Research Notebook

1. Research Notebook

2. I. Purpose and Importance • A complete record of research ideas, activities, and findings. • A contemporaneous record, i.e. recorded at the time, not from memory. • Permits later re-analysis of data. • Legally admissible in disputes about: • intellectual property • patents • fabrication or falsification of results

3. II. Types of Notebooks • Minimum requirements • Graph paper • Numbered pages • Bound • Optimal attributes • Duplicate pages

4. III. Content • Err on the side of too much detail • Table of contents • Update every few days • Date all entries • Each entry has abbreviated title • Observations • Experimental protocol in detail • Include figures, diagrams where needed • Information on instruments • Sample calculations, etc. • Data – ALL of it

5. III. Content • Data • Ways to put in data: • Narrative form • Repetitive data? • Table • Data sheet • Tape, all 4 sides, and outline area in notebook • Refer to their presence in your narrative • Data Analysis

6. III. Content • Modifications to protocol • Actual measurements if they differ from intended values in the protocol • Unusual findings • Conclusions, speculations, hypotheses • Ideas for future research • General thoughts (relevant ones, please)

7. IV. Do's and Don'ts • Use a pen • Bring your notebook every time you might do any research. • Make entries while you are in the lab, or very soon thereafter. No “catching up.” • Sign every page when it is finished. • Always write entries directly in notebook • Keep a copy in a separate location*

8. IV. Do's and Don'ts • Make photocopies of data transferred into the notebook - be sure to include the source of the information • Don't copy data from one page to another; photocopy and tape instead • Try to be legible. But it’s not a beauty contest. DO NOT take rough notes elsewhere and recopy.

9. IV. Do's and Don'ts • Never tear out an original page • Don't erase or conceal a mistake. Cross out (one single line) so that erroneous text remains legible. • Don’t let your notebook become a folder of loose data sheets. If they belong in the notebook, attach them permanently. • Don't include your literature search results • Avoid irrelevant information (shopping lists, to-do lists, love notes).

10. Project #1: Competition in Mycophagous Flies

11. Project #1: Competition in Mycophagous Flies I. Pattern in Nature: - 10-15 species of mycophagous flies use soft-bodied mushrooms as larval resources

12. Project #1: Competition in Mycophagous Flies I. Pattern in Nature: - 10-15 species of mycophagous flies use soft-bodied mushrooms as larval resources - these resources are ephemeral; they rot fast

13. Project #1: Competition in Mycophagous Flies I. Pattern in Nature: - 10-15 species of mycophagous flies use soft-bodied mushrooms as larval resources - these resources are ephemeral; they rot fast - sometimes, the mushroom is consumed completely by larvae

14. Project #1: Competition in Mycophagous Flies I. Pattern in Nature: - 10-15 species of mycophagous flies use soft-bodied mushrooms as larval resources - these resources are ephemeral; they rot fast - sometimes, the mushroom is consumed completely by larvae - the last two points suggest that competition might be intense, yet the coexistence of so many species suggests that it is either rare, or species have adapted to it, or partition resources and don’t compete.

15. Project #1: Competition in Mycophagous Flies I. Pattern in Nature: Questions: - Do species compete for food at the larval stage? (or do they partition resources and NOT compete?)

16. Project #1: Competition in Mycophagous Flies I. Pattern in Nature: Questions: - Do species compete for food at the larval stage? (or do they partition resources and NOT compete?) - If so, what effect does competition have?

17. Project #1: Competition in Mycophagous Flies I. Pattern in Nature: Questions: - Do species compete for food at the larval stage? (or do they partition resources and NOT compete?) - If so, what effect does competition have? - decrease food availability - increase larval period? - decrease larval period of survivors? - reduce survivorship (to pupation and to adulthood) - decrease mean mass of survivors? - increase mean mass of survivors? (If only the largest survive).

18. Project #1: Competition in Mycophagous Flies I. Pattern in Nature: Questions: Additional Patterns in Nature: - D. putrida abundance increases during droughts - D. putrida emerges later than D. tripunctata - D. putrida is smaller than D. tripunctata, and may survive at small fractions of ideal body mass and water content.

19. Project #1: Competition in Mycophagous Flies Working hypothesis: Competition within and between these species will cause a decrease in survivorship and mean size.

20. Project #1: Competition in Mycophagous Flies Working hypothesis: Competition within and between these species will cause a decrease in survivorship and mean size. Alternatives: - no effects - increase in survivorship and or mean mass (Allee Effect) - decrease in survivorship, increase in mean mass – only large ones survive. - effects differ across life cycle stages

21. Project #1: Competition in Mycophagous Flies • II. Experimental Design: • Overview: • First instar larvae placed on mushroom sections (1.0g) in Drosophila vials with moist wood chips. • Incubate for 2 weeks @ 26oC • Collect pupae and adults

22. Project #1: Competition in Mycophagous Flies • II. Experimental Design: • Overview: • -Treatments: • 1: 20 D. putrida larvae • 2: 40 D. putrida larvae • 3: 20 D. putrida larvae and 20 D. tripunctata larvae • 4: 40 D. tripunctata larvae • 5: 20 D. tripunctata larvae

23. -Treatments: 1: 20 D. putrida larvae 2: 40 D. putrida larvae 3: 20 D. putrida larvae and 20 D. tripunctata larvae 4: 40 D. tripunctata larvae 5: 20 D. tripunctata larvae -Measured Dependent Variables: Number of pupae of each species Number of adults of each species Mean dry mass of individuals of each species

24. -Measured Dependent Variables Number of pupae of each species Number of adults of each species Mean dry mass of individuals of each species -Analyzed (including derived) Dependent Variables: % survivorship to pupation (# pupae/number of larvae) % survivorship to eclosion (#adults/number of larvae) % pupal survivorship (#adults/#of pupae) mean dry mass/individual/species

25. -Treatments: 1: 20 D. putrida larvae 2: 40 D. putrida larvae 3: 20 D. putrida larvae and 20 D. tripunctata larvae 4: 40 D. tripunctata larvae 5: 20 D. tripunctata larvae -Treatment Contrasts (for each dependent variable): (1 vs. 2 vs. 3) 1 vs. 2: Intraspecific density effects on D. putrida 1 vs. 3: Interspecific density effects on D. putrida 2 vs. 3: Relative effects of intra- and interspecific density on D. putrida (3 vs. 4 vs. 5) 5 vs. 4: Intraspecific density effects on D. tripunctata 5 vs. 3: Interspecific density effects on D. tripunctata 4 vs. 3: Relative effects of intra- and interspecific density on D. tripunctata

26. -Treatments: 1: 20 D. putrida larvae 2: 40 D. putrida larvae 3: 20 D. putrida larvae and 20 D. tripunctata larvae 4: 40 D. tripunctata larvae 5: 20 D. tripunctata larvae -Treatment Contrasts (for each dependent variable): 1 vs. 5: Differences in habitat suitability at low density 2 vs. 4: Differences in habitat suitability at high density

27. -Treatments: • 1: 20 D. putrida larvae • 2: 40 D. putrida larvae • 3: 20 D. putrida larvae and 20 D. tripunctata larvae • 4: 40 D. tripunctata larvae • 5: 20 D. tripunctata larvae • -Treatment Contrasts (for each dependent variable): • 1 vs. 5: Differences in habitat suitability at low density • 2 vs. 4: Differences in habitat suitability at high density • Statistical Tests: • All comparisons will be mean comparison tests, using multiple t-tests / ANOVA, or a suitable non-parametric test (Mann-Whitney / Kruskal-Wallis test).