Phylogenetics Using MEGA

 For today’s lab we are going to work with the Molecular Evolutionary Genetic Analysis program (https://www.megasoftware.net/home) to examine the phylogentic relationship of the cytochrome oxidase I (COI) gene in several ants. These 10 ants were collected by amateur entomolgists in south Florida, five were collected from one location (ants 1-5) and five were collected from another location (6-10). The DNA was extracted from all of these ants and the COI gene was amplified and sequenced in order to compare the two populations. We were also supplied with sequence from Formica rufa a close relative of the ants being sequenced. Your goal is to identify each of these ants (using BLAST) (Camponotus atriceps_1) and create two distance matrices and two phylogenetic trees (using MEGA) to compare these populations and identify if these two populations are actually one giant population. In order to proceed, you will need to download the MEGAX program from https://www.megasoftware.net/ . You will then make a MEGA alignment for the 10 ant species and the outgroup species (Formica rufa) using the sequence files provided. You will need to trim the sequences and correct any errors in the sequences by using the editing functions in MEGAX.