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Welcome to the Molecular Marker Wiki on Deepfin

This service is meant to allow public collaboration regarding molecular markers best suited for phylogenetic studies of fishes. It should answer the "million dollar question" (what marker(s) should I use to resolve the phylogeny of my favorite taxa?). Your are encouraged to let everybody else know which one(s) worked for you! See the marker list page for current entries and to edit or add more information. Please note you must log in to Deepfin and retrieve the wiki edit password from your MyDeepfin page before you can add or edit pages!

When adding a marker please make sure to include the following information if possible:

  1. gene_name
  2. gene_function (e.g., exon/intron/RNA/microsatellite)
  3. fragment_length (number of bp amplified and sequenced)
  4. taxonomic_level at which it has been applied (intraspecific/species/genus/family/order/supraordinal, etc)
  5. taxonomic groups that were studied using this marker, for which a "good" phylogeny was obtained.
  6. PCR_primers = a list or table of matching primer_name= primer_sequence
  7. narrative describing methods and results; how good of a phylogenetic resolution was obtained; PCR conditions; were PCR products cloned?

...and additionally, if possible:

  1. Lit_reference= if they were published, give journal citation
  2. GenBank_accession = provide if DNA sequences for this marker have been deposited
  3. divergence_level1= max, min, and average p-value among ingroup taxa
  4. divergence_level2= max, min, and average p-value between ingroup an outgroup taxa
  5. Potential_problems = narrative describing potential paralogy o non-stationarity or other (alignment)

You can add your information by going to the marker list page and following the instructions from there.

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Page last modified on July 25, 2008, at 10:21 AM