There is no clear-cut difference between population variation and the early stages of speciation. You would need to monitor variation over time to test if the different variants tend to occupy different ecological niches and if the divergence between them is increasing through time. On the other hand population genetic studies, using molecular markers can tell you if gene flow is occurring at the same rate within the different morphs as between them. Is there is evidence for partial genetic isolation between the morphs, you might suspect incipient speciation.

I agree with Pierre Meerts.

This is exactly one of the issues with species delimitation.

Often the variation between different populations are just under the usual variation considered inter-specific (i.e. the super discussed COI 3% threshold for insects) but quite higher than the usual intra-specific one.

Depending on what you are working on, testing populations of closely related species could help. The barcoding gap could give you an insight, too. If multiple populations of similar species show a similar genetic variation, then you could at least assume to be in the same situation.

However, you still cannot really know if you are looking at early stages of speciation or at genetically variable populations of the same species.

What are you working on?

Thank you sir. I am working on Lepidoptera

Have you tried to compare the COI barcode region of the species you are interested in? Are the results very variable?

One approach is to employ multilocus nuclear genotyping and population genetic analyses to answer the question whether morphs of interest represent (semi)isolated gene pools in sympatry, or not.

Thanks Meerts, Martoni and Strelkov.

F. martoni Now i am using this DNA Barcode tool. It is in progress

Dear Santosh

Please read The Ernst Mayr Book, Principles of Systematic Zoology, specially chapters 5 and 6. You can find some important information.

Truly

Alireza