Update on recent work

On June 18th I had a look at one of the RAxML trees that had recently finished.  The following taxa were removed from the tree because of LBA:

  • Vh4Virid–Gastromermis
  • T28Steat–Thornia
  • B91Spec3–Aporcelaimellus
  • M65Tenui–Capillaria
  • Eu6Dispa–Eucoleus
  • S94Batur–Soboliphyme
  • TbuHopei–Tobrilus hopei
  • AjrSpec2–Trophotylenchulus

The following species were also removed because they were short (~300bps) and they seemed to be quite unstable in the tree:

  • Enospec3
  • Enobrun2
  • Enospec2
  • Aopspec4
  • Aopspec5

Database 18June_EnopTreeEdits.arb now has 771 taxa left in Enoplid tree after these edits.  The Enoplid trees were then resubmitted to RAxML:

  • Job #573613 19June_EnopTreeEdits_ML.phy GTR + G
  • Job #573618 19June_EnopTreeEdits_ML.phy GTR + G + I

And same taxa were then submitted to CIPRES:

  • 19June_EnopTreeEdits_Bayes.nxs  GTR + G  
  • 19June_EnopTreeEdits_Bayes.nxs  GTR + G + I

On June 19th I downloaded outgroup alignments from SILVA (775 taxa from four Phyla: Kinhorhyncha, Nematomorpha, Priapulida, Tardigrada), and these downloaded alignments are in the file named SILVA_SSU_Outgr_19June.arb.  Birgit also used the Gastrotricha and Chaetognatha as outgroups in her thesis, but I decided not to use these groups because the Dunn (2008) paper indicated that they weren’t as close relatives as the four phyla I chose.

I had to merge two databases, and to facilitate the process I created two new field:

  • Created the ‘Tree’ field, and wrote ‘fullnem’ to this field for all the 1796 nematode taxa currently in the tree
  • Created the ‘outgroups’ field and wrote ‘outgroups‘ for all the 775 SSU taxa downloaded from SILVA

The tree in the merged database initially contained 2571 species (Fullnems plus outgroups) in the first tree that I bult.  I then removed all the uncultured tardigrades–there were 2031 taxa left after this step.  Next I removed some redundant outgroup taxa–there were 1946 taxa left after this step.  This merged database is named 19June_MergeOgr.arb

In order to merge the databases, I had to reassign all the short names for all the taxa in the database.  The file SSU_OGstaxalist.alpha lists the taxa labels for the reduced outgroup taxa list.  The file SSU_renamedFullNemforOGtree_taxalist.alpha lists the new names for all the Nematode taxa in the tree in the merged database.  I also changed all the Us to Ts in 19June_MergeOgr.arb

The following RAxML jobs should be discarded–they were run before I realised I had forgot to change the U’s to T’s:

  • Job#576226 (Fullnem +all OGs)
  • Job #576267 (Fullnem +Kinorhyncha)
  • Job #576299 (Fullnem +Nematomorpha)

After realising my mistake, I re-ran all the outgroup options in RAxML–these are the correct job numbers [all were run with only GTR + G]:

  • Job #576466 19June_FullNem_allOgs1.phy (1946 taxa)
  • Job #576486 19June_FullNem_Kinorhyncha.phy (1806 taxa)
  • Job #576540 19June_FullNem_Nematomorpha.phy (1815 taxa)
  • Job #576602 19June_FullNem_Priapulida.phy (1810 taxa)
  • Job #576705 19June_FullNem_Tardigrada.phy (1903 taxa)

I also started work on the LSU database.  I built the PT server and imported my Enoplids into the tree (even though its really messy…). 

The D2/D3 segment in the  LSU aligment is:

  • Begins from approx. position 71593  [E.coli 442]
  • Ends at approx. position 81886 [E.coli 810]

Today I edited the following species and removed a lot of duplicate species:

  • Longidorus, Xiphinema, and Bursapelenchus (fully edited)
  • Pellioditis, Hopolaimus, Pratylenchus–removed some sequences but didn’t edit fully
  • Oncholaimus/Viscosia, Bathylaimus

On June 20 there were 1145 taxa cool after reductions.

For the CIPRES MrBayes results, the following explains the different file types you get back:

  • .nxs file contains all the final trees from the analysis
  • .p file–not sure what this is!
  • tmp. file is the temporary trees from the analysis
  • Best scoring tree is the best tree, obviously!



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