Phylogeny Report

Expose you to real issues surrounding the analysis and interpretation of phylogenetic
data. It is not intended to be a review of recent literature on a specific topic, nor a critique of an
existing paper or set of papers. Rather, it should be your best attempt to address a specific issue in
phylogenetic biology by analyzing real data.
Structure: Each project will be required to analyze a minimum of 1-2 specific species. The
project should be organized around a standard lab report, with an Introduction section outlining
the purpose of your analysis, a Methods section summarizing the types of analyses and
computer programs used, a Results section summarizing results, and a Conclusion or
Discussion section. The paper should have a bibliography with at least 4 references on the
characters studied, the taxonomic group of interest, the computer programs used and any other
useful information.
Timeline and strategy: The best strategy is to start your project early! I recommend consulting
recent papers from systematics journals of your favorite organisms, as well as journals like
Science, Nature, PNAS, PLoS Biology, etc. Choose a study that makes its data public - most
commonly, this will be DNA sequences deposited in GenBank. One way to begin to decide on a
project is to pick your favorite group of organisms and consult GenBank, TreeBASE and
literature databases (according to instructions given in labs) to see what data sets are available.
Once you have decided on a topic, the following questions can be used to help structure your
project. They assume that your project consists of reanalysis of data from a published paper. Most
likely you will be able to approach these data with different questions or improvements in mind.
Questions 1-3 can serve as guides leading up to the main questions 4 and 5.

1. What was the specific or general question that the authors were trying to answer? 2. What
   computer programs were used by the authors to determine the phylogeny of the group in
   question?
2. Are there any peculiarities about the mode of evolution of the gene that was used by the
   authors that might make phylogenetic analysis by their methods difficult or misleading? 4.
   What novel methods of analysis can you bring to bear on the problem. and how do your
   results differ from those already published?
3. What kind of data would be needed to make the conclusions more reliable?
   Suggestions and example projects
   Phylogeny of a group of organisms: re-analysis of published molecular and/or morphological
   data, e.g.:
   ∙ How are zebras related to horses?
   ∙ How are sperm whales (Physeter) related to other whales?
   ∙ Domestication of animal species
   ∙ The red fox domestication experiment
   ∙ From wolves to dogs
   ∙ Relationships among animals, plants and fungi
   ∙ How many times has carnivory evolved in flowering plants? How many different structural
   adaptations have evolved for carnivory?
   ∙ Phylogenetic analysis of molecular evolution
   ∙ Evolution of genes involved with the immune system
   ∙ Evolution of genes involved with development
   ∙ Evolution of genes in species living at extreme temperatures
   ∙ Molecular clock comparisons among species differing in generation time or ecology ∙
   Examining methods of phylogenetic analysis
   ∙ Do analyses of different kinds of data (e.g. morphology and DNA sequences) yield the
   same phylogeny?
   ∙ Effect of differences in nucleotide base composition on phylogenetic analysis ∙ Effect of
   assuming different models of character evolution on inferring phylogenies ∙ Effect on
   phylogenetic analysis of sampling only a few representative species from a particular
   taxonomic group