Does the outgroup affect the structure of the tree? - The in-group relationship was changed when I used different outgroups (Mar/20/2007 )
Hello,
Sorry for disturbing. Is there anybody who can kindly tell me why the structure of the my phylogenetic tree was changed within the group after I only changed outgrouop-sequence?
I used CLUSTALW to contruct a phylogenetic tree for all beta-proteobcteria related clones from an environmental sample using partial 16S rRNA sequences and simply selected one corresponding sequence from alfa sub-class of proteobactria as the outgroup. What I am confused is when I only replaced the sequence of this outgroup with another 16S RNA sequence from Actinobacteria, the structure of the tree within beta-proteobacteria has also been changed. It is my first time to construct a phylogenetic tree. As my understanding, the outgroup does not affect the in-group structure if we select a proper sequence as the outgroup, isn't it? Did I make the tree in an improper way?
I will be very grateful if you could give me some comments!
Sorry for disturbing. Is there anybody who can kindly tell me why the structure of the my phylogenetic tree was changed within the group after I only changed outgrouop-sequence?
I used CLUSTALW to contruct a phylogenetic tree for all beta-proteobcteria related clones from an environmental sample using partial 16S rRNA sequences and simply selected one corresponding sequence from alfa sub-class of proteobactria as the outgroup. What I am confused is when I only replaced the sequence of this outgroup with another 16S RNA sequence from Actinobacteria, the structure of the tree within beta-proteobacteria has also been changed. It is my first time to construct a phylogenetic tree. As my understanding, the outgroup does not affect the in-group structure if we select a proper sequence as the outgroup, isn't it? Did I make the tree in an improper way?
I will be very grateful if you could give me some comments!
I am not very familiar with tree building mechanisms, but perhaps your outgroup do interfere too much with the other data/sequences, i.e. it is not a "real" outgroup. Other possibilty may be that tree is looks as if arranged new, but it is not really (same dependencies/grouping but order of sequences/groups is different, hope you know what I mean).