This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Gene Phylogeny Versus Species Phylogeny”.
1. A gene phylogeny only describes the evolution of a particular gene or encoded protein.
Explanation: One of the objectives of building phylogenetic trees based on molecular sequences is to reconstruct the evolutionary history of the species involved. However, strictly speaking, a gene phylogeny (phylogeny inferred from a gene or protein sequence) only describes the evolution of that particular gene or encoded protein.
2. Evolution of a particular sequence _______ correlate with the evolutionary path of the species.
a) does not
c) does not necessarily
Explanation: The sequence may evolve more or less rapidly than other genes in the genome or may have a different evolutionary history from the rest of the genome owing to horizontal gene transfer events. Thus, the evolution of a particular sequence does not necessarily correlate with the evolutionary path of the species.
3. The species evolution is the ______ of evolution by _____ in a genome.
a) combined result, multiple genes
b) result, single genes
c) result, sole genes
d) distinct results, single gene
Explanation: In a species tree, the branching point at an internal node represents the speciation event whereas, in a gene tree, the internal node indicates a gene duplication event. The two events may or may not coincide.
4. To obtain a species phylogeny, phylogenetic trees from a variety of gene families need to be constructed
Explanation: To obtain a species phylogeny, phylogenetic trees from a variety of gene families need to be constructed to give an overall assessment of the species evolution. Phylogenetic trees drawn as cladograms (top) and phylograms (bottom).
5. It is often desirable to define the root of a tree. There are two ways to define the root of a tree. One is to use an outgroup, which ______
a) is a sequence that is homologous to the sequences under consideration
b) is separated from those sequences at an early evolutionary time
c) is generally determined from independent sources of information
d) is generally determined from similar or related sources of information
Explanation:Here, option c and contradict and it can be explained as follows. For example, a bird sequence can be used as a root for the phylogenetic analysis of mammals based on multiple lines of evidence that indicate that birds branched off prior to all mammalian taxa in the in group. Outgroups are required to be distinct from the in group sequences, but not too distant from the in group.
6. Which of the following is incorrect statement about the Kimura model?
a) It is a model to correct evolutionary distances and is a more sophisticated model
b) In this, the mutation rates for transitions and transversion are assumed to be different
c) According to this model, occur more frequently than transversions
d) According to this model, transversions occur more frequently than transitions
Explanation: This provides a more realistic estimate of evolutionary distances. The Kimura model uses the following formula dAB = −(1/2) ln(1 − 2pti − ptv) − (1/4) ln(1 − 2ptv). dAB is the evolutionary distance between sequences Aand B, pti is the observed frequency for transition, and ptv the frequency of transversion.
7. Which of the following is incorrect statement about Choosing Substitution Models?
a) There is one substitution at a particular position, in divergent sequences
b) The evolutionary divergence is beyond the ability of the statistical models to correct
c) The statistical models used to correct homoplasy are called substitution models or evolutionary models
d) For constructing DNA phylogenies, there are nucleotide substitution models available
Explanation: The caveat of using these models is that if there are too many multiple substitutions at a particular position, which is often true for very divergent sequences, the position may become saturated. This means that the evolutionary divergence is beyond the ability of the statistical models to correct. In this case, true evolutionary distances cannot be derived. Therefore, only reasonably similar sequences are to be used in phylogenetic comparisons.
8. The second step in phylogenetic analysis is to construct sequence alignment. This is probably the most critical step in the procedure because it establishes positional correspondence in evolution.
Explanation: Incorrect alignment leads to systematic errors in the final tree or even a completely wrong tree. For that reason, it is essential that the sequences are correctly aligned. Multiple state-of-the-art alignment programs such as T-Coffee should be used. The alignment results from multiple sources should be inspected and compared carefully to identify the most reasonable one. Automatic sequence alignments almost always contain errors and should be further edited or refined if necessary.
Sanfoundry Global Education & Learning Series – Bioinformatics.
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