I have DNA sequence data of two closely related marine species (one coastal and other oceanic). The samples has been collected from two different geographic location of same ocean, seperated by 650 miles. Now since one species is oceanic and other is confined to coast, i wish to study their genetic divergence.
Can anyone help me in this regard
I don't understand what is your doubt. But, yes, is possible to compare genetic divergence between two species even if from different localities (tough different countries or continents). And you can use various methods, how fingerprint with markers (SSR, ISSR, AFLP, RFLP), or phylogeography using mtDNA (for animals) or cpDNA (for plants) sequences, or still phylogeny approach, depends on how many budget and infrastructure you have.
I don't understand what is your doubt. But, yes, is possible to compare genetic divergence between two species even if from different localities (tough different countries or continents). And you can use various methods, how fingerprint with markers (SSR, ISSR, AFLP, RFLP), or phylogeography using mtDNA (for animals) or cpDNA (for plants) sequences, or still phylogeny approach, depends on how many budget and infrastructure you have.
Why dont u simply go for phylogenetic analysis.. If you find good similarity between them then you cn use its non conserved domains to study their divergence. as you r saying that they are from same ocean then their cn be a great corelation as it is the water of c=ocean that sweeps the coast...
If you want to evaluate phylogeographic patterns, or if your species have geneflow, that could be a bad idea indeed. If that is the case, you need more samples
Simplest way would be find some conserved part of the genome. Then sequence those region. Do, the phylogenetic studies. Else deign some RAPD primers and amplify and analyse banding pattern with softwares. U can find correlation.
Hi Swaraj
I also agree with Fabio...you need to analyze more number of samples per species ...and if possible from multiple locations..you'll find several papers now-a-days where considerable intra-species divergence has been reported due to a variety of factors and often geographical locations is also cited one of the important factor...so best way is to try to analyze multiple samples per species..
bye
You can study the genetic divergence for those species, but the data of only one population per species may not be enough to conform your finding. You had better to use more populations from many locations to study the genetic divergence of two species. Because even same species from different locations showed the genetic divergence.
Two parameters are sometimes enough, specially when you using sequences. The problem is when you take very conservative or very variable fragments. For you good marker could be cytochrome and AT-rich region or rDNA introns. Be careful if you are using only RFLP - frequently two markers are not enough.
Thanks Prof. Kijewska for your reply. The marker in this case is mitochondrial DNA D-loop region,. This particular region is amplified and sequenced for two population containing 50 each. I wish to study population structure of the species based on that.
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