I've obtained the mRNA sequences for bobwhite (Colinus virginianus) and Japanese quail (Coturnix japanonica) myoglobin. I was advised to make a phylogenetic tree with them, so I got the sequences for turkey and chicken which were the only other Galliformes whose myoglobin mRNA I could find. I'm using MEGA 6 with maximum likelyhood (bootstrap - 5k) and finding it hard to settle on a tree.
Of particular issue is finding an acceptable outgroup. Originally I was advised to use a loon because of their ancestral nature, but after reading about them it seems that Galliformes and Anseriformes (duck-like) are the oldest orders for birds and loons are actually more modern. The only Anseriforme with myoglobin mRNA available appears to be the general mallard. When using it with my tree I end up with a very weak node. Should I stick with the loon as an outgroup or keep my tree with the weak node? Maybe I'm using the wrong method for just 4 highly related groups and an outgroup?
My background in phylogenetics/bioinformatics is pretty much next to nothing so this has been quite trying. Any help would be appreciated.
This link might help you out? I know BGI is getting ready to publish ~ 40 new avian genomes. They might be some pre-released data out there. I have felt your pain in tree building. Hang in there.