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.
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.