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This homework is due the Tuesday after Spring Break, March 19.


You will analyze a (real) data set of five flowering plant sequences. Three sequences are from plants in the poppy family: Sanguinaria (Bloodroot), Eschscholzia (California Poppy), and Bocconia (Tree Poppy). The remaining two sequences are from monocots: Oryza (Rice, grass family) and Disporum (Fairy Bells, crocus family). The 2 monocot taxa are distantly related to the 3 dicot taxa in the poppy family.

What to do

Download the following data file (sequence alignment) to your account on the cluster:

curl -O https://gnetum.eeb.uconn.edu/courses/phylogenetics/hw8.nex

Load the paup/4.0a-166 module. The analyses you will carry out comprise the following steps:

  • use the alltrees command to perform an exhaustive search using maximum likelihood (using the default model, which is HKY85 with trs:trv ratio 2 and empirical nucleotide frequencies);
  • use the lscores command to obtain the log likelihood of the best tree; and
  • use the bootstrap command to perform a bootstrap analysis (1000 replicates).

Do all of the above for each of these three sets of sites:

  1. Left half: Include only sites 1-180
  2. Right half: Include only sites 181-402
  3. Concatenated: Include all sites (1-402)

What to turn in

  1. For each of the three analyses, draw (using your hand, not FigTree!) the bootstrap consensus as an unrooted tree and show the bootstrap frequencies on the internal edges. To save writing, you can abbreviate the taxa as follows: S (Sanguinaria), E (Eschscholzia), B (Bocconia), O (Oryza), and D (Disporum).

  2. Add together the log-likelihoods for the “left half” and “right half” and compare it to the log-likelihood from the “concatenated”. Is the data less surprising if you allow each half of the gene to have its own tree topology or is the data less surprising if all sites share the same topology?

  3. Which of the 3 bootstrap analyses yields the highest confidence? Does this agree or disagree with your answer for question 2?

Food for thought

Think about how you might go about explaining these results. You do not need to tell me your thoughts: we will discuss this in lecture after everyone has finished it.