This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Forms of Tree Representation”.
1. Which of the following is an incorrect statement?
a) In a phylogram, the branch lengths represent the amount of evolutionary divergence
b) Trees like cladogram are said to be scaled
c) The scaled trees have the advantage of showing both the evolutionary relationships and information about the relative divergence time of the branches
d) In a cladogram, the external taxa line up neatly in a row or column
Explanation: In a cladogram, the external taxa line up neatly in a row or column. Their branch lengths are not proportional to the number of evolutionary changes and thus have no phylogenetic meaning. In such an unscaled tree, only the topology of the tree matters, which shows the relative ordering of the taxa.
2. Which of the following is an incorrect statement about Newick Format?
a) It was designed to provide information of tree topology to computer programs without having to draw the tree itself
b) In this format, trees are represented by taxa excluded in nested parentheses
c) In this linear representation, each internal node is represented by a pair of parentheses
d) For a tree with scaled branch lengths, the branch lengths in arbitrary units are placed immediately after the name of the taxon separated by a colon
Explanation: Trees are represented by taxa included in nested parentheses. In this linear representation, each internal node is represented by a pair of parentheses that enclose all member of a monophyletic group separated by a comma.
3. Sometimes a tree-building method may result in several equally optimal trees. A consensus tree can be built by showing the commonly resolved bifurcating portions and collapsing the ones that disagree among the trees, which results in a polytomy.
Explanation: Combining the nodes can be done either by strict consensus or by majority rule.
In a strict consensus tree, all conflicting nodes are collapsed into polytomies. In a consensus tree based on a majority rule, among the conflicting nodes, those that agree by more than 50% of the nodes are retained whereas the remaining nodes are collapsed into multifurcation.
4. The number of rooted trees (NR) for n taxa is ______
a) NR = (2n− 3)!/2n+2 (n− 2)!
b) NR = (2n− 3)!/2n (n− 2)!
c) NR = (2n− 3)!/2n−2 (n− 5)!
d) NR = (2n− 3)!/2n−2 (n− 2)!
Explanation: The number of potential tree topologies can be enormously large even with a moderate number of taxa. The increase of possible tree topologies follows an exponential function. In this formula, (2n−3)! Is a mathematical expression of factorial, which is the product of positive integers from 1 to 2n − 3. For example, 5! = 1 × 2 × 3 × 4 × 5 = 120.
5. For unrooted trees, the number of unrooted tree topologies (NU) is ________
a) NU = (2n− 5)!/2n−3(n− 5)!
b) NU = (2n− 5)!/2n−3(n− 3)!
c) NU = (2n− 5)!/2−2(n− 3)!
d) NU = (2n− 5)!/2n(n− 3)!
Explanation: The number of possible topologies increases extremely rapidly with the number of taxa. For six taxa, there are 105 unrooted trees and 945 rooted trees. If there are ten taxa, there can be 2,027,025 unrooted trees and 34,459,425 rooted ones.
6. It can be computationally very demanding to find a true phylogenetic tree when the number of sequences is large.
Explanation: Because the number of rooted topologies is much larger than that for unrooted ones, the search for a true phylogenetic tree can be simplified by calculating the unrooted trees first. Once an optimal tree is found, rooting the tree can be performed by designating a number of taxa in the data set as an outgroup based on external information to produce a rooted tree.
7. Which of the following is incorrect statement about Molecular Markers?
a) For studying very closely related organisms, protein sequences are preferred
b) The decision to use nucleotide or protein sequences depends on the purposes of the study
c) For constructing molecular phylogenetic trees, one can use either nucleotide or protein sequence data
d) The decision to use nucleotide or protein sequences depends on the properties of the sequences
Explanation: The choice of molecular markers is an important matter because it can make a major difference in obtaining a correct tree. For studying very closely related organisms, nucleotide sequences, which evolve more rapidly than proteins, can be used. For example, for evolutionary analysis of different individuals within a population, noncoding regions of mitochondrial DNA are often used.
8. For studying the evolution of ________ divergent groups of organisms, one may choose either ______ nucleotide sequences, such as ribosomal RNA or protein sequences.
a) less widely, slowly evolving
b) more widely, slowly evolving
c) more widely, rapidly evolving
d) less widely, rapidly evolving
Explanation: If the phylogenetic relationships to be delineated are at the deepest level, such as between bacteria and eukaryotes, using conserved protein sequences makes more sense than using nucleotide sequences.
9. In many cases ______ sequences are preferable to ______ sequences because they are relatively ____ conserved.
a) protein, nucleotide, less
b) nucleotide, protein, less
c) protein, nucleotide, more
d) nucleotide, protein, more
Explanation: Protein sequences are preferable to nucleotide sequences because protein sequences are relatively more conserved as a result of the degeneracy of the genetic code in which sixty-one codons encode for twenty amino acids, meaning thereby a change in a codon may not result in a change in amino acid.
10. Protein sequences can remain the same while the corresponding DNA sequences have more room for variation.
Explanation: The protein sequences can remain the same while the corresponding DNA sequences have more room for variation, especially at the third codon position. The significant difference in evolutionary rates among the three nucleotide positions also violates one of the assumptions of tree-building. In contrast, the protein sequences do not suffer from this problem, even for divergent sequences.
11. DNA sequences are sometimes more biased than protein sequences because of preferential codon usage in different organisms.
Explanation: In this case, different codons for the same amino acid are used at different frequencies, leading to sequence variations not attributable to evolution. In addition, the genetic code of mitochondria varies from the standard genetic code. Therefore, for comparison of mitochondria protein-coding genes, it is necessary to translate the DNA sequences into protein sequences.
12. In Jukes–Cantor Model to correct evolutionary distances, A formula for deriving evolutionary distances that include hidden changes is introduced by using a logarithmic function. It is ____
a) dAB = −(3/4) log[1 − (4/7)pAB]
b) dAB = −(3/4) ln[1 − (5/3)pAB]
c) dAB = −(3/4) log[1 − (4/3)pAB]
d) dAB = −(3/4) ln[1 − (4/3)pAB]
Explanation: The simplest nucleotide substitution model is the Jukes–Cantor model, which assumes that all nucleotides are substituted with equal probability. dAB is the evolutionary distance between sequences A and B and p AB is the observed sequence distance measured by the proportion of substitutions over the entire length of the alignment.
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