PART I

PART II

PART III

INTRO PAGE

LEMURS OF MADAGASCAR

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.

  1. Shown below is an unrooted tree for five species. Draw all of the rooted trees that are compatible with this tree.

  2. Shown below is a rooted tree. Draw all of the unrooted trees that are compatible with this tree.
  3. 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?

  4. Given below are the character states (A or A’) of species 1-6.

    Which of A and A’ is ancestral, and which derived, in the clade (1,2)? Assess the relative certainty of the inference in the three cases.

  5. Imagine four species A, B, C, and D. Each species has five unique character states; 25 characters are shared by A, B and C; 15 characters are shared by A and B; and 100 characters are shared by all four species. What is the minimum number of evolutionary events implied by each of the possible unrooted trees for the four species?

    6.  

  6. 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

    a. Estimate the shortest possible unrooted tree from the matrix.
    b. Produce the most parsimonious rooted cladogram.
    c. Which implicit character state polarisation did you use in producing the tree?
    d. Compare the character polarisation between (A(B(CD))) and (D(C(AB))).
    e. Which derived character states unique to one taxon (autapomorphies) are present?
    f. Which role do these derived character states unique to one taxon play in resolving trees?
    g. Which derived character states shared by two or more taxa and held to reflect their common ancestry (synapomorphies) are present?
    h. Do these derived character states (synapomorphies) help to resolve a tree?
    i. Does the tree contain excess changes resulting from parallel or convergent evolutions and from character state reversals (homoplasy)?

  7. Use the rooted tree (A,(B,(C,(D,E)))).

    For all characters 0 is the ancestral state.
    A
    B
    C
    D
    E
    1
    1
    1
    0
    0
    1
    2
    0
    1
    0
    1
    0
    3
    0
    1
    1
    0
    0
    4
    0
    1
    1
    0
    1
    5
    0
    0
    1
    1
    1

    Optimise the character state distributions onto the tree, using optimisations:

    a. unordered
    b. single origin
    c. irreversible

  8. Which character state distributions give different results for the different parsimony criteria?

  9. Do the same for the multistate character state distributions:

    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

    Again, 0 is the ancestral state for all characters.

    a. ordered: 0>1>2>3
    b. unordered
    c. For which characters do the results differ?

  10. Consider the following matrix:

    Toothcomb1

    Ever growing incisors2

    Ringed tail3

    Tonal group alert calls4

    Form of the skull5

    Opposable thumb6

    Daubentonia madagascariensis
    0
    1
    0
    0
    1
    1

    Oryctolagus cuninculus
    0
    1
    0
    ?
    1
    0

    Lemur Catta
    1
    0
    1
    1
    2
    1

    Indri Indri
    1
    ?
    0
    1
    2
    1

    Character description: 1= number of teeth in toothcomb (0= toothcomb absent or two teeth in toothcomb; 2= more than two teeth in toothcomb). 2= ever growing incisors (0= absent; 1= present). 3=ringed tail (0= absent; 1= present). 4= tonal group alert calls (0= absent; 1=present). 5= form of the skull (1= rodentlike; 2= foxlike). 6=opposable thumb (0= absent; 1= present) More about these characters

    a. Draw all possible unrooted trees for the four taxa.
    b. Root each tree, using Oryctolagus cuninculus as the outgroup.
    c. Calculate the length of each tree, assuming w1=1, w2=2, w3=1, w4=2, w5=1, w6=1, and assuming diff(xk,j,xk''j) = 1 for all branches k and for all characters j.
    d. Which topology is most parsimonious?
    e. How many changes would your tree have if every character were an unambiguous synapomorphy (i.e. no homoplasy)?
    f. If the c.i. (consistency index) is simply (minimum length of a tree)/(actual length of a tree), then what is the c.i. for your tree?
    g. Is it possible to infer, using Maximum Parsimony, what the character states might be for the taxa which have question marks?
    h. Look at the pictures of the four taxa.Do you think your tree reflects the true evolutionary relationships of these species?