Phylogenetics project write-up
Follow the details provided in the lab to analyze your project.
Note that each of you has been assigned an order of flowering plant families to analyse phylogenetically and compare your results to the phylogeny on the angiosperm website.
Your write-up should be formatted like a scientific publication.
In your write-up:
Abstract
Begin with a short summary of your project (usually write this after you've written up the whole project).
Introduction
Begin with short description of the angiosperm order you are analysing perhaps indicating the geographic distribution of the families, and any notable features of species within the order. For example, if there are species with uses in agriculture, or forestry, or medicine, etc.
Present the phylogeny of your order from the Angiosperm website and state the objective(s) of your project (something along the following lines: In this project I will explore phylogeny of the order xxxx using parsimony and maximum likelihood methods…).
Methods
Describe the analyses you have conducted, the outgroup or outgroups you've decided to use. How you did your sequence alignments etc. When you did bootstrapping, how many bootstrap replicates did you use (1000? 500? or whatever you did). How did you determine which ML analysis (model) to use?
Include a table listing the species you've chosen, and indicate to which family the species belongs. Remember that you should rename the sequences with an informative name prior to running your analyses (i.e. the family to which the species belongs).
Results and Discussion:
Figures and Tables:
Present figures(diagrams) of the phylogeny. At a minimum, you should have four of these, plus a table of the top five ML models from your model test. A figure from the parsimony analysis. Then another figure from parsimony analysis, but this time it is the consensus tree from bootstrapping. A figure from the maximum likelihood analysis.
Then another from the maximum likelihood but this time it’s the consensus tree from bootstrapping.
If you explored the effects of different outgroups on the analysis, and the results differed, you could indicate this by showing the phylogeny with the different outgroup, and/or you could just describe the differences (if there were any), or simply state that using a different outgroup didn't change the resulting phylogeny. What were the results of your model test?
Describe any differences between your phylogenies.
So, here I would compare the results of your analysis using parsimony to the one using maximum likelihood. Are they different? If so, how do they differ.
Then compare your phylogenies to the one you copied from the Angiosperm website.
Do your results agree with the phylogeny on the website. Describe the differences if any. (e.g. I find families x and y seem to be sister groups or are more closely related than families x and z, as indicated on the Angiosperm phylogeny website etc.).
References.
You should have a short reference list citing any literature (and computer programs) you have used. Both in text and reference list should be in the format of a scientific publication.
Note: For those wishing to extend the scope of this project beyond the Maximum likelihood and parsimony analyses, you could try any of the following: The effect of different outgroups on the analyses, running a few of the ‘top’ models for maximum likelihood analysis, running the analysis using a different gene, including more than one species per family, etc.