Dear Uxia,

Do you have the sequence data of each genotype? If so you can use the sequence to deduce the TMRCA with mean mutation rate of the microsatellite. Otherwise, it is impossible to do to my knowledge. However, you can use ABC model to test the population demographic history, which will give you the TMRCA of the populations. But if you only have one population, it seems also impossible.

Best wishes,

Jie

Thanks for your quick answer, I am afraid I only have the data obtained from these 10 STR loci for cases and controls and I dont have any sequence data... could you recommend any other methods to infer TMRCA from microsatellite data different from the linkage desequilibrium based ones? Thanks a lot!

Dear Uxia

Perhaps you can try https://github.com/arjun-1/BEASTvntr with Beast2.

And I am sure there is a way to do it in Beast1.8 too, using methods from Wu and Drummond (2011) Genetics, but I have not used it.

A google search with "beast phylogeny ssrs" will give you several journal references that seem to apply these methods.

Hope it helps

Pablo

You can try use the genetic distance and mean mutation rate of microsatellite to estimate the divergence time of your control and case, but I do not think the results are reliability. If the TMRCA is really needed for you?

Jie

Hello Pablo, I already tried that without any productive result. Jie I already did that, the age of the MRCA is the thing I am looking for..I was just trying to get a different approach. Thanks a lot for your suggestions!

What did you try? BEASTvntr? According to the BEAST2 webpage there seems to be some issue  with it (look into a table comparing what BEAST1 and BEAST2 can do), but it is not clear enough.

I have been looking into BEAST1.8 and it seems there is a direct way to import the data; i.e., after opening BEAUTI, go to import file and there you can select microsat data. After that, you should fill the options in the upper part of BEAUTI to produce the xml file needed by BEAST to obtain your MRCA. Now, if you want to use this, you will have to guess which data format is needed (it says only tab-delimited txt files, but in Genpop format? or Structure format? or...

Pablo

Jus found the microsat format to import into BEAUTI. 

Once you download Beast1.8, go to examples/Data and there it is the fiel microsat_data.txt

Cheers

Pablo

Yes, I tried Beast1.8.4, I followed the example of microsatellite.txt, I tried many options with fixed molecular clock, fixed mutation rate, linking the tree, the drumond option, etc. I think my results arent accurate cause I also used other methods to calculate TMRCA and they are not even close; I made this question cause I dont know exactly which are the criteria we have to consider when analyzing this kind of data. Thanks Pablo!!

Hola Uxia Saraiva-Esperón , lograste correrlo en beast2 o que estrategia seguiste? Se que es viejo el post pero tengo la misma incógnita y tu consulta es de lo primero que ha aparecido, tengo experiencia con beast y paquetes adicionales pero no he aplicado aun msat + beast.Gracias