Same data set, different K
Agostina DEL CANTO
I’m conducting a genetic variability analysis on a fungal population. I’ve used ISSR on 100 individuals. First, I analyzed different values for the Burn-in Period and MCMC using K 1:10 (10 iterations). The final results suggested that my organisms grouped into three different subpopulations. I was able to reach these results with a Burn-in Period of 20,000 and 100,000 MCMC steps. I took a course, and the professors suggested that I enhance those values, as they considered them not very accurate. I repeated my analysis using the same dataset but applying a Burn-in Period of 100,000 and 1,000,000 MCMC steps, with K 1:10 (10 iterations). This time, the highest deltaK value (Evanno test performed in Pophelper) was 2 instead of 3. To be completely sure, I ran Structure again using the same dataset and parameters but choosing K 1:4. Results showed that the highest deltaK value corresponded to K=3.
To sum up, I would be very pleased to hear (or read) suggestions on how to proceed. Should I look at other parameters to choose the best results? Is there something else to do, or should I just repeat the analysis one more time?
P.S.: In the last analysis, deltaK values are very similar; deltaK for K=2 is 433.667, and for K=3 it is 494.391.
Thank you very much in advance. Any suggestions will be appreciated.
Agostina Del Canto
Microbiologist, PhD Student.
Basu Umer
As you have repeated analysis, difference deltaK values for
K=2 and K=3 is small, it could suggest that K=3 is actually most supported
option. The fact that the deltaK for K=3 is higher than for K=2 by a small
margin suggests that the 3 pop model is more good. Remember that deltaK is not
always a perfect indicator of the correct no. of pops/clusters. It is an empirical
approach and might not always align with biological or ecological actualities.
Consider whether the three subpopulations that you have have now make sense based on
other criterias like geo distribution, known genetic differences, or ecological differences.
Umer Basu
Northwest Agriculture and forestry University
Xi'an China
--
You received this message because you are subscribed to the Google Groups "structure-software" group.
To unsubscribe from this group and stop receiving emails from it, send an email to structure-softw...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/structure-software/7dd9bb1d-6c05-4acf-b717-c2012f645511n%40googlegroups.com.