Evolutionary Biology

• Definition of Homology in Computational Biology:
• In bioinformatics and evolutionary genetics, homology strictly means sharing common evolutionary ancestry between genes, proteins, or morphological structures.
• Homology is a qualitative attribute (sequences are either homologous or not homologous; they cannot be '80% homologous').
• Homologous genes are subdivided into:
• Orthologs: Homologs separated by a speciation event (often preserving function).
• Paralogs: Homologs arising from gene duplication events within a genome.
• Conclusion: Homology refers to Evolutionarily related genes or proteins (Option 3).

Correct option: (3) Evolutionarily related genes or proteins

• Phylogenetic Tree Terminology:
• Branches or Edges: The connecting lines in a phylogenetic tree representing evolutionary lineages over time. (True)
• Internal Branch: A branch connecting two internal nodes (representing an ancestral lineage prior to subsequent divergence events). (True)
• Root: The basal node representing the unique common ancestor of all operational taxonomic units (taxa) present in the tree. (True)
• Conclusion: All (A), (B) and (C) are true (Option 4).

Correct option: (4) All (A), (B) and (C) are true.

• Number of Possible Unrooted Trees:
• For $n$ operational taxonomic units (taxa), the number of distinct unrooted bifurcating phylogenetic trees ($N_u$) is given by the double factorial formula:

$$N_u = (2n - 5)!! = 1 \times 3 \times 5 \times \dots \times (2n - 5)$$

• For $n = 5$ taxa:

$$N_u = (2 \times 5 - 5)!! = 5!! = 1 \times 3 \times 5 = 15$$

• (By comparison, the number of rooted trees for $n = 5$ is $(2n - 3)!! = 7!! = 105$).
• Conclusion: The number of unrooted trees for 5 OTUs is 15 (Option 2).

Correct option: (2) 15

• Phylogenetic Analysis Terminology:
• Topology: The branching pattern and connectivity of a phylogenetic tree, independent of branch lengths. (True)
• Internal Branch: The lineage/edge connecting two internal nodes. (True)
• Root: The basal node representing the most recent common ancestor of all operational taxonomic units in the tree. (True)
• Statement in Option 4: The lines in a tree are called nodes. $\implies$ NOT correct.
• The lines connecting entities in a tree are called branches (or edges); the intersection or branching points and terminal tips are called nodes (vertices).
• Conclusion: Option 4 is not correct.

Correct option: (4) The lines in a tree are called nodes.