This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Phylogenetics Basics”.
1. Phylogenetics is the study of the evolutionary history of living organisms using treelike diagrams to represent pedigrees of these organisms.
a) True
b) False
View Answer
Explanation: Tree branching patterns representing the evolutionary divergence are referred to as phylogeny. Phylogenetics can be studied in various ways. It is often studied using fossil records, which contain morphological information about ancestors of current species and the timeline of divergence.
2. The descriptions of morphological traits are often _____ which are due to _____
a) ambiguous, multiple genetic factors
b) lucid, more than one genetic factors
c) clear, multiple genetic factors
d) ambiguous, one or two genetic factors
View Answer
Explanation: Thus, using fossil records to determine phylogenetic relationships can often be biased. For microorganisms, fossils are essentially nonexistent, which makes it impossible to study phylogeny with this approach.
3. Which of the following is incorrect regarding the advantages of Molecular data for phylogenetics study?
a) They are more numerous than fossil records
b) They are easier to obtain as compared to fossil records
c) Sampling bias is involved
d) More clear-cut and robust phylogenetic trees can be constructed with the molecular data
View Answer
Explanation: There is no sampling bias involved, which helps to mend the gaps in real fossil records. Therefore, they have become favorite and sometimes the only information available for researchers to reconstruct evolutionary history. The advent of the genomic era with tremendous amounts of molecular sequence data has led to the rapid development of molecular phylogenetics.
4. To use molecular data to reconstruct evolutionary history requires making a number of reasonable assumptions. Which of the following is incorrect about it?
a) The molecular sequences used in phylogenetic construction are homologous
b) The molecular sequences used in phylogenetic construction share a common origin
c) Phylogenetic divergence cannot be bifurcating
d) Parent branch splits into two daughter branches at any given point
View Answer
Explanation: Here, option “Phylogenetic divergence cannot be bifurcating” and “Parent branch splits into two daughter branches at any given point” contradict. Another assumption in phylogenetics is that each position in a sequence evolved independently. The variability among sequences is sufficiently informative for constructing unambiguous phylogenetic trees.
5. Building phylogenetic tree involves bifurcation and multifurcation.
a) True
b) False
View Answer
Explanation: Multifurcation is normally a result of insufficient evidence to fully resolve the tree or a result of an evolutionary process known as radiation. Sometimes, a branch point on a phylogenetic tree may have more than two descendents, resulting in a multifurcating node.
6. Which of the following is incorrect regarding the terminologies of phylogenetics?
a) The connecting point where two adjacent branches join is called a node
b) Node represents an inferred ancestor of extant taxa
c) At the tips of the branches are long lost species or sequences
d) The lines in the tree are called branches
View Answer
Explanation: At the tips of the branches are present-day species or sequences known as taxa (the singular form is taxon) or operational taxonomic units. The bifurcating point at the very bottom of the tree is the root node, which represents the common ancestor of all members of the tree.
7. Which of the following is incorrect regarding the terminologies of phylogenetics?
a) A group of taxa descended from a single common ancestor is defined as a clade or monophyletic group
b) In a monophyletic group, two taxa share a unique common ancestor shared by other taxa as well
c) Lineage is often synonymous with a tree branch leading to a defined monophyletic group
d) When a number of taxa share more than one closest common ancestors, they do not fit the definition of a clade. In this case, they are referred to as paraphyletic
View Answer
Explanation: In a monophyletic group, two taxa share a unique common ancestor not shared by any other taxa. They are also referred to as sister taxa to each other. The branch path depicting an ancestor–descendant relationship on a tree is called a lineage.
8. Which of the following is incorrect regarding the terminologies of phylogenetics?
a) The branching pattern in a tree is called tree topology
b) When all branches bifurcate on a phylogenetic tree, it is referred to as dichotomy
c) In case of dichotomy, each ancestor divides and gives rise to multiple descendants
d) An unrooted phylogenetic tree does not assume knowledge of a common ancestor
View Answer
Explanation: Sometimes, a branch point on a phylogenetic tree may have more than two descendents, resulting in a multifurcating node. The phylogeny with multifurcating branches is called polytomy. A polytomy is an be a result of either an ancestral taxon giving rise to more than two immediate descendants simultaneously during evolution, a process known as radiation, or an unresolved phylogeny in which the exact order of bifurcations cannot be determined precisely.
9. Because there is no indication of which node represents an ancestor, there is no direction of an evolutionary path in an unrooted tree.
a) True
b) False
View Answer
Explanation: To define the direction of an evolution path, a tree must be rooted. In a rooted tree, all the sequences under study have a common ancestor or root node from which a unique evolutionary path leads to all other nodes.
10. Molecular clock is an assumption by which molecular sequences evolve at varying rates.
a) True
b) False
View Answer
Explanation: Molecular clock is an assumption by which molecular sequences evolve at constant rates so that the amount of accumulated mutations is proportional to evolutionary time. Based on this hypothesis, branch lengths on a tree can be used to estimate divergence time. This assumption of uniformity of evolutionary rates, however, rarely holds true in reality.
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