Computational Molecular Microbiology (MBIO 4700) Quiz

Phylogenetic Tree Analysis and Ancestral Sequence Reconstruction

• The provided data includes a phylogenetic tree of small mushroom species, with bootstrap support values at the leaf nodes.
• A Newick notation is used to represent the phylogenetic relationships between the species.
• The text discusses the use of various tools for visualizing and interacting with phylogenetic trees, such as iTOL, TreeView, FigTree, and others.
• Ancestral sequence reconstruction is mentioned, with references to the FASTML Server for computing Maximum Likelihood ancestral sequences.
• The concept of selection (dN/dS) and sequence logos is explained, with an emphasis on examining evidence of change due to chance or selection.
• SYNSCAN analysis, a program for estimating if a gene is under selection or drifting, is described with its application in determining functional constraints.
• The text discusses the neutral theory of evolution and its application in analyzing rates of substitutions and codon bias.
• The requirements for conducting SYNSCAN or MEGAX analysis are outlined, including the need for a codon-based alignment in fasta format.
• The text explains the implications of specific dN/dS ratios, with dS > dN indicating purifying selection or functional constraint.
• The program is useful for identifying nonfunctional genes (dN = dS) or those gaining new functions (dN > dS).
• It is highlighted that dN values for entire genes might only be slightly higher than dS, as changes to gain new functions may occur in only a small part of the protein.
• The variability of dN/dS ratios is noted, as sometimes only a small part of the protein changes to gain a new function, leading to variable ratios.

Test your knowledge on computational molecular microbiology topics including sequence databases, sequence comparison, pairwise alignment, multiple sequence alignment, phylogenetic tree, and Newick notation.