Cox1 Treebuilding and SSU Alignment Edits

Cox1 Tree building—23 May 09

Note: in previous Cox1 treebuilding (files from 4th-11th May), the correct Cox1 alignment to be used is named ‘Align_4May_nts_truncnames

 Today I imported all the cox1 sequences I could find from genbank—the full list of species and accession numbers are listed in the file ‘Cox1_Genbank_Acc_nos’.  The files I worked on are as follows:

  • Genbank_cox1nems.mas (protein sequence alignments—you CANNOT back translate this file to nts in MEGA for some reason)
  • Genbank_cox1nems_ntseq.mas (nucleotide sequence alignment—all sequences had to be re-downloaded from Genbank)
  • Cox1_GBplusEnop_23May.mas (combines all my Enoplid sequences with all the Genbank files I downloaded)
  • Cox1_GBplusEnop_23Maya.mas (removed the following bad sequences: BUS 4, JCC 59, LCL 3, OUS 14, TCR 69, AND WUS 3)
  • Cox1_GBplusEnop_23Mayc.mas (added more Pellioditis sequences from Genbank, and also deleted more sequences as follows: B. ruftipennis, S. lupi, H. muscae, S. sp, R sp., P. sp., C. nassatus, T. skrjabini, G. binucleatum [2 seqs], T. native, C. briggsae, R. iyengari.  These sequences were either too short or looked too divergent to be fitted into the alignment.)
  • Cox1_GBplusEnop_23Mayd.mas (additionally removed the following taxa, which were a bit divergent: O. volvulus, D. immitis, B. malayi, R. lichstensfelsi, B. debrae)

I ran likelihood analyses in PhyML using the divergent and tight alignments (23Mayc and 23Mayd, respectively). I first aligned the translated protein sequences in each .mas file using CLUSTAL in MEGA (default parameters).  The output nucleotide alignments are saved as 23Mayc_DNAaln and 23Mayd_DNAaln.

Alignments had to be saved as sequential PHYLIP files to be run through PhyML—alterted parameters were as follows: HKY model, Ts/Tv ratio estimated, invariable sites estimated, 4 categories of nt substitution, sequential input sequences.


Nematode groups edited in the ARB alignment on 22 May 08:

  • Trichura
  • Trichinella
  • Bathyeurystomina
  • Enchelidiidae
  • Pareurystomina
  • Thoracostomopsidae
  • Enoploides
  • Calyptronema
  • Oxystomina
  • Thalassoalaimus
  • Litinium

 The species Birgit used in her paper (Meldal 2007, A revised phylogeny of the phylum Nematoda; I searched for all the accession numbers listed in the appendix [saved as ‘Meldal_appendix_acc_nos.pdf’]), were annotated with the phrase ‘Meldal’ under the field ‘publication_doi’.  Two species weren’t in my ARB database: Trigulla aluta and Belondira apitica.  Somehow, though, although Birgit listed 214 species, I only have 211 marked in ARB (minus the two not found, I missed one somewhere?)