Morphology and Measuring Phenotype II Study Notes

Morphology and Measuring Phenotype II

1. Mathematics

1.1 F Test / Levene Test

  • Purpose: Tests for differences in variance between two groups, not means.

  • Definition of Variance:

    • ext{Variance} = ( ext{Standard Deviation})^2

  • Requirements for Tests:

    • F-Test Requires Normality: If the data is not normally distributed, use the Levene test instead.

  • Null Hypothesis:

    • States that the variances of the two groups are equal.

1.2 Pearson Correlation Test

  • Purpose: To determine if two continuous variables move together.

  • Null Hypothesis:

    • Asserts that there is no linear relationship between the two variables (no correlation).

2. Biology

2.1 The Extended Phenotype

Concept Overview:

  • Phenotype is defined as more than just the gross morphology of an organism; it encompasses a range of characteristics including:

    • Scale: Various levels of biological organization (whole organism, organs, tissues, cells, organelles).

    • Physiological: Involves the physical and chemical processes that govern the functioning of living organisms, tissues, and cells.

    • Behavioral: Actions and reactions of the organism in response to internal and external stimuli.

    • Phenological: Concerns the timing of life cycle events in organisms.

  • The concept of the extended phenotype:

    • Proposed by Richard Dawkins, suggesting that the gene is the unit of selection.

    • It involves not only the organism's direct interactions with the environment but also how it influences and modifies the behavior of other organisms.

3. Lab Activities

3.1 Fun with Leaves!

Stomata Preparation:

  • Choose a leaf for sampling.

  • Apply a 2cm x 2cm square patch of nail varnish on the underside of the leaf.

  • Allow the varnish to dry (~5 minutes).

  • Use sticky tape to attach to the nail varnish and peel off to obtain a replica for microscopic analysis.

  • Label the slide and cut off excess tape.

3.2 Stomata Analysis Under Microscope

  • Set the scale in ImageJ for 0.75mm, counting stomata at 40x magnification (total magnification = 400).

  • Pixel count example:

    • Diameter of field of view is 0.75mm.

    • Distance in pixels recorded as 2390.785; known distance is 0.75.

    • Measurement of stomata width can be conducted based on pixel counts, with a pixel aspect ratio of 1.0.

3.3 Statistical Testing in Lab

  • Each table will utilize dependent variables of stomatal abundance and size.

  • Perform at least 6 measurements for both stomatal abundance and width from two different groups.

  • Conduct Student's t-tests on both datasets:

    • Set up hypotheses in the form: "If (independent variable), then (dependent variable)."

    • Use the link provided (https://ij.imjoy.io/) for ImageJ data analysis.

4. Presentations

  • Requirements for presentation slides:

    1. Slide 1: Shapiro-Wilk normality test results and t-test results (Figure 1 from the previous week).

    2. Slide 2: Shapiro-Wilk normality test and t-test results (Figure 2 from the previous week).

    3. Slide 3: Analysis of stomatal density and size, including Shapiro-Wilk, t-test, and Levene’s test results.

    4. Slide 4: Pearson correlation results and associated figure.

  • For each slide, articulate the hypothesis and whether the results supported it.

  • Note: The grading criterion does not focus on whether results are significant.