053-2008

MO640 - Multiple-choice question

The table below specifies 4 species and 4 characters for them, that can undergo state changes of the form 0 -> 1 or 1-> 0. Identify the FALSE alternative for the mutations in the tree shown besides the table, using maximum parsimony criteria:

Species Characters 1 2 3 4 Alpha 1 0 0 1 Beta 0 0 1 0 Gamma 1 1 0 0 Delta 1 0 1 1

1. For character 3, just one change in this tree is enough to explain all states.
2. For character 4, just one change in this tree is enough to explain all states.
3. The total number of changes for all characters in a most parsimonious reconstruction of this tree is 5.
4. This tree is optimal for the given table.
5. None of the above.

Original idea by: Tiago Takamoto

032-2015

MO640 - Multiple-choice question

Using the genomes and topology below, considering the SCJ distance, and solving the small phylogeny problem, the distance between G1, G2, G3, G4, and G5 and their parents are, respectively:
a) 3, 1, 1, 2, 0
b) 3, 1, 1, 1, 0
c) 3, 1, 1, 1, 1
d) 1, 1, 1, 1, 1
e) None Of The Above

Original idea by: Cicero Silva Luiz Júnior

059-2008

MO640 - Multiple-choice question

Mark the alternative that renders the following matrix ultrametric:

	a	b	c	d	e
a	0	2	A	1	1
b	-	0	2	B	2
c	-	-	0	1	1
d	-	-	-	0	C
e	-	-	-	-	0

1. A=1 ; B=2 ; C=1 
2. A=1 ; B=1 ; C=2
3. A=2 ; B=1 ; C=2
4. A=2 ; B=3 ; C=1
5. NDA

Original idea by: Tiago Takamoto

057-2008

MO640 - Multiple-choice question

Consider the tree with branch lengths and its corresponding distance matrix below:



Regarding the following statements:

I. The value of X in the matrix is 2,5.
II. The value of Y in the matrix is 1,5.
III. The matrix is additive.
IV. The matrix is ultrametric.

Which alternative lists exactly the true statements?

1. I, II, III, IV.
2. I, III.
3. I, III, IV.
4. II, III, IV.
5. NDA

Original idea by: Fabio L. Usberti

020-2006

MO640 - Multiple-choice question

	Character
Object	c1	c2	c3	c4	c5
A	1	1	0	0	0
B	0	0	1	0	1
C	1	1	0	0	1
D	0	1	1	1	0
E	1	1	0	0	1

Given the feature matrix above, and assuming that states can transition in the direction 0 --> 1 only, we can say that:

1. It doesn't admit a perfect phylogeny, because characters c1 and c2 are not compatible.
2. It doesn't admit a perfect phylogeny, because characters c2 and c3 are not compatible.
3. It doesn't admit a perfect phylogeny, because characters c4 and c5 are not compatible. 
4. It admits a perfect phylogeny
5. None of the above

Original idea by: Mirela Dal Col Silva
Translation help by: Jessica Akemi Matsuoka

018-2015

MO640 - Multiple-choice question

Regarding phylogeny reconstruction, which alternative is correct:

a) - The Big Phylogeny Problem is an easy problem that is usually solved with fast algorithms
b) - The Small Phylogeny Problem has the goal of finding a phylogeny that represents the  minimum amount of evolution
c) - The loss or gain of a specific character can happen just once in evolution
d) - There are two ways to root a tree: by using an outgroup or by assuming a molecular clock
e) - None of the above

Original idea by: Guilherme de Mello Barsoti

017-2015

MO640 - Multiple-choice question

Which assignment of ancestor states yields the minimum number of changes, given the topology and the species vs. characters matrix below:

Characters Species C1 C2 S1 1 1 S2 1 0 S3 0 0 S4 0 1

a)

	C1	C2
X	0	0
Y	1	1
Z	0	0

b)

	C1	C2
X	1	0
Y	1	0
Z	1	0

c)

	C1	C2
X	0	0
Y	1	0
Z	0	0

d)

	C1	C2
X	0	1
Y	1	1
Z	0	0

e) None of the above.

Original idea by: Miriam Ito

016-2015

MO640 - Multiple-choice question

Considering the following species vs. characters matrix:

What is (are) the most parsimious tree(s) among the
 three 
possible 
unrooted
 trees 
for 
four 
taxa,  
shown below?

1. Trees 2 and 3
2. Tree 1
3. Tree 3
4. Trees 1 and 3
5. None of the above

Original idea by: Shagali Huanca Vargas

015-2015

MO640 - Multiple-choice question

Considering the "Species vs. Characters" matrix below, what is the number of changes in the most parsimonious tree?

1) 8
2) 10
3) 15
4) 18
5) None of the above

Original idea by: Leandro Tacioli

014-2015

MO640 - Multiple-choice question

Given the data set and tree below, choose the right answer with respect to most parsimonious reconstructions.

1. The minimum overall state changes needed is 7.
2. The minimum overall state changes needed is 8.
3. Reconstructions of character 2 need two state changes.
4. Reconstructions of character 5 need two state changes.
5. None of the above.

Original idea by: Leandro José de Bortoli

016-2006

MO640 - Multiple-choice question

Methods that use parsimony to build phylogenetic trees aims at:

1. Find the phylogeny that has the minimum number of homoplasies.
2. Find the phylogeny that has the maximum possible number of species in the tree leaves, i.e., species that didn't originate any other species.
3. Find an unrooted phylogenetic tree.
4. Finding the phylogeny that has the minimum number of outgroups among the analyzed species.
5. None of the Above

Original Idea by: Mirela Dal Col Silva

Translation help by: Jéssica Akemi Matsuoka

016-2011

MO640 - Multiple-choice question

What is the best phylogeny for the following matrix of states and characters?

	Characters
individual	c1	c2	c3	c4	c5	c6
A	0	0	0	1	1	0
B	1	1	0	0	0	0
C	0	0	0	1	1	1
D	1	0	1	0	0	0
E	0	0	0	1	0	0

(Consider that labeled edges mean that the named character has changed state)

a)

c)

---

b)

d)

---

e) None of the above

Original idea by: Felipe Holanda

Translation help by: Cristiano Borges Cardoso

012-2015

MO640 - Multiple-choice question

Consider the phylogenetic trees below.

Assume that C1, C2, C3, and C4 are all binary, unordered characters.  Which of the topologies could be a most parsimonious tree possible for a given input table?

a) I, II, and III
b) I and II only
c) I only
d) III only
e) None of the above

Original Idea by: Mario Akita