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Mark A. Davis

Professor of Biology
Macalester College
email: davis@macalester.edu

SEMINAR IN ADVANCED ECOLOGY

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SEMINAR IN ADVANCED ECOLOGY

Syllabus AssignmentsUFIs (Useful Flyers of Information for students)

Spring 2005    
Office: OlinRice 219; 651-696-6102                                            

Office Hours:    M 2:00-3:30; W 1:30-3:00


GENERAL INFORMATION

            In this seminar students will examine many of the ideas and theories that have and are currently defining the fields of ecology and related fields such as conservation biology, restoration ecology, behavioral ecology and landscape ecology.  Often controversial, these ideas are the basis for much of the cutting edge research currently being conducted by ecologists around the world.  Using books and ecological journals as the primary source material, students will explore in detail ideas, theory, and empirical data involving topics such as: extinction processes, efforts to restore degraded habitats, the evolutionary basis of behavior, the impact of possible climate change on communities and ecosystems, and species invasions.  Classes will consist of lectures, discussions, student presentations, a class field exercise and an occasional field trip.  During the class, students will gain experience writing ecological research proposals.  (Note: this syllabus and other class information can be found at http://www.macalester.edu/~davis/ecosem.htm/

MEETINGS:  Tuesday 1:00-4:15 OlinRice 270  <>
            Attendance at class meetings is required and students are expected to attend all class sessions during the term.  Students will be expected to inform Mark prior to a class if they will be unable to attend due to some emergency.  Absences will result in a significant loss of points.


TEXTS:  Rosenzweig, M. 2004. Win-win Ecology.   Corson, C. 2004.  The Secret Life of Lobsters.  Plus readings from the primary literature.             

READING, WRITING, DISCUSSION AND GRADING

            Students will do extensive reading, will write regularly, and will be expected to contribute actively to class discussions. There will also be a group field project. The primary written product will be a field ecology research proposal that will be written in accordance with the guidelines of the National Science Foundation. Students will also maintain an Ecology Journal in which they will enter on a weekly basis a summary and critical review of ecological material they have read that week.  Students will take turns preparing and leading class discussions and teaching the class new material via a more typical lecture format.  In addition, students will write bi-weekly memos to one another on issues raised in the course.  Finally, during one week in April, students (working in pairs) will lead an environmental lesson for young children at a nearby elementary school.  There will be no exams in this seminar.  Students will be graded on the quality of their research proposal (40%), ecology journal (30%), participation in class discussions (20%), memo writing (5%), and attendance.

CLASS SCHEDULE

Date                                         Topic/Activity                                                   Reading

                                                                                                (To be read prior to class)

  NOTE:  Each class will begin with about a 30 minute “current ecological events” discussion.  Students’ journal entries for that week will also be handed in at that time.

January 25        Hour 1:  Introduction to class/Overview of Research Proposal Assignment and
                                     Ecological Journals/Selection of Lecture Presentation Topics & Groups
                        Hour 2: Examples of Research Projects


February 1        Hour 1:  Discussion (The Secret Life of Lobsters)           Chapters 1-9    
                        Hour 2: Introduction to Landscape Ecology and Class Project
                   

February 8        Hour 1:Discussion (The Secret Life of Lobsters)             Chapters 10-Epilogue

                        Hour 2: Lab--Brief presentation of Research Project Topics

                                            Preparation for field data collection (review procedures and bird identification)


February 15      Field Data Collection (preceded by 30 minute current ecological events discussion)

February 22      Field Data Collection (preceded by 30 minute current ecological events discussion)

March 1            Introduction to correspondence analysis; presentation of analysis of groups’ data, and group debriefing about the project and findings.

March 8            Hour 1: Bring Us Up to Date:  Student Lecture Presentation I.                            
                         Hour 2: Bring Us Up to Date:  Student Lecture Presentation II.


March 15          Hour 1: Bring Us Up to Date:  Student Lecture Presentation III
                        Hour 2: Introduction to ecological modeling using Excel

SPRING BREAK                                                                                          

March 29          Ecological Modeling using Excel (continued)

April 1 (Friday) (1st draft of research proposal due)

April 5              Hour 1: Panel Reviews and Summaries of Research Proposals
                        Hour 2: Ecological Ethical Conundrums


April 12            Hours 1 & 2  Ecologist’s Public Duty: Informing grade school kids about ecology issues.
                        (Students take over classes at Randolph Heights Elementary School) 
 

April 19          Hour 1: Student Presentations of Proposals
                      Hour 2: Student Presentations of Proposals
 

April 26            Hour 1: Student Presentations of Proposals        
                        Hour 2: Discussion     Win-Win Ecology


May           Hours 1 & 2:     Spring Wildflower and Birding Field Trip and PDPs
 

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ASSIGNMENTS

Landscape Ecology and Multivariate Analysis Project Research Proposal Instructions for Reviewing Proposals Student Ecology Journal

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GRANT WRITING ASSIGNMENT

Seminar in Advanced Ecology
Davis

Background. In ecology, other disciplines, and many other worldly enterprises, one often must compete for funding through grant writing. This activity involves making a case to some funding organization or agency that you have a really good idea, so good in fact that the organization or agency should give you money to make your idea a reality. Since almost everyone would like to be given money, funding organizations are usually (though not always) deluged with proposals. In this competitive environment, one needs to understand the funding process very well and to write a very persuasive proposal.

Before one even begins the proposal writing process, one should contact the funding organization and get as much information as possible about the application process--forms, timetables, types of projects the organization typically funds, etc. Many unsuccessful grant writing efforts simply come from applying to the wrong organization. To be successful, you need to characterize your goals and ideas in terms that reflect the priorities of the granting group.

The Assignment. Since this is an ecology class, you will be writing a scientific research proposal. The proposal will be written according to the grant proposal guidelines of the National Science Foundation, the single largest funder of ecological research in the United States. Ecology is one of the Programs under Ecological Studies, which in turn is part of the Division of Environmental Biology (DEB) (which in turn is part of the Directorate for Biological Sciences). Information about DEB and its programs is attached.

To write a research proposal, one needs to be familiar with the existing research on and related to your topic. Your proposal should build on existing knowledge while also proposing to advance the knowledge in the field. Thus, the first thing you need to do is to select a general area of research. Then, you need to review the literature in this area. Then, you need to develop the specific focus of your proposal (one that would advance the knowledge in this area of research). And finally, you need to write the proposal. The best ecology proposals are those that advance both ecological theory (generalizations about how the natural world works) and ecological knowledge about a specific species, community, or ecosystem.

Your proposal should set your proposed study into the context of the field, emphasize the new knowledge that will be gained by your study (your specific goals and objectives), and describe the methodology you will use to obtain this knowledge. More information about writing the proposal, including specific sections to include are described below.

SECTIONS OF THE PROPOSAL
(This information has been taken directly from the NSF Grant Proposal Guide--NSF 99-2).

Project Summary - Proposal Section A

The proposal must contain a [one page] summary of the proposed activity suitable for publication, not more than one page in length. It should not be an abstract of the proposal, but rather a self-contained description of the activity that would result if the proposal were funded. The summary should be written in the third person and include a statement of objectives, methods to be employed and the potential impact of the project on advancing knowledge, science and mathematics education, and/or human resource development. It should be informative to other persons working in the same or related fields and, insofar as possible, understandable to a scientifically or technically literate lay reader.

Table of Contents - Proposal Section B

Project Description - Proposal Section C

The main body of the proposal should be a clear statement of the work to be undertaken and should include: objectives for the period of the proposed work and expected significance; relation to longer-term goals of the PI's project; and relation to the present state of knowledge in the field, to work in progress by the PI under other support and to work in progress elsewhere. The statement should outline the general plan of work, including the broad design of activities to be undertaken, an adequate description of experimental methods and procedures and, if appropriate, plans for preservation, documentation, and sharing of data, samples, physical collections and other related research products.

The statement should also indicate any broader impacts of the proposed activity, addressing the following: indicate how the project will integrate research and education by advancing discovery and understanding while at the same time promoting teaching, training, and learning; discuss any ways in which the proposed activity will broaden the participation of under represented groups; if relevant, discuss how the project will enhance the infrastructure for research and/or education, such as facilities, instrumentation, networks, and partnerships; indicate how the results of the project will be disseminated broadly to enhance scientific and technological understanding; and, identify potential benefits of the proposed activity to society at large.

Brevity will assist reviewers and Foundation staff in dealing effectively with proposals. Therefore, the Project Description may not exceed 15 pages. Visual materials, including charts, graphs, maps, photographs and other pictorial presentations are included in the 15-page limitation. Conformance to the 15-page limitation will be strictly enforced and may not be exceeded unless a deviation has been specifically authorized.

The Metric Conversion Act of 1975, as amended, and Executive Order 12770 of 1991 encourage Federal agencies to use the Metric System (SI) in procurement, grants and other business-related activities. Proposers are encouraged to use the Metric System of weights and measures in proposals submitted to the Foundation. Grantees are also encouraged to use metric units in reports, publications and correspondence relating to proposals and awards.

References Cited - Proposal Section D

Reference information is required. Each reference must include the names of all authors in the same sequence in which they appear in the publication, the article title, book or journal title, volume number, page numbers and year of publication. Proposers should be especially careful to follow accepted scholarly practices in providing citations for source materials relied upon when preparing any section of the proposal.

While there is no established page limitation, this section should include bibliographic citations only and should not be used to provide parenthetical information outside of the 15-page project description.

Biographical Sketches - Proposal Section E

Biographical sketches are limited to two pages each and are required for all senior personnel. (See Appendix C for definition of Senior Personnel.) The following information must be provided:

a. Vitae, listing professional and academic essentials and mailing address;

b. List of up to 5 publications most closely related to the proposed project and 5 other significant publications, including those accepted for publication. Patents, copyrights or software systems developed may be substituted for publications. Additional lists of publications, invited lectures, etc., should not be included. Only the list of 10 will be used in merit review.

c. A list of ALL persons (including their organizational affiliation), in alphabetical order, who have collaborated on a project or a book, article, report or paper within the last 48 months, including collaborators on the proposal and persons listed in the publications. If there are no collaborators, this should be so indicated.

d. A list of persons (including their organizational affiliation), over the last five years with whom the individual has had an association as thesis advisor or postdoctoral scholar sponsor. A summary of the total number of graduate students advised and postdoctoral scholars sponsored should also be included.

e. The names and institutions of the individual's own graduate and postgraduate advisors.

The information in c, d, and e is used to help identify potential conflicts or bias in the selection of reviewers.

Proposal Processing and Review

NSF evaluates proposals using a process known as peer review. As indicated by the words, ecologists evaluate one another's proposals. We will do the same in this seminar. That is, you will review one another's proposals. The specific process followed by NSF is described below. (This information is taken from the Grant Proposal Guide, NSF 99-2.)

Proposals received by the NSF Proposal Processing Unit are assigned to the appropriate NSF program for acknowledgment and, if they meet NSF requirements, for review. All proposals are carefully reviewed by a scientist, engineer, or educator serving as an NSF Program Officer, and usually by three to ten other persons outside NSF who are experts in the particular field represented by the proposal. Proposers are invited to suggest names of persons they believe are especially well qualified to review the proposal or persons they would prefer not review the proposal. These suggestions may serve as one source in the reviewer selection process at the Program Officer's discretion. Program Officers may obtain comments from assembled review panels or from site visits before recommending final action on proposals. Recommendations for awards are further reviewed by senior NSF staff.

NSF REVIEW CRITERIA

The National Science Board approved revised criteria for evaluating proposals at its meeting on March 28, 1997 (NSB 97-72). The criteria are designed to be useful and relevant across NSF's many different programs, however, NSF will employ special criteria as required to highlight the specific objectives of certain programs and activities.

The merit review criteria are listed below. Following each criterion are potential considerations that the reviewer may employ in the evaluation. These are suggestions and not all will apply to any given proposal. Each reviewer will be asked to address only those that are relevant to the proposal and for which he/she is qualified to make judgments.

What is the intellectual merit of the proposed activity?

How important is the proposed activity to advancing knowledge and understanding within its own field or across different fields? How well qualified is the proposer (individual or team) to conduct the project? (If appropriate, the reviewer will comment on the quality of prior work.) To what extent does the proposed activity suggest and explore creative and original concepts? How well conceived and organized is the proposed activity? Is there sufficient access to resources?

What are the broader impacts of the proposed activity?

How well does the activity advance discovery and understanding while promoting teaching, training, and learning? How well does the proposed activity broaden the participation of underrepresented groups (e.g., gender, ethnicity, disability, geographic, etc.)? To what extent will it enhance the infrastructure for research and education, such as facilities, instrumentation, networks, and partnerships? Will the results be disseminated broadly to enhance scientific and technological understanding? What may be the benefits of the proposed activity to society?

DIVISION OF ENVIRONMENTAL BIOLOGY (DEB)

The Division of Environmental Biology "supports fundamental research on the origins, functions, relationships, interactions, and evolutionary history of populations, species, communities, and ecosystems. Scientific emphases include biodiversity, molecular evolution, mesoscale ecology, computational biology (including modeling), conservation biology, global change, and restoration ecology."

The Division of Environmental Biology is divided into two sections, 1) Systematic and Population Biology and 2) Ecological Studies. In turn each of these sections is subdivided into specific programs. These are described briefly below.

SYSTEMATIC AND POPULATION BIOLOGY

"Supports research on the patterns and causes of diversity within and among populations and species. Research projects may involve any group of organisms, including terrestrial, freshwater, and marine taxa, and range in subject from microbes to multicellular plants, animals, and fungi. Research areas are arranged in the following groups.

Population Biology: "Focus areas include (1) molecular population studies including analyses of the causes and consequences of variation and change in biochemical characteristics; RNA and DNA sequences; the population genetics of mobile elements; the evolution of genic and genomic organization and functioning; and the evolution of organismal development; (2) population and quantitative genetics directed at understanding the genotypic and phenotypic variation of populations during microevolution; geographical differentiation; organismal adaptation to changing environments; natural hybridization; and speciation; and (3) studies from an ecological and evolutionary perspective of the life history and life cycle phenomena of terrestrial, freshwater, and wetland organisms; animal and plant demography of age- and stage-structured populations; and population dynamics including linear, nonlinear, and stochastic approaches."

Systematic Biology: "Focus areas include (1) phylogenetic analyses that produce or test phylogenetic hypotheses or models and the use of derived phylogenies to elucidate patterns of structural, developmental, or molecular evolution; (2) studies that lead to improved classifications, better methods of taxonomic identification, contributions to classificatory theory, and nomenclatural reform; (3) understanding of processes that underlie the origin and maintenance of taxonomic diversity; and (4) theoretical and empirical studies of biogeographical, co-evolutionary, and paleobiological patterns to develop models of the origin, diversification, distribution, and extinction of species and evolutionary lineages and to determine the tempo and mode of evolutionary change."

Biotic Surveys and Inventories: "Focuses on collecting and recording the diversity of life on Earth. Permanent, well-curated collections and computerized databases are strongly encouraged as products of the program's support."

ECOLOGICAL STUDIES

"Supports research on natural and managed ecological systems, primarily in terrestrial, wetland, and freshwater habitats. Research areas include experimental, theoretical, and modeling studies on the structure and function of complex biotic-abiotic associations and the coupling of small-scale systems to each other and to large-scale systems. Projects are encouraged that develop conceptual and synthetic linkages such as theoretical and modeling studies, that are conducted at one or more scales of ecological organization, and that synthesize empirical and theoretical findings into new ecological paradigms. Research areas are arranged in the following groups."

Ecosystem Studies: "Supports mechanistic or empirical investigations of whole-system ecological processes and relationships in the following areas: (1) biogeochemistry, such as studies of decomposition, global and regional elemental budgets, and biotic versus abiotic controls of nutrient cycles; (2) primary productivity, particularly ecophysiology within an ecosystem framework; and (3) landscape dynamics with an emphasis on quantitative models of disturbances, ecosystem resilience, and successional patterns."

Ecology: "Supports community ecology and population interactions in such areas as (1) dynamics and processes within specific communities or habitats; (2) food-web structure and landscape patterns formed by community dynamics; (3) paleoecology; and (4) organismal interactions such as mutualism, plant-animal interactions, competition, predation, co-evolution, and chemical or evolutionary ecology."

Long-Term Ecological Research (LTER): "Supports investigations of whole ecosystems and their component organisms and processes at sites that represent major biomes. Projects are multidisciplinary and actively encourage collaborative research with nonecological investigators. The deadline date for submission of proposals is announced only via special solicitations; unsolicited proposals will not be accepted."

Long-Term Research in Environmental Biology (LTREB): "Supports smaller studies that focus on evolutionary or ecological phenomena and that require long-term investigation. These awards are designed to provide funding to help maintain an on-going long-term research project; LTREB awards are not a source of start-up funds to initiate long-term research nor does DEB envision that LTREB projects will be the main source of extramural support for investigators."

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INSTRUCTIONS FOR RESEARCH PROPOSAL REVIEW PANELS

Students will be divided into panels consisting of three or four student reviewers. Each panel will receive three or four proposals to review. Each student in a panel will review each of the proposals assigned to that panel, and each student will be the lead reviewer for one of the proposals. Reviewers need to bring to the panel meeting a hard copy review of each of the proposals in their panel. At the panel meeting, each of the proposals will be discussed in turn, with the discussions being led by the lead reviewer. The initial basis for the discussion will be issues raised by the reviewers in their own reviews, however it is expected that the discussion will help synthesize the various points made by the different reviewers. In some cases, new issues may arise out of the discussion. It will be the lead reviewer's job to take notes during the discussion and to write up a summary review based on the discussion. The author of the proposal will receive the summary review and copies of all the individual reviews prepared by the panelists.

Discussions of individual proposal should take about fifteen minutes. The lead reviewer will begin the discussion by briefly summarizing the proposal, including the objectives and proposed methodology. The lead reviewer will then summarize his/her review of the proposal, followed by brief summaries by the other panelists of their respective reviews. The discussion will continue as panelists respond to the points made by other panelists, e.g., agree, disagree, etc. During the last two minutes, the panel needs to come to a consensus on what the lead reviewer will include in the summary review.

The individual and summary reviews should be approximately 150-250 words in length. They should address positive aspects of the proposal as well as weak points. Reviewers and panels should feel free to make specific recommendations about particular aspects of the proposal, e.g., methodology or experimental design. Reviewers and panels should pay special attention to several aspects of the proposals, including the literature review (context for the proposed study), clarity of objectives and/or hypotheses to be tested, thoroughness of the methods description, and appropriateness of the methodology described, i.e., would the proposed methodology enable the author to accomplish the stated objectives?

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LANDSCAPE FEATURES AND HABITAT CHOICE BY OVERWINTERIN BIRDS:
DISCERNING PATTERN FROM COMPLEX DATA SETS

(Introduction to Landscape Ecology, Multivariate Analysis, and Winter Birds Via a Group Field Project}



Background. The ultimate goal of ecologists is to recognize and describe patterns of ecological phenomena and to explain the causes of these patterns. The challenge faced by ecologists is to accomplish this goal in the face of extensive variation in ecosystem processes, community structure, population dynamics, and the phenotypes and genotypes of individual organisms. Basic statistics (e.g., regressions, contingency table analysis, t-tests, ANOVAs) is one method ecologists can use to discern ecological pattern from environmental noise. However, in many cases these analyses are not sufficient.

A common data set in ecological studies consists of species lists at many different sites. A basic question from such a data set is whether the species vary in any ordered fashion among the different sites, and if they do vary in an ordered fashion, is there any plausible ecological explanation for the observed pattern of species distribution. A large data set of this type might include dozens of sites with more than 100 species among the sites. Although certain patterns of individual species might be discerned by inspection of the data, some general analysis method is needed to systematically process all the species at all the sites in order to reveal any comprehensive patterns. Many such analyses exist; these fall under the umbrella term multivariate analysis.

Multivariate Analysis. Multivariate analysis, sometimes referred to as ordination, aims to reduce the complexity of a data set in order to reveal a few of the most important general trends or patterns. Normally, one of the results of an ordination is a graph consisting of one, two, or three axes on which individual sites and species are plotted. The proximity of sites and species to one another on the ordination graph is usually interpreted as an indication of their similarity. For example, sites close to one another would indicate that they tended to share similar species while species close to one another would indicate that they often were found together (and not found together) at sites. Species plotted close to particular sites would indicate that those species were often found at those particular sites. As just described, such an ordination normally would be part of an exploratory analysis in which the ecologist's primary goal would be to identify some patterns of species abundance among different sites. If a pattern is discerned with the aid of multivariate analysis, the ecologist is then often able to formulate more specific hypotheses regarding the ecological causes for the pattern observed. These hypotheses can then be tested by other studies. These subsequent studies could be experimental in nature with the data being analyzed using traditional statistics (ANOVAs, etc.), or they could be other observational studies with the data being analyzed using other multivariate techniques. See the handout on ordination for more information on multivariate analyses.

Landscape Ecology:  The discipline of landscape ecology studies patterns in the landscapes, what processes produce those patterns, and how those patterns influence other processes and patterns.  Landscape patterns include such things as patchiness, corridors, edges, and connectivity.  These elements can be such things as ponds, forest patches, roads, rivers, agricultural fields, and borders between these.  Landscape patterns can be produced by natural events such as fires, floods, and earthquakes, or by humans through deforestation, agriculture, and urban development.  These patterns can greatly affect biological processes such as dispersal and migration of plants and animals, the flow of nutrients from one place to another, and the size, diversity, and composition of plant and animal communities.

The Project. As a class, we will do an exploratory analysis of the overwintering bird community at various sites around the Twin Cities that vary in certain landscape features, such as overall tree density, the number of tree patches, the size of tree patches, the amount of tree edges, and whether or not the habitat percolates (is fully connected).  Questions we will try to answer are:

Field Equipment: aerial photograph, road map,100 m tape measure, binoculars, bird book, notebook, pen or pencil, warm clothes <>Field Procedures. Working in pairs, you will be assigned a particular location in St. Paul or Roseville (a park, golf course, or cemetery) at which you will collect data. (You will use a map and aerial photograph as a guide to help you find your assigned study area.) Once you have found your study site, you will determine the boundaries of your 200 x 200 m observation plot.  Then you will systematically walk through your observation plot (8 200 m transects) and record all birds that you observe.
Try to aim for about 7-8 minutes per transect.  Finally, estimate approximately what proportion of the trees in your 200 x 200 m observation plot are evergreen.

Data Compilation. For each of the two observation days, record the number of birds of each species that you saw.  Include mammals as well, if you saw any. Return these data to Mark directly upon your return to campus each Tuesday afternoon.

Landscape AnalysisUsing your aerial photographs and the grid provided, calculate the following landscape features:  number of (clusters) patches of trees, largest cluster, total outside edge of tree patches, total inside edge (if any) of tree patches, and total area covered by tree patches. Also, indicate if your landscape percolates.  Then, produce 15 random landscapes using the same 8 x 16 grids, and calculate the mean, standard deviation, and 95% confidence intervals for the same six landscape attributes you calculated for your actual landscape.  Also record how many of your random landscapes percolated.  Then compare your actual landscape attributes with the values obtained from your random landscapes to determine whether your site differed from a neutral landscape model, and, if so, in what landscape parameters did it differ.  Provide Mark with the landscape attributes for your observation area and your random landscapes, along with your comparison of your site with the neutral landscapes no later than the 2nd Tuesday afternoon of the field data collection.

Data AnalysisWe will do the data analysis in class using a multivariate analysis method known as correspondence analysis. 

Supplemental Readings. The following sources provide background on landscape ecology and winter bird habits, and also include a study of habitat fragmentation on bird distributions as well as an example of applying correspondence analysis to a study of bird distributions.

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STUDENT ECOLOGY JOURNALS

Background

Research in any discipline is primarily defined by a comparatively small group of key questions, concerns, and controversies. As these issues change over time, the field continually redefines itself.   Regular reading in the discipline is necessary if one wishes to understand these defining concepts. Ecologists, like all professionals, continually read in their discipline. They read recent research publications, review articles, research proposals and articles submitted for publication (as peer reviewers), books, and popular articles in newspapers and magazines. As part of their own research, they also read articles and books published in the past. The ongoing learning that takes place in the rapidly changing discipline of ecology is partly what makes being an ecologist so intellectually stimulating. Ideas and theories are always being challenged. Some ideas persevere in the discipline while others are discarded for ones that better explain the evidence. With ongoing thoughtful reading in the discipline, ones own understanding of the natural world changes over time as well. Sometimes the changes are gradual, if occurring at all, while at other times ones view can change dramatically in a short time (a process not unlike evolution itself).

Besides the intellectual stimulation involved in remaining current with the discipline, understanding the currently defining concepts has important practical ramifications. In order to publish papers and secure funding for your own research, you need to link your own work to these same defining concepts. Publication and grant funding is very competitive. Far more articles are submitted for publication than are published and even more grant proposals are submitted than are funded. Decisions for publication and funding in ecology are based on a peer review process, in which your colleagues evaluate the importance of your article or proposal. Thus, to be successful, you need to know what ideas and what types of research the discipline currently regards as important and of high priority.

The Journal

Throughout this class, students will keep an ecology journal. This will be a folder, in which you regularly enter descriptions, thoughts, and commentary on ecological material you have read. Each entry should be dated. These accounts are similar to the class memos except that they are written for yourself and not for someone else in class. The subject matter is a bit narrower than memos as well. Journal entries should primarily be focusing on the ideas, concepts, theories, and findings of the discipline of ecology, along with your effort to make sense of them. More personal reflective commentaries, e.g., on environmental issues, personal experiences on internships or study away programs, career plans, etc., are excellent topics for memos, but not for the journal.  At the end of class, a good journal will provide a map of your intellectual journey and growth during the course.  Entries will be collected each week and put into your folder.
 

Your journals will be graded. In fact, evaluation of the journals will represent a large portion of your grade in the class, 30%. Thus, you are encouraged to take them seriously. In most cases, entries will probably be associated with a particular article, book, essay, etc. that you have read. However, it will likely also be common for you to make an entry addressing a couple of related readings. In general, entries should include both a descriptive or expository component and a commentary component. In the expository section, you will briefly describe the essential features of the piece on which you want to focus. For example, these might be findings, interpretations, hypotheses, methodology, or objectives of the report or study. In the commentary, you will then reflect on whatever it was you wrote in the expository section.  You might explain why you disagree with the author(s); you might explain how this report relates to other reports on the same topic (e.g., is supportive or contradictory); you might comment on what you believe is a strength or weakness of the report; you might explain how the report has affected your thinking on the subject; you might comment on how you think this and related research is affecting the discipline, etc.

Subject matter for your memos can include the required readings for the class, material read for your research proposal, and additional reading you do on your own. While some entries can be based on articles in newspapers and popular magazines, most should be based on scientific journals, reports, and books. Commentaries on popular reports might address how accurate you believe the reporting is based on what you know of the scientific literature.  You are encouraged to check out new issues of ecological journals that are put out on the periodical shelves on the main floor of the library. These journals are listed on the attached page.  In addition, you should get in the habit of perusing SCIENCE each week. While covering all scientific disciplines, this journal is probably regarded as the premier publication for most scientists. To be published in SCIENCE, ones work clearly must be of a discipline defining nature. Thus, any coverage of ecological research in SCIENCE will be of cutting edge ideas and findings that have important ramifications for the discipline.  Another great source to check weekly is the Science Tuesday, a special section of the New York Times produced every Tuesday.  It usually has one or more very interesting and timely reviews of something ecological.  Given that the class meets Tuesday afternoon, it is always great to check out Science Tuesday and get something hot off the press.

Your journals will be evaluated on the quality of your descriptions and commentaries and on the nature of the sources used as the basis of your entries. While there is no specific length requirement, comprehensiveness, as well as quality, will be considered in the evaluation. That is, high quality entries consisting of a single page account of a single source each week would not receive a high evaluation. Low quality entries (e.g., lacking substantially in either the expository or commentary sections) of several sources per week likewise would not receive a high evaluation.  Journals which include entries involving readings not required for the class or related to the student=s research proposal will evaluated more highly than ones without such entries. Journals will be collected about four weeks into class and returned promptly with preliminary comments regarding your entries.

Ecology Journals to which Macalester subscribes:

American Journal of Botany (includes some ecological articles)
American Midland Naturalist
American Naturalist (emphasizes theory)
Behavioral Ecology
Biodiversity and Conservation
Biological Conservation
Bioscience (excellent review articles by the scientists themselves)
Canadian Journal of Fisheries and Aquatic Sciences
Conservation Biology
Ecological Monographs (same as Ecology, but this contains the longer articles)
Ecologist
Ecology (the signature journal of the Ecological Society of America, ESA)
Environmental Forum
Evolution
Evolutionary Ecology
Global Biodiversity
Journal of Animal Ecology
Journal of Ecology (the signature journal of the British Ecological Society)
Journal of Mammalogy
Journal of the North American Benthological Society
Journal of Wildlife Management
Limnology and Oceanography
Loon (natural history of birds journal published by the Minnesota Ornithological Union)
Natural History
Nature (the European version of SCIENCE; leading publisher of all scientific disciplines)
New Scientist
Oecologia (through 12/98)
Proceedings of the National Academy of Sciences of the U.S. of America
Restoration and Management Notes
Trends in Ecology and Evolution (Library Edition)
Wilson Bulletin
Annual Review of Ecology and Systematics (great bibliographies)
Ecological Applications
Environment
Environmental Biology of Fishes
Environmental Conservation
International Journal of Sustainable Development and World Ecology
Journal of Environmental Education
Natural Areas Journal
SCIENCE (the leading journal in the US of cutting edge science in all disciplines)
Wilderness America
Wildlife Conservation
 
 

ORDINATION

Introduction. Ordination refers to a variety of multivariate analysis techniques developed to help simplify certain complex data sets. A common type of ecological data set consists of a list of species at many different sites. The general ecological question of interest usually is whether there is any sort of pattern to the distribution of species among the sites. More specific questions include: are certain species often found together; are certain species seldom ever found together; are certain sites quite similar in their species composition; are certain sites very different in their species? One could examine species in a pair-wise fashion to answer some of these questions and one could perform pair-wise comparisons of sites using simple ecological indices, such as the Coefficient of Community or Percent Similarity. But this approach is very time consuming and does not provide a holistic overview of the entire system--all the species and all the sites.

There are many different types of ordination, but they all provide this holistic examination of the data. While the specific calculations vary among ordination types, the nature of the output is usually the same. Normally, an ordination graph is produced (in one, two, or three dimensions) on which sites and/or individual species are plotted. The production of an ordination graph usually involves a dramatic reduction in the dimensionality of the data, thereby providing a spatial display of the data which can be presented on a two dimensional surface. (Very few of us are capable of visualizing spatial displays of data in more than three dimensions.) The ordination analysis calculates "distances" between sites and species based on the number of individuals of each species at each site. For example, many ordination techniques determine distances using a chi-square type of calculation. Whatever the method used, ordination can display on a single graph sites and/or species at various distances from one another. The relative distance sites and species are from one another is indicative of how similar they are to one another.

The one problem with ordination is that the axes produced for the ordination graph have no ecological meaning. For example, an ordination might lump sites into three distinct groups distributed horizontally across the graph. In this case, it would be nice to know what the x axis represented in order to provide a context for understanding the shift in the location of the three groups. In other words, do the axes represent some environmental gradient?

Gradient Analysis. Ultimately an ecologist wants to know not just the spatial pattern of species distributions but the environmental explanations behind the patterns. Efforts to discover underlying environmental factors that may be contributing to changes in species abundance across space are often referred to as indirect gradient analyses. In these analyses, the ordination calculations are performed solely on the species data (number of each species at the respective sites). No environmental data regarding the sites is incorporated into the calculation process. After the ordination is completed, the ecologist may decide to determine whether the axes may have some ecological meaning. To find out if the x axis represents a particular environmental gradient, one can perform one or more simple linear regressions using the x coordinates of the respective site points as the dependent variable and one or more environmental measurements recorded at the respective sites. If one or more of the regressions are significant, one then has an ecological context to interpret the x axis. For example, if the regressions were significant for soil nitrogen (negative slope) and for elevation (positive slope), one could envision the x axis as a combined elevation and soil nitrogen gradient, with sites and species on the far right of the graph characterized by high elevation and low soil nitrogen while sites and species on the far left characterized by low elevation and high soil nitrogen. One could conduct similar regressions with the y axis (and z axis if one were interested) to see if the sites and species were sorted out vertically along one or more other environmental variables. For example, the y axis might be positively associated with annual precipitation. In this example, one would now have an excellent ecological context (involving elevation, precipitation, and soil N levels) in which to interpret the distribution of sites and species in this two-dimensional space.

One could run other regression analyses using the abundance of individual species at the respective sites as the dependent variable and the corresponding environmental measurements at the sites as the independent variable. These analyses would indicate whether the abundance of certain species predictably increased or decreased along the environmental gradients.

There are many types of ordination that are examples of indirect gradient analyses. Two of the techniques most commonly used by ecologists are Principal Components Analysis and Correspondence Analysis. These, and the other indirect gradient analyses, are used fundamentally as exploratory tools. They are used to identify spatial patterns of species distributions and to identify environmental factors that might be responsible for the patterns. Note that the development of hypothesized causes for the spatial patterns occurs after the data are collected. This is quite different from analyses which are specifically testing causal hypotheses that were articulated prior to the study. There is nothing wrong with this approach, which is very commonly pursued by ecologists. But it is important to understand that when one conducts an indirect gradient analysis, one is developing, not confirming, hypotheses.

If one knows ahead of time (e.g., from other studies) what are the driving environmental variables, one can incorporate environmental measurements into the ordination calculation itself. This is called direct gradient analysis, or sometimes constrained ordination, since the ordination calculations (e.g., calculated distances between sites) are actually constrained by the respective environmental measurements at the sites. The ordination graphs produced by these analyses include not only plots of the species and sites but also vectors (arising from the graph's origin) representing each of the environmental variables. The direction of the arrows indicates the direction of the respective environmental factors on the graph. Thus, graphs produced by constrained ordination include the ecological context as part of the output.

One advantage of direct gradient analysis is that one is able to test a priori hypotheses. The most common type of direct gradient analysis now being used by ecologists is Canonical Correspondence Analysis. This analysis permits the ecologist to calculate p values for null hypotheses stated prior to the experiment. An example of a null hypothesis would be: species distributions are not related to a specified set of environmental factors.

In conclusion, although the phrases multivariate analysis and gradient analysis sound imposing, the purpose of these techniques is really quite simple--to produce a visual display of data in three or fewer dimensions and to provide an ecological context for interpreting the display.

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