Absolutely, adding samples to your analysis will often change the trees that are drawn, especially if the sample is not easily related to the ones already in the analysis.
prabhubct, on 05 September 2012 - 02:54 AM, said:
I mean to ask whether it is possible that we make relations between sequences distorted. As stated if A->B-> C-> D ( I guess it means A-> C too) is tree drawn by parsimony. could e,f,g (mutant) make it go as e->B-> D->f-> A->g-> C ? whether it would mean as B->D->A->C
Is it possible that you have making it confusing by how you are explaining this? Are you talking about efg as mutant forms of A, B and D? If so, they would be better described as A*, B* and D* or something similar
You can't state whether or not the order of the changes is possible from the analysis; a completely non-related sample where you only have efg,and no ABCD, should form its own clade, joined only at the base (if you are drawing a based tree). If the efg mutant also contains the ABCD traits, and the ABCD non-mutants, contain basal forms of the efg traits, then it is entirely possible that there will be a change in the tree drawn.
You must, must, must, understand that this is only minimum number of changes analysis - it may have no bearing on what actually happened. It makes the assumption that the changes proceed by a minimum number of steps, when in fact the traits could have formed several times completely independently. For instance if you look at the kingdom Animalia - you have three major groups of flying organisms - insects, birds and mammals (bats). If you did an analysis where you looked at the form of locomotion, trait A could be walking/ running, trait B could be swimming, and trait C could be flying. Under this analysis, flying insects, flying birds and bats would all group together - yet if you go and look at the actual animals, it is very very obvious that they have evolved the trait independently, whales, dolphins, frogs and fishes would also group together - yet so far as we know, fish have never left the water, whales and dolhins used to inhabit the land, and frogs are somewhere inbetween...
Do you see where this is going?