I think there are several factors including:

1. It depends very much on the group of organisms. Karyotype is difficult and expensive data to get for many organisms. It is also uninformative or of limited taxonomic value in others.

2. Generating karyotype data would usually require tissue collected or cultured correctly.

3. Understanding of how to generate and interpret the data is becoming rare.

Dear Rob

Thank you for adding an answer for my question, by the way i think when we used karyotype aproach and found a difference it proves flawless as the two population groups are different species, However realized the compareason by sequencing of genes remains circumstantial evidence. What do you think?

In most cases of taxonomic work, living material is not availalable. You need living material for karyotype examination, but for sequencing, dried (dead) material is fine, too. One can get DNA even out ot specimens that are centuries old.

Besides Robs point that, in many taxa, karyotype is not informative.

Hi Semir

Are you thinking of a specific case? Consistent karyotype differences between populations certainly suggests that they are different species. However, it is still important to try and correlate these differences with other characters and keep in mind that very complex situations can exist in nature and some organisms are remarkably variable in their chromosome characters.

Differences in sequences can also reflect intraspecific variation and need to be considered carefully. Sequence differences between morphologically (or otherwise) distinguishable groups in sympatry is strong evidence for distinct species (provided the organisms are outcrossing), but small sequence differences between allopatric populations are to be expected within a species. So, I agree with you that sequences in isolation are only circumstantial evidence.

An example of a complex situation where neither sequences nor chromosomes provide a satisfactory taxonomic answer is detailed in de Lange et al. (2008) "Biosystematics and Conservation: A Case Study with Two Enigmatic and Uncommon Species of Crassula from New Zealand",  Annals of Botany 101(6):881-99. This paper is available on ResearchGate. I have worked on several plant groups where sequence differences were found, but could not be correlated with other characters and do not seem to be a good basis for taxonomy, but that Crassula study is one where chromosome data turned out to be much more complicated than was anticipated at the beginning.

cheers

Rob

Hi, Norbert

Tank you for your explanation, but when you have a choice what do you do? KARYOTYPE OR SEQUANCING?

Short answer is that it depends on the group of organisms and what prior knowledge is available.

Hi, Rob

Thank you for all those informations. I'll download the reference and try to have clearer ideas. I take this occasion to say, we try  to organize an international workshop on plant genetics and microorganisms which you will find more information on the attached file.

I'd try to identify taxa with morphology first. Then, the question would be, why a specimen is needed to be identified. The problem in general is, that one needs a reference for identification, meaning, a karyotype or DNA sequences of a correctly identified specimen. In most cases, the karyotype is simply not known, and DNA might give you a better hint, which taxon you are dealing with (family, genus etc.) If there is a good density of karyotype data that allows discrimination between subspecies, then it might be useful, but this is likely only rarely the case.

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