I am constructing the phylogenetic tree of a monogenean parasite called Macrogyrodactylus species (28 isolates)(MEGA original) but always I found the outgroup lies inside the ingroups.I used several parasites species which looks related but from diffferent genera and families of monogenea bu again the outgroup lies inside the ingroups (inside the tree). I would be most grateful if you could help me in getting the outgroup outside the tree?
Choose something really distant like human, mouse or Drosophila.
Dear/ Dr. Mohammed
I attached a file containing some notes in Arabic about Outgroup selection. I hope they can help.
Best Regards
Hi,
I don't know much about flatworms, but for a great many types of organisms, including invertebrates and vertebrates, the mitochondrial genomes and even more often mitochondrial genes such as nadh and cox-1 are studied for phylogenetic classification and taxonomy.nomenclature. I searched GenBank for Macrogyrodactylus and only found one mitochondrial genome. I then used BLAST with the cox-1 gene from that genome and again found only one Macrogyrodactylus plus a few related flatworms. I aligned the cox-1 genes and have attached the alignment and tree here.
As for outgroups, in general you should select the next closest relative of the group you are interested in, and not something very distant like mouse or insect, for many reasons. Even within the flatworms, the 0.5 scale bar in my attached tree indicates a huge distance between these organisms. You can see that within a species (G. lucii, G. botnicus) there are variable degrees of diversity which is probably more of a nomenclature issue than a biological issue.
I have also attached an alignment and tree of the same gene (mitochondrial cox-1) of some mammals for comparison. So you can see for example the distance between gorilla and Homo sapiens in comparison to distances between flatworm species.
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