Hello Asif,

Allozyme markers are codominant markers. I, myself worked with them back when I was an undergraduate.Therefore they are suitable for genetic diversity and structure analysis. Overall, they are good indicators of inbreeding levels and heterozigosity. However, they have limited coverage, since only a few loci are able to examined. It is very laborious and given the current sequencing technology, I would not go there even for a species that has not population genetic study.

One of the drawbacks on this technique is the detection of null alleles. They might interfere in the determination on allele frequencies and might lead to misinterpretation of heterozigosity and genetic structure. One must be very skilled at identifying null alleles.

If you desire to study a codominant marker, I promptly advise microsatellites, since they are also codominant and are a direct representation of the genome. Many loci can be examined at once as well. High heterozigosity levels might be detected. Accurate genetic structure and paternity tests might be performed with such markers. So, I would recommend going for microsatellites instead of allozymes for a deeper study. 

Of course, for a broad panorama and some history behind populaton genetics, you should read these classics: 

Hamrick, J. L.; Godt, M. J. W. Allozyme diversity in plant species. It is a book chapter in: Plant population genetics, breeding, and genetic resources. 1990 pp. 43-63

Lewontin RC, Hubby JL. A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura.Genetics. 1966 Aug;54(2):595-609.

Have a good study!

Thank you for such a informative response. Many thanks!!

I published some papers on genetic structure of marine species in the 1990s. Successive genetic work on the same species carried out with DNA techniques provided new information on particular aspects of population genetics, but basically corroborated the results on their genetic structure I obtained with allozymes. So, given the right Eneas' consierations, I believe that allozymes can be effective nuclear genetic markers. Their major drawback is that "they are considered old-fashioned markers", so it is difficult to publish allozyme results in good journals. In the 70s biologists thought that allozymes would have solved any problem; in the 90s they thought that DNA sequencing, SNPs, etc. would have solved any problem; and now they are thinking that NGS will solve any problem.... Maybe there is not a "philosophical genetic marker"!

Thank you very much for you response. My main concern was that epigentic regulation or environmental stress could alter protein production and therefore could interfere with results. My assumption was that looking at the raw DNA sequences would give a better picture and clearer resolution of population genetic structure. 

I have some experience with isozyme and DNA markers in plants. Isozymes markers have been replaced by DNA markers. However they have been fundamental in population genetics and the pattern of diversity found with the two types of markers are consistent.

Beside they are old-fashioned and labour-costly, you have caught a main drawback of isozyme markers, the lack of ontogenetic stability. It means that a certain locus or allelic variant (isoforms) could be not constantly expressed (and thus detected) in every tissue and developmental stage. Of course, the expression pattern can be the result of epigenetic regulation. This issue strongly limits the transferability of methods and results across independent experiments.

Thank you