Managing and conserving populations of fish and wildlife species is a complex process. It requires obtaining accurate information concerning the size of the population, its distribution, its age structure and sex ratio, and the rates of production and mortality. Often this information is not available or must be inferred from crude indices. To sift and evaluate this information, the biologist must use his/her knowledge of population dynamics, quantitative and analytical skills, computer models and good measures of intuition and common sense to arrive at a proper strategy for conserving and managing the population. The purpose of the field/analysis project is to give you practical experience in various aspects of this process.
In previous years I have encouraged students to work on a species with which they are very familiar and particularly interested. Depending upon the species that you select, your efforts may concentrate on some of the following areas: gathering population data in the field, gathering harvest data, evaluating previous trend or harvest data, designing a scheme for gathering population data in the future, evaluating reproductive and mortality rates, modeling the growth of a population, modeling the response of a population to changes in harvest, evaluating the long-term viability of a population, or asking a new population question with published data.
This year we have a unique opportunity to contribute to the understanding and management of a fish and a bird species of great interest and importance in the region. We will assist in analysis of excellent long-term datasets on breeding populations of Greater Sage-grouse (Centrocercus urophasianus) and Chinook Salmon (Oncorhynchus tshawytscha) based on lek and redd counts respectively. The studies that we conduct will be used by biologists responsible for management of these 2 species in this region.
The following sections outline various considerations to bear in mind while designing, conducting, and writing up your project.
Determine the status, causes of declines and potential for recovery to earlier abundance of 2 populations of either greater sage grouse or chinook salmon based on analysis of long-term lek or redd counts. If you choose to work on sage grouse then select one population (or sub-population) from Idaho and a second population from another state or province. For chinook you should select one population (consisting of fish spawning in a small section of a stream or adjacent streams) from the Clearwater basin and a second population from the Salmon River basin. I will post a list of the populations where you may sign up for your selected populations to insure that each person (or pair of people) works on different populations and we analyze as many populations as possible.
The lek and redd count data you will use for your projects are the data gathered by biologists and managers working on these species over the past 50 or more years. The data will be found in an Excel or Access dataset stored on the K: drive under /WLF/448/Salmon/Chinook or /WLF/448/Sage Grouse. You can calculate rates of change for the population over single years or over longer time periods such as a generation to use as a population response. I placed Excel spreadsheets in the same directories that show you how to calculate annual instantaneous rates of change (rt) for each population (Lemhi Spring Chinook MVP.xls and Sage-grouse Lek Counts 1960-2005 - Rate of Change.xls). The Lemhi Spring Chinook spreadsheet shows the calculations presented during lecture as well as2 better ways to do it. One calculates rates of change by generations of (5-yr lag incorporated into Rt). The second extra column applies an approach put forward by Holmes (2001) in which you use the 5-yr running sum as an index to total population size across all age classes present in a year. The Sage-grouse Lek Counts 1960-2005 Rate of Change file uses a really neat trick to calculate annual rates of change from all the lek counts possible in a pair of years so that missing lek counts in a particular year do not bias the estimates or keep you from using data for a lek with a few missing values. You will need to copy the data for your populations into the appropriate spreadsheet so that you can use it to calculate these annual instantaneous rates of change. To those you can add data on potential predictors such as density, habitat, weather, water flows, hatchery releases, harvests, fires, ocean conditions, etc. to evaluate reasonable hypotheses concerning the patterns and causes of population change. Take another look at the Powerpoint lecture stored on the K: drive under lectures (Sustainable harvest of sage-grouse-Short.ppt) and see if you can't figure out how to add other predictors to the model:
such as habitat or weather variables the way that I added harvest (bHt) and plant communities (ci). For those of you working on Greater sage-grouse, I put a pdf of the species assessment we completed last year for WAFWA in the same directory. You might consider using our approach to all the individual leks within your population or sub-population that we used: we summed the lek counts in each interval (year t to t+1) for leks which were counted in both of those years to estimate rt so that missing values would only influence the counts adjacent to them rather than requiring that we delete all data for a particular lek because it had a few missing values amongst many years of data.
Note that there are invaluable resources on the web for you to use in your analysis. For example, all the weather station data is available at http://www.ncdc.noaa.gov/oa/climate/stationlocator.html which you use to locate data from a station by choosing a state, then a county, etc. and it provides maps to locate stations too. I have put the most recent and most comprehensive map of sagebrush habitat on the K: drive with the grouse data under sagestitch. There is one phenomenally useful site for coverages of spatial data in the sage dominated region called sage map (http://sagemap.wr.usgs.gov/). this site has hundreds of coverages of things like rivers, cities, land cover types from GAP programs, topography, etc. Choose get GIS data, List all data, by theme type to find a list and links to download everything on the site. The one hassle is that you will need to convert it to match the Albers projection of your lek/population/subpopulation coverages. There are super statistics available for salmon at http://www.cqs.washington.edu/dart/dart.html and that is a quick link to find things like the Pacific Coastal Upwelling Index (CUI) that Mark Scheurell from NOAA has related to ocean survival. The Fish Passage Center (http://fpc.org) has tremendous data on hatchery releases etc. and http://tao.atmos.washington.edu/pdo/ at UW presents a measure of the Pacific Decadal Oscillation commonly called El Niņo.
You may work individually or with up to 3 other students to plan your project and gather your data and do your analysis but you will work with 2 populations per person (i.e. 2 people working together analyze data for 4 populations, etc.). Thus it will be an advantage to work on more populations but choose your coworkers carefully! A group of 2 or 3 will be expected to perform proportionately more analyses than a single individual but they will have a better chance of identifying interesting relationships. Single individuals are free to work on more than 2 populations if they wish. Groups will submit a single proposal but for your final report you must complete your own individual analysis and write up your results, discussion, and conclusions independently.
You should look at a recent article published in the Journal of Wildlife Management (JWM) or North American Journal of Fisheries Management (NAJFM). Both guidelines are available on the web at http://www.wildlife.org/publications/index.cfm?tname=journal http://www.fisheries.org/html/publications/styleguide/styleguidetoc.shtml
or on the K:\\ drive in the 448\2004\Science Writing folder.
**Note: The format for a submitted publication is different than the format that appears in the printed journal but they are similar. Your paper will need to be in the format of a submitted publication (i.e. all text must be double-spaced except in Tables). Any proposal not meeting the guidelines will be returned for revision. Final reports not meeting guidelines will be graded accordingly.
Most journals now require submitting papers electronically and we will move toward that standard by requiring that you submit your final report both in printed form (1 copy which may be duplexed if you desire) and electronically. Electronic submissions also have the benefit of allowing you to submit more extensive material in the form of appendices which are commonly made available through the society web site associated with the online form of the publication. For this project submit your Word or WordPerfect document as an attachment to an email to ogarton@uidaho.edu and include attachments of appendices consisting of your final Excel files of your data set as well as the statistical files with input data, command files and output files from SAS, SYSTAT, SPSS, S, R, or other stat package used.
The proposal is the first component of the project. As a wildlife, fisheries or conservation biologist, manager, or researcher you will probably write numerous proposals during your career. Such proposals will likely contain the following four parts required for this exercise plus an additional part; a budget. (Note: This is different than requirements in other classes and does not include a budget.)
Title page - Indicate title, class title and semester, members of the group, date, instructor. **Note: This is the only page that will not follow the guidelines for submitting a paper. The rest of the paper should follow those guidelines exactly.
Introduction (Justification) - This section should present a review of the history of the population and any pertinent literature review of the subject, an indication of why the study should be conducted (not because it's required!), and the purpose and/or objectives of the study. Please note that conducting an in-depth literature review must be a key part of preparing any proposal. You have excellent resources available to you at the Univ. of Idaho library. Enter the address of the University of Idaho's library web portal to databases to which UI subscribes for our use: http://db.lib.uidaho.edu/databases/ In essence, convince me the study is worth doing and be very precise in the objectives you hope to accomplish.
Description of the Study Area and Population - A short and concise verbal description of the study area and population should be presented along with any pertinent maps. Basic habits should be described and percentages given, if obtainable.
Methodology - This is the "meat" section of the proposal. Many studies are "doomed" before they ever get going simply because the investigator did not take sufficient time to develop a good plan of attack. Present any assumptions you may have to make about your population(s). Present the statistical analyses you plan to use (e.g., model selection criteria, confidence intervals around estimates of the population, chi-square or Students t tests, etc.). Be precise in designating exactly what you are going to do. Put your biometry to use!
Literature Cited - You must cite the source for all information that you did not gather personally. Follow the format of Journal of Wildlife Management (JWM) or North American Journal of Fisheries Management (NAJFM) exactly. Note that personal communications and unpublished reports on the internet or in gray literature are not considered reputable sources because they are not peer-reviewed with attendant standards of scientific credibility and reliability. Such citations should never constitute more than 10-20% of your sources and are not listed in your Literature Cited section. Make use of your free access to searching the fish and wildlife literature through ABSEARCH to find previous peer-reviewed literature relevant to your project. If you can't find at least 5 peer-reviewed publications to cite you haven't made an adequate effort to review previous work on your topic of interest.
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Deadline for turning in proposals is 5:00 p.m. on Monday, Oct. 29, 2007. Submit one printed copy of your proposal. For each day the proposal is late, 5 points will be deducted from the determined score to a maximum deduction of one half the points. Part of a day is considered a whole day. |
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Students working as a group should submit one joint proposal and all students will receive the same grade for the proposal. Note that such a proposal will be expected to evidence proportionately more creative thought and effort than proposals from single students. |
Title Page: 5 points - based on completeness, clarity of title, and neatness. Title should be 10 words or less.
Introduction (Justification): 10 points - this should be limited to a maximum of 3 pages double spaced. Grade based on clarity, completeness, and conciseness.
Description of Study Area: 10 points - verbal description should be limited to 1 page. Maps must be in black ink and neat.
Methodology: 20 points - show me how good a planner you are and present it to me in a clear, concise manner so that anyone could go out and repeat the study in the same way, if necessary. Results of any "pilot" studies may be included.
Literature Cited: Pay attention to detail.
Overall Impression: 5 points - proposals are often made or lost on the grounds of the initial or overall impression of the reviewer.
Total points = 50.
The report will consist of eight parts, of which the first four will have been presented previously in the proposal, but must be presented here in a condensed and/or modified version. Remember that "groups will submit a single proposal but for your final report you must complete your own individual analysis and write up your results, discussion, and conclusions independently" as stated above. Each student in a group will submit an individual report (i.e. written personally and individually) based on his/her own analysis and conclusions from analyzing the data.
1. Title page (Same as your proposal except you should make your name bold or underlined).
2. Abstract (see below)
3. Introduction
4. Description of study area
5. Methodology
6. Results (see below)
7. Discussion and Conclusions (see below)
8. Literature Cited (see below)
Abstract (#2)
Give only the very pertinent pieces of information. Check journal guidelines for length restrictions. Do not under-estimate the importance of a well-formulated abstract - it is often the only part of a paper people read (not me, in this case, however!).
Results (#6)
In this section, you will present what you found. The section is expository. That is, the investigator explains to the reader in a simple, concise, scientific way, what was found. The data are analyzed statistically, if appropriate. If the results of more than one subject are presented (e.g., population estimates, age structures, model results, etc.), they are categorized and presented separately. In essence, you expose the facts found in the study. Why particular objectives or results were or were not obtained may be presented, but a discussion as to how the facts relate to other published works is not presented here; this "discussion" is reserved for the next section. Clarity is absolutely essential in this section. If the results can be misinterpreted, they will. Do not use flowery adjectives or adverbs as they only add confusion or take up valuable space in a journal. Words such as very high, highly significant, or strongly correlated are relative to the reader and unnecessary. When appropriate and necessary, use probability levels to indicate how "strongly" the results were correlated, or how significantly different the population means were. For example, you might want to say: "The age structure of the harvested population changed during this period of time (C2 = 4.92; P < 0.05)."
Discussion and Conclusions (#7)
This section allows the investigator to relate his/her material to other published works. Do the results reconfirm other similar studies? How do the results differ? If they differ, why? Here again you should be citing other people's results from the refereed literature. Although speculation is generally frowned upon in many scientific journals, it will be allowed in this paper. Do not be afraid to "stick your neck out" and philosophize a bit on your results. Since you are the expert on your subject, offer your opinion, where appropriate, on the possible interpretation of your results, but be sure to note that it is your opinion. Make recommendations for the future management of this population.
Literature Cited (#8)
All references cited in the body of the paper must be reported correctly and completely in this section. Editors are very "nit-picky" on this section, and readers are very irritated when they want to use a source and find it to be incorrect, incomplete, or missing. It is the responsibility of the writer to double check every source, preferably from the original, so that it is cited correctly. Be sure to check this after typing, virtually letter by letter, comma by comma, before handing in the report. Editors used to require use of standard abbreviations for names of journals - but now JWM requires full titles rather than abbreviations. ! If in doubt, follow the style in the Journal of Wildlife Management. Remember, if you have someone else type the paper, it is your responsibility to see that everything in the manuscript is correct. Misspelled words (typos) are frowned upon. Note that you do not cite any internet sources or web sites in your literature cited unless they constitute a peer-reviewed scientific publication such as Conservation Ecology or other publications of reputable, permanent organizations or institutions. Typical internet sources are cited in the body of the text just like personal communications (see above under Literature Cited section of Proposal).
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Deadline for turning in final reports is Monday December 3, 2007 in class. For each day the report is late, 5 points will be deducted from the determined score up to a maximum deduction of one half of the points. Part of a day is considered a whole day. |
GRADE BREAKDOWN (FOR FINAL REPORT):
Format: 15 points. Based on exact adherence to JWM, NAJFM or Conservation Biology guidelines.
Abstract: 10 points. Based on conciseness.
Sections from Proposal (Title page, Justification and Introduction, Description of Study Area, and Methodology): 10 points
Results: 30 points - maximum 3 pages. Based on clarity of presentation, not only verbally, but use of tables and figures will also be considered. Note: Use figures to show a trend and tables if you think it necessary for the reader to see specific data. Use of appropriate statistical tests will be evaluated.
Discussion and Conclusions: 20 points - maximum 3 pages. Based on clarity, brevity, interpretation of data and comparison with other published work.
Literature Cited: 10 points - 1-2 page(s) should be sufficient. Based on correctness (as determined by style in JWM or NAJFM).
Overall Impression: 5 points - Is the manuscript worthy of publication?
One last comment on style - for many of you, this may be the first time you have written a paper in scientific form. It is quite different than writing a standard term paper in English 102. For instance, do not use footnotes at the bottom of a page. Footnotes are acceptable in tables if correctly done and used sparingly. Look at a recent article in the Journal of Wildlife Management or the North American Journal of Fishery Management. Note the title is all in caps, is left justified, and does not contain a scientific name. The author's name and address is left-justified with the authors capitalized. The abstract is single spaced with the word "Abstract" in bold italics. Scientific names are used here when all common names are first introduced. After the abstract there is a solid line all across the page, etc., etc. WATCH THE DETAIL! Jon Horne posted an article he recently submitted to JWM on the K:\\ drive under ...448\2004\Science Writing for you to look at if you are having trouble understanding the guidelines.
Most journals now require submitting papers electronically and we will move toward that standard by requiring that you submit your final report both in printed form (1 copy which may be duplexed if you desire) and electronically. For this project submit your Word or WordPerfect document as an attachment to an email to ogarton@uidaho.edu and include attachments of appendices consisting of your final Excel files of your data set as well as the statistical files with input data, command files and output files from SAS, SYSTAT, SPSS, S, R, or other stat package used.
“A fundamental goal of education is to produce students who can evaluate ideas – both analysis and synthesis – and who can produce significant original thoughts. Plagiarism is simply repeating words or thoughts of other people, without adding anything new. Therefore, submitting a plagiarized paper – in addition to the wrongful conduct – does not demonstrate the level of understanding and skill that an educated person is reasonably expected to have.” (R. B. Standler. 2000. Plagiarism in colleges in USA. http://www.rbs2.com/plag.htm
“Plagiarism means using another’s work without giving credit. You must put others’ words in quotation marks and cite your source(s) and must give citations when using others’ ideas, even if those ideas are paraphrased in your own words.” (http://sja.ucdavis.edu/sja/avoid.htm)
“Plagiarism is a form of theft. Taking words, phrasing, sentence structure, or any other element of the expression of another person’s ideas, and using them as if they were yours, is like taking from that person a material possession, something he or she worked for and earned.” (J. Cochran, Wake Forest University, http://www.guilford.edu/original/ASC/TWZ/define.html)
“Note that the intent of a plagiarist is irrelevant. It is no defense for the plagiarist to say “I forgot.” Or “It is only a rough draft.” Or “I did not know it was plagiarism.” (R. B. Standler. 2000. Plagiarism in colleges in USA. www.rbs2.com/plag.htm)
Plagiarism violates the University of Idaho code of academic conduct. The departmental policy is consistent with the UI policy, regulation O-2, “Consequences for academic dishonesty may be imposed by the course instructor. Such consequences may include but cannot exceed a grade of “F” in the course.”
Some potentially useful web sites (in addition to those cited above):
http://www.wiu.edu/users/miwrite/wiu/citation.htm Citing electronic texts
http://webster.commnet.edu/mla/plagiarism.htm Examples of what is and is not plagiarism
http://www.its.uidaho.edu/english/comp/plagiarism.htm UI English Department site
http://www.plagiarized.com/index.shtml Commercial site for detecting plagiarism
http://www.canexus.com/eve/index.shtml Site for tracking down plagiarism
"Plagiarism is a serious issue. Plagiarism will not be tolerated. Even a sentence or two plagiarized in a long document is inexcusable. If you are uncertain about how to cite sources, or have other questions about potential cases of plagiarism, visit with me prior to handing in an assignment."
How do I avoid plagiarism? you might wonder. The answer isn't too complicated. Just think back to your basic study skills training: Start your writing effort well ahead of the final deadline, take good notes on what you read rather than grabbing text off of electronic sources like the internet, then simply place everything that is an exact or close-to-exact quote in quotation marks and scrupulously cite your sources. Most cases of plagiarism are quite obvious and the commercial sites available on the internet now make it fairly simple for faculty to find the source of your plagiarized material. One of the most serious risks occurs when you do a joint project with other students. Even if you personally did not plagiarize if you sign your name to a joint project proposal containing plagiarized material you become personally liable for the plagiarized material. Don't do it yourself and make sure it doesn't happen on a group project. I and other faculty in the Fish and Wildlife Dept. consider plagiarism such a serious breach of professional standards (comparable to illegal harvest of fish and game) that any student proven to have committed plagiarism will receive an F and 0 points on the assignment, may fail the course and will be tainted by this unethical behavior on any recommendations for jobs, graduate positions, etc. in the future.
Amy Campbell's 2003 Project on Viability of Checkerspot Butterflies
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Revised: 18 August 2008
