No idea what genes should be taken in plants but yes multiple genes can provide better results….and then you can derive the phylogeographic idea about the concerned species using sdiva etc. Hope this helps

Sir, I couldn't get that answer. I have gone through some papers where researcher took genes as well as non-coding regions/IGS. As I do not know ABC of this, could you kindly elaborate. Thanking you Sir.

Hi biswajit I am suggesting you that take multiple genes and construct phylogeny. let me know if i can be of any help….mail me at [email protected] if you have any doubts...

Hi Biswajit,

Here are some paper that can help you to plan your study:

1- Buckley, D., 2009. Toward an organismal, integrative, and iterative phylogeography. BioEssays 31, 784-793.

2- Carstens, B.C., Brennan, R.S., Chua, V., Duffie, C.V., Harvey, M.G., Koch, R.A., McMahan, C.D., Nelson, B.J., Newman, C.E., Satler, J.D., Seeholzer, G., Posbic, K., Tank, D.C., Sullivan, J., 2013. Model selection as a tool for phylogeographic inference: an example from the willow Salix melanopsis. Mol. Ecol. 22, 4014-4028.

3- Hickerson, M.J., Carstens, B.C., Cavender-Bares, J., Crandall, K.A., Graham, C.H., Johnson, J.B., Rissler, L.J., Victoriano, P.F., Yoder, A.D., 2010. Phylogeography’s past, present, and future: 10 years after Avise, 2000. Mol. Phylogenet. Evol. 54, 291-301.

4- Knowles, L.L., 2009. Statistical phylogeography. Ann. Rev. Ecol. Evol. Syst. 40, 593-612.

Hi Biswajit

Maybe you can do a scan with all the individuals from one population, in order to find "intrapopulation" diversity and therefore, decide how many individuals are necesarry in each population/marker.

Hi Biswajit,

That`s depends on the geographical coverage of your samples and the main question of your study. How many species are you intending to use? If your main question is about speciation of these related-species, you may use small samples and just few points distant from each other to have a general idea. Then you can use molecular clock approaches to define time of these speciations, such as it is implemented in Beast software.

If you want to study just this species, it is a totally different approach. You may need more points of collection and more individuals per point to make population genetics and history of these populations. A good start-point is to analyze 10-20 individuals/site.

It is not a good idea to make a phylogenetic analysis using ITS-2, as this marker is probably under a concerted evolution (i.e. is not a neutral marker), and usually it is present in multiple copies in the genome.

As Niladri said, multiple genes can provide better results, but unfortunately I don`t know which markers are frequently used in plants. Maybe you can make a literature revision and look at the markers that are commonly used to answer scientific questions related to yours.

If you need anything else, mail me [email protected]

As no one has mentioned it: using haploid markers like mitochondrial or chloroplast DNA are good... At least as a starting point...

Hi Biswajits,

I suggest you,

1. analyse cpDNA for your samples which will give the initial genetic diversity and geographic distribution on the basis of organelle DNA, you can define main

groups and subgroups

2. on the basis of cpDNA results, use multiple nuclear genes (must give phylogenetic signal) you will test gene flow among groups. According to results, you can increase your sample size.

3. join your analysis from both markers to test phylogoegrapgy and speciation.

Hope this help,

Çiğdem

Hi biswajit, I have no idea what type of genes normally use in plant for the reason of phylogenetics. I work on mushrooms and the ideal region will be ITS, and even it is non-coding nominated as efficient DNA barcode. I recently published a paper that shows establishment of a phylogenetic study using multiple regions (either coding gene or non-coding) can increase the chance of success (u can find my publication in my profile).

Another thing is about sample size, I wanna say if you are trying to barcode a species, one sample also sufficient, but if you wanna establish a complete phylogenetic study, at least 5 samples per location required. However, the proper results obtain when we have samples as more as possible. Some people believe that 20 samples each region can be sufficient.

if you need any manual of phylogenetic analysis, I have written one and i can send to you,

I hope this helps you,

best wishes

Farhat

Respected Sir/Mam, Thank you all for your support. I need your support more.

Farhat, I badly need your manual. I am learning step by step of phylogenetics, but, phylogeography....Hmm, its really tough, BEAST software n all.

Respected Márcio Pavan, Boris Fumanal and Ciğdem Akın Mam, thank you for helping me and I have read all your publication.

Respected David Buckley Sir, Thank you for sharing the valuable publications and I am making my concept from there.

I want to work with psbA-trnH intragenic spacer, trnL-F spacer as they are not so big and variable. Because sequencing charges is a problem in case of phylogeographical study due to sample size/population. I am working on closely related alpine species as there are some nomenclatural problem and those species are highly medicinal and as we know active compound vary from species to species. In my phylogenetic study, I got a lot of morphological variation spanning in western-eastern Himalayas and I am expecting some new species too. I have taken ITS1,ITS2, rbcl a, matK,trnL gene andabove two IGS.

Now, what really to do start with my phylogeographycal study. I want to do molecular clock analysis and want to know the glacial refugia/movements of those alpine plants.