Nematode Report Instructions
The report that you are to write for this experiment should be no more than 1500 words (excluding references, tables, figures) and is to be written individually. The report is not a group activity even though you are using data collated from the whole class, and you have worked in pairs for some steps.
1. Title that is descriptive without being overly long
2. Introduction: Must address:
Effective population size (Ne)
a. what is it?
b. what are the consequences, in terms of genetic drift, of reductions in Ne for
i. genetic diversity (loss/fixation of alleles) within populations
ii. increase in divergence between populations
c. what are the other major determinants of genetic diversity? In particular, what are the effects of population bottlenecks and allele starting frequencies?
Nematodes (Caenorhabditis elegans)
a. what are they... very brief statement about life history
b. why are they useful for this experiment (things like ease of culture, timing of development etc)
The final part of the introduction should be a clear and concise statement of the aim(s) of the experiment in your own words AND a brief hypothesis (eg. That variation in population size and/or genotype starting frequency will influence direction and magnitude of genetic change in populations). Simply quoting the manual, or saying "This experiment aims to illustrate evolution" will not suffice.
3. Methods section.
All that is required is "Refer to GEN2EGE practical notes". You do not need to summarise or paraphrase the lab manual.
4. Results section:
The Results section must contain the following elements:
- The tabulation of the complete class data. This is the total counts of cleaved/non-cleaved alleles for each treatment (3 worm population, 9:1 genotype ratio; 3 worm population, 1:1 genotype ratio; 30 worm population, 9:1 genotype ratio; 30 worm population, 1:1 genotype ratio). Note that these counts are the observed values that you use in the statistical analysis of the data.
- A statistical analysis of the expected and observed ratios of each phenotype for each of the populations using a X 2 (chi-square) test of significance for each population
(see Appendix I Pp. 109-112 for information on how to calculate chi-square).
- Note that for every statistical test you use, you should record ALL of
(a) the null hypothesis (may not be the same for every test)
(b) the test used,
(c) the test statistic X2
(d) degrees of freedom
(e) p value estimated from the value of X2 and
(f) is the null hypothesis accepted or rejected
- AlleleA1 data that explore the impact of population size (one of your worm experiment variables), genotype ratios at G0 (also one of your worm experiment variables) under a range of fitness differences (no difference, small (<5%?) difference and large (25%?) for large or small (150 vs 20?) generations. In other words, use AlleleA1 to simulate an ideal population (infinite size, no fitness differential, many generations) and then populations that are closer to the experimental.
- The keys to a good Results section are to be selective about the data you display (do not simply dump all the AlleleA1 output into your Results), and to be concise in your description of the most important features of the data. Note however that you need to have two elements in your Results section: tables and/or figures that illustrate the data and a verbal description of the main features of those data that refers explicitly to the relevant table and/or figure that displays those data. If you are unsure, check the Results sections of some the papers covered in the class talks.
- Do not confuse the statistical null hypothesis that is tested using the X 2 statistic (the statistical expectation) and the population genetic hypotheses that you may make (eg that, according to population genetic theory, selection is weak in small populations and may be overwhelmed by genetic drift in those populations, or that population bottlenecks promote drift and the loss of rare alleles). Note also that it is the observed data that are to be described and analysed statistically while AlleleA1 provides illustration of the theoretical framework that you will use in your Discussion.
5. Discussion section that addresses the following:
- if the observed experimental data differ significantly (in the statistical sense) from the expected values that you calculated using the initial allele frequency, is the deviation related to the population size and the severity of the bottleneck? For example, consider whether the "3 founder" worm populations deviated more, or less, from the statistical null hypothesis than the "30 founder" worm populations.
- similarly, do the total class data do show any relationship between the degree of variation in the observed allele frequencies at generations 1 and 3, and population size? How might this be accounted for by population genetic theory? Think about sampling theory and population size. A simple way of looking at this is to ask how likely it is that the minor allele in the 1:9 genotype ratio 3 and 30 worm replicate populations disappears completely, then comparing this to your expectation of "fixation" frequency in the number of 1:1 genotype ratio populations. Why might the starting allele frequency and/or the population size affect the fixation rate (think about the results from the AlleleA1 exercise, and about sampling theory)?
- Was there any evidence of selection occurring during the experiment? If so, was it obvious in all populations? Only in the 30 worm populations? Sensitive to genotype starting frequency?
- The last part of the Discussion must bring it back to the Aims and the population genetic hypothesis (NOT the statistical hypothesis) stated in the Introduction. Were your data consistent with the hypothesis? If so, how? If not, what alternative hypothesis could you propose that is consistent with the data? And, to really impress, you could suggest what the next experiment(s) might be and why.
6. Acknowledgments: your practical partner.
7. References, listed alphabetically by first author's last name in the La Trobe version of Harvard. I recommend strongly that you use Endnote. Then there are no quibbles out what does or does not equal Harvard style.
8. Supplementary data - raw data tables if you need to refer to them directly, and additional AlleleA1 files to which you refer. Do not simply dump everything you think might be relevant into a supplement. Be selective.
Format
Font: Times New Roman Size: 12 point
Lines: Double spaced