I am conducting a molecular phylogenetic analysis on closely related Bivalve species using COI, Cytb, 16s, 18s & 28s.
Are there known to be similarities or what could be described as "Haplotypes" between genes and not just within genes. Are there any sorts of homology that can be traced between two different genes or their rate of evolution?
You might want to consider using supermatrix and/or supertrees methods.
There is no recombination in the single-stranded mtDNA, so as Artur said, all mt genes are linked. As such, phylogenetists consider the entire mt strand a single locus. Depending on how closely related these bivalves are, the 16s, 18s, and 28s loci may be uninformative or even identical. I have found about 1 phylogenetically informative mutation in these genes for every 3 million years of divergence. The COI and CytB will likely be more informative, and a concatenated approach (supermatrix) may be the best way to incorporate the slowly evolving loci.
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