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Welcome to Biocore 302 Evolution, Ecology, and Genetics Lab!

Biocore Lab Courses Are All About The Process Of Science
You may be familiar with the model for scientific investigations known as the "Scientific Method." The model presents a logical sequence of steps leading from an initial observation to an experiment and interpretation of data. However, few scientists actually carry out investigations according to the rigidly defined linear sequence of steps. What they do is to engage in the following activities: 1. Making Observations and Generating Testable Questions: Making Observations takes a careful, keen eye and experience in differentiating subtleties and slight differences in whatever you are sensing (visually or smell, touch, taste too!). Through careful observation, we notice patterns that provide the basis for inferring explanations, predictions and cause-effect relationships that result in questions that can be tested or measured in an empirical way. 2. Formulating Hypotheses Supported By A Rationale: Forming hypotheses requires stating tentative explanations or answers to your testable question based on background knowledge about the system you are investigating. A hypothesis is not simply an educated guess. It must be supported by a substantive rationale (what we will refer to as a biological rationale), have explanatory power, and make a prediction that can be tested. 3. Designing And Conducting An Investigation: This process includes planning the methods and procedures for gathering data to answer a question, evaluate a hypothesis, or challenge a theory. You test hypotheses by designing manipulative experiments or making careful systematic observations that evaluate the actual outcome against the predicted outcome. The type and design of your investigations is based on the questions you ask as an investigator, your knowledge of the study system, AND the general knowledge available in the scientific literature. In short, you need to understand the complexity of the system before measuring it. 4. Analyzing and Interpreting Data: Investigators attempt to find patterns and provide meaning in a group of data in a particular context. When working with data in this class, we will emphasize the need to make connections between your data, the concepts and context underlying the project, and the assumptions you are making in your experiment. Interpretation of data should bring you back to your hypothesis, which you can either support or reject. 5. Constructing New Knowledge: If you reject your hypothesis based on the interpretation of your data, you may conclude that the assumptions you made about the system are not valid or that the way you are thinking about your system is incorrect. You have not failed or made a mistake if your experiment leads you to reject your hypothesis. Nor have you proven your hypothesis true if your data supports your prediction. You have simply supported or accepted your hypothesisunder this specific situation. With more precise measurement, different statistical tests, or repeated experimentation in different environmental conditions with different organisms etc... your data may force you to reject your hypothesis. This should lead you to a new, more sophisticated hypothesis as you increase your knowledge about the system. You might even find that the patterns that you see run counter to what you read in the scientific literature, in your textbooks, or even are in opposition to what your instructors think (gasp!). If
Biocore 302, Fall 2013

2 thats the case, you have just learned or discovered something new! Now that is exciting and.that is the process of science. 6. Communicating your Science: As you question your analysis/ interpretation, or when you talk about or write about your understanding, you expose your ideas to discussion and debate. This is sometimes uncomfortable but is an essential form of feedback, and it helps to clarify fuzziness in our thinking. Communicating and receiving feedback on your science, and reviewing scientific work of your peers provides essential quality control and expands the knowledge we have collectively as a scientific community. In practice, above and beyond meeting expectations for a grade-- communicating your science clearly and effectively provides a vehicle for sharing and constructing new knowledge with others, and allows the next generation of scientists (AKA next years Biocore students) to stand on the shoulders of giants (Sir Issac Newton).

How this Applies to Biocore 302-Course Goals & Outcomes

As instructors, we are here to help you and to facilitate your learning of biology and your development as a scientist in an active way, but ultimately you bear the responsibility for learning the material, developing skills and taking ownership of your education. We will challenge you to go beyond simple memorization of details, to interconnect concepts, applications and problems; to ask meaningful questions; to test well-developed hypotheses; and to communicate your findings to your instructors and peers within the realm of science. These are lofty goals! We set high standards for you because we expect that you can reach them! Our overall goals in this course are to: 1. Give you experience applying and expanding upon the concepts discussed in Biocore 301 2. Engage you in the process of science as described above 3. Give you experience working with the tools and procedures of ecology, genetics, and evolutionary biology 4. Improve your scientific communication skills and your capacity to give and receive feedback on your ideas. 5. Improve your capacity to work as a member of a productive, collaborative research team. 6. Give and receive constructive feedback using professional communication and effective interpersonal skills 7. Contribute to a safe, sustainable, socially and ethically responsible research and learning environment At the end of two (three)* semesters of Biocore labs, students should be able to: *Students are only required to take two of the three Biocore labs. Many choose to take all three! 1. 2. 3. 4. 5. 6. 7. 8. 9. Make careful, systematic observations Ask testable, relevant, creative scientific questions Search, sort and gather relevant background information from texts and primary literature Make predictions and formulate clear, testable hypotheses Develop protocols that test hypotheses Evaluate assumptions associated with experimental design and the biological system Analyze data and make logical conclusions utilizing statistical reasoning Communicate effectively about science through writing and oral presentations Do productive group work

Biocore 302, Fall 2013

3 In the process, we hope you will begin to see your instructors as people who bring special skills and a vast array of experiences to complement the class rather than as authorities who know all the answers. In addition, we hope you can hone your group work skills given that science is not a solitary process but one that relies heavily on collaboration and teamwork. Four Strategies for Doing Well in Biocore Labs 1. Be prepared. Do Pre-lab assignments and read the relevant section of the lab manual carefully ahead of your laboratory meeting time and be sure you understand the question(s) the project is attempting to answer and the approach you will be taking to answer these questions. Careful preparation will save you a great deal of time both during lab and in writing assignments. Pre-lab assignments are designed to help in this process. 2. Make the most of the time you have in lab. Collect the necessary data and make detailed notes in your lab notebook. In many cases we have allowed time in class for you to begin analyzing and discussing your data, preparing presentations and getting feedback from peers and instructors. Take advantage of this opportunity and resist the temptation to leave early. This is where the most learning takes place. 3. Start writing your lab papers well before the deadline and pay attention to the many tips from your instructors, in the lab manual, and Biocore Writing Manual. We emphasize writing in this course not only because communicating your ideas is part of the scientific process, but also because writing about a subject helps you understand more clearly and at greater depth. This takes time. Many times during the semester you will have the opportunity to have your paper reviewed by a peer before turning it in for a grade. This is an excellent opportunity to remedy problems before turning in a final copy. If your peers cannot understand what you have written it is unlikely that the instructor will understand. 4. Cultivate a relationship with your Biocore peers. Your peers are an incredible resource and have much to offer you in the way of support and advice in this course. These are the people you can depend on for the next three semesters!

Biocore 302, Fall 2013

Biocore 302: Ecology, Genetics and Evolution Laboratory - Fall 2013 Schedule
Week/ (date) Topic Disc Activities and InClass Check Assignments Lab Activities Graded and Check Assignment due in Weight* Lab (done individually unless specified)

Pre-Semester Assignment: Review syllabus, read Preface and Chapters 1 & 2 of Biocore 302 lab manual BEFORE lab. Do the Pre-Semester assignment on p. 23 of lab manual. How do you DO the Process of Science in Ecology Genetics and Evolution?
Prairie Sept. 3-6 Ecology I Prairie Ecology II ECOLOGY: How do you generate testable questions? NO Discussion Sections Field trip to Biocore Pre-lab assignment due in lab Prairie (meet in 341 Choose prairie experiment in lab Noland) 4%

*Field work at Biocore Paper review worksheet (1/pair) Experimental design Prairie- (meet in 341 & Group Effort Analysis (GEA) form worksheet before disc Noland) Material & Schedule *Experiment set up and sheet (1/team) data collection *Hypoth/ Expected Results Activity How do you work with data? Data Analysis *Data entry and Intro to Analysis of Biocore Data Analysis Prelab (Intro to Sept. Excel Prairie Data Descriptive Stats) 16-20 Discussion & Conclusion Activity How do you communicate scientifically? Urban Biocore Prairie paper & GEA & Formal Peer Review: Field work at Willow Stream Creek & University Bay Authors response due 48 h after disc& Exchange paper drafts Sept. 23- Ecology I (meet at Willow Creek) Peer Review (PR) with partner and 27 complete review at least Tentative research question for 24h before disc. Willow Creek proposal (1/team) *Focus on Peer Review (PR): our expectations How do you measure complex systems? Urban Materials and schedule sheet Experimental design Informal Feedback Sept. 30- Stream Presentations - Willow detailing how, when, and who will worksheet due in disc Oct. 4 Ecology II *Identifying knowledge Creek research proposal perform each step of experiment (1/team) gap activity *Teams prepare Revised Experimental design feedback presentation worksheet due 48h after lab (1/team) slides How do you construct new knowledge? Urban Preparing for field work Willow Creek Field Individual conferences with TA for Oct. Stream Work Biocore Prairie Paper- outside of class 7-11 Ecology III (meet at Willow Creek) Sept. 913 ECOLOGY INTO GENETICS: How do you generate testable questions? Cell Division and Plant Willow Creek Paper Formal peer review: Life Cycles & authors response & GEA Exchange paper drafts & peer review due 48 h after disc with partner and complete review at least 24h before disc. Cell, flower & fruit drawings and observations Genetics I: *Basics for gene Introduction to Brassica FastPlants/ Genetics pre-lab due in Intro to expression & signal rapa (FastPlants)- life lab Quantitative transduction cycle, plant breeding, and *Group work/behavior- phenotypes and genetics F1 phenotypic measurements Mendelian check in (1/team) Genetics with * Mid-semester evals Tentative independent variable to Brassica rapa investigate Cell Division & Life Cycles: Genetic Variation


12% 2%


15% 2%

Oct. 1418


Oct. 2125

Oct. 28Nov 1

Genetics II: Proposing and Starting Experiments

*Begin Brassica rapa experiments outside of lab time How do you work with data and communicate scientifically? in a CONCISE way? Genetics III: Formal peer review: Preliminary data Practice Data Analysis Nov Collecting collection Worksheet Exchange proposal 4-8 preliminary poster drafts with data Brassica proposal posters (minipartner and complete posters) due Friday Nov. 8 review at least 24h before disc. Genetics IV: *Complete Brassica *Discussion/ Conclusion Complete Brassica rapa Nov Data Analysis data collection Activity for B. rapa experiments 11-15 and Poster *Introduction to the Development Galapagos and finch evolution field trip to Evolution I the Zoology Museum ECOLOGY & GENETICS INTO EVOLUTION: How do you measure complex systems? Nov Evolution II: Informal peer review *Introduction to historic Tentative research question for 18- 22 Using data to final posters- outside data on Galapagos evolution grant proposal (1/team) develop finches questions Evolution activity *Group Time- work on Brassica final posters (mini-posters) research question, gather &GEA due in disc literature, analyze historic data, prepare to Evolution pre-lab due in lab share progress in lab Nov. 25- Evolution II: Experimental design Thanksgiving Recess 29 Using data to worksheet due in disc No Labs develop questions Evolution III: *Teams prepare Finch evolution proposal Dec Developing feedback presentation Powerpoint feedback 2- 6 hypothesis session and rationale Evolution IV: *Writing group paper Finch presentations Formal Grant Proposal Dec. 9Presenting Informal peer review: presentations (1/team) & GEA 12 work practice presentation in forms discussion (group peer review) Finals Evolution Grant Proposal (1/team) & GEA due Sunday Dec. 15- electronically to TA week Team work, class participation and check assignments

*Teams prepare feedback presentation Brassica rapa experimental design (1/team)

Brassica rapa proposal Powerpoint feedback session

Materials and schedule sheetdetailing how, when, and who will perform each step of experiment (1/team)


15% 4%


15% 3%

Operating Principles & Procedures

Class Attendance and Time Management

Each week you will attend a 50-minute discussion section and a 3-hour lab. You should also plan to spend time outside of regular class hours to work on literature searches, project development, some data collection, data analysis, PowerPoint and poster preparation, paper writing, and peer review. Lab Etiquette For use of 341 and 334 lab rooms: Access and use of lab rooms outside of class time is a key component of our Biocore learning environment and community, but it comes with responsibility. You may use 341 for group or quiet study when no classes or meetings are in session. Use 334 for doing experiments and meeting with lab research teams. Both 341 and 334 lab rooms have key lock boxes that you will be given access to after the start of the semester. If there is any misuse or suspected misuse of the rooms, if the rooms are not cared for or left

untidy or down right dirty, or if equipment/ books/ furniture are out of place or missing we will no longer be able to allow student access to these rooms outside of class time hours. In short, be good Biocore citizens and take care of your lab rooms! For use of the printer in 341 lab: Reserve only for critical lab work. Do not print your lab papers or primary literature papers on this printer unless you ask your instructor. At NO TIME should you be printing lecture course notes or materials for any other course. For use of computers: You will have access to 11 PC laptops. The laptops are located in a room adjacent to 341 and can be checked out (with your student ID) by request of your instructors. Do not download applications to these computers and do not store your valuable files on the hard drive (the drives are wiped clean regularly). During presentations and discussions: Your presence and participation in class is extremely important for your learning and the establishment of a positive, effective learning environment for everyone (students and instructors). With this in mind, we ask that you DO NOT have your computers open, use electronic devices or study for other courses during our class meeting time. Group work & Participation Learning to work as a productive collaborative team is an essential skill for all professions. Collaboration increases the number of perspectives focused on a complex problem, and it increases creativity and capacity for productive work! Unfortunately, group work can sometimes be unproductive if team members do not value or invest in the team or shared goal. We consider collaboration a skill that needs practice to become competent. Throughout the semester you will be assigned to different groups by your instructors, therefore giving you an opportunity to practice working with different personalities and approaches. Part of working productively as a team member is being independently accountable for the knowledge you gain & the work you do while respecting and encouraging the work of others. Although we expect you to discuss ideas and work through problems and analyses with your teammates, you need to demonstrate your accountability for the project by writing proposals and final papers individually- on your own. Note that the first assignment (paper review), revised experimental design worksheet, final finch presentation and finch grant proposal are all group grades, and so 27% of your final semester grade results from "Team" efforts. Your team & class participation grade will be based on the quality of your check assignments, attendance and participation in class discussions and research team efforts. This grade is determined by input from both your instructors and from your teammates with a Group Effort Analysis (GEA) form and weighted as 3% of your final semester grade. Papers & Posters Written assignments will be done in the form of a scientific research proposal or final paper, poster, or grant proposal and are graded using the rubric criteria described in the Biocore Writing Manual. Collaborators must be listed on all papers and posters submitted individually (highlight author) or by the research team. Presentations As a Writing Intensive/ CommB course, Biocore 302 provides a number of opportunities for you to improve your oral communication skills about your science. You and your research teams will prepare and present three informal, PowerPoint feedback presentations in the format of a research proposal when you are planning your research projects (similar to what graduate students do in their research labs). These presentations are not graded, but will allow you to receive essential and valuable feedback from your instructors and peers prior to you doing your experiment AND prior to writing a research proposal. Although not graded, feedback presentations are where a great deal of learning happens- for both the presenters and the audience. You and your team will also give one formal presentation at the end of the semester to summarize your finch evolution project. This presentation is graded and requires presenters to focus on both the scientific rigor of the project as well as how it is presented to the audience. (See the 2012 Biocore Writing Manual for our expectations.)

Peer review You will have 3 opportunities to be a peer reviewer (as well as to have your work reviewed) this semester. Formal peer reviews (listed in the syllabus) are done in discussion and require partners to exchange draft papers at least 24h before discussion to allow time for thorough review. You will turn in a copy of the review you received with each assignment, along with an authors response form that briefly explains major revisions as well as what advice you took and did not take from your reviewer, and why. Your peer review grades will be based on the rubric on p. 40 of the Biocore Writing Manual. Even when not required, we strongly encourage you to use the peer review process before turning in papers or posters. Late Assignment Policy Papers & assignments must be handed in at the specified/ place time unless you have contacted your TA ahead of time to request an extension due to emergency or extenuating circumstances. Otherwise, we will deduct one grade per day it is late from the grade you would have received (e.g., A->AB for one day late). Note that even an F paper (one week late) counts more than 0 (not handed in at all) when we total the final grades at the end of the semester. Late papers should be given directly to your TA, Janet Batzli, or Seth McGee (NOT put in a mailbox or submitted electronically). If you know of a religious observance or other commitment this semester that will keep you from attending class, let your TA and Janet Batzli know as soon as possible. Honor and Honesty, Ethics and Social Responsibility is essential The validity and accuracy of scientific findings are open to review. Your data is NOT PERSONAL, data is neither correct/incorrect or good/bad and should therefore not be associated with a personal value judgment. We have had some problems in labs with students fabricating or changing data. We consider this a serious violation not only of ethics but also of scientific principle. You are not graded on your results but rather on how you analyze your data. It is absolutely essential that you report your data honestly and accurately. In addition, we have had several instances where students have copied and pasted segments and whole sections of their classmates papers, changed the wording/order a little, and claimed the work as their own, either in drafts for peer review and final papers or in pre-lab assignments. Not only is it plagiarism, claiming credit for the intellectual work of others is highly disrespectful and erodes trust within our Biocore learning community. If you find yourself tempted (especially late at night just hours before a paper is dueweve all been there) JUST DONT DO IT. It is much better to ask for an extension, receive a slightly lowered grade for a late paper, or even receive a zero for a missing assignment than to plagiarize your classmates or someone elses work. You agreed to this when you signed the Biocore Honor Code during the first week of Biocore 301and will be held accountable for violations according to UW Academic Code of Conduct 14.03 How you earn your final grade We use an absolute grading scale in 302 (no curves!). You will be participating in both individual assignments (73%) and group assignments (27%). Assignments, due dates, and assignment weight in percent are detailed in the schedule above. Pre-lab assignments are graded on a point percentage basis. Papers and posters are graded using rubric criteria described in the Biocore Writing Manual and reported to you as a letter grade (A&, A, AB, B&, B, B-, BC, C). Letter grades are converted to numeric values when final grades are tallied at the end of semester (e.g. AB=89, B&=87). Check () assignments are scored simply adequate or inadequate. Your final percentage score will be converted to a final letter grade as follows: Final Assignment % Letter Grade 90-100 A 80-89 B 70-79 C 60-69 D
*For those few individuals that are on the borderline at the end of the semester, we will assign intermediate grades (AB and BC) based on our evaluation of your participation (in both lab AND discussion), teamwork and your effort.

Chapter 1. How do we know what we know in science? Introduction to Designing Scientific Investigations
Author: Janet Batzli Our first laboratory is designed to introduce you to scientific inquiry through the perspective of an ecologist, and to prepare you for the field projects that we will be taking during the next 6 weeks in the Biocore Prairie and in Willow Creek. These labs will provide the basis for the study of ecology and introduction to scientific inquiry.

Learning Objectives
By the end of this lab unit you should be able to: 1. Explain the importance of sampling, replication, controls and sound experimental design. 2. Evaluate, revise and develop a testable question 3. Work in a group to discuss, evaluate, and generate an experimental design for a prairie project 4. Generate a specific hypothesis and biological rationale aligned with a testable question Key terms: testable question, systematic observation, manipulative experiment, abiotic factors, biotic factors, independent and dependent variables, replicates, sample, population.

How do we know what we know in science? Focus on Testable Questions, Biological Rationale, Hypothesis and Scientific Investigation
Inquiry of any type starts with observations and questions. We all ask questions because we are naturally curious about the world around us. Scientific inquiry begins the same way...starting with general observations, information and questions that become more specific as you learn more about the system and the context you are working in. Although these initial questions are essential, not all questions can be answered using scientific investigations. Therefore, we need to distinguish between broad questions, that begin the process of inquiry but are not testable, and testable questions -- questions that can be answered through measurement and observation. Testable questions include an independent variable (something that is changed, manipulated, selected), and a dependent variable (something that is measured) Basic criteria for testable questions: 1. Testable questions can be answered through investigations that involve manipulative experiments or systematic observations (studies where nothing is being manipulated, but some element or process is being observed carefully over time or in different environments). 2. Testable questions are answered by measuring something using a standardized or calibrated approach 3. Testable questions relate to scientific ideas rather than personal preference or moral values. Biocore 302, Fall 2013

5 4. Testable questions do not relate to the supernatural or to non-measurable phenomena. Once you have a testable question, the next step is to generate a biological rationale and hypothesis. The hypothesis and biological rationale work together to lead up and frame your investigation. The biological rationale is your reasoning that explains why you think your hypothesis is true and your experiment is logical. [This is a tough concept! Be patientwe will unpack the concept of biological rationale in the coming weeks.] In short, your rationale combines what you know about the system, what you learn from the literature, and makes clear important assumptions that outline the knowledge gap that your investigation will address. The hypothesis leads directly from your rationale, providing a very clear prediction of the outcome of your scientific investigation. The hypothesis spells out in specific detail, the independent variables to be compared, the dependent variables that will be measured (with units), the direction of the outcome, and the system that you will be working in for your particular investigation. Perhaps an example of the flow of these elements is in order ... Table 1: An example flow of logic from broad question to design of a scientific investigation. Elements leading up to an scientific investigation
Broad question (non-testable) Testable question Biological rationale

Why do hummingbird pollinators prefer some flowers over others? Is high sucrose concentration in floral nectar of tabacco (Nicotiana sp.) associated with greater number of hummingbird visits? Sucrose based nectar concentrated in nectaries of tabacco flowers serves as an attractant and reward for many species of bee pollinators (Tyler 2005). Careful sampling of nectar from different tabacco flowers blooming on the same plant suggests that high sucrose concentration (above 40% sucrose w/v) is found in newly opened flowers and that sucrose based nectar concentration varies with age of flower (Sutherland 2010). Although hummingbirds are frequent visitors of tobacco flowers, it is unclear how variation in sucrose concentration in different flowers of the same age influences the number of hummingbird visits. Increasing concentration of sucrose in nectar of tabacco flowers [INDEPENDENT VAR] is positively correlated with greater numbers of hummingbird visits [DEPENDENT VAR]. Grow tabacco plants in a location where hummingbirds naturally frequent. Upon flowering, label and sample floral nectar from 20 different tabacco flowers of the same age using micro-pipet and refractometer technique (Broyles 2004). Observe number of hummingbird visits to labeled flowers over 2 hours following nectar sampling.

Hypothesis Experimental Approach

Introduction to Experimental Design

Get to know your system After you have developed a testable question, but before you run out to the field or into the laboratory to start collecting data, you will need to do quite a bit of background reading and take some observations to get familiar with the system you are studying. Biocore 302, Fall 2013

6 For instance, imagine you are investigating how variation in sucrose concentration of plant nectar affects the number of hummingbird pollinator visits on different plant species. To begin your background research, start by drawing a model of your system to describe the general variables you know about and identify where you need to gather more information (Figure 1).

Figure 1. Start diagramming your model with dependent variable at the top, and then classify your independent variable as either biotic or abiotic. Next consider all the other relevant variablessome that you need more information about (look in literature), some that could be confounding.

Based on your literature search you understand that hummingbirds are attracted to red flowers. You select two red-colored flowering plant species to observe. From what you read in your textbook, one species is thought to have relatively low and the other has relatively high sucrose concentration in floral nectar. You spend three months counting hummingbird visits to many flowers of both high and low nectar species across a field. At the end of the season, you find that most plants on the north side of the field have statistically significant more hummingbird pollinators regardless of plant species. What you didnt to realize is that there are a set of homes less than 100m from the south side of the fieldall with large hummingbird feeders in their yards such that the distribution of hummingbirds is not random! In addition, you discovered from your reading of literature that soil moisture is highly correlated with nectar sucrose concentrationthe north end of the field slopes and is shaded from direct sunlight and is more moist. Although you learned a lot and your data shows some interesting patterns it is quite variable. At the end of the summer you surmise that proximity to hummingbird feeders and soil moisture were confounding variables for testing your hypothesis on the influence of nectar sucrose concentration. In addition, you wished you Biocore 302, Fall 2013

7 had measured plant nectar sucrose concentration directly to confirm that random variation in between species was greater than variation within species (that your high species was actually high and low was actually low in the context of your study system). Careful analysis of your study site and the study system can decrease the impact of confounding variables and random variation, and can help focus your project by identifying variables to control. When you are doing field studies, there is a great deal of random variation and there may be many confounding variables that may affect your investigation. One way to get to know your system better is to do pilot studies. Once you have a hypothesis in mind, you can try out different methods, refine your question, test feasibility and scope of what you can reasonably do given restraints of time, funding and available technology. In Biocore 302, we are restricted in all three areasbut particularly by time. Discussions with your research team and instructors will help you decide what is practical. Rule of thumb for designing all investigationsKEEP IT SIMPLE! And remember that there is no such thing as a PERFECT STUDY. Direct vs Indirect Measures In ecology or any scientific discipline, it is often difficult to measure what you think is causing differences in your system directly. For instance, if you are interested in measuring the amount of nectar a hummingbird gets from each visit to a flower, rather than measuring the volume of nectar directly transferred from flower to bird (very difficult to measure!) you might consider time spent feeding as a surrogate or proxy measure. Although this makes data collection easier, you must evaluate how good the proxy is as an intermediate representative for the direct measure. Keeping measurements as direct as possible strengthens your evidence and the conclusions you can make. Controls Controls are used to identify (and sometimes to correct for) results that are not due to your independent variable. For example, suppose that you have learned that burning a field within prescribed limits is sometimes an effective tool for combating invasive species, and you want to design an experiment to test whether burning will decrease the Canada thistle that is taking over your favorite wetland. To gather evidence on the effectiveness of prescribed burning on reduction of Canada thistle, you would not simply burn the wetland and see what happens because a reduction in Canada thistle could be due to something other than your burn treatment. For example, it could be due to an influx of plant pathogen that targets thistles or to the dry weather that year. It would be important to leave part of the wetland unburned as a control. You can then compare the burned and unburned parts. Different types of controls are often necessary in studies to make sure that methods or treatment works the way it is supposed to (i.e. positive control) and when the treatment is not given (i.e. negative control). For systematic observational studies, in some cases, there may not be an obvious control for the variable you are measuring.

Developing a MethodThings to Think About:

In the next week, you will be using the information about prairies above in addition to other resources to develop a testable question and begin a scientific investigation at the Biocore Biocore 302, Fall 2013

8 Prairie. The following section stresses some important experimental design and statistical principles that will help you in thinking about how to test your question.

Populations and Samples

Once you have come up with a question, you will need to develop a method and protocol for testing. In Biocore you will gather data from small samples (perhaps 5-20 measurements), which represent larger populations (or the whole system) for which you want to make general conclusions. Heres an example to help you understand the difference between samples and populations: Lets say you are interested in the effects of chemical runoff from a local carwash into Willow Creek. Your lab instructors have suggested that the common waterflea, Daphnia magna, a well-studied zooplankton (small < 2 mm long aquatic invertebrate) species, may be highly sensitive to toxins in runoff and would serve as an excellent model species to test this question. Upon examination of literature on ecotoxicology and D. magna you find that these organisms may exhibit altered morphology, changes in survivorship, and reproduction upon exposure to carwash runoff. As a result, you have chosen all of the D. magna in Willow Creek to serve as your population. A population is the set of all individuals of interest in a particular study that you plan to make conclusions about.*

Obviously, in Willow Creek it would be an impossible task to capture, expose and examine the entire population of D. magna. A more logical approach would to be to study a smaller representation of the D. magna population and then generalize your conclusions to the whole population in Willow Creek. In other words, you need to collect a sample of D. magna from the large population in Willow Creek, collect their offspring, and expose the offspring to carwash runoff to determine toxicity. A sample is a representative selection of a population that is examined to gain statistical information about the whole.

Figure 1 helps to illustrate the relationship between the population and the sample. The population is composed of all the possible individuals of a particular group of interest, such as the D. magna of Willow Creek. The sample is a smaller subset of D. magna from the population. If the sample is representative of the population, the study results can be used to generalize about the population.

Biocore 302, Fall 2013

Fig. 1: An illustration of the relationship between the population and a sample. The population is made up of all the possible sampling points or individuals, which are represented by the Xs and Os. The various shapes represent the individual differences in the variable of interest (e.g., heart rate, body size, or location in a creek). The sample is a smaller subset drawn from the population. If the sample variation is representative of the population variation, the sample data and conclusions can then be used to generalize about the population.

It is important to carefully define the population of interest, taking into account your research question, experimental design, and resources. For example, the population can be defined as all the D. magna in Willow Creek, as opposed to all the D. magna that live in Lake Mendota or Wisconsin lakes more generally, or those D. magna that have been reared inside in a laboratory for generations. Table 2 (below) provides some examples of appropriately defined samples from a specified population (keep in mind that these are only possible examples; sample sizes and definition may vary for a particular population). Table 2: Three examples of a specified population and a possible representative sample. Population Sample 150 students from the UW campus who All UW-Madison students (male and reflect the diversity in gender, fitness, age, female) enrolled in classes during Fall and race within the Fall 2011 student 2011 between the ages of 18 and 22 population All 2500 Galapagos Finches on the island of Isabela All of the yeast cells in a 500mL beaker 75 Finches capture from locations around the entire island After stirring to evenly distribute the yeast in a liquid medium, 10 ml of yeast are removed as a representative sample of the beaker population

Replication and Evaluating Variation

In chemistry you probably are used to controlling all the potential confounding variables except the one you want to test. This usually is not possible in complex systems (e.g., the top of the hill may be different from the bottom of the hill). Ecologists try to minimize the effect of random variation as much as they can by using replication in their experimental design. For example, in designing an experiment to compare three methods (burning, mulching and mowing) for removing weeds from the Biocore Prairie prior to planting prairie species, we divided an area into nine (rather than three) plots and randomly assigned one of the three treatments to each plot. With 3 replicates of 3 treatments we hoped to reduce the effect of known and unknown random site variation (e.g. non-uniform distribution of weedy species) to reveal obvious real differences among treatments. Biocore 302, Fall 2013


One fundamental criteria of replication is designing or selecting independent replicates. Going back to the flower and hummingbird example mentioned in Table 1, the nectar sucrose concentrations of individual flowers on the same stem are all dependent on the health and the metabolism of the individual plant itself and therefore can not be considered independent replicates in the context of the hypothesis being tested. If treated as independent replicates in data analysis they would be labeled as pseudoreplicates. As an alternative, you could use individual flowers on the same plant as subreplicates, and calculate average nectar sucrose concentration per plantsuch that the individual plant becomes the replicate. Experimental results must be repeatable in order to be accepted as valid. This is done both by including replicate points in the design of the experiment and by repeating the entire experiment. Laboratory experiments are usually repeated many times before they are published. Field experiments are usually repeated or are carried out at more than one site. Replication is especially important in field experiments. Ecological systems vary dramatically in space and through time. Replication helps the experimenter differentiate between natural variation and changes caused by the experimental treatment. We are generally looking for changes above and beyond the natural random variation.

REPLICATES?? How many samples should you have? How many measurements should you take?
When thinking about the number of replicates to use in an experiment, there are ways to figure outa good rule of thumb to keep in mind is that three samples is the absolute minimum for replication. Ideally, you should measure many more than three replicates when you are attempting to make generalizations about a population, especially when you know that the population or the system you are working in is quite variable (think 20-30 replicates). The more replicates you take, the better your estimate of variation, the greater your confidence in your conclusions!

Unique Aspects of Sampling for Field Studies

When we do an experiment, we generally are using samples to try to answer questions more generally about a larger population. To illustrate this point, lets say we wanted to know how repeatedly mowing a field early in the spring influenced the height of weedy Canada thistles. To run a controlled experiment, you mow half of your large field but leave the other half un-mowed as a control each area or plot being 16m x 10m in size (example 1). Then you count the number of thistle plants that return following mowing relative to the number growing in the non-mowed area. Seems simple..yes? This design would be appropriate only if all components in the mowed and non-mowed areas are absolutely identical to begin with including soils, number of original thistle plants, composition of the other plants, available moisture and nutrients etc.... Example 1. Simple Mow Biocore 302, Fall 2013 Non-mow


But lets say now that the far west side of the field has slightly greater soil moisture (indicated by the gray shading in example 2) than the center or eastern sides of the plot. In order to account for this natural variation, we can alter the experimental design so that there are mow and non-mow areas in both the wetter and drier areas of the field with plot sizes of 8m x 5m as in example 2 below. This design attempts to systematically control for the variation in moisture. Example 2 Systematic Nonmow Mow Mow Nonmow Nonmow Mow Mow Nonmow

If you are setting up a field experiment and there is no apparent environmental differences in your site, you would still do well to split the area up into smaller plots and thoroughly randomize the assignment of plots to treatments as in example 3, or stratify the randomization so that plots are randomized within the rows as in example 4 (within each row there are 2 mow and 2 nonmow). Example 3 Random Nonmow Mow Nonmow Mow Nonmow Mow Mow Nonmow

Example 4 Stratified Random Nonmow Mow Nonmow Nonmow Mow Mow Mow Nonmow

Sampling Design It is usually not feasible or efficient to count, measure and map each plant (and animal) in an ecosystem to characterize the type and abundance of species present. Therefore, you must define a smaller area that you feel is representative to sample. A quadrat (note there is no N in this word- quadrat NOT quadrant) is a square area (usually 0.5m2 in this lab) defined to represent a small portion of the ecosystem you are sampling. For instance, we might count the number of thistles growing in 4 randomly selected 0.5m2 quadrats within each of the mowed and nonmowed 8 x 5m plots in the stratified random design shown above. Decisions about the appropriate size and shape of quadrats to use are based on the size, number, and rarity of species at the site as well as on practical considerations. If you are surveying trees in a forest community, your quadrats may be upwards of 10m x 10m in size, for shrubs you may use 4m x 4m. In the Biocore Prairie, we generally are surveying grasses and forbs (smaller plants), so 0.5m2 (0.71m x 0.71m) quadrats are more appropriate. Biocore 302, Fall 2013


It is important that the placement of quadrats on the site not introduce bias. Studies have shown that humans tend to over sample rare species and species in flower. Therefore, quadrats should be located randomly or by spacing them at equal distances across the site (the latter runs the risk of accidentally overlaying a preexisting pattern, such as former planting rows in the case of the Biocore Prairie). Another method to use is stratified random quadrats. This differs from random in that one first divides the plot into sections and then samples randomly within each section. For instance, each 8m x 5m mowed or non-mowed plot in Example 3 above could be subdivided into 4m x 2.5m subplots where 0.5m2 quadrats would be randomly located. A transect is a measured line that cuts through an ecosystem and represents the variability (of soil, vegetation, environmental conditions) of that ecosystem. During our stream ecology unit (Chapter 4), we will sample at random points along a line (transect) placed parallel to the stream. We could also use a transect if we wanted to measure how plant height of rosinweed varied on the border of the prairie as it merges with forest. In that case we might stretch a measuring tape across the border area (~50m of prairie into 50m of forest) and measure height of rosinweed plants if they are within 1 meter of the transect line. The new knowledge yielded by your study is a puzzle piece that contributes to the greater understanding of the system as a whole!

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Chapter 2. Biocore Prairie Restoration Project

Authors: Janet Batzli and Seth McGee The material in this Chapter provides specific information about prairie ecology, the Biocore Prairie, the history and management of the area, as well as guidance on assignments culminating in the generation of a final paper based on your research in the Biocore Prairie. Results and ideas from your project will contribute to our continuing restoration efforts and even (perhaps) inspire a larger project in summer months. Learning Objectives By the end of this unit you should be able to: 1. Recognize several native prairie plant species and explain how they are adapted to life in a tallgrass prairie ecosystem. 2. Recognize several non-native weed species and explain how their adaptations allow them to survive and grow even after attempts to remove them from the prairie. 3. Conduct field research study on prairie ecology 4. Work in a group to discuss, evaluate, and generate an experimental design for a prairie project 5. Generate a specific hypothesis and biological rationale for your research 6. Develop a plan and carry out a scientific investigation that will address your hypothesis 7. Use tools and procedures for measurement of biotic and abiotic properties of the prairie environment.

Schedules and Logistics

Field trips to Biocore Prairie will take place the week of September 4 (excluding Labor Day 9/3) and September 13. We will go rain or shine, so please come dressed appropriately for the weather. We recommend wearing long pants, long sleeves, and close-toed shoes (not sandals) for all of our field labs because we may encounter insects, scratchy brush, and/or poison ivy. We also recommend a water bottle, sunscreen and/or a hat since we will be outside for several hours. Also, bring a camera if you have one- it is always beautiful out there! Meet in the lab (341 Noland) promptly at the beginning of your lab. We will go to the prairie, rain or shine, in several groups in university vans. Bring your lab manual, carbonless lab notebook and a pencil. When we reach the prairie, we will go on a short tour, discuss prairie ecology, organisms, and adaptations, and demonstrate sampling techniques. Then, you will work with a group to explore project ideas you would like to explore further the next week. One aspect of the prairie that you should notice is that vegetation on trails/firebreaks and prairie borders often have different species than those in the interior. These path species are adapted to trampled soil and the movement and presence of people, and are, therefore, not representative of the rest of the prairie community. The prairie is composed of a different set of species that mix with path species at the interface or ecotone resulting in higher diversity than present in either path or field. This is called the edge effect. When you are making observations to represent the prairie, be sure to keep this in mind and dont trample like a buffalounless that is part of your experiment!

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How do we know what we know in the science of Ecology? Introduction to Prairie Ecology Some background information to help in the formation of a scientific investigation in the Biocore Prairie
Prior to European settlement, the uplands of southern Wisconsin were a shifting mosaic of vegetation, including prairies (a community of grasses and non-grassy herbaceous plants with few to no trees), deciduous forest, and oak savanna, a community with widely scattered trees (usually white and burr oaks) and an understory often dominated by grasses. Prairies once occupied up to two million acres in Wisconsin, sometimes existing in large patches and at other times occupying the rocky soils of small hilltops. By the 1900s rich prairie soils had been plowed and used for agriculture. Fires that maintained prairie plant communities were suppressed. Today, prairie ecosystems in Wisconsin are very rare and endangered. Following agricultural settlement- it is estimated that only one half of one percent of the original prairie still remains in small patches called remnants. Prairie restorations are an attempt to reintroduce flora into areas known historically to support prairie and savanna, but whole ecosystems are made up of more than flora. The ultimate goal and biggest challenge for most prairie restorations is to create a system that provides suitable habitat and encourages natural interaction among plants, animals, microorganisms, and the physical environment that characterizes prairie. In some cases, this goal may be unrealistic since the total area undergoing restoration is small, the space between restorations is interrupted by agriculture and human dominated landscape, and the introduced invasive species impose strict competition difficult for natives to overcome. Despite these challenges, there are many restoration projects underway.

Abiotic Environment
Most prairie soils are rich due to the abundant, deep root growth and subsequent decomposition. Wind is ever present and unyielding in prairie given few trees and relatively flat landscape. The drying force of wind is a challenging element for which most prairie plants have evolved adaptations to mitigate. Fire is a natural disturbance in prairies, discouraging non-native plants and tree growth. Precipitation, in the form of rain and snow, play a crucial role in the development of prairies. On the high plains, short grasses thrive in the rain shadow east the Rocky Mountains. In the Midwest plains states that receive higher precipitation, mid-sized to tall grasses dominate the landscape.

Biotic Environment
Prairie Plants The dominant plants in prairies are perennial grasses and forbs (non-grass flowering plants). These plants are perennial meaning that they live more than one year as opposed to annuals that complete their whole life cycle in one year. Prairie perennials retain permanent underground structures (roots and underground stems) from year to year but die down to the soil surface each winter.

Figure 1. Left image of prairie leaves -grasses and forbs including compass plant (big lobed leaves) and small delicate leaves of purple prairie clover.

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15 Grassland vegetation is adapted to a drier climate than temperate deciduous forest. Typical leaf adaptations are compound or highly lobed leaves to decrease the leaf surface area exposed to the hot summer temperatures (Fig. 1). Some species have thick, hairy leaves that help plants conserve water. Prairie plants have highly adapted root systems to the often droughty soil conditions. Plants may have several thick tap roots or a mass of fiberous roots all penetrating to great depth (Fig 2). Some species roots may grow as deep as 15 feet allowing them to tap remote moisture reserves not accessible to plants with surficial root systems like those of many weedy and invasive annual or perennial species. The deep root system of prairie plants are also a means of energy storage after frequent disturbances such as fire. Fires are a natural part of the prairie ecosystems and most prairie species have special adaptations that allow them to survive frequent fires.
8 7 6 5 4 3 2 1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

Lawn grass

Fig 2. Root systems of prairie plants. Compare the roots of lawn grass on the far left with the deep tap and fiberous roots of prairie plants. Scale on the left indicates the number of linear feet above and belowground.

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16 Prairie Animals and Interactions Animals that live in prairies are adapted to grassland habitat. There are a large number of bird species that are found in prairies- some as permanent and others as temporary residents. Birds such as gold finches, eastern meadowlark, bobolink, and sandhill cranes eat a large array of prairie seed or insects, and utilize diverse vegetation for perch and nesting sites. Although few restorations are large enough to sustain large animals such as bison and elk, smaller mammals such as deer, coyotes, rodents are plentiful in many restorations. These animals often have specific adaptations of body structure, color or behavior that help them survive in different prairie habitats. Some grazing mammals, have broad, flat-topped teeth or teeth that grow continuously (rodents) especially adapted to feed on tough prairie grasses containing silica. Many birds and small mammals such as Peromyscus leucopus (white footed mouse) and Microtus pennsylvanicus (meadow vole) utilize insects and seeds of prairie plants as a major source of nutrition, and exploit different microhabitats in the prairie to avoid competition or predation. For example, meadow voles tend to burrow and tunnel in dense prairie vegetation and are most active at night which helps conceal their presence from predators, while deer mice may forage at anytime and in more exposed locations. Insects are, by far, the most numerous animals in the above ground part of prairies and include many species of bees, moths, butterflies, beetles, and grasshoppers. Some insects are specialists to prairies, others are more general to many communities found in Wisconsin. Pollinating insects such as bees, flies, butterflies, and moths are attracted to flowers through numerous mechanisms including flower color, size, fragrance, pollen, UV light reflectance (fig 3) and the promise of a nectar reward. Ground dwelling insects such as grasshoppers, crickets, ants, beetles may spend much of Fig. 3 Image of frost aster flowers exposed to UV light 365nm. The tiny speckles are UV light reflective pollen that serves to their life cycle in the soil or surface litter attract insect pollinators. (photo credit Seth McGee) (decomposing leafy debris). These insects feed on leaves, stems and roots, on decaying material or on other insects. Below ground in the soil, you will find bacteria, fungi, insects, earthworms and nematodes (tiny <2.5 mm long, soil worms AKA round worms) (Fig 3.) that are crucial for soil turn over and formation. Soil nematodes are numerous with high densities in most soils. They can be beneficial or detrimental (plant parasitic nematodes), and vary in abundance and distribution based on plant compounds and the abundance of particular microorganisms (bacteria or fungi) present in the soil. Earthworms are familiar to anyone who has dug in the garden or has done a little fishing. Important fact: Earthworms are not native, but rather were introduced to the upper Midwest and Canada from Europe. Earthworms digest large amounts of dead plant material, pulling fallen leaves and stems underground, producing nutrient-rich casings, and mixing and aerating the soil as they move. Their voracious appetite for dead plant materials has drastically altered soils organism communities and the way nutrients cycle through forest and prairie ecosystems. Soil microorganisms are essential to the

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17 health of the soil and the plant community. Soil microbes breakdown decaying plant and animal remains creating humusa nutrient rich component of soil important to plant growth and nutrition. Interactions of Prairie Organisms Prairie animals and plants interact in a dynamic way. Animals utilize prairie plants for food, cover, and a structural environment in which to interact with other animals and microorganisms. Many, but not all, prairie plants rely on animals for pollination, seed dispersal, aspects of soil formation and nutrient acquisition. Some animals eat prairie plant seed and, therefore, influence the number and types of seed that will remain to germinate in a restoration. Although there are many positive or mutualistic interactions, some plant- animal- microbe interactions are not mutually beneficial. Prairie plants utilize a variety of defense mechanisms to avoid being eaten. Spines, thick hairs, gooey resins, waxes, and toxic chemicals all act to deter herbivores from eating most plants. However, many animals have evolved mechanisms to overcome these challenges. For instance, some insects have developed chewing or piercing mouthparts that allow them to tear through thick leaf cuticle (outer leaf covering) and the tough plant cell walls to tap into the sugary plant vascular system for a meal. Monarch caterpillars can eat and store toxic latex Figure 4. Image and illustration above of produced by milkweed plants, which results in monarch goldenrod gall and emerging goldenrod gall fly caterpillars and butterflies being toxic to potential (Eurosta solidaginis). predators. Another example is the goldenrod gall flies that have evolved the capacity to feed exclusively on goldenrod plants and induce the plant to create a gall tumor in which the insect makes its home (Fig. 4). Some plants produce antibiotics or other antimicrobial compounds to confer resistance to bacterial or fungal pathogens. Prairie plants have long been sought after for their medicinal value and are now a focus in the on-going search for new pharmaceutical drugs. Finally, and importantly, many forb plants produce brightly colored, patterned, or fragrant flowers while others produce large quantities of high sucrose nectar, all of which are alternative mechanisms to attract different types of pollinating insects.

Biocore Prairie Restoration Background and History

As far as the site records go back, the area where the Biocore Prairie is situated at the base of Picnic Point supported savanna and upland forest. In the early 1900s, the area was part of a private farm that was turned over to the University for establishment of the College of Agriculture experimental farm and orchards. When the experiment station was moved to central Wisconsin, this area was left fallow, allowing 40-50 years of weed seed to accumulate in the soil. In 1997, the Biocore program staff, students and volunteers began restoring this old agricultural field to tall grass prairie for ecological educational research opportunities as well as public outreach and enjoyment. The Biocore Prairie is a central research site for Biocore 302, for undergraduate independent research projects offered under directed study, Biocore Bird Observatory, service learning opportunities, and collaborative research and teaching efforts with other UW-Madison programs and departments. Over the last 13 years, the Biocore Prairie team has been hand-pulling weeds, burning, preparing soil, sowing prairie seed, transplanting prairie seedlings, and mowing

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18 fields and fire breaks. Happily, we can report that our hard work is paying off with a growing area of establishing prairie. Summer 2012 was very interesting as a result of early spring warm up and extreme summer drought. March 2012 temperatures were in the 70-80F for over two weeks initiating early spring growth. Without rain from April to mid-July, much of SW Wisconsin fell 3-8 inches below normal in precipitation resulting in severe drought. The extreme weather of 2012 will surely impact your observations of flowers, pollinating insects, and other prairie organisms this fall. It will be interesting to study what is going on! The following pages are provided as a brief record of our accomplishments to date and to give you a feel for where we are today. The Restoration Process: Establishment of a functional prairie ecosystem is a very complicated and multifaceted process. The items listed below are just a few of many considerations when undertaking a prairie restoration and management project. 1. Site Preparation- We have used several different methods to prepare the site for planting including; rototilling/plowing, growing Roundup Ready soybeans and spraying Roundup herbicide, growing cover crops, black plastic mulching, and addition of high carbon substrates (e.g. sawdust). One important thing to consider is the severity of the weed problem. If there is a tremendous amount of weed seed in the soil, you do not want to turn the soil over and bring weed seed to the surface where it can germinate and produce more weed seed. 2. Selection, collection, and planting of prairie seed- After reviewing historical documents describing the composition of prairies in South-central Wisconsin prior to settlement, we have selected a set of species that we feel are representative of the plant diversity of that time. Plant materials have been collected from other near-by restorations, from prairie remnants, and purchased from seed companies. Seed was hand broadcast or drilled into the ground in late fall or early spring. 3. Hand planting seedlings- We have grown and transplanted young seedling plants of rare species that are difficult to establish from seed. This process is very laborious and expensive, since we often must water the new seedlings through dry summers. 4. Interseeding- After the restoration is underway, we have found that some prairie species establish well, while others are missing. In these cases, we have gone into an area and have seeded specific species of interest (e.g. wood lily Lilium philadephicum, difficult to establish species). 5. Weed Control There are several techniques that we have used to control weeds on the Biocore Prairie. Each technique is specific to the types of weeds that are of concern. The most effective weed control usually uses a combination of techniques including: Prescribed burning- Burning is very important for our restoration. Areas are burned regularly, often on an annual basis, in young restorations to help control weeds remove woody plants that are not fire adapted. Burning encourages prairie plant growth by burning dead organic material and exposing soil to sunshine and warming temperatures in early spring. To have a successful burn, the restoration has to have built up a
Fig. 5 Spring 2007 prescribed burn

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19 significant amount of dead plant material to serve as fuel. Forbs often decompose rapidly, leaving little to burn. Dead grass stems and leaves, on the other hand, tend to remain through the winter and serve as an optimal fuel source. Since 2004 we have attempted to burn areas of the prairie each spring, sometimes successfully and sometimes not. Spring 2007, 2010 and Fall 2011, 2012 were all very successful burns at the Biocore Prairie (Fig. 5). Mowing- timed to cut weeds before they flower and go to seed. Mowing does not remove or kill roots, but generally reduces the weeds energy reserve and keeps weeds under control. Mowing is particularly good for controlling annual weeds that depend on annual seed dispersal for reproduction. Mowing is not effective for grasses or other weeds that have growing points (meristems) close to the ground. Hand pulling- this technique is reserved for more problematic weeds that have large energy reserves stored in roots, are biennial or perennial or can reproduce asexually. Hand pulling is obviously very labor intensive, and not efficient in most cases. However, we do hand pull weeds if the problem is not wide spread. (good for burdock, curly dock, sweet clover, bull thistle, garlic mustard) Herbicide- this is a good choice (and last resort) for the most tenacious weeds (crown vetch, reed canary grass, leafy spurge, Canada thistle) that continue to be a problem after we have tried other control techniques. Much care goes into choosing and applying herbicides, since some can be very toxic to non-target organisms.

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20 Description and Restoration History of Areas in Biocore Prairie

We have established 3 general areas in the prairie as depicted in Figure 6. Although we do not expect you to be intimately familiar with each Area, we provide the following information to introduce you to the site and for background on what you will see in the field. The following page describes these areas in greater depth.

Figure 6. June 15, 2004 aerial photo of Biocore Prairie restoration showing the three different restoration areas. Area1a seeded in 1998, Area 1b was sown with prairie seed in June 2004. Area 2 planted in 2000 Area 3 (outlined in white) was planted in prairie seed in November 2005. This area has been subdivided into Area 3a, 3b, 3c given the different soil, slope and micro-environment. In Spring 2007, the garden peninsula was rototilled and will soon be incorporated into the prairie planting.

Area 1: oldest area established in 1997 subdivided into Area 1a and 1b.

o Area 1a (~0.5 acres)- land sloping toward Lake Mendota. Prairie plant community is currently dominated
by Canada goldenrod and lacking in grasses required to fuel a strong burn. The area is susceptible to invasion by non-native weeds and woody plants given its proximity to foot trails and forest. The Biocore staff and students have concentrated on hand pulling of problematic weeds and planting seedlings in this area.

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21 o Area 1b (~0.4 acres) This area was rototilled in spring 2004 and split into six plots for an experiment
testing different prairie plant seed mixes. After a slow start and heavy infestation of weeds such as Canada thistle, the area is progressing.

Area 2: (~0.9 acre) This area was an old dirt pile placed on the site during the construction of the UW Hospital. The dirt pile in combination with the underlying sediment provides a nutrient poor, yet, heterogenous soil for prairie plant establishment. In 2000, this area was plowed repeatedly and seeded in a cover crop of oats and planted in prairie plants in spring 2001. Over the last several years, Biocore staff and student workers have transplanted hundreds of young prairie plants into this area and watered them during dry periods. The team hand weeded problematic weeds such as garlic mustard, thistles, Queen Annes lace, sweet clover, burdock and curly dock. This area currently supports most of the 57 prairie species originally planted as surveyed by Biocore 302 students in fall 2005. Area 3:(~11 acres) has 3 subareas; Area 3a, 3b and 3c. The entire area was planted in Round-up Ready soybeans during summers 2003, 2004, and 2005 and treated three times each season with Roundup herbicide to control weeds in preparation for seeding with prairie plants. The soybean planting and repeated herbicide treatment appeared to diminish the Canada thistle, a problematic weed. In November 2005, 53 species of prairie plants were hand planted into Area 3 by 45 Biocore 301/302 students (plus friends and family!).

o Area 3a: Summer 2006-2010 have been a great growing seasons- with plenty of rain, seasonal drought,
and warm weather. From our management teams observations and vegetation analysis, we have counted 50 prairie species (of 53 planted). In 2010, prairie grasses and forbs continued to grow and establish. This is very exciting and remarkable to see, particularly following a couple of rough years and poor success in the beginning! The problematic weed in Area 3b continues to be Canada thistle.

o Area 3b: Although the rest of Area 3 is doing well, area 3b was plagued with tenacious weeds including

stinging nettle, crown vetch, and Canada thistle. This areas deep organic layer is rich in nitrogen and other nutrients that encourage weed growth. In fall 2008, 2009 and summer 2010-12, this area was deep plowed to turn over and bury all vegetation, both weeds and prairie plants. In spring and summer 2009, the area was planted in oats, mowed and sprayed with herbicide to reduce growth of weeds (particularly crown vetch, Canada thistle, reed canary grass). In fall 2012, we plan to plant winter wheat with the intention of depleting the nutritive content of the soil, making it less fertile for weed growth. We will continue weed control in this area for at least one more growing season before replanting prairie. species. It slopes to the west with relatively dry soil. The upper one-half of the site was planted in short grass species including little blue stem, prairie dropseed, and side oats grama together with many forbs. Whereas the bottom one-half, sloping toward a moist ditch was planted with tall grass species including big blue stem and Indian grass. Although planting in this part of Area 3 was somewhat later than Area 3a and 3b, the prairie plant community is starting to establish. Problematic weeds in Area 3c are Canada thistle, leafy spurge, and reed canary grass.

o Area 3c: This area is unique and particularly well suited to grow dry adapted or short-grass prairie

Garden Peninsula: In 2010, the Biocore Prairie enlarged to include a small area previously part of the Eagle Heights Community Garden. This area has many remnants of the garden including sprouts of herbs and vegetables, and regular long depressions in the soil as evidence of many years of rototilling and row cropping. The area has been plowed and mowed through summer 2012. We will continue weed management and site preparation for prairie planting in 2013. Demo gardens & Nursery: In 1999 and 2000 we set up two demonstration gardens and a nursery area as a point of interest for visitors, as a visual reminder of our goal, and as a source of seed in the new planting areas. These areas now have many thriving prairie species that are producing seed and expanding their vegetative

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growth. They also attract many seed eating birds, butterflies and other insects. These areas are used extensively by the Biocore Bird Observatory group led by Dr. Mara McDonald who monitors migratory and resident bird populations that move through the Biocore Prairie (see website for data collected by this group Fig. 7 Grid Map of Biocore Prairie In summer 2004, a civil engineering surveying class did a detailed survey using high accuracy GPS (global positioning system) resulting in a permanent, 20x20 meter grid overlay map of the entire prairie that is geo-referenced to the Dane County coordinate system (accurate to 5cm). Brass monuments were installed at the corners of each grid square to help us start to map the data we are collecting in a systematic way. This work establishes a valuable base map from which students can accurately locate study plots, and analyze spatial correlations of soils, hydrology, and vegetation.

*NOTE about further study in the Biocore Prairie: The Biocore Prairie Restoration offers many opportunities to pursue independent study projects or senior thesis work in future semesters. Although we will only be at the Biocore Prairie for two lab periods in Biocore 302, students are a huge part of the success of this project and we hope you take pride in the site, returning with friends and family, coming out to volunteer, or frequenting the area during a run. Let us know about your interests and we will help you get involved! Contact Janet or Seth to volunteer for activities like seed collecting, monitoring long-term experiments, prairie planting, or prairie burn at the Biocore site.

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Schedule Your Assignments:

A great deal of effort and resources have gone into this project. We hope to establish a prairie ecosystem on the site and provide ample opportunities to study ecology in this living laboratory. We also want to learn as much as we can about the restoration process, not only to guide our own efforts as we expand the prairie in the future, but also to help others undertaking prairie restorations on similar sites. For this reason it is important to document exactly what we have done and the results of our data collection. Your data is valuable!!

Pre-lab assignment to do BEFORE attending first lab class (check assignment): Review the seven questions below. Select TWO questions that interest you and revise each one as a testable question. Use information from previous descriptions in this chapter for background. Indicate what the independent variable and dependent variables are in each of your testable questions. Bring your questions to the first lab period and hand in for check assignment credit. 1. Does the development of gall growths on Canada goldenrod divert significant energy from plant growth? 2. What prairie plant species in the Biocore Prairie contain anti-microbial chemicals? 3. Do different concentrations of nectar from prairie forbs attract different insect pollinators? 4. Are there different communities of ground dwelling insects in the prairie than in the neighboring forest? 5. Does seed consumption by small mammals in Biocore Prairie restoration impact the areas that have been newly seeded with prairie plants? 6. Are there natural additives (plant-based compounds) that can be included into prairie seed mixtures to help prevent loss of seed through herbivory? 7. Does an area that has been burned more recently have a greater amount of grasses than forbs? Week 1: Part A. Experimental Design Worksheet (check assignment- 1/individual) o Download a copy of the Experimental Design Worksheet from Biocore Prairie subdirectory on Biocore 302 in Learn@UW. o In lab, your research team will choose one of seven research topics to pursue based on questions described above. The projects were done by former Biocore 302 students serving on the Summer 2010 - 2013 Prairie Crew. Each prairie crew member wrote up a short paper describing their project and preliminary results. The papers were written in an INFORMAL style but provide important information (i.e. background, biological rationale, hypothesis, methods, preliminary results) and suggestions for further research. This is where you take over! o On your own, complete the experimental design worksheet to draft an idea for an experiment that would expand on what was done by crew members. Come to your first discussion section prepared to share your worksheet with your team. o You will then work with your research team during discussion to share and combine ideas. By the end of discussion, come to consensus on ONE investigation to pursue for your project. Note: You may be asked to change your question and/or your protocol based on practical limitations. We appreciate your flexibility! o Turn in your group material and schedule worksheet to TA for check assignment credit.
Biocore 302, Fall 2013

24 Part B. Paper review and critique (4% assignment- 1/two person pair) due in second lab period: Go to Biocore 302 Learn@UW and download a copy of the paper review worksheet and electronic copies of Prairie Crew papers With a partner (determined in the first lab), select one paper to review. Important note on the Prairie Crew Papers- These are not complete, formal papers. They only include the Title, Introduction, Methods, and Literature Cited, and are written in an INFORMAL style. All of the papers are in the needs work category. Follow guidelines in the paper review worksheet. Hand in paper review and critique plus a Group Effort Analysis (GEA) form (also found on Learn@UW) in lab. Week 4: Formal Peer Review (2% assignment): A draft of your final research paper focusing on your investigation proposed in your practice paper is due the week of Sept. 28 (see syllabus for details on peer review and final paper due date). You will be doing a formal peer review (for a grade) on a draft of your partners final paper prior in discussion. Your grade on this assignment will be based on how well you peer review your partners paper. Be sure to exchange contact information with your partner during lab (week Sept. 17) and exchange your paper with your partner at least 24 h before discussion. (This means you have to have an almost completed draft to exchange 24 h before discussion!). Have your review written out and be ready to discuss with your partner during discussion. Blank peer review forms can be found on Biocore WebSpace in the class handouts file. Final paper (12% assignment): Your final paper includes the following sections- title, visual model of the introduction including biological rationale and hypothesis (see example on p. 11 of Biocore Writing Manual), methods, results, discussion, literature cited. Please use the Biocore Writing Manual (especially the final paper rubric) as your guide. Pay close attention to the content and format of figure/table legends. Due 48h following discussion week of Sept 28 (in Wed lecture or in Wed/Thurs lab). Your final paper should follow the format described in the Biocore Writing Manual and should be no more than 5 pages long (not including your figures). The purpose of this paper is: To give you an intimate introduction to the Biocore Writing Manual, specifically the instructions for writing a scientific paper and using rubrics. To give you experience developing a research question, biological rationale, hypothesis, method to test, analyzing data, presenting data in the form of figures, and formulating conclusions. To give you practice deciding what details are of greater or lesser importance in writing a scientific paper (i.e. what is the variable, what is the context of the study, what is the question, why is the variable important in the context of the study, how will you test your question) The appropriate format and style for your paper are described in the Biocore Writing Manual. You should concentrate your reading on the Structure of a Lab Report and Final Paper Rubric that offer a detailed guidelines that will be used by your peers and TA to review (and grade) your paper. It is essential for you to study the writing manual carefully before completing the assignment. Your paper needs to be complete yet concise. This means that you need to think carefully about what information is essential and what is unnecessary. For this assignment, we expect you to utilize (and cite!) the information included in the prairie crew paper you are following, the lab manual (primarily information from Chap. 1 and Chap. 2) as well as at least one (1) primary literature paper that logically supports your background, biological rationale
Biocore 302, Fall 2013

25 and discussion. You may include more literature if you like. In addition, you may need more in-depth information about the topic you choose to investigate even if you do not use this information in your paper. If there are terms or ideas you come across that you are not familiar withLOOK THEM UP! (this is standard for any assignment). Feedback on your paper from your peers and your TA will be based on the criteria presented in the Biocore Writing Manual (starting on Receiving Feedback). Be sure to bring your writing manual to your first discussion section and be prepared to ask about anything you are unsure about concerning your writing of this paper or general questions about writing in this class. Helpful Tips for Paper Writing: If you are having trouble starting, seek out your classmates to discuss assignments. Be sure you understand the scope of the assignment BEFORE you start to write. Use the FINAL PAPER RUBRIC in the Biocore Writing Manualrefer to it often during the writing process. Make bulleted notes or an outline with ideas for appropriate content for each section For example: INTRODUCTION- subunits: background information about factor/variable and system, observations/question, assumptions about the study system associated with variable, biological rationale, hypothesis and approach; METHODS-further description of system (if necessary), sampling location(s), experimental design, procedure, and replication. Etc.] In each section, write notes and questions to yourself concerning what you know and what you dont know, and what you need to investigate further. Look up any terms or concepts you are not familiar with. PUT PEN TO PAPER (or keyboard to software) and start to WRITEknowing that the key to writing a good paper is to write, reread, reflect, rewrite, get feedback, revise and edit. Writing is a multi-step process that is not accomplished without spending a great deal of time and effort doing it! TOPIC SENTENCES -use them for each paragraph. Each paragraph should develop a single coherent idea, and each piece of information in the paragraph related to the topic sentence. When you have drafted sections of your paper READ IT OUTLOUD TO YOURSELF. REVISE. REPEAT. Wording, grammar, organization, unnecessary sentences, the flow of ideas and many other problems will jump out at you. BACKWARDS OUTLINE Once you have completed a draft, test the structure and logical flow of ideas by making a backwards outline. Read through each paragraph and write a 3-4 word phrase describing the gist of the paragraph. When you have gone through the whole paper, string together your phrases. Do they make sense? Are their gaps in the logic calling for additional information? Could you have said the same thing with fewer words? TRANSITIONS At the sentence level, test to seed if the first few words of a sentence connect to the end of the prior sentence, and that last few words present new information. At the paragraph level, do the ideas from the last sentence of one paragraph introduce the topic sentence of the next paragraph? At the document level, the discussion section should begin by connecting clearly to the question/ hypothesis in the introduction and then move to further develop your findings. Although transitions sound like more words, they can actually help you be concise. Look for additional tips for Writing a Biocore Paper collected from former students on the last page of this chapter. There are many helpful books, texts, field guides and research articles about prairie restoration in the bookshelf at the back of the lab room (341 Noland). Please do not remove resources from lab!

Biocore 302, Fall 2013

Top Ten Tips for Writing a Biocore Paper From former Biocore 302 student (2008) and uTA (Kristen Fox)
As previous Biocore students, we understand how difficult learning to write scientific papers can be. The follow tips were collected from suggestions from previous peer mentors, students, TAs, and professors. We hope that they will help you become awesome writers. Good Luck! 1. Follow the writing manual. Everything you need to know is in there. Do yourself a favor and read the manual BEFORE you start to write noting the main points. When you begin your first paper, make an outline using the writing manual to make sure that you have the main ideas. As you write, refer back to it often and compare your draft to the examples. 2. Start Early! Biocore papers are intense and require lots of thought and time. You've heard it 1,000 times but seriously, don't leave this to the last minute! 3. Use your peers. Get together with your group and draft an outline of your papers together. Share good references and ideas with each other. Remember, you're not graded against each other so be generous with your knowledge! 4. Know how to use a journal search engine. Web searching can be a huge waste of time if you don't know what you're looking for. Use specific engines like Pub Med, Web of Knowledge or Google Scholar. Be specific with your search terms, and use the search optimizing info from the librarians. 5. Start with your textbook and review articles. Familiarize yourself with a new topic by reading general literature/ a review article. This will give you important background knowledge as well as lead you to new sources that will help you develop your rationale. Circle the references in the review that are relative to your paper and then go read those articles. This can save you lots of time by cutting back on paper searching! 6. Be an efficient reader. Sometimes titles can be misleading and you can waste a lot of time reading an irrelevant paper. First, read the abstract to see if the paper is really talking about what you're looking for. Next, read the introduction and glance at the figures/ discussion. If after reading, the paper is still relative, go back and pick out the important information. 7. Think persuasively and logically. When you're writing a proposal or final paper, you are trying to convince someone that your project is/was valid and worth doing. Set up an "argument" and take your reader through it step by step. Try making a flow chart to organize your thoughts and to make sure everything connects. As you go through each section of your paper, think about how it supports your argument. Caution: Let you data do the talking! Don't be overly emotional and avoid exaggerated interpretations. Always be objective and critical of your experiment. 8. Do your graphs and tables first! Before you try to write your results and discussion, make your graphs. It is very hard to make conclusions from raw data. Once you have your data organized, you will be able to see the relationships more clearly and interpret the data intelligently. 9. Don't make laundry lists. Every experiment could use more replicates, time, and accuracy so don't spend too much time discussing these in your paper. When you evaluate your data/ design acknowledge any of these flaws but don't stress over them. Instead, think about the components of your experiment that you had control over. Did you employ the proper controls? Were your assumptions appropriate? Did you use the right read outs? A discussion that includes these points demonstrates a deeper understanding of your experiment and shows that you can think critically beyond technical problems. 10. Don't freak out about your grades on papers. Your TA will grade tough and you may not be happy with your first grade. Your TA knows how much time and effort you are putting into these papers so don't get the impression that they are just trying to make your life difficult. They grade hard because they are trying to help you develop your writing skills. When you get a paper back, READ the comments. Make notes on your areas of weakness and review these when you write your next paper. If after the first few papers you are still not happy with your scores, meet with your TA and go over your writing, they will be more than happy to help.

Biocore 302, Fall 2013