Hi! Luis,

As you mentioned though there are reports that AFLP markers are unable to distinguish polyploids look at the following article, these authors used MCMC (Markov chain Monte Carlo) algorithm

Inference of population structure using multilocus genotype data: dominant markers and null alleles

http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2007.01758.x/pdf

in the following some used cytometry and others RAPD apart from AFLP

ORIGINS, DISTRIBUTION, AND LOCAL CO-OCCURRENCE OF POLYPLOID CYTOTYPES IN SOLIDAGO ALTISSIMA (ASTERACEAE)

http://www.amjbot.org/content/95/1/50.full.pdf

Genetic Analyses of Chinese Cynodon Accessions by Flow Cytometry and AFLP Markers

http://naldc.nal.usda.gov/download/3554/PDF

The use and limits of AFLP data in the taxonomy of polyploid wild potato species in Solanum series Conicibaccata

http://www.vcru.wisc.edu/spoonerlab/pdf/Solanum%20series%20Conicibaccata%20AFLPs.pdf

these authors say "AFLP analysis is an efficient technology for assessing genetic diversity among wheat cultivars", by using methylation sensitive and methylation insensitive restriction enzymes for AFLP analyses .

AFLP-Based Genetic Diversity Assessment among Wheat Cultivars from the Pacific Northwes

https://dl.sciencesocieties.org/publications/cs/abstracts/38/5/CS0380051261

Assessment of genetic diversity in a Morus germplasm collection using fluorescence-based AFLP markers

Theoretical and Applied Genetics. November 2000, Volume 101, Issue 7, pp 1049-1055

by the way what is your model organsim

Dear Jetty,

Thank you very much for the information, you seem to be very well informed :). My model is an earthworm, I not meant to underestimate it is value but I was expecting it to be less complex than what I found.

What I also have been found is that, first of all, you should at least know the ploidy of your target, in my case I found that all populations show the same ploidy number which make things easier for diversity comparison, otherwise it would be impossible to compare the diversity indexes, even with a mixture of ploidy numbers. We are know trying to implement the method for assessing the exact karyotype number, but with no success until know and if anyone have a protocol I would be very happy to get it.

Thanks again for the attention

Luis

Hey! Luis,

First of all what is your sample size, how many species...you are saying all are same ploidy, may be some times it happens, you can not see any variations. In the following paper they mentioned becuae of parthenogensis and in Lumbricidae it is widley studied and 4 genetic systems are investigated

go to page 170

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1013674/pdf/jmedgene00298-0001.pdf

you are asking for some protocol just have look at the following

Karyotype analysis of ....

http://www.zin.ru/journals/compcyt/pdf/2/polyakov.pdf

the following is in Russia

[Genetic structure and peculiarities of earthworms Aporrectodea (superspecies) caliginosa (Oligochaeta: Lumbricidae) complex on the territory of Ukraine].

http://www.ncbi.nlm.nih.gov/pubmed/19140431

both mentioned 2n= either 36 or 54 and in the Russian paper clones fromed are allotetraploids.

in the following they say "polyploid Lumbricidae in the East-European plain, except for the Volga region, are represented mainly by parthenogenetic forms of other genera"

[Polyploid races of earthworms (Lumbricidae, Oligochaeta) in the East European plain and Siberia].

http://www.ncbi.nlm.nih.gov/pubmed/18771028

in the following too it is mentioned female germline is inactive

[Consequences of experimental triploidy on the fertility and sexual differentiation of a normally amphigonic and diploid lombrician, Eisenia foetida Sav].

http://www.ncbi.nlm.nih.gov/pubmed/405115

most of the article are in russia n other laguage