I want use outgroup for these bacteria. and I don't know is this possible that I use all of them in one tree?
Pseudomonas chlororaphis
Pseudomonas putida
Pantoea agglomerans
Stenotrophomonas maltophilia
Chryseobacterium elymi
Rhodobacter ovatus
Rhizobium sp.
Bacillus infantis
Bacillus cereus
Microbacterium oleivorans
Guide me please...
Regards
It is possible to construct a phylogenetic tree across even greater diversity than the eubacterial species you are describing here. For example, it is possible to make a tree including eubacteria, archaebacteria, and eukaryotes. Using ribosomal RNA sequences (or the genes endocing them) plus genes for DNA polymerase and other highly conserved genes that are very often sequenced from many different species, and which tend not to be horizontally transferred between diverse groups, is important. With a diverse group of species such as those on your list, the choice of an outgroup depends on why you want to use an outgroup. A good alternative is to use midpoint rooting for your tree. No matter what bacteria you choose for an outgroup, you are likely to create a "long branches attract" problem where the outgroup will join this group on the longest branch within this group (the ingroup). This will tend to bias your view of the evolution of this ingroup if you do not understand the long branches attract problem.
Another potential issue to deal with is to make sure that genome composition bias (A+T rich organisms, compared to G+C rich for example) does not bias the results. Bacteria can have very large differences in DNA base composition which can tend to make the AT-rich organisms group together away from the GC-rich ones, or at least bias the results if there are both types of genomes in your data set. The DAMBE phylogenetic analysis package has some good tools for exploring other aspects of the data, in addition to providing phylogenetic analyses.
http://dambe.bio.uottawa.ca/dambe.asp
Hi dear Dr. Foley
Thank you so much for your kindly guidance
that was so useful...
Regards
Kamal S.
Kamal, you question is not informative enough to give you a correct answer. You should describe the methods of analysis you expect to apply. You can study all your bacteria together by very general methods only (16S rRNA-like). If you want to get information about bacteria diversity on subspecies-strain group level you must use methods like MLST/MLSA, AFLP, etc. For such purpose, outgroup and type strains will be different for each named genera of bacteria.
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