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I am required to create a phylogenetic tree(s) of my genes of interest and am currently blasting (tblastn) my genes of interest from S. mediterranea against model systems before expanding my search.

Problem I get something like the attached which does not look like right. What am I doing wrong? I'm aligning via MUSCLE, and running Maximum Likliehood Protein models and consequentially, using the correct model (JTT, for instance). enter image description here

Greatly appreciate any help in advance.

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  • $\begingroup$ Which gene is it? $\endgroup$
    – M__ ♦
    Sep 29, 2019 at 10:00
  • $\begingroup$ Anyway yes it's possible, I'm confused by your Tblastn because that will give nucleotides, JTT is s protein model $\endgroup$
    – M__ ♦
    Sep 29, 2019 at 10:17
  • $\begingroup$ @MichaelG. tblastn gives protein, not nucleotide. It takes a protein query and blasts it against a translated nucleotide database. The results are protein alignments. $\endgroup$
    – terdon ♦
    Sep 29, 2019 at 10:47
  • $\begingroup$ @zaci, could you explain what looks wrong? Why would there be something wrong here? You seem to be aligning small parts of each protein, so it makes sense that you're not finding the "real" species tree. $\endgroup$
    – terdon ♦
    Sep 29, 2019 at 10:48
  • $\begingroup$ I suspect it's gene duplication. Helminths and insects are in the right place as basal metazoa $\endgroup$
    – M__ ♦
    Sep 29, 2019 at 11:23

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Anyway the chances are this is gene duplication. It will be a housekeeping type gene or else histone that sort of thing. You simply map the different genes onto the various metazoan classes. In your case nematodes and arthropods are basal metazoan, so their is correct given the clade they form part of all all representatives is that gene.

There is nothing weird you just need to read the deep phylogeneticists work like Tom Caveliar-Smith and Sandy Balfour, possibly Blair-Hedges

There are alot of eukaryotes prior to the invertebrates, just look at the Cambrian explosion

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  • $\begingroup$ How about the tri-furcation at the branch giving rise to RFX5-RFX7, Smed RFX15486 and Dmel Uncharacterized...? Isn't there a problem there? $\endgroup$
    – haci
    Sep 29, 2019 at 16:23
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    $\begingroup$ No, its simply a polytomy, increase the amount of data and resolution will sharpen to a bifurcation. From recollection the arthropod - worm boundary isn't well resolved. Might have changed with genome availability $\endgroup$
    – M__ ♦
    Sep 29, 2019 at 16:53
  • $\begingroup$ I think Blair-Hedges was the person most related to this $\endgroup$
    – M__ ♦
    Sep 30, 2019 at 13:10

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