The Genetic Differences Between European Fire Ants & BC Fire Ants
A while back I had written an article where I compared the genetic similarities and differences of the European Fire Ant’s here in BC. During the analysis process we thought it would be interesting to research the origin of the BC fire ant. More specifically, where in Europe did the BC fire ants originate from?
To answer this question I needed to get fire ant sequences from different parts of Europe. Unfortunately, I was given a firm no when I offered to go on a two week trip to Europe to get said sequences :) Fortunately, a similar study had been done by Leppãnen et al. (2011) where they collected fire ant DNA from different areas of Europe and stored the accession numbers for the COI and CytB genes.
There were over 400 accession numbers for the CO1 gene, which would have taken a long time to compute. A more efficient approach would be to choose countries that had trading routes with BC. I felt that sequences originating from those countries would most likely result in relationships being shown. I ended up with 37 fire ant accession numbers that corresponded to fire ant sequences obtained from different regions of Europe.
From there it was a simple matter to write a short script that would connect to Genbank, enter the accession numbers and obtain the corresponding fasta sequence. These sequences were then saved in a text file.
I combined those sequences with all the BC fire ant COI sequences that were gathered from my previous analysis.
With all my sequences in the correct format I could import them into MEGA for further analysis. Similar to my previous analysis I aligned the sequences using MUSCLE with the default settings chosen. The Tamura 3-parameter model was used to generate estimation distances. Lastly, bootstrap testing was run 100 times to determine the reliability of each node of the tree. The end result is what you see below with the BC ants being circled in red.
To me it definitely looked like the ants from BC are much more closely related to each other instead of any of the ants from Europe. The most likely explanation was that enough time has past such that that BC ants have diversified genetically.
While this explanation was plausible I felt that there should be some closer relationships present. As such, I had to tweak my original approach to include all of the 420 fire ant sequences. The data was originally downloaded as a word document so I started by exporting it into a excel spreadsheet.
I then modified my original script to read directly from the CSV file. An extra step was added that formatted and saved the accession number and location into an array. In the previous version of the script this part was done manually.
From there the process was the same. The script connected to Genbank, entered the accession numbers, obtained the corresponding fasta sequence and saved all the sequences in a text file. Since there were over 400 sequences to read and save the script took a couple minutes to run.
Analyzing the sequences in MEGA was again very similar. Adding gamma distribution to the Tamura 3-parameter model was the only difference compared to the previous analysis. Generating the tree using all 420 sequences took just under two hours.
Due to the size of the generated tree it’s a tad difficult to see the relationships. However from the close up it appears that BC ants are in fact their own entity.
This was an awesome side project and I had a blast working on learning how to making the script work! You can check out the scripts that were used and the fire ant data on my github. As always, feel free to comment with your thoughts. Thanks for reading :)
