Murray, K.G. 1988. Avian seed dispersal of three neotropical gap-dependent plants.
Ecological Monographs 58: 271-298.
5. Murray, K.G. 1987. Selection for optimal fruit crop size in bird-dispersed plants. American
Naturalist 129: 18-31.
4.1.1.1 ii. Other significant products:
1. Murray, K. G., S. Kinsman, and J. Bronstein. 2000. Plant-animal interactions. In
Monteverde: Ecology and Conservation of a Tropical Cloud Forest. Oxford University Press,
New York. Edited by N. M. Nadkarni and N. T. Wheelright. Pp. 245-302.
2. Wheelwright, N.T., W.A. Haber, K.G. Murray, and C. Guindon. 1984. Tropical fruit eating
birds and their food plants: a survey of a Costa Rican lower montane forest. Biotropica 16:
173-192.
3. Lepczyk*, C. A., K. G. Murray, K. Winnett-Murray, P. Bartell*, E. Geyer*, and T. Work*.
2000. Seasonal fruit preferences and digestive correlates in American Robins. The Auk
117: 709-717.
4. Murray, K.G., S. Russell*, C.M. Picone*, K. Winnett-Murray, W. Sherwood*, and M.L.
Kuhlmann*. 1994. Fruit laxatives and seed passage rates in frugivores: consequences for
plant reproductive success. Ecology 75: 989-994.
5. Murray, K.G., K. Winnett-Murray, E.A. Cromie*, M. Minor*, and E. Meyers*. 1993. The
influence of seed packaging and fruit color on feeding preferences of American Robins.
Vegetatio 107/108: 217-226.
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(d) Synergistic Activities:
Training of undergraduate research students: Since 1987, 83 undergraduate students from
Hope College and elsewhere have collaborated with Murray on research in Costa Rica or
the U.S., many with NSF support. All have presented or coauthored presentations at
scientific meetings, and most have or will coauthor publications resulting from the
collaborations.
Curriculum development for ecology and general biology courses: Murray is very active in
curriculum design at the undergraduate level, having developed investigative laboratory or
field exercises used in 7 courses at Hope College and at other institutions across the U.S.
Five of these have been published formally.
Interdisciplinary curriculum development: Murray also developed, with support from NSF, an
interdisciplinary mathematical biology course that focuses applications of linear algebra and
partial differential equations to modeling in population biology and disease. Murray also
teaches a course in Marine Biology and Biophysics with Dr. Peter Gonthier (Physics, Hope
College), and has taught a course in Island Biology and Geology with Dr. Brian
Bodenbender (Geology and Environmental Sciences, Hope College).
Interdisciplinary research: with funding from NSF and the Howard Hughes Medical Institute,
Murray has collaborated with three chemists (Drs. Kenneth Brown, William Mungall, and
Michael Short), a microbiologist (Dr. Aaron Best), and a parasitologist (Dr. Dereje Desta) to
study the roles of toxic seed chemicals in the demography of soil seed banks at
Monteverde, Costa Rica.
Panelist for NSF Conservation Biology and Field Station and Marine Labs proposals since
1990.
(e) Collaborators and other Affiliations:
i. Collaborators: Dr. Aaron Best (Hope College), Dr. Kenneth Brown (Hope College), Dr.
Thomas Bultman (Hope College), Dr. Dereje Desta (Hope College), Sr. J. Mauricio Garcia
C. (Organization for Tropical Studies, Dr. Peter Gonthier (Hope College), Dr. Carlos F.
Guindon (Monteverde Conservation League), Dr. William H. Haber (Missouri Botanical
Garden), Ms. Deborah Hamilton-DeRosier (Monteverde Institute), Ms. Lori Hertel (Hope
College), Ms. Katherine Horjus (UC Santa Cruz), Ms. Adrienne Hull, Dr. Mark Kuhlmann
(Hartwick College), Dr. Jianhua Li, Dr. Tammy Long-Robinson (Michigan State University),
Ms. Laurie K. McNamera, Mr. Dr. Randall Myster (University of Puerto Rico, Rio Piedras),
Dr. Graham Peaslee (Hope College), Mr. Mitchell Plosz, Mr. Jason Roberts, Dr. Garth B.
Rotman, Dr. Michael Short (Hope College), Dr. Debbie Swarthout (Hope College), Dr.
Joseph Veldman (University of Florida), Dr. Kathy Winnett-Murray (Hope College), Dr.
Brian Yurk (Hope College), Ms. Willow Zuchowski (Monteverde Institute).
ii. Graduate Advisors and Postdoctoral Sponsors: Dr. James Dole (California State
University, Northridge; M.S. advisor); Dr. Peter Feinsinger (University of Florida; Ph.D
advisor)
iii. Thesis Advisor and Postgraduate-Scholar Sponsor: Mr. Keiller Kyle, Purdue
University (I served as outside committee member on his M.S. committee).
iv. Undergraduate Research Students: 83 since 1987.
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5
Current and Pending Support
Brian Yurk
Bringing the latest science to Michigan’s Management of our coastal dunes. Michigan
Department of Environmental Quality Office of the Great Lakes Coastal Zone Management
Program. $92,200. Funded. PI: Brad Garmon. Yurk is senior personnel on this grant, which
funds work during 2013. Yurk will devote at most half-time developing mathematical models of
dune ecology, particularly focusing on Pitcher’s thistle for 10 weeks during summer 2013.
NSF-REU Site: Creating and sustaining a mathematical learning community. National Science
Foundation Research Experiences for Undergraduates. $225,774. Pending. PI: Darin Stephenson.
Yurk is senior personnel on this proposal. If this proposal is funded, and if notification is early
enough, some student support for the research proposed here may from this source.
K. Greg Murray
NSF-REU Site: Microbial Interactions in a Tropical Cloud Forest – Integrating Next-generation
Genetic Sequencing, Analytical Chemistry, and Community Ecology. National Science
Foundation Research Experiences for Undergraduates. $962,332, Pending. K. Greg Murray is
the PI on this proposal, and if it is funded, biology students will spend approximately two weeks
in the summer collecting samples in Monteverde before returning to the U.S. to analyze plant
extracts and microbial DNA samples. Murray is committed to 1.0 person-months per year from
1 April 2014 to 31 March 2018 for this project, and that commitment would be fully compatible
with the present request.
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