I have two data sets, one chloroplast SSR and one nuclear SSR, both with 20 populations and I would like to run a Barrier analysis (Barrier 2.2) separately once on nuclear and once on chloroplast. as I know I need a Fst or Gst matrix and a bootstrap matrix and GPS coordinates of the pops. Unfortunately, I don't know R software, so I need a something which can create these matrices from my data set. Any suggestions?
Dear Endre
I have used Barrier analysis in one of my study. You can obtain Fst matrix from Arlequin. If you want to obtain bootstrap value for each of the candidate barriers, you should calculate lots of Fst value from your data set. If you want to do this you have to calculate Fst values under the different model assumption.
Good luck
SArp
Dear Sarp Kaya,
I have calculated Fst matrix with Arlequin as you mentioned, Thank you for the help! Now, I only suffer to prepare the bootstraps. I have no clue how to do it and I would be glad if someone can help me!:)
I have also tried Nei's genetic distance and actually that showed explainable results, while Fst showed very complex barriers. Probably, because of the calculation method...
Bootstrap analysis in Arlequin will give you probabilites for each Fst-value in your matrix. However, BARRIER will not take into account those probabilities. So, if your aim is only to run BARRIER, you do not need to bootstrap Fst values.
Dear Ferruccio Maltagliati and Sharp Kaya,
Thanks you for the help, advices and suggestions!:) I finally solved the problem, this is my recipe:
I have looked for an old computer, which were able to run MICROSAT software. Unfortunately it does not prefers Win 7 and 8, 8.1, but it runs well on Win XP. It is able to calculate several (8 or 10, can't recall) distance matrices and bootstraps also. Here are some possibilities, which one I tried: Reynold's Fst, Delta mu squared (Ddm), Nei's standard Gst, Slatkins Rst...I have looked for such a software for ages...
So I calculated 100 bootstrap with a four mentioned genetic distances. Last, only the change the file format and some editing in Excel needed....and done!:) From the 100 bootstraps its clearly visible which barrier is the strongest supported, so which is significant:)
Dear Endre,
Do you still have the MICROSAT software? I am having the same problem generating Fst or Rst bootstrap matrices with cpSSR data... It would be very helpful to have MICROSAT!
Thank you very much!
email: [email protected]
Dear Alfredo López Caamal ,
I attache here the MICROSAT software version 1 and 2. But, I would recommend to generate the distance matrices with a different software called Microsatellite Analyzer (MSA). This software is simple and runs under newer operation systems such as Win 8.1 and 10. I used this to calculate DA the Nei's chord distance, which used in several studies for Barrier analysis. This also capable to generate over 100 bootstrap matrices. If you check my publication Tóth et al. 2017 in Tree Genetics and Genomes I used this software in it. It is available for several platforms, including Mac, Win...etc.:
http://i122server.vu-wien.ac.at/MSA/MSA_download.html
I hope you find it useful!
Best wishes;
Endre
Endre,
I downloaded MSA... It's so easy to use! I generated the bootstrapped matrices quite fast. I've already used them in Barriers software. Thank you very much. This was so useful!
Alfredo
Excuse me, can someone tell me a new link where I can find MSA to download? What I knew doesn't work anymore. Thank you very much Olga
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