I think its pretty impossible to conclude from genetic diversity, that it is indigenous. Particularly with anthropogenic influences, indigenous species can be diverse or not, depends on the case. The same is true for invasive species, where maybe a bottlenecked founder population shows low diversity, but by age & geneflow/ multiple introductions etc increases it. If the founding population was big enough the genetic diversity can also be high.

It's very interesting question. Plant DNA accumulates insertions/deletions, inversions, base changes and and other chages occured all time with different speeds. Sometimes molecular methods can be used to confirm origin of some species. Based on DNA plasticity and maybe epidenetic characteristics you can observe some differences which can be used as markers in your study. But I think it is quite impossible to make the conclusion based only on genetics about ingenuousness of a species. You need to combine different methods, thechniques and approaches to solve this problem.

Thank You Eckart and Andrii for answers.

Same thing I was thinking before that it is impossible to conclude indigenity of a species only with the help of genetics.

I am agree with your answers. Thank you.

Please tell me if any other method to prove the indigenity of plant species.

I evaluated with other partners the genetic diversity of cultivated chestnut tree (grafted) in the Iberian Peninsula using SSRs, with most of the trees over 300 years old, and structure revealed a geographical differentiation in correlation with climatic variations (cold and humid vs. warmer and drier environments), being able to discriminate introgressants from other areas, including new hybrids made on the 50's. Cultivars were originated from the local wild populations and those could be indigenous to me.

AUTORES (p.o. de firma): Pereira-Lorenzo, S.; Lourenço Costa, R.M.; Ramos-Cabrer, A.M.; Marques Ribeiro, C.A.; Serra da Silva, M.; Manzano, G.; Barreneche, T.

TÍTULO: Variation in grafted European chestnut and hybrids by microsatellites reveals two main origins in the Iberian Peninsula

REF. REVISTA/LIBRO: Tree, Genetics & Genomes (2010) 6:701–715 DOI 10.1007/s11295-010-0285-y

AUTORES (p.o. de firma): SANTIAGO PEREIRA-LORENZO, RITA MARIA LOURENÇO COSTA, ANA MARÍA RAMOS-CABRER, MARTA CIORDIA-ARA, CARLA ALEXANDRA MARQUES RIBEIRO, OLGA BORGES, TERESA BARRENECHE

TÍTULO: Chestnut cultivar diversification process in the Iberian Peninsula, Canary Islands and Azores

REF. REVISTA/LIBRO: Genome (2011), 54: 301-315. Doi:10.1139/g10-122

I do not know if I understand your question, but yes, it is possible. However, for such inferences, you need a high number of individuals. Still, I think dangerous infer or not infer the ancestry of species from a study of molecular markers only.

Read more in my profile. I publisher two papers maybe that need you.

It is generally possible to compare the probability of alternative biogeographic hypotheses or scenarios using molecular data. However, these scenarios must differ in the genetic signal they are expected to leave in your population and your data set (sampling design and choice of markers) must be powerful enough to pick up that signal. For example if you are defining "indigenous" simply as originating from natural colonisation (in contrast to human mediated introduction) there is no principle difference in terms of population genetic signal and consequently you can't test their relative likelihood. You therefore need additional information to distinguish the two scenarios. For example if humans might have colonised a certain area 1000 years ago. Therefore, if a molecular dating analysis reveals that your population has split from adjacent geographic areas 5000 ybp you have evidence to support the indigenous scenario. However this also requires comprehensive phylogeographic information. There are also more rigorous approaches which test the likelihood of a number of population trees such as implemented in the software DIY-ABC. A good example is Pedreschi et al. (2013) Journal of Biogeography

Thank You sir... Thank you all..

I will check the publications suggested.

Is it possible to infer the species being indigenous based on Likelihood/ phylogenetic trees based on chloroplast gene sequences? Chloroplast genome is 'pass-on' to the offspring from mother cell, even though there is recombination. The clusters may show correlation with the geographical distribution or at least idea about distribution at continent level. Apparently, it will require huge data, molecular as well as from other disciplines also.

It is not possible to tell whether the species is indigenous from genetic diversity study of a plant genus.But the molecular diversity study of the species from the same genus like the ITS region sequences of the genomic DNA gives some good idea about the closeness of the species.The Evolutionary relationships of taxa using ITS region's sequences in MEGA5 software gives a very good idea about the phylogeny of the species under study. If the collection history of the studied species are known some idea on the indigenous species are possible. But confirmation is required after getting the idea. That could be possible to get from literature search.A good numbers of species study and following this path i think it is possible to be sure.

Diversity analysis per se is not a good idea to conclude about the origin. Phylogenetic relations however can give idea about the probable age on evolutionary tree based upon the likelihood of changes in genomic regions and the time required to take such events to happen. The records may be (paleobotanic) of same period also support the presence of species or its relatives in that particular area.

I have some doubt that phylogenetic relations can give the idea of age on evolution.

Naresh, I agree with you, that we can 'estimate' the range of time period of species origin. But, from that, we cannot conclude the 'area' where it must have originated. Thank you all for answers. I think the conclusion is, we cannot use genetic diversity as a tool to determine the species being indigenous. What other tools we may use for that?