Unknown sepiolids and the GenBank blues

Discussion in 'Sepiolidae' started by thom, Feb 22, 2006.

  1. thom

    thom Blue Ring Registered

    Joined:
    Apr 8, 2004
    Messages:
    38
    Likes Received:
    4
    Hello all!

    I had a chance to look at a specimen of Sepiola sp. , that was found recently in the North Sea; morphologically it resembles a S. atlantica, but it’s mantle length was longer than expected. After having sequenced a bit of mitochondrial DNA, I went on to pubmed’s genbank and did a BLAST search.
    While aligning the sequences of related species for a phylogenetic analysis, I found that there are unexpectedly many identical sequences of this particular COI gene for a number of sepiolid species, such as S. robusta, S. atlantica, S. intermedia and Heteroteuthis dispar. What’s more is that S. affinis and S. ligulata showed only a few base pairs of variation.
    More worrying was the fact that S. atlantica has two representatives for this gene on GenBank, and they are both quite different, showing more intra-species variation than I knew to expect. What’s going on here?
    This is not a research project as much as it is just a little first venture into molecular analysis and phylogeny on my part, as a second year bio student. It got me thinking though; How are your experiences with GenBank? Is it reliable?
    Is there a decently resolved phylogeny of the sepiolids out there already, so that I might be able to place my specimen more accurately?

    Thanks,

    Thom.
     
  2. main_board

    main_board Vampyroteuthis Supporter

    Joined:
    Feb 5, 2003
    Messages:
    373
    Likes Received:
    7
    I have a question for you that is completely unrelated to your dilemma (sorry, don't know enough about phylogenetics to help out).

    At a CIAC workshop, a woman doing a Ph.D (I believe) on Oegopsid phylogenetics said that using COI gene in cephs might not be such a good idea as cephs are supposed to have two copies of that gene. However, during the conference, basically everyone who presented studies on ceph genetics used the COI gene in their evaluation. Naturally, I found this very confusing. I was wondering if you could comment on the validity of using COI genes in cephs, and why such determination to use this one gene. I believe I understand that the desire to use this gene come from using it in other creatures with great success. Is this true?

    Cheers!
     

Share This Page