I would like to know if it is possible to combine haplotype sequence data with multilocus microsatellite genotypes data into a unique STRUCTURE (Pritchard et al., 2000; Hubisz et al., 2009) simulation. If yes, which is the best way to compute the analysis, considering that I have analyzed a different number of individuals with mtDNA and microsatellite DNA?
(I guess you mean "haploid sequence data", since haplotype is something completely different...)
If you model the lack of recombination and in the case of mtDNA the maternal inheritance... go for it. But I'd rather do a phylogenetic analysis using the mtDNA data and do STRUCTURE only with the autosomal data.
Yes I mean haploid sequence data, I made a mistake explaining the question I was asking for. So you suggest me to not combine the data from mtDNA and nuclear DNA. Probably I will carry on separate analyses for both molecular markers and then I will try to combine them when I will discuss the results. Thank you really much for your advises. Cheers.
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