Nicole C.

Mendoza Jerez
MEGA (Molecular Evolutionary Genetics Analysis) is a comprehensive software
package designed to conduct molecular evolutionary analysis and building phylogenetic
trees. Using the information gathered in the previous assignment 3.2.1 the Multiple
Sequence Alignment was evaluated with the MEGA software. So, as the first step, we
input all the 9 protein sequences into MEGA which were downloaded in FASTA format
cause, as we learned in class, protein-based phylogeny in most cases may be more
appropriate than DNA based phylogeny. Second, we did the Multiple Sequence
Alignment using the MUSCLE algorithm that calculates pairwise distances between
sequences and measures similarity. In this alignment we also removed gaps or
ambiguous positions ensuring that homologous positions are correctly matched across
all sequences. After that, we use the MEGA model test tool to evaluate the best fitting
model for the dataset as is shown in the screenshots below. The MEGA software
determined that the best models for the accuracy of the phylogenetic tree were the
LG+I and the cpREV+G+I. For the phylogenetic tree construction, the MEGA
software provides several character and distance- based methods including Maximum
Likelihood (ML), Neighbor-Joining (NJ), and Maximum Parsimony (MP). So, the
chosen distance-based method was the Unweighted Pair Group Method with Arithmetic
Mean (UPGMA) which follows an agglomerative hierarchical clustering approach, and
the used character-based method was the Maximum Likelihood (ML) which is based on
analyzing the discrete character data at each position in the aligned sequences. The
major differences observed between the two formed trees are that the Maximum
Likelihood tree specifies in more detail the outgroup rooting in many branches
estimating their lengths and substitution rates based on the data, making it more
accurate for more diverse sequences and complex evolutionary scenarios. The UPGMA
assumed a constant rate of evolution over time and assigns equal branch lengths to the
tree and it’s possible to lead into wrong results when analyzing highly divergent
sequences or in the presence of rate variation among different lineages.
Phylogenetic tree constructed with the distance-based method: Unweighted Pair Group
Method with Arithmetic Mean (UPGMA)

Phylogenetic tree constructed with the character-based method: Maximum Likelihood

(ML)