Biology 600 - Seminar in Conservation Genetics

(2 Units: Graded)

Last Updated 23 March, 1999

Instructors:Dr. Lee McClenaghan (594-3751; lmcclena@sunstroke.sdsu.edu) & Dr. Tod Reeder (594-7826; treeder@sunstroke.sdsu.edu)

Time & Place:  9:00-11:40 on Fridays; LS 235.

Objectives: 1) To learn about conservation genetics by reading and evaluating the current literature; 2) to develop critical thinking skills; and 3) to develop skills of oral presentation and response to questions in a professional setting.

Possible topics:

  • Genetic variation, heterozygosity and fitness.
  • Genetic variation in populations and species: how is it measured? how is it maintained?
  • Inbreeding and inbreeding depression.
  • Outbreeding depression.
  • Importance of gene flow and migration in conservation.
  • Hybrization and introgression.
  • Systematics and conservation genetics.
  • Captive breeding programs and re-introductions.
  • Genetic drift; founder and bottleneck effects.

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    Grading criteria:  2/3 seminar presentation; 1/3 questions asked/discussion.

    Seminar format:
        Class lasts 100 minutes (1 hour and 40 minutes). Please be prompt; if we start late, we end late. That time period will be divided as follows (subject to modification):

    10 -15 minutes:
        If needed, wrap-up from previous week's speaker. Opportunity to answer questions, present material inadequately answered/presented in the previous week.

    30 minutes:
        Thorough presentation of primary journal article and possibly peripheral journal articles or book chapters. The presenter should generally have handouts to distribute beforehand with a brief outline of the topic, photocopied illustrations (if appropriate), and pertinent literature cited (both of the paper and other articles or books).
        Summarize and critically evaluate: 1) Objectives proposed and questions asked; 2) methodology used; and 3) conclusions presented (see below). Explain material to the general audience; don't assume foreknowledge.
        Thoroughly evaluate how the article relates to and/or can be applied to one's own research interests.
        It is strongly recommended that the speaker use PowerPoint for their presentation. Use of overheads and/or slides is optional.

    20 minutes:
        Critical questions from students enrolled in the course: Students are required to ask one pertinent question. These will be asked in an order determined by the instructors, which will rotate each week. Questions may include clarification of points in the journal article, clarification/explanation of what the speaker said, or general questions about the topic or field (e.g., things that you do not understand or have expertise in).

    30 minutes:
        Critical questions from the instructors (and other faculty or students present). These may include both specific questions related to the article and questions that the instructors feel the student should know as general knowledge.

    5 - 10 minutes:
        Wrap-up. Distribution of topic/paper(s) for next week.

    10 minutes +:
        Meeting of instructors with speaker to comment on quality of presentation, where improvement can be made, and possible questions to answer more adequately the following week.

    Hints for preparation:

  • Read the abstract thoroughly, several times. Mark what you think are the objectives, methods, and conclusions. Jot down (in the margin or on paper) any questions you have about anything in the abstract ( e. g., something you do not know or do not understand, something you think is faulty.
  • Stop and recite to yourself (orally or in writing) the paper title, authors, journal, and year. Then recite the gist of the paper: Objectives, methods, and conclusions.
  • Next, look at all the figures and tables. Read the captions thoroughly. Ask yourself if you understand these figures and tables, how the data were obtained and what is being described or analyzed. Again, jot down any questions you have about these figures and tables.
  • Now read the article from start to finish, with one objective being to answer the questions you have written down. If you are limited for time, skim through certain sections (e. g., lengthy descriptions).
  • Get into the habit of looking up at least some of the literature cited. If interested or if pertinent, obtain one or more of these articles for further reading.
  • Critique the paper by jotting down if you thought the author(s) attained the objectives, answered the questions posed, used the correct methodology (including type of analysis), and had a valid basis for the conclusions presented. How might you approach the problem differently, or what different or further problems/objectives would you propose?
  • Think about how the paper, related topics, or specific methodology or knowledge relates to your own research or research interests.

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    What everyone should bring to the seminar:

  • Copy of the article.
  • Notes of questions you have (at least as many as students enrolled in course), whether you thought the author(s) attained the objectives of the paper.
  • Thoughts about what would you have done/concluded differently?

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    Critical Thinking
    Critical thinking in science means forming a judgment about a piece or research, rather than simply accepting it at face value. It does not, however, mean just trying to find fault with it. The following are guidelines to help assess the value of a scientific paper.

    General Issues
    1. What specific question does the paper address?
    2. In what framework or context is this an interesting question?
    3. Does this paper open new avenues of research, test rival hypotheses, or present basic data of little conceptual interest?

    Data Collection
    4. What methods are used to answer the research question?
    5. What kind of data were collected and are these appropriate to address the research question?
    6. From your own experience (or imagination), what problems may have been encountered during collection of the data? How might they have influenced the results?

    Analyses
    7. What analyses were performed and what conclusions may be drawn from them?
    8. Were analyses used appropriately?

    Conclusions
    9. What do the authors conclude?
    10. What is the chain of logic leading the authors to their conclusion? Does it contain unfounded assertions, tautologies, or inconsistencies?
    11. What is essential and what is unnecessary to the conclusions? Discussion sections often include material that is interesting but not crucial to the conclusions. Don't get waylaid by this when assessing the value of the research.
    12. What implications does this research have for the way we think of the natural world?
    13.  Are there other possible interpretations of the data?

    Some Pertinent Journals in Conservation Biology and Genetics (articles from more specialized journals may also be acceptable):
    Molecular Ecology
    Genetics
    Bioscience
    Conservation Biology
    Evolution
    Science
    Nature
    Ecology

    Papers Discussed:

  • Walker, D., G. Orti, and J. C. Avise.  1998.  Phylogenetic distinctiveness of a threatened aquatic turtle (Sternotherus depressus).  Conservation Biology 12:639-645.
  • Garcia-Rodriguez, B. W. Bowen, D. Domning, A. A. Mignucci-Giannoni, M. Marmontel, R. A. Montoya-Ospina, B. Moreales-Vela, M. Rudin, R. K. Bonde, and P. M. McGuire.  1998.  Phylogeography of the West Indian manatee (Trichechusmanatus):  How many populations and how many taxa?  Molecular Ecology 7:1137-1149.
  • Fitzsimmons, N. N., S. W. Buskirk, and M. H. Smith.  1995.  Population history, genetic variability, and horn growth in bighorn sheep.  Conservation Biology 9:314-323.
  • Bouzat, J. L., H. H. Cheng, H. A. Lewin, R. L. Westemeier, J. D. Brawn, and K. N. Paige.  1998.  Genetic evaluation of a demographic bottleneck in the Greater Prairie Chicken.  Conservation Biology 12:836-843.
  • Templeton, A. R., S. K. Davis, and B. Read.  1987.  Genetic variability in a captive herd of Speke's Gazelle (Gazella spekei).  Zoo Biology 6:305-313.
  • Coltman, D. W., W. D. Bowen, and J. M. Wright.  1998.  Birth weight and neonatal survival of harbour seal pups are positively correlated with genetic variation measured by microsatellites.  Proceeding of the Royal Society of London, B 265:803-809.
  • Fischer, M. and D. Matthies.  1997.  Mating structure and inbreeding and outbreeding depression in the rare plant Gentianella germanica (Gentianaceae).  American Journal of Botany 84:1685-1692.
  • Haig, S. M., J. D. Ballou, and S. R. Derrickson.  1990.  Management options for preserving genetic diversity:  Reintroduction of Guam Rails to the wild.  Conservation Biology 4:290-300.
  • Roy, M. S., E. Geffen, D. Smith, and R. K. Wayne.  1996.  Molecular genetics of pre-1940 Red Wolves.  Conservation Biology 10:1413-1424.