Lemurs of Madagascar - Part I

PART I: INTRODUCTION

This is the first part of the lemur practical. Write (and draw) your answers on a sheet of paper. Don't forget to write your name and student # on each sheet you submit.

Shown below is an unrooted tree for five species. Draw all of the rooted trees that are compatible with this tree.
Shown below is a rooted tree. Draw all of the unrooted trees that are compatible with this tree.
Suppose you are studying four species whose true evolutionary relationships are shown below: After studying many characters of these four species, you produce the unrooted tree shown below: Your next goal is to determine the order of evolutionary branching. That is, you want to root the tree. You choose an outgroup species that you think probably has ancestral states of the characters you have studied. However, due to convergent evolution, your outgroup actually shares many derived characters with species C. What will your rooted tree look like? How will it differ from the true tree?
Draw these two trees. (If this is completely mysterious, try
this backgrounder ) on this way of representing trees.
(((A:1,B:1):2,(C:2,D:2):1,E:1):1,((F:1,G:1):1,(H:3,I:3):1):1);
(((A:1,B:1):2,((C:2,D:2):1,E:1):1):1,((F:1,G:1):1,(H:3,I:3):1):1);.
These two differ at one node. What is the difference?
Does the first tree contain more or less information than the second? Why?
Given below are the character states (A or A') of species 1-6.
Using the two pass approach for MP reconstruction, what is the inferred state at the node in the clade (1,2) for character (A,A')? Try to assess the relative certainty of the inference in the three cases (there are several ways to answer this second question).
Imagine four species A, B, C, and D. Each species has unique character states for five characters; A, B and C share character states for 25 characters; A and B share character states for 15 characters (and C and D share a different character state for these same characters); and for 100 characters, the states are the same for all four species. What is the minimum number of evolutionary events implied by each of the possible unrooted trees for the four species?
Consider this matrix:
```
            [   1 2 3 4 5 6 7]
            A   1 0 0 0 0 0 1
            B   0 1 0 0 0 1 1
            C   0 0 1 0 1 1 1
            D   0 0 0 1 1 1 1
          
```
1. Estimate the shortest possible unrooted tree from the matrix.
2. Produce the most parsimonious rooted tree.
3. Did you have to make some sort of assumption about ancestral vs. derived states when you produced the rooted tree? If so, what?
4. Which derived character states unique to one taxon (autapomorphies) are present?
5. Which role do these derived character states unique to one taxon play in resolving trees?
6. Which derived character states shared by two or more taxa and held to reflect their common ancestry (synapomorphies) are present?
7. Do these derived character states (synapomorphies) help to resolve a tree?
8. Does the tree contain excess changes resulting from parallel or convergent evolutions and from character state reversals (homoplasy)?
Use the rooted tree (A,(B,(C,(D,E)))); and the following matrix - for all characters 0 is the ancestral state:
```
            [   A B C D E]
            1   0 1 2 3 3
            2   0 2 2 1 3
            3   1 3 1 2 3
            4   2 3 3 1 2            
          
```
Optimise the character state distributions onto the tree, using optimisations:
1. ordered: 0 -- 1 -- 2 -- 3. This means that to get from 0 to 3, evolution has to go through 1 and 2.
2. unordered (one is no more suprised for a 3 to evolve from a 0 than for a 1 to evolve from a zero state.
For which characters do the optimizations differ (changes are put in different places)?

Consider the following set of species: Daubentonia_madagascariensis,Oryctolagus_cuninculus, Lemur_catta, Indri_indri.
Here are photos of them.
Here is a matrix of characters (More about these characters):

           
            [                                 1 2 3 4 5 6]
            A.Daubentonia_madagascariensis    0 1 0 0 1 1
            B.Oryctolagus_cuninculus          0 1 0 ? 1 0
            C.Lemur_catta                     1 0 1 1 2 1
            D.Indri_indri                     1 ? 0 1 2 1
            
            [ Character legend:            
                1 = number of teeth in tootcomb
                    0 = toothcomb absent or two teeth
                    1 = more than two teeth in comb
              
                2 = ever growing incisors
                    0 = absent
                    1 = present
            
                3 = ringed tail
                    0 = absent
                    1 = present
            
                4 = tonal group alerts
                    0 = absent
                    1 = present
            
                5 = skull form
                    1 = rodentlike
                    2 = foxlike
            
                6 = opposable thump
                    0 = absent
                    1 = present
            ]

Assume the tree is of the form "(B,(A,(C,D))"

Draw the tree. What is wrong with the parenthetical (newick) format above? Give the correct newick form.
How many changes would your tree have if every character were an unambiguous synapomorphy (i.e. no homoplasy)?
If the c.i. (consistency index) is simply (minimum number of changes)/(actual number of changes), then what is the c.i. for these data on this tree?
Is it possible to infer, using Maximum Parsimony, what the character states might be for the taxa which have question marks?

In this final section of part 1, we'll interpret a recent tree of the Lemuridae (Primata). Some background on Madagascar and the lemurs can be found here. (Pictures and data by ETI ). The descriptions of these species are very old (1999) IUCN redbook reports. Note that these reports follow an old - and taxonomically speaking incorrect - nomenclature for the taxa.
Download and open a .pdf of our recent lemuridae tree , created in 2010 by Renske Gudde and Jeff Joy.
Download the most recent IUCN taxonomy of lemurs . This is a .csv (comma-separated) file that you can open in Excel or in a text editor.

What type of tree is this (rooted/unrooted; cladogram/additive; ultrametric/nonultrametric)? What are your clues?
Are any genera non-monophyletic on this tree? Which? Are any families? Which?
What taxa seem to have had the most taxonomic inflation since 1999? Do you see any pattern to this inflation? Can you give a reason for any pattern?
Is there anything about this tree that strikes you as particularly interesting or noteworthy?