Well, the difficult question is "what is a subspecies"? Since it is in fact already complicated to agree on what a species would be, it is certainly all the more difficult (and subject to the application of conventional criteria) to recognize boundaries between subspecies, which make less biological sense. Of course the opinions will differ depending on who you talk to (splitters or lumpers). Anyway, below please find the link to a paper which you might find interesting in case you haven't seen it yet. It regards molecular recognition of tiger subspecies:

https://www.researchgate.net/publication/279511593_Planning_tiger_recovery_Understanding_intraspecific_variation_for_effective_conservation

I hope this helps, all best

Danilo

Article Planning tiger recovery: Understanding intraspecific variati...

It may depend of a lot of variables; first the group in which you are working on (recent papers shows that molecular data in some groups do not work until very high levels, etc.). and what you consider a subspecies. Another important thing is in what kingdom of organims are you working on, because the species-subespecies concepts can vary tremendously. 

Thanks to Danilo for mentioning our paper. While our paper deals with a precise question regarding the tigers here is also a quite interesting paper by Colin Groves which - although directed at Primate taxonomy - deals with more general issues of species concepts and their application. 

Best regards

Joerns

Article Primate Taxonomy: Inflation or Real?*

I agree with the other commentors: Given the controversy on even the species concept ( e.g.:  "species concepts and phylogenetic theory: a debate"), deriving certain percentages of molecular difference as a deliminator of subspecies seems like a tricky business to me, or, more specifically, an empirically derived rule of thumb for a certain group of organisms with sufficiently even genomic constitution. So, I´d say: If it is possible, and, if so, where a satisfactory threshhold would be situated, may depend on the group of organisms and maybe even the group of genes you are looking at.

best regards

Paavo

http://cup.columbia.edu/book/species-concepts-and-phylogenetic-theory/9780231101424

Hello Harsimran,

I understand what you are asking and why, but I think it is perhaps worth while going back to the pre-molecular era and considering what subspecies were designed for - I say "designed for" because they are of course a taxonomists' concept, not a biological one.  Classically, subspecies are geographical races of a widely distributed species which are reliably distinguishable on some morphological character or character set. I suppose you could translate this into molecular terms by saying that a subsp. is a geographical race  of a species with a distinctive sequence.  However, the two critical components are a) the geographically limited distribution and b) the distinguishability. In my own work (on grasshoppers) I was able to show that previously described subspecies  were all  significantly different from each other in some morphological parameter. However, the differences were not enough to RELIABLY assign any individual specimen, as  the variance within the individual subspp. meant that there was always overlap. Only one population was so different from the nominate race that all its members could be reliably assigned to its (geographical) source, and that was the only one that I recognised as a subs. in my revision. If you would like a copy of that paper, let me know.   Hugh Rowell.. 

Hello Harsimran,

As Hugh Rowell rightly pointed, subspecies were (and still are) delimited on morphological traits, frequently quantitative traits (like larger, darker, wider, more mottled etc.).

All this characters, if we exclude the influence of the environment that can lead to distinct phenotypes of the same or similar genotypes, are the result of some genetic differentiation too.

The problem is  that molecular studies at intraspecific level are usually done on markers that are frequently neutral (such as mtDNA, introns, ITS), as they are sufficiently variable. This markers do not have the same pattern of geographic variability as the gene(s) that lead to that morphological traits used to recognize the subspecies. Because of this, most phylogeographic studies show no correspondence between morphologically defined subspecies and molecular clades.

See for instance this paper and its introduction

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0041058

Concerning your question, I think that if you know your group well, you might find a threshold that indicate the limit between species and intraspecific variability. But it is group specific and every time there will be a few exceptions (like a pair of good biological species that are indistinguishable on the molecular marker you use or a single species that has strong geographic structuring at molecular level).

All the best,

Lucian

In plants the concept of subspecies varies. However,  the concept of geographical  distribution is generally taken into consideration.

I am expecting  precise answer to the question of Harsimran Singh:

I mean can molecular data tell the authenticity of subspecies in a taxon ? Like it is a convention that difference of 2% genome leads to distinction of two populations as a separate species. Can it be inferred that between 1.5-2% difference in genome leads to conclusion of sub species ? Is there any molecular basis of recognition of sub species ?

With best wishes and regards to all of you,

Subir.

There is a whole new emerging area on coalescent methods for species/sub-species delimitation nowadays. You can get, for example, a Bayesian posterior probability for the recognition of a lineage as a distinct species using bGMYC or the software BPP. 

There is a molecular basis for the recognition of sub-species and species, but it depends on the data you have available and the group you are working on. So the precise answer, in evolutionary terms, would be: it depends on the coalescence of the loci you have available to test the hypothesis "are my lineages different species/sub-species?". The use of these methods are much more reliable and statistically sound than an artificial threshold based on the researcher experience.

I would strongly recommend the recent review by Carstens et al. 2013 (and references therein), that discusses the available methods and good practices to use species delimitation methods.

Best Regards, Fabricius

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Thank you every one for participation and kind guidance. It is really helpful. Regards.

The designation the subspecies as taxon must have a very good reason. The subspecies is almost species. Probably molecular biological methods can only be used as additional arguments in this task. Consult the experts in studied group of organisms. It is important that only your competence will allow You to make the right decision.

We addressed the question of molecular data in subspecies concepts in a recent publication attached.

 I agree completely with Dr. Goncharov! A so-called subspecies is mostly a species and therefor a useless taxon "level". It is mostly used by a taxonomist who is uncertain if he is dealing with a (new) species or not...

In zoological nomenclature, the names of subspecies do not have a special status. The International Code of Zoological Nomenclature is only dealing with taxa of the species group, which comprises species and subspecies according to Art. 45.1, which "are subject to the same provisions irrespective of rank within the species group" (Art. 45.2).

Subspecies have usually been used when the author was uncertain whether a taxon was distinct. In recent years, conservation issues became more important, and the usage of subspecies has complicated these a lot. For conservationists, it is often not clear whether a subspecies needs a special conservation status, or whether it is enough to provide a conservation concept for the species, disregarding the subspecies.

In fishes, we have raised most subspecies to the species level during the past decade. I would recommend to follow this example for other groups as well. A continued use of the subspecies level seems unadvisable. At least, there is no objective need for that level, and it causes more confusion than it is worth.

Having read the question and answers, I have two remarks:

1) The “convention that difference of 2% genome leads to distinction of two populations as a separate species” is based on a serious misunderstanding: species are fragments of evolutionary lineages, defined as reproductively isolated groups of populations, recognizable as such by non-overlapping range of variability of one or more characters; thus, decisive is the presence of a separating hiatus, but its “width” is perfectly irrelevant!

2) As to subspecies, it is morphologically recognizable, geographically delimited group of populations within a species, so it not only need not, but as a rule must not be separated with hiatus from others – if it is, we have almost certainly to do with distinct species! So a subspecies should be identifiable as a population (individual specimens often cannot be reliably determined), and again the degree of morphological difference is not decisive, and molecular sequences simply irrelevant.

More extensive discussion of these points may be found – among others – in my publications (attached):

2010. Taxonomy and the mediocrity of DNA barcoding: some remarks on Packer et al. 2009: DNA barcoding and the mediocrity of morphology. Arthr. Syst. Phyl. 68, 1: 143-150

and (the last chapter of)

2005. Philosophy of science from a taxonomist’s perspective. Genus 16, 4: 469-502

Article 2010. Taxonomy and the mediocrity of DNA barcoding: some rem...

Article 2005. Philosophy of science from a taxonomist’s perspective ...

As people have already said, before you worry about subspecies, you need to decide what your species concept is.  If you adopt a Biological Species Concept based on the capacity to interbreed, then likely you will see lots of intraspecific variability, and some of that may be reflected by DNA characters as well as morphology.  If you adopt a phylogenetic species concept (by which I mean the diagnosable differences one of Cracraft, Wheeler and Nixon, etc.), then probably any consistent variation you find will be diagnostic of species and not subspecies.  If you are asking whether there is some magic number, like the "barcode gap" that separates subspecies, then I do not think so.

Certainly not in the strict sense of a species in the biological sense