Research Proposal for Plant Ecology (Description)

Detailed Description of the Experiment

Introduction
Materials and Methods
Questions for Further Thought and Discussion
References and Links
Tools for Assessment of Student Learning Outcomes
Tools for Formative Evaluation of this Experiment

Introduction:

The final goal for this semester’s plant ecology lab is a proposal for research. This proposal will detail the experimental designs to answer a set of 4 hypotheses / questions concerning the distribution and abundance of plants in an experimental garden plot. This proposal will include:

background information (a literature review),
the significance or importance of this research,
general goals of the research,
specific hypotheses / questions to be investigated,
background about the experimental plots,
data of the current plant abundances and distributions,
details of the proposed experimental designs to investigate hypotheses / questions,
expected results, and
references.

       Since you will spend the majority of laboratory time on developing these research proposals, you will probably want to know why this is a worthwhile goal. Most of you will take one of several career paths after undergraduate school: a profession position related to biology, medical school, or graduate school. In any of these careers, you will likely read and evaluate research or research proposals or you will write research proposals and do research. Developing and writing a research proposal in this course will improve your evaluation and writing skills in general and specifically for research proposals. Even if you do not take any of the above career paths, there is something in this for you: improved writing skills and a writing intensive credit, improved interpersonal skills from working with a group, experience using field and laboratory techniques, and improved evaluation and interpretation of research literature. I also believe that the detailed development of hypotheses, an essential precursor to good research, is often simplified when teaching the scientific process. In short, much of this laboratory is about learning and practicing how science is done.

       There are a wide range of questions that you might investigate as plant ecologists. Any question investigated in plant ecology focuses on the patterns, causes, and consequences of plant abundance and / or distribution in nature. Early plant ecologists investigated questions about the patterns or distribution of groups of species (i.e. community ecology). More recently, plant ecologists started investigating the patterns and causes of population abundances and / or distributions (i.e. population ecology). In addition, ecologists now have many technologies to help answer questions about individual plant physiology and how it changes as the environment changes (i.e. ecophysiology). In other words in this class, we might propose to investigate questions about groups of plant species, populations of individual species, or the interaction of individual plants with their environment.

       The factors affecting plant abundance and distribution fall into two broad categories: abiotic and biotic causes or variables. Abiotic factors are any variable in the environment that is not living. These abiotic factors include, but are not limited to, light intensity, temperature, variation in temperature, length of growing season, fire regimes, soil moisture, rain fall, and seasonal variation in rain fall. Biotic factors are any variable in the environment that is created by another living organism. Biotic factors include, but are not limited to, competition, herbivory, mutualism, and disease. The basis for your research proposals will be hypotheses about relationships between 2 or more of these variables and individual plants, plant populations, or plant communities.

       From my perspective, there are many practical reasons for understanding more about plant ecology. Many of these reasons are conservation issues. One worldwide issue is the loss of species in communities of plants and animals. What are the causes and consequences of this change of species abundance in nature? Another worldwide issue is invasive species or non-native species of plants and animals that enter a community. What are the causes and consequences of the introduction of these invasive species into established communities? A third broad concern is that human population growth and development have placed many pressures on the natural habitats of plant and animal species. One of the most commonly stated causes of species endangerment is “loss of habitat.” The wide spread degradation of natural habitats makes restoration ecology an important application of many topics in ecology (Palmer et al. 2004).

       We will use a plot of land at Belmont Estates to motivate our hypotheses / questions about plant abundances and distributions. This may immediately raise the question, “What can investigations on a 60 m² plot tell us about the loss of biodiversity or habitat restoration? These processes happen at quite large scales.” One response is, “We have to start somewhere….” More specifically we can learn much about what is happening on large scales from processes at small scales. For example, past research shows that the plant species found in different climatic regions of the world (i.e. species growing on the northern tundra or species growing in Mediterranean climates) show broad adaptations to the abiotic conditions (e.g. seasonal air temperatures and length of growing season) created by those climates. These abiotic conditions are felt by individual plants. In addition, biotic factors like competition often help determine the abundance and distribution of the plants growing within broader regions. If two plants are adapted to grow in the same climatic region, but one of the two plants out competes the other, the better competitor may be more abundant. The process of competition acts over very short distances between neighboring plants. In short, to begin understanding ecological processes happening at large scales, we can start our investigations at small scales.

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Materials and Methods:

Study Site(s).

Students used an experimental garden plot on a college property close to campus. The garden was created on the grounds of Belmont, the Gari Melchers Estate, in Falmouth, VA. The plot was a 2 m X 30 m rectangular plot. The plot was historically an unmanaged pasture and has been mown, but not seeded or fertilized for several years. Two applications of Round Up, a general purpose herbicide, were applied to the plot, covered predominantly in perennial grasses, and the soil was roto-tilled to about 1 inch depth. This light till of the soil uprooted most of the dead vegetation and exposed the soil to direct contact with new seeds.

A mixture of forb, grass, and legume seeds were seeded into this plot. The list of seeded plants, purchased from “Prairie Nursery” in Wisconsin, is shown below. The seed mixture was applied at 1/3 greater than the recommended rate of seeding (rate recommended by the vendor = 1 lb. / 4400 ft²). Each of the plant types (i.e. forbs, grasses, and legumes) was applied separately. Plant types were seeded separately because the types have very different sizes and masses. The total seed allotment for each plant type was divided into ten equal parts by weight and added equally to ten-3 m sections of the plot. Seeds were hand cast at the beginning of the summer and the plot was left unmanaged for the summer. By the fall, the plot was well covered with plants from the planting and self established local species or volunteers. The herbicide, roto-till, and seeding treatments were one time treatments completed in 2001, followed by a controlled burn of the plot in spring 2003.

List of plants seeded into plots at Belmont
Forbs Smooth aster New England aster Pale purple coneflower Purple coneflower Rattlesnake master Ox eye sunflower Showy sunflower Bergamot Smooth penstemon Yellow coneflower Black eyed susan Sweet black eyed susan	Grasses Big bluestem Canada wild rye Indiangrass Switchgrass	Legumes Canada milk vetch Blue false indigo White false indigo Wild senna Purple prairie clover Canada tick trefoil Roundhead bushclover

Overview of Data Collection and Analysis Methods.

Prior to Lab

As currently organized, “Week 1” of this experiment, which is described below, starts in the second week of the semester (see Appendix1_syllabus_fall2003.doc, 36kb). Students learn the line transect method and practice developing hypotheses during the first week of the semester. I give a short lecture describing the characteristics of a good hypothesis and the line transect method. I also provide a handout describing the technique and goals for this lab (Methods for Line Transect Sampling). The students set up 3 meter line transects across the edge of a lawn and a woodlot. Groups of 3 - 4 students measure percent cover of all the species on the transect and describe patterns they measure in the plant species composition across the transition from lawn to woodlot. They have now used a quantitative technique to describe plant abundance and distribution. They also propose hypotheses for the causes of their measured changes in species composition.

Week 1: Introduction to Plant Community Plots.

Students visit the site of the experimental plot. They are given background information about the goals of the laboratory, and the creation of the plot and neighboring grassland (details provided above). It is important for students to first get the “lay of the land” before they do any measurements for background data on this plot of land. A combination of my description and their observations familiarizes the students with the plot, the plants on the plot, and the area of land surrounding the plot. I describe the plot and how it was created. I also describe a larger, adjacent grassland that was created similarly to the experimental plot.

I have several objectives for this first visit to Belmont:

describe the plot treatment so far,
observe a similarly treated grassland,
observe / name plants in the plot,
create a class herbarium,
describe plants in herbarium for future identification,
make qualitative observations of plants currently in the plot,
make qualitative observations of the plot itself

The students finish this lab by making qualitative observations of the current abundances and distributions of the plants in the plot. The qualitative observations by students are a visual inspection of the plants in the plot and the physical environment of the plot. Observations of the plants can be guided by a series of questions such as

“About how many species of plants do you see in this plot?”
"Are different species of plants distributed evenly across the plot? Are they distributed in obvious clumps?
"Are there any species of plants that seem relatively rare in this plot?"
"Do any of the species grow in only a small section of the plot?” and
"Do you see any changes in the composition of plant species as you move from one end of the plot to the other?”

       Observations of the physical environment include slope, adjacent land features and plants in the vicinity of the plot. For example, during the first year of this experiment, there was a garden beside the experimental plot and several species seen in the plot were also observed planted in the garden. These kinds of observations may spark ideas about how these plants came to grow in the experimental plot.

Week 2: Decide on Variables of Interest. Clarify and Quantify Observations.

       Groups of 2 - 3 students use line transects, a technique introduced prior to “Week 1” of this experiment, to quantify the abundance and distribution of the plant species in the garden (see Week 2: Quantifying Observations for formatting suggestion).

       Each group is then assigned to a section of the plot. Although it is not always necessary to identify plant species for this exercise, the class develops a reference herbarium for this experimental plot. As students find new species on their line transects, they bring specimens for identification and preservation. When possible, plants are identified to species. Otherwise, each species is given a generic name (e. g., grass 1, grass 2) that is consistently used by all student groups. This reference herbarium allows groups of students to compare and compile species specific data among different transects. After students have completed their transects, we return to the campus laboratory, and students share the data they have collected. Students must also state what abiotic variables they wish to collect in and around the experimental plot. This defines the equipment needs for the next week. Students start working in their research groups during the “Week 2” lab. Although the data collected here and next week are shared by the whole class, I believe it is useful to have students start working in their research groups now to get to know each other and develop their group relationships.

Week 3: Clarify and Quantify Observations. Measure Abiotic Variables.

       Students identify and map rare plants in the plot. Rare is defined by plants distributed such that they do not or are not likely to fall on a line transect. These rare plant data supplement the quantitative data collected the previous week. They may motivate students’ questions about causes of rarity or low abundance in plants. Students split into small groups to take abiotic variable measurements or to collect samples for abiotic variables. For example, one group of students will typically measure quantum flux at different levels in the herbaceous canopy. Students also typically wish to know something about soil moistures across the plot. Therefore, a group of students takes soil core samples for subsequent treatment and analysis. All students participate in the treatment and analysis of samples in the laboratory. For example, soil samples for soil moisture content must be weighed before and after drying in an oven.

Week 4: Statement of Hypotheses / Questions. Literature Reviews Begin.

       Students complete treatment and analysis of samples. They also share data from these analyses. Students decide among themselves how they will organize and move data between them. Students, in their research proposal groups, must state at least four (4) different hypotheses / questions. Student groups develop their own hypotheses / questions through a bounded inquiry. I work interactively with the research groups as they generate specific questions. During this process, I ask questions to clarify the dependent and independent variables that the students are working with. I also ask questions like, ”Are your independent variables biotic or abiotic variables?” “Are your dependent and independent variables measurable?” “How will you measure your variables?” “How are your 4 hypotheses / questions related to one another?” This last question is important because I want each research group to propose an integrated set of research questions. After agreeing on hypotheses, each group sends me an email copy of their hypotheses for my records. Sometime during this session, I give a 15 - 20 minute primer on the use of the college library’s online databases of the primary literature (see Week 4: Library Research Strategies).

Week 5: The Proposal - Content and Form.

       During this session, I preview my expectations for the full research proposal (see Week 5: Guidelines for Research Proposals) due at the end of the semester. This preview includes a description of the different sections of the proposal, some requirements on content, and examples (see Week 5: Example Research Proposal - Appendix3_proposal_example.doc (156k)). The research proposal must clearly state the 4 hypotheses / questions that were developed by the research group. Experiments must be proposed to answer each of these 4 hypotheses / questions. Students continue their literature reviews.

Week 6: Data Analysis and Presentation.

       I give a 15 - 20 minute primer on the use of spreadsheet software to generate graphs. This primer includes how to create a graph from scratch, as well as, some specific information on the format requirements for graphs (i.e. “instructions to authors” information). Editorial formats of graphs and bibliographies follow the conventions of Ecology and Ecological Applications and the examples in the research proposal guidelines (see above). Students also receive a description of annotated bibliographies (see Week 6: Guidelines for Annotated Bibliographies), which includes other examples of the correct bibliographic style.

Week 7: Experimental Design.

       I give a 20 - 30 minute primer on experimental design. This primer includes a review of dependent and independent variables, experimental units, the significance of randomization, types of variation, and several specific designs. I discuss completely randomized designs, blocked designs, factorial designs, and a strategy to eliminate repeated measures in experimental designs.

       Students also get a preview of the oral presentation requirements during this lab class. The presentation requirements and information on developing a quality oral presentation are covered in more detail in the “Tools for Assessment of Student Learning Outcomes” section below.

Week 8: Annotated Bibliography Due.

       Students hand in their first assignment, an annotated bibliography. This assignment is meant to provide most of the information students will need to write the background section of their proposal.

Week 9: Oral Presentation #1.

       Each oral presentation is given as a research group. But, individuals are given individual assessment for their part in the presentation. The focus of this presentation is literature review, background data, and a specific statement of hypotheses / questions. Students are assessed (see Week 9: Oral Presentation Midpoint Assessment Form) on the quality of their presentation organization and style. I use this exercise partly as a formative assessment to give students feedback on the content they have gathered so far. The presentation length is 15 minutes.

Week 10: Data Presentations Due.

       Students hand in any graphs and/or tables they will include in their final research proposal. These data are preliminary data collected from the field site or relevant data collected from other sources. An example of other relevant data would be local, monthly, mean air temperatures or average length of growing season. All students must present a graph of the plant distributions in the experimental plot, as this data was the original motivation for hypotheses / questions. Any other data collected from the plot or external sources (e.g. local mean high temperatures) that are relevant must be handed in at this time. Before this, students have been given instruction on the criteria for and examples of good graphs and tables. My assessment focuses on editorial requirements (e.g. fonts, font sizes), clarity of data presentation, and completeness of the title / caption.

Week 11: Peer / Supervisor Review.

       A complete rough draft of the final research proposal is due at this meeting. Students exchange a copy of their drafts with 2 students not in their research group. I have not made this an anonymous review process, although this could easily be done. Each student chooses their 2 student reviewers. I provide guidelines or criteria (see Week 11: Guidelines for Peer Reviews of Research Proposals) for this review by peers. I also review papers at the request of authors. Many questions about experimental design come up at this time and I can use this as formative feedback on experimental designs.

Week 12: Oral Presentation #2.

       Each oral presentation is given as a research group. But, individuals are given individual assessments (see Week 12: Oral Presentation Final Assessment Form) for their part in the presentation. A literature review and statement of questions are given, but briefly, because they were covered in the first presentation. This second presentation focuses on expected outcomes, experimental designs, and potential benefits. Students are assessed on the quality and organization of the presentation. Students are assessed on the quality of their literature review, statement of questions, and appropriateness of experimental design, but not during this oral presentation. The quality of their literature is assessed in their annotated bibliography. The quality of their questions is formally assessed in the research proposal, but I’ve provided enough feedback before this to work out most problems. Lastly, I use this oral presentation as a formative assessment to give students feedback on experimental designs. They are then given time to incorporate these design changes into their written research proposals. I do this for two reasons. First, creating experimental designs to answer specific ecological questions is little known or completely unknown to most of our students. Therefore, they need the time and feedback to work out the details. Second, students have given me feedback on evaluations that a week between the second oral presentation and the written research proposal is very important for them to make necessary changes to their experimental design, based upon my comments during oral presentations.

Week 13: Final Paper Due.

       Students hand in their final research proposals and do the course evaluation. Student experimental proposals are assessed based upon a grading rubric (see Week 13: Research Proposal Final Assessment Form).

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Additional Documents Are Available in the Links Below.

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Questions for Further Thought and Discussion:

Discuss the relationship between a factorial experimental design and the concept of interactions we’ve talked about in lecture.

The experimental garden at Belmont was populated by plants seeded into the plot and volunteers that may have been in a seed bank. How would you describe the different processes that determine the presence or absence of these different plants to this plot. What experimental designs might you use to distinguish among the processes that determine the presence or absence of seeded or seed bank plants?

Describe the broad goals of your experimental program and the specific hypotheses / questions to be answered by your experiments. State how these goals and questions are different from one another by relating them to your background concepts and your experimental design.

Pick your favorite abiotic dependent variable and your favorite biotic dependent variable. Also, choose some independent variable like (don’t limit yourself to my list) growth rate, carbon fixation, or seed production. Describe your expected results from a simple 2x2 factorial experiment. I would like you to describe 2 possible outcomes: results to show no interaction between the two variables and results to show an interaction between the two variables.

As a plant ecologist let’s say you are interested in conserving populations of a Federally endangered plant. How would you suggest going about doing the research that would help restore the populations of this rare plant? Would you approach it from a population ecology perspective (i.e. investigate the factors that impact the population dynamics of this single plant)? Would you approach it from a community ecology perspective (i.e. investigate the community and community dynamics in which the populations of the plant live)? Describe at least 2 advantages and disadvantages of each approach to restoring populations.

The hypotheses / questions you have proposed have probably dealt with the distribution and/or abundance of plants in space. Take one of your hypotheses and restate it so that it looks at the distribution and/or abundance of plants in time. Describe how you would have to change your experimental design to test this new hypothesis / question.

*** Note: Answers to many of these questions and numerous other comments by the contributing author can be found in the "NOTES TO FACULTY: Comments On Questions for Further Thought" page.

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References and Links:

Terrestrial Plant Ecology

Science

Annual Review of Ecology and Systematics

Annual Review of Ecology, Evolution, and Systematics

Journal of College Science Teaching

Bounded inquiry description

Table describing "Inquiry Framework: Levels of Student Ownership"

Web page on Learner Centered Teaching and syllabus development (www.cte.iastate.edu/tips/syllabi.html)

digital.library.okstate.edu/oas/oas_pdf/v71/p43_45.pdf

Aeschynomene virginica

Plant Ecology

www.geobotany.uaf.edu/teaching/biol474/lesson14slides.pdf

www.serg.sdsu.edu/SERG/techniques/mfps.html

biometrics.hri.ac.uk/experimentaldesigns/website/hri.htm

www1.agric.gov.ab.ca/$department/deptdocs.nsf/all/sag3024?OpenDocument

www.tfrec.wsu.edu/ANOVA/

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Tools for Assessment of Student Learning Outcomes:

       Students are assessed on two oral presentations and three written assignments. The integrating assignment for the semester is a written research proposal of a standard form. This proposal does not include a budget. Different portions of the research proposal are collected as the semester progresses. This modular development of students’ proposals is designed to give students feedback on segments of the proposal before the complete proposal is due at the end of the semester. This strategy allows students to improve the content and format of their proposals through formative assessments from their instructor and peers. This section is organized first by assignment and second by assessment goal.

Assessment by Assignment

       The first assessment due is an annotated bibliography. The goal of this assessment is for students to organize their background research in order to focus on their hypotheses / questions. Students receive a description of an annotated bibliography (see Week 6: Guidelines for Annotated Bibliographies). Annotated bibliographies must be in alphabetical order by the first author’s last name. The bibliographic style must match that of Ecology and examples are given in the annotated bibliography handout and the proposal guidelines (see Week 5: Guidelines for Research Proposals). Students are graded on style and organization of their bibliographies. The content of the annotation is graded based upon how well it is focused on the questions and results of the bibliographic reference. In addition, the annotation is graded based upon how it is related to the student’s hypotheses / questions.

       The second assessment is the first of two group oral presentations. The grading sheet used for oral presentations should be shown to students the week before their presentations (see Week 9: Oral Presentation Midpoint Assessment Form). This explicitly shows them the criteria for the assessment of their performance. On the grading sheet, positive feedback and constructive criticism are particularly important as they should give the speaker a clear statement of how to improve the content and organization of their presentation, as well as goals for improving their public speaking skills.

       The third assessment is data presentations the authors will place in the final proposal. Students primarily have graphs and few tables. This is because most of the data we collect is best presented in graphs and I also stress that data should be presented graphically whenever possible. The evaluation of these graphs is straight forward. I have seen many if not most of these graphs previously and had a chance to comment on the format and titles / captions. My main criteria for a quality title / caption is “Does this title / caption allow the data presentation to be understood when it stands alone?” In terms of form and formatting, I provide examples of graphs that are consistent with Ecology editorial standards and I also provide copies of Ecology.

       The fourth assessment is the second group oral presentation. The second presentation focuses on the segments of the experiment proposal not covered during the first presentation. These are also the segments of the proposal that the students have been working on since the first presentation. The grading sheet used for oral presentations should be shown to students the week before their presentations (see Week 12: Oral Presentation Final Assessment Form). They should also have copies of their assessment from the first presentation.

       The final assessment is the students’ written proposal. Most sections or elements of this proposal have been seen several times before it is handed in for assessment. That said, it remains a complex writing task for most of the students. Proposals are assessed objectively for both form, about 25% of the total grade, and content, about 75% of the total grade (see Week 13: Research Proposal Final Assessment Form).

Assessment by Goal

Goal: Students present information orally
Assessment: Oral presentation scoring rubric; instructor and peer review
Overview: Effective public speaking skills are an integral part of many, if not most, of the professional and/or post-graduate positions our students will hold. Students are given criteria for their presentation assessment (see above), so they know the elements of public speaking on which they will be graded. There are many strategies for evaluating public speaking and criteria can change over time. Students are also provided several resources to guide them through preparing presentations. Our campus has a well appointed Speaking Center (http://www.umw.edu/spkc/center/) where students can go to practice and get detailed feedback on any aspect of their presentations, from initial organization to final presentation. Students also are given access to documents produced by the UMW Speaking Center staff that provide guidance for this process:

Goal: Students formulate research questions / hypotheses
Assessment: Instructor / student interactions, oral presentation assessment, and written proposal assessment
Overview: Some student feedback suggests that, of all the components of science methodological skills, they have had the least practice formulating clear and precise research hypotheses / questions. Students formulate their questions, in collaboration with peers in groups of 2 or 3. Research groups also consult closely with the instructor. My input in the process is meant to focus students’ attention on the dependent and independent variables in which they are interested and the measurability of these variables. I also guide students to ask questions that are, in some way related to each other. This relationship provides each research group with a larger perspective for their research proposal. Once these questions have been formulated and agreed upon by each group and the instructor, each group sends an email that records the agreed upon questions. Research questions are formally assessed within the context of the group oral presentations and the written proposal. Assessment of questions in the written proposal goes to how well students describe the relationship among their questions and whether or not their experiments answer those questions (see Week 13: Research Proposal Final Assessment Form).

Goal: Students apply appropriate designs to specific research questions / hypotheses.
Assessment: Oral presentation assessment and written proposal assessment.
Overview: These are the guidelines for the students’ experimental designs: 1. Some of the proposed experiments must be controlled experiments in the field, 2. At least one of your experiments must be an experiment that will answer all or part of a particular hypothesis, and be a laboratory or greenhouse experiment, and 3. Observational experiments can be proposed, although they are not required. Students are encouraged to use experimental designs they have found in papers on related research and they are encouraged to use factorial designs. During the 7th week of the exercise, I provide criteria for design of good experiments. I provide feedback to the research groups during their 2nd oral presentation and formally assess designs while grading the final proposals (see Week 13: Research Proposal Final Assessment Form). Questions about experimental design consistently arise during the peer reviews.

Goal: Students self organize for data collection tasks and data sharing among themselves.
Assessment: Peer comments and assessment.
Overview: Students are given free rein to organize the class for data collection and data sharing, once they are clear on the requirements. I have not done any formal assessment of this process. Two things seem to happen during data collection and sharing. Either a group of leaders forces the class the pause and think about efficient ways to collect and share or a group realizes how inefficient they have been and tries to remediate.

Goal: Students critically assess peers’ research proposals.
Assessment: Peer assessment.
Overview: It is critical that students learn self assessment and peer assessment skills. Each student seeks 2 peers, not in their research group, to review a rough draft of their proposal. This is done during lab time. Each student is given criteria for their review of the proposals orally and in writing (see Week 11: Guidelines for Peer Reviews of Research Proposals). This is an exercise primarily for students to develop evaluative skills. Secondarily, students read their peers’ work for comparison to their own writing.

Goal: Students organize and write a research proposal.
Assessment: Scoring rubric on proposal sections and final proposal. Peer review of written proposal.
Overview: While students have received considerable feedback and assessment on components of the written proposal, the writing and integration of the final proposal is a complex task. Early in the semester, I describe the components of the proposal in detail (see Week 5: Guidelines for Research Proposals) and provide an example of a good proposal (see Week 5: Example Research Proposal). I will also make good student proposals available for examination as I gather them into my files. The proposals are assessed according to the proposal grading rubric (see Week 13: Research Proposal Final Assessment Form), as stated before.

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Tools for Formative Evaluation of this Experiment:

To date, I have received formative evaluation of this experiment in the context of my student course evaluations. This instrument (i.e. the course evaluation) is not designed to give consistent formative evaluation.

An extensive discussion on Evaluation appears in the Teaching section of this site.

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