I am using dominant markers (AFLP) to assess the genetic diversity of a plant. I don´t have reliable information about the mating system, so I´d like to estimate gene diversity assuming both Hardy–Weinberg equilibrium and total inbreeding. POPGENE is supposed to do that, but when I do the analysis with the assumption of HWE or total inbreeding i get exactly the same results. What I am doing wrong?
The link below may possibly help
http://dendrome.ucdavis.edu/help/tutorials/gdiversity.php
You may like to check this reference too http://cc.oulu.fi/~jaspi/plantpopgen/Arctophila_ConsGen.pdf
Hi Ziva. The process is as follows. First you have to score the marker data in a binary matrix either manually or using softwares like Phyelph. Then you will have to prepare the data matriix following the format of popgene.Then you will have to feed the data into popgene software. You have to run the software using a minimum of 1000 iterations and you will get the data enlisted under various heads like shannon diversity index, neis gene diversity index. You will also get the gene flow value. Actualy, its very simple but you will have to be very precise while making the matrix. If you have any further queries feel free to message me.You can also follow my publications.
dear Ziva,
you should use AFLPSurv (http://www.ulb.ac.be/sciences/lagev/aflp-surv.html) which explicitly gives to options to calculate gene diversity of AFLP markers with the assumption of either total inbreeding (option 1) or HWE (options 2..4), the latter again with different approaches to estimate allele frequencies.
regards
Walter
Dear all,
thank you for your comments. I didn't have any problems with the datamatrix in POPGENE, the problem was that I was getting the same results...
I am now doing the analysis in AFLPsurv and it seems to work, but I had to discard 1 population because it had to much missing data on some loci which made the program crush... Thank you Walter!
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