Advanced Biological Data Analysis

Vakinformatie

Advanced Biological Data Analysis

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/G0F87AE.htm

Examenvragen

6 januari 2019

Tom Wenseleers - oral (you receive the questions in an R file)

1. Researchers were interested to test if queen pheromones of the honeybee, which in that species are emitted by the queen to stop the workers from reproducing, would also inhibit the reproduction of either workers or queens in the bumblebee. They hypothesized that such cross activity might be observed in the event that these compounds exploit conserved physiological pathways linked with the regulation of reproduction. To test this hypothesis, the researchers exposed bumblebee queens and bumblebee worker groups (groups of 20 workers each) to either a blank solvent-only control or a solution of honeybee queen pheromones for a period of 2 weeks. Subsequently, they dissected the queens and workers and measured the size of the largest oocyte in their ovaries to be able to test for any effects on ovary development. For each of the worker groups, these measurements were averaged over all individuals. In terms of experimental design, genetic background was controlled for by doing the experiment in a paired fashion, whereby the worker groups exposed to each replicate control and queen pheromone treatment were derived from the same source colony and similarly, the queens exposed to each replicate control and queen pheromone treatment were taken to be sisters of each other (colony or sibgroup is encoded as variable "id" in the dataset). In your analysis, take into account this non-independence through the inclusion of a random effect term, and use a model with the appropriate error distribution.
   • Aim: Test whether honeybee queen pheromones inhibit ovary development and whether this effect is caste dependent. (cf. dataset "data.csv").
   • Specific questions:
     • A. Display your data using "spaghetti plots", i.e. plot oocyte size in function of treatment, using two different panels for caste, and connect points that are measured from individuals from the same colony (for workers) or sib-group (for queens). Make this plot both using lattice's xyplot and ggplot2.
     • B. Fit a model of oocyte size (SIZE_OOCYTE) in function of TREATMENT and CASTE, either considering a possible interaction effect between both or not, taking into account possible random effects and use a model with the appropriate error distribution. Decide which model is best based on the AIC criterion. What is the name of the type of model you fitted? (in this case a linear mixed effects model was ok, since the distribution or errors was normal: lme() or lmer())
     • C. Make effect plots of the effects in your model and explain what these imply.
     • D. Carry out the relevant tests for the significance of the different effects. What do these tell you? Also carry out Tukey posthoc tests to test the effect of treatment for each of the two castes. What would the conclusion have been if you would have ignored the dependency in your data (variable ID, i.e. colony or sibship)? WOuld the effect of TREATMENT have been more or less significant then and why? (just do a normal lm here)
     • E. Test whether the residuals of your model conform to your assumed error distribution. (he wanted to see a histogram of the residuals)

Hans Jacquemyn (in a Word document)

1. Evolutionary theory predicts that coexistence of two closely related plant species can have a major impact on floral morphology and plant mating systems. To test this prediction, floral morphology of a large number of individuals from both allopatric and sympatric populations of Common centaury (Centaurium erythraea) and Seaside centaury (C. littorale) (Fig. 1) were investigated along the Belgian coast. For each individual seven floral traits were measured (Table 1). (Data set: Centaurium.xlsx) (Table 1: Floral traits measured in allopatric and sympatric populations of Centaurium erythraea en C. littorale along the Belgian coast. (Given traits and variables were: Total length of the flower (mm), Total Petal length (mm), Petal width (mm), Ovary length (mm), Style length (mm), Length of the anthers (mm), Level of herkogamy (mm))
   • A. Investigate whether floral morphology differs significantly between flowers of Centaurium erythraea and C. littorale.
   • B. Illustrate graphically which variables best explain variation in floral morphology between both species and indicate which variable most determines the difference between the two species.
   • C. Can you notice a difference in floral morphology between allopatric and sympatric populations? Is this difference determined by the identity of the species? If yes, explain how and illustrate with the appropriate graph.
   • D. Based on your results, can you conclude that allopatric populations can as easily discerned from sympatric populations for C. erythraea as for C. littorale? And which floral traits are best suited to discern allopatric from sympatric populations?