I’ve been always interested in evolutional and phynogenic studies, I read some ABCs before I went to bed on that last night, and woke up this morning thinking, “why not try it out myself”?
Well, you know, a cladogram is something you see on a biology text book that shows how human evolves from ancient apes, and how we’re related to modern ones. Watching a well and carefully constructed cladogram is a great pleasure, because it reveals the evolutionary events happend millions of years ago. However, constructing it is another story, it appears to be very simple and actually the basic principle is simple. But there’re still many problem to be solved before we can make a reasonable tree, and conclude something base on it. The biggest headache may be choosing the gene. Luckily, many scientists have done lots of experiments to prove that using mitochonrion genes for phylogenetic purpose usually works because they change fast enough to see the difference between species from a genus, and conserved enough to see their common ancester. Plus it is mainly materinherited.
Forget about the aboves, I just wanna try out some softwares that I may be using in the future. So, I visited GenBank, and fetched some published mtDNA sequences. The gene I chose was the one encodes cytochrome b, it’s totally random, I don’t know which to use actually. I collected sequence information for 10 species, 9 of which are gobies(Gobiidae) and one Perciform Aspasma minima was chosen as outgroup. Again, I don’t have tons of theory to choose this one, I just want to see how things would turn out.
Next, I need a program to align the sequences and compute the tree. After trying out some of the many, I find phyloWIN easy to use and also powerful. The data file is attached in this blog, you can download it here. With just several clicks, a tree is drawn. The result turns out satisfying, which reflects the some main groups in Gobiidae.