What is the purpose of multiple sequence alignment in phylogenetic analysis?

• To select sequences for study

• To construct a phylogenetic tree

• To align sequences for analysis

• To evaluate tree accuracy

In a phylogenetic analysis, branch lengths represent the number of nucleotide substitutions per site that have occurred along that branch. If Species X has a much longer branch length than Species Y from their most recent common ancestor, which of the following is the most likely interpretation?

• Species X is more closely related to the common ancestor than Species Y.

• Species X has accumulated more genetic changes since diverging from their common ancestor than Species Y.

• Species X diverged from the common ancestor more recently than Species Y did.

• Species X and Y have evolved at the same rate since divergence.

Which method is NOT a distance-based method?

• BLOSUM62

• Neighbor joining

• UPGMA

• Maximum parsimony

In UPGMA, what is used to derive the ideal tree topology?

• Character states

• Bootstrap support

• Distance matrix values

• Likelihood scores

What does maximum parsimony assume about tree construction?

• All taxa evolve at different rates

• All characters contribute equally

• The most complex tree is the best

• The simplest tree is the most plausible

What is the main focus of maximum likelihood methods?

• Minimizing the number of substitutions

• Evaluating the probability of an evolutionary model

• Aligning sequences accurately

• Constructing the simplest tree

What is bootstrapping used for in phylogenetic analysis?

• To draw the phylogenetic tree

• To conduct multiple sequence alignment

• To evaluate the robustness of clade membership

• To select sequences for analyses

What does a 100% bootstrap support indicate?

• The data is generated from DNA sequences

• The query cover between the sequences in the clade is 100%

• The clade was reproduced in 100% of the bootstrap replicates

• The % identity between sequences in the clade is 100%

How can phylogenetics be applied in cancer biology?

• To study evolutionary relationships of species

• To understand tumor evolution

• To analyze protein structures

• To evaluate genetic diversity

Which of the following is TRUE about choosing DNA vs protein sequences for phylogenetic analysis?

• Protein sequences are always preferred regardless of species divergence.

• DNA is always more reliable because it evolves slower than proteins.

• Protein sequences are more suitable when comparing widely divergent species.

• DNA sequences cannot be used to study non-coding regions.