Phylogenetics on scyphozoans

Basic steps:

You take photographs, take tissue samples, preserve whole specimens, ship to CnidToL (request reimbursement).

CnidToL identifies specimens to Genus and species using current morphological taxonomy, extracts DNA, PCRs and sequences target genes, then provides you with a proof-read electropherogram and text file of the sequence.

You also should check that the elecropherogram and text file match, by opening the file with any of several softwares, for example:
Chromas - http://www.technelysium.com.au/chromas.html
(Chromas is freeware, but is limited to looking at only one sequence at a time.)
ChromasPro - http://www.technelysium.com.au/ChromasPro.html
(ChromasPro allows you to align multiple sequences, but has only a 60-day free trial period)
BioEdit - http://www.mbio.ncsu.edu/BioEdit/bioedit.html
(Freeware comparable with Chromas)
Sequencher - http://www.genecodes.com/
(Superior commercial software; $$$)
DNAStar - http://www.dnastar.com/
(Superior commercial software; $$$)

After checking that the sequences are correct, the next steps are alignment of multiple sequences, phylogenetic analyses in any of several programs (e.g. PAUP*, MEGA, Phylip, MrBayes), interpretation of phylogenetic trees, species descriptions, and comparison with other data. Many of these steps require specialist training, so may require additional collaborations with either researchers in CnidToL or other phylogeneticists. How much you collaborate with CnidToL, and the lists of acknowledgements and authors can be discussed on a case-by-case basis. Whether you use data for individual projects (e.g. species descriptions) or group projects (e.g. regional biogeographic comparisons) is up to you. We hope this workshop will facilitate international collaboration. This may be encouraged further by training in molecular phylogenetics (e.g. by visiting UC Merced to work on specific projects, or during workshops at UC Merced or overseas).


Molecular Phylogenetics Michael N Dawson
Basic steps: You take photographs, take tissue samples, preserve whole specimens, ship to CnidToL (request reimbursement). CnidToL identifies specimens to Genus and species using current morphological taxonomy, extracts DNA, PCRs and sequences target genes, then provides you with a proof-read electropherogram and text file of the sequence. You also should check that the elecropherogram and text file match, by opening the file with any of several softwares, for example: Chromas - http://www.technelysium.com.au/chromas.html (Chromas is freeware, but is limited to looking at only one sequence at a time.) ChromasPro - http://www.technelysium.com.au/ChromasPro.html (ChromasPro allows you to align multiple sequences, but has only a 60-day free trial period) BioEdit - http://www.mbio.ncsu.edu/BioEdit/bioedit.html (Freeware comparable with Chromas) Sequencher - http://www.genecodes.com/ (Superior commercial software; $$$) DNAStar - http://www.dnastar.com/ (Superior commercial software; $$$) After checking that the sequences are correct, the next steps are alignment of multiple sequences, phylogenetic analyses in any of several programs (e.g. PAUP*, MEGA, Phylip, MrBayes), interpretation of phylogenetic trees, species descriptions, and comparison with other data. Many of these steps require specialist training, so may require additional collaborations with either researchers in CnidToL or other phylogeneticists. How much you collaborate with CnidToL, and the lists of acknowledgements and authors can be discussed on a case-by-case basis. Whether you use data for individual projects (e.g. species descriptions) or group projects (e.g. regional biogeographic comparisons) is up to you. We hope this workshop will facilitate international collaboration. This may be encouraged further by training in molecular phylogenetics (e.g. by visiting UC Merced to work on specific projects, or during workshops at UC Merced or overseas).