The way forward?

So I’ve been thinking about how we’re going to proceed towards publication with the data analysis we’ve done so far.


  • The RAxML trees using all 95A OCTUs came out alright, but as expected you can’t infer much about higher phylogeny.  Basically things cluster into ‘Metazoa’ or ‘Non-metazoa’.  Some of the major clade groupings are recovered–Nematoda seems pretty robust–but the bootstraps are abysmal and you get sequeces out of place everywhere (hinting at alignment errors or an untrustworthy BLAST result).  Also, hello long branch attraction!
  • I’m having concerns about our BLAST matching system; sometimes when I BLAST an OCTU sequence I get a completely different hit versus what the OCTUPUS pipeline churned out.  Also, my new hit normally corresponds with the phylogenetic placement in ARB (an erroneous observation is why I re-BLASTed the OCTU in the first place).
  • The possiblity that a lot of sequences aren’t ‘real’ and can’t be fixed by simple alignment tweaks–e.g. when an OCTU sequence is missing 10-20 bps in a conserved rRNA region!  Are these chimeras or are these sequencing errors?


  • I like the individual OCTU phylogeny approach that Kelley came up with.  It seems to be working really well and gives a good idea of the geographic distribution when you break things down.
  • Need to liaise with Pari regarding a database that will run this phylogeny approach.  At the very least I need to learn how to manipulate FASTA headers and add on information from excel spreadsheets so that I can run some of this stuff myself.

Phylogenetic species concept

  • Need to read papers.  The microbial people seem to think we can do this with pairwise identity cutoffs? (e.g. 98%?)  But I’m sure there are other algorithms based on branch lengths, etc. that would be worth trying
  • Progress on mtDNA arrays?  Ordering oligos? I know this is a whole other can of worms, but additional loci will be important in determining species boundaries/community compostions in the long run.

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