I want to study genetic relatedness among fresh water fishes, so which molecular marker would be best for this study?
There are many suitable markers. I suggest you to consider also 1) the costs and 2) the effective application to related species.
Hi. You should look at which markers have been used for your group of interest and what is the mutation rate for them. Then you choose those having sufficient polymorphism for your question (i.e. whether resolving deep or shallow nodes). Mitochondrial loci are more polymorphic and have been extensively applied for interspecific/intergeneric relationships whereas nuclear coding genes have been applied for interfamilial/deeper clades. Choosing a marker is essential for a good project so be sure you are choosing those which will respond your question. All the best.
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