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PostPosted: Thu Mar 10, 2011 2:54 pm 
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Joined: Fri Jan 29, 2010 9:57 am
Posts: 37
Location: San Jose,CA,USA
i've been digging around lately and found out that the scalare mitochondrial cytochrome b sequence is actually available since 2007. the GENBANK accession numbers of the Pterophyllum scalare cytochrome b sequences are AY843353 (Rio Ariau, Brazil) and DQ990688 (Rio Ucayali, Peru). probably this can be utilized to differentiate "controversial" angelfish species.


you can actually have a fragment sequenced for just $6. but before that is done you need to :

1.isolate DNA
2. have specific DNA fragments synthesized so you can make several copies of a portion of the cytochrome b sequence
3.perform a Polymerase Chain Reaction (PCR) in order to make many copies of the fragment of the cytochrome b sequence to be analyzed ( if you have a scientist friend with the reagents and equipment you can have it done for free)
4. isolate the cytochrome b pcr fragment through agarose gel electrophoresis and a DNA clean up kit.

interestingly, when i aligned the two available sequences there were 2 amino acid differences (look for the BOLD letters those are the two differences):

scalare_str MANLRKTHPLLKIANDALIDLPAPSNISAWWNFGSLLGLCLAAQILTGLFLAMHYTSDIA
scalare_IF1 MANLRKTHPLLKIANDALIDLPAPSNISAWWNFGSLLGLCLAAQILTGLFLAMHYTSDIA


scalare_str TAFSSVAHICRDVNYGWLIRSMHANGASFFFICIYLHIGRGLYYGSYLYKETWHVGVILL
scalare_IF1 TAFSSVAHICRDVNYGWLIRSMHANGASFFFICIYLHIGRGLYYGSYLYKETWNVGVILL


scalare_str LLVMMTAFVGYVLPWGQMSFWGATVITNLLSAIPYIGNSLVQWLWGGFSVDNATLTRFFA
scalare_IF1 LLVMMTAFVGYVLPWGQMSFWGATVITNLLSAIPYIGNSLVQWLWGGFSVDNATLTRFFA


scalare_str FHFLLPFVIAAMTMVHLIFLHETGSTNPAGLNSDTDKVSFHPYFSYKDLLGFALLLIALI
scalare_IF1 FHFLLPFTIAAMTMVHLIFLHETGSTNPAGLNSDTDKVSFHPYFSYKDLLGFALLLIALI


scalare_str SLSLFSPNLLGDPDNFTPANPLVTPPHIKPEWYFLFAYAILRSIPNKLGGVLALLFSILI
scalare_IF1 SLSLFSPNLLGDPDNFTPANPLVTPPHIKPEWYFLFAYAILRSIPNKLGGVLALLFSILI


scalare_str LMLVPILHTSKLRALTFRPLTQILFWLLIADVAILTWIGGMPVEHPFIIIGQIASFLYFF
scalare_IF1 LMLVPILHTSKLRALTFRPLTQILFWLLIADVAILTWIGGMPVEHPFIIIGQIASFLYFF


scalare_str IFLILLPITGLVENKMFA
scalare_IF1 IFLILLPITGLVENKMFA

the scalare_str is scalare from Rio Ariau, Brazil while scalare_IF1 is from Rio Ucayali, Peru.

so from this preliminary data one can probably/possibly use cytochrome b sequence data to differentiate geographical populations of angelfish.

interestingly you can attempt to correlate this data with the Schultz table. Rio Ariau will most likely be placed in the Manaus area whereas Rio Ucayali will be most likely placed in the Peruvian amazon area. Compare the merisitcs data and you will see there seems to be a slight but appreciable difference in meristics between the angelfish in this regions.

reference:


Perez,G.A., Rican,O., Orti,G., Bermingham,E., Doadrio,I. and Zardoya,R. Phylogeny and biogeography of 91 species of heroine cichlids (Teleostei: Cichlidae) based on sequences of the cytochrome b gene Mol. Phylogenet. Evol. 43 (1), 91-110 (2007)


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