Hi all, I'm working on an intra-species phylogeographic study of Rays using only sequence data from GenBank. My goal is to assess genetic diversity across different geographic regions of the same species.
Since COI is quite conserved, I'm considering using rRNA genes (e.g., 12S or 16S) to identify haplotype diversity. Would rRNA markers alone be sufficient for this purpose, or should I look for more variable mitochondrial regions like Cyt b or the control region?
Also, I plan to use PopArt for haplotype networks and Arlequin for population genetic analyses. Does Arlequin work smoothly on Windows?
Any guidance would be appreciated!
Either 12S or 16S is fine. However, I find for vertebrates, the phylogenetic information is quite noisy (too many conflicting sites). COI, ND1, ND2 and cytb are some of my favorites. Depending on how closely related the taxa are and how many taxa you include in your tree, one complete gene may not have enough information. You may wish to concatenate a few genes with separate models for each gene. I would use the control region if the species are closely related or if you are looking at different populations in the same species.
Regarding Arlequin, I do not use Windows so would have to let someone else cover that.
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