I know how to calculate genetic similarity between genotypes, but I do not know how to calculate genetic similarity between groups.

From cluster analysis, I found seven groups. Now, I need to calculate genetic similarity between these groups. How should I go about doing this?

  • $\begingroup$ Maybe I don't know enough about the analysis of genotypes, but I find it hard to follow this question. The first thing that occurs to me is to use whatever method works for you with individuals, & use that with the group centroids. Have you tried that? Is there a reason it wouldn't work? Can you say more about what you have tried & the problems you're facing? $\endgroup$ – gung - Reinstate Monica Aug 12 '12 at 2:24
  • $\begingroup$ Thanks for your reply. Actually after cluster analysis I found 7 groups. Each group consists of different number of members/genotypes. Now, if I would like to see lower similarity or higher similarity between groups(between one group to another) how should I calculate. Because finally, I have to conclude selecting parents from groups for further breeding. Many thanks. If possible pls help. I have used NTsys Program.I used SSR markers.how can I put the data combinedly for a group? to put it in NTSYS> $\endgroup$ – Sirajul Mazid Aug 12 '12 at 3:30
  • $\begingroup$ What similarity did you use for clustering? $\endgroup$ – Anony-Mousse Aug 12 '12 at 3:32
  • $\begingroup$ Why can't you check the similarity between the group centroids? Are you worried about the variability in the groups? $\endgroup$ – gung - Reinstate Monica Aug 12 '12 at 3:33
  • $\begingroup$ No I don't know how to do that, No I am not worried about the variables. Actually centroids is quite new to me. Thanks $\endgroup$ – Sirajul Mazid Aug 12 '12 at 3:34

I had the same problem. In fact, I had to use free genetic software, Arlequin for this purpose.

If you already have each genotype assigned to any cluster, then use AMOVA technique (genetic version of ANOVA) in order to find out if there are significant differences between clusters or if some are overlapping.

Moreover, Arlequin also computes differences between populations (clusters) using many indices.

If you also want to use any genetic software for clustering, then I recommend to use another free genetic software, Structure.

Genetic data should be analyzed with genetic software or special genetic packages since they often need special measures of similarity of special methods of analysis (AMOVA, model-based clustering in Structure software).

  • $\begingroup$ I've used Structure for studying population substructures. Do you have a pointer describing where it can be used to analyze genetic similarity between arbitrary groups and how it compare to, say, other methods? $\endgroup$ – chl Oct 9 '12 at 11:00
  • $\begingroup$ It is not so easy, since in this area, I have no information about any comparison study, which method is best and when to use which one. But here is link to my poster where we used Structure and other clustering approaches and compared validity of partitions. Best results were from hierarchical approach, self-organizing map and multi-dimensional scaling. $\endgroup$ – Miroslav Sabo Oct 9 '12 at 11:11

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