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The correct option is (d) According to this model, transversions occur more frequently than transitions

Easiest 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 thefrequency of TRANSVERSION.

Right choice is (C) Phylogenetic divergence cannot be bifurcating

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.

Correct answer is (C) Sampling bias is involved

The best 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.

Right answer is (a) For studying very CLOSELY related organisms, protein sequences are preferred

For explanation I would say: 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.

Right CHOICE is (a) There is one substitution at a particular POSITION, in divergent sequences

To elaborate: 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.

Correct option is (a) True

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.

Right CHOICE is (a) True

For 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.

Right answer is (a) True

Easiest 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.

The CORRECT choice is (b) In this format, TREES are represented by taxa excluded in nested parentheses

For explanation I would say: 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.

The correct choice is (b) Trees like cladogram are said to be scaled

Easiest 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.

Right ANSWER is (a) True

Easiest 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.

Right option is (d) dAB = −(3/4) ln[1 − (4/3)pAB]

Best 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.

Correct ANSWER is (c) protein, nucleotide, more

To explain I would say: 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.

Right answer is (b) False

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.

Right OPTION is (b) more widely, slowly evolving

To explain: 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.

Right option is (C) At the tips of the BRANCHES are long lost species or sequences

The best I can EXPLAIN: 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.

Right ANSWER is (a) ambiguous, multiple GENETIC factors

The BEST 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.

Right answer is (a) True

The best 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.

Correct choice is (a) COMBINED RESULT, multiple genes

The explanation is: 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.

The CORRECT choice is (B) In a monophyletic group, two taxa SHARE a unique common ancestor shared by other taxa as well

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.

Right ANSWER is (a) True

Best 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).

Right answer is (a) True

Best 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.

The correct choice is (a) True

The best 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.

Right option is (d) is generally determined from similar or related sources of information

For explanation I would SAY: Here, the option “is generally determined from independent sources of information” 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.

Correct answer is (c) In case of dichotomy, each ANCESTOR divides and gives rise to multiple descendants

The 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.