I'm doing analysis of phylogeography with a plant that can be either diploid, triploid or tetraploid. I get AFLP results. If I use Nei or Jaccard index there is a bias because a tetraploid has more chance to show any given allele than a diploid. Then knowing the ploidy of every sample, how do I compute a distance unbiased by ploidy?

Who could advise me on the relevant publications about the choice of diversity index?

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