Hi Muhammad

Well that depends on your aim, species, budget, and a number of other variables.

I should say that there is no such a thing as "silver bullets". All markes have their strengths and drawbacks.

For instance, if primers are available for your species, microsatellites would bring you some valuable information on intraspecific variation. Microsatellites (SSR) are usually very polimorphic and stable, but are also expensive and laborious to develope in the first time. They are good to compare intraspecific variations but are less and less useful to compare interespecific relationships as your species get more distant in a phylogeny.

If you want to compare two species from different families or orders, you'll need homologous markers phylogenetic conserved, like gene sequences from mtDNA as you named, coi, cytb or nuclear genes as well... You might chose sanger sequencing, but I recomend you take a look at NGS based markers.

NGS markers have become more and more accessible and have a tremendous potential for information and are very flexible as well. However what you will be able to do with that has a lot of "ifs" involved.

You should first clarify what exactly is your aim in it, your budget, time, n of samples... To only measure variation, almost any marker will help you, what is going to constraint you is what kind of conclusion you wanna reach.

Please take a look at:

https://link.springer.com/article/10.1007%2Fs10709-005-2485-1

And

https://doi.org/10.1111/eva.12288

I hope it helps you.

Cheers

Wilson

Dear Wilson Frantine-Silva

Thank you very much for such a detailed answer. These recommended articles were much needed.

Kind regards

Abrar

For genetic diversity analysis, multi-locus markers seem to be right choice since theses markers will provide more information and wide coverage of the genome than the locus specific markers.

I suggest RAPD.

Dear mam, we are considering RAPD too.

Good, definitely you can see variation exists. But need to check with different Primers as some of the primers do not show any variation.

Probably you might have started screening.

Good Luck!

Jetty Ramadevi yes mam, I am working on it.