Re-running jobs for BMC Enoplid Paper

I’ve been re-running all the jobs for the BMC paper, now including the Rhabdolaimidae for the Enoplid-only tree.  However, inclusion of these sequences has caused some (previously resolved) nodes to become unresolved.  So I’ve modified two new RAxML jobs to include 1000 bootstrap replicates and another with an extended majority rule consensus tree.  I’m also re-running the Enoplid Bayes tree to run for 4 million generations.

Did something similar with the Nematomorpha tree (Bayesian), using the nexus file for the thesis job Holly_longjob2 (CIPRES Bayes folder on old Dell).  Running this for 3 million and 4 million generations.

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Big Updates

Been doing a lot of updates over the past week or so. 

There are now separate ARB databases for the Enoplid-only tree (12June_EnopTree.arb)and the Full nematode tree (14June_FullNemTree.arb).     Firstly, I severely cut down the Full Nem SSU tree to 1798 taxa, and further to 1796 taxa on June 18thThe Enoplids-only tree now contains 784 taxa.

On the 12th June I edited the following genera in the Full Nem tree, during the process of cutting down taxa:

  • Oscheius
  • Phasmarhabditis
  • Plectus
  • Ancylstoma
  • Protorhabditis
  • Mesorhabditis
  • Schistonchus
  • Aphelenchoides
  • Camallus/Procamallus/Spirocamallus
  • Brugia
  • Toxocara
  • Philonema
  • Poikilolaimus
  • Howardula
  • Pratylenchus
  • Hirschmanniella
  • Basiria
  • Helicotylenchus
  • Cephalob*
  • Zeldia
  • Philometra/Philometroides
  • Nacobbus
  • Eumonhystera
  • Oxydirus
  • Labronema
  • Clavicaudoides
  • Robbea
  • Laxus
  • Caenorhabditis
  • Rhabditis
  • Panagrolaimus
  • Anguina
  • Aphelenchus
  • Adoncholaimus
  • Daptonema
  • Theristus

The Enoplids Only tree contains the following species:

  1. All Enoplea (I searched in tax_embl field for ‘Enoplea’ and selected all results)–includes Enoplida, Dorylaimia, etc.
  2. Chromadoridae (searched in tax_embl field for ‘Chromadoridae’)–represents outgroup
  3. Holly Enoplids (All sequences–no duplicates removed)

The total of the above Enoplids was 989 taxa.  This was then cut down to 784 by removing excess sequences in some taxa (but none of Holly Enoplids were removed) Some of the removed taxa are listed in the file 12June_removedEnop.alpha, but more were removed that aren’t listed in that file.

The alignment was checked for ALL Enoplid sequences by systematically going down the tree.  On June 13th (after all edits were finished), all Enoplid taxa left in tree (784 taxa) were submitted to RaxML:

  • Job 533582 –> 13June_EnopFulledit, GTR + G
  • Job 533583 –> 13June_EnopFulledit, GTR +G +I

On June 14th, the same Enoplid taxa were submitted for Bayesian Inference analysis via the CIPRES web server.  The taxa need to be exported from ARB in PAUP format, and then you need to add a) MrBayes command block b) Remove some info from the header (change RNA to DNA, delete some characters for missing data):

  • File 14_June_EnopBayes.nxs, GTR + G
  • File 14_June_EnopBayes.nxs, GTR + G +I

The next few days have been spent editing ALL taxa alignments in the Full Nem SSU tree.  These edits were finished on June 18th, and the Full Nem tree (no outgroups added yet) was submitted to RAxML:

  • Job 569141 –> 18June_FullNem.phy, GTR + G
  • Job 569160 –> 18June_FullNem.phy, GTR + G + I

I tried submitting the Full Nem tree to the CIPRES server for MrBayes, but it appears the file size is too big for the server to accept–I have to contact the administrators if I want them to run the job.

Cox1 ML and Bayesian Treebuilding

 

Model choice for ML –> Use Modeltest 3.7 (chooses between 56 models)

  • Cox1_28May_aln.nex –> Cox1 Enoplids only with 6 Pellioditis spp. (105 taxa  total)

Ran on modeltest:

  1. First execute data file (Nexus) in PAUP
  2. Execute file ‘modelblock PAUP b10’ to compare models—this makes an output file called  ‘model.scores’ and you can change this filename afterward to reflect your data
  3. Deposit the ‘model.scores’ file into C:\bin folder and then run modeltest <inputfile.scores> outputfile.out
  4. If successful, the command line will revert back to C:\bin and the outfile is written to the bin folder.

For Cox1_28May_aln.nex the AIC selected GTR +I +G as the appropriate model for Cox1 data

 

Modeltest for MrBayes –> Use MrModelTest2.3 (chooses between 24 models)

  1. Execute data file (Nexus) in PAUP
  2. Execute ‘mrmodelblock’ in PAUP to compare models.  This makes an ooutput file called ‘mrmodel.scores’
  3. Deposit the ‘mrmodel.scores’ in the bin folder, and run the command mrmodel2  <inputfile.scores> outputfile.scores
  4. If successful, the command line will revert back to C:\bin and the outfile is written to the bin folder.

For Cox1_28May_aln.nex the AIC selected GTR +I +G as the appropriate model for Cox1 data

 

PhyML run 29 May

  • Used file ‘Cox1_29May.phy’ (sequential  file format, 105 taxa)
  • GTR + I +G model, estimated invariable sites, estimated gamma distribution, 4 nt substitution categories, base frequency estimate was empirical
  • Loglikelihood from stat file = -11260.10740

Running files in MrBayes:

  • Save as a sequential Nexus file (PAUP 4.0) from Mega
  • No need for alteration to MrBayes block—use the default one from the Barry Hall Book (chapter 8 folder).  For Cox1 I used the one with codon partitions.
  • Ran file ‘Cox1_28May_aln.nex’ using GTR +G+I with a codon partition model. Ran for 1,000,000 generations, final average standard deviation was 0.042370.
  • Burnin=1250 (should have increased this for 1,000,000 gen), sampplefreq=100 (records tree/parameters every 100 gen), printfreq=1000 (prints to screen every 1000 gen), nchains=4, temp=0.2

 

Bayes_datafile_changes