If long branches are found to be sister taxa when analyzed using ML & a best fitting model, what can one say about the possibility of LBA artifacts?
As I mentioned in class, one can never be sure if one is suffering from LBA, although some cases have been clearly found (especially when MP joins long branches but ML doesn’t). However, ML isn’t immune to LBA so it will sometimes fail as well. If you’ve used the best model and used ML and the long branches are still together you can say either you are suffering from an unusually hard LBA problem (hard enough that ML won’t help!) or the long branches belong together – (Farris zone).
