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Redundant Haplotypes doubt

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Hi there! 

I come here because a doubt about Redundant Haplotypes and his repercussions.

I have been doing my thesis for the grade of Biologist about the Evolutionary Significant Units, this are populations of organism that were genetically isolated and have a diferent genetic variability. To make a delimitation of ESUs we indentificate reciprocal monophyly on a genetic tree, in this case whit COI and some of this ESUs have redundant haplotypes with some other locations.

¿ This redundant haplotypes make this reciprocal monophyly no viable?¿ This redundant haplotypes indicate a genetic relation?

I have this dudes because i read, that is very difficult to have the same two haplotypes frommutations or another mechanisms, and that make this ones good to make filognenetic reconstructions.  i not have literature about redundant haplotypes.

I'm not a native speaker, i hope my doubt was cleary explain.

Gretings from Chile! 

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I'm not sure if you're asking about technical problems of genome mapping, or about the evolutionary significance of genetic redundancy?

For the technical side, does this help? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937319/

For the evolutionary significance, the simplistic answer is that redundancy increases the chances of survival if a chance mutation proves to be deleterious. A "back up plan" so to speak.

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