I am trying to establish a genetic monitoring program for an endangered fish species. The genetic diversity baseline was set 5 years ago. My study is a follow-up looking at impacts of a changing environment on the diversity of the species. I was wanting to run an AMOVA to look for any evidence of molecular variance explained by a temporal aspect.
There are several packages like ade4, pegas, poppr etc. Check out their tutorials.
However, I strongly recommend to first understand any statistical test, function and your dataset before just follow the tutorial and run the analysis. This will help in the interpretation of the results in a correct way.
Hi. there,
I can suggest you to calculate the genetic variability within each locality or environmental condition, and then perform CCA. (Canonical correspondence analysis), which gives you an idea that how genetic diversity changes towards environmental conditions. CCA can be done by PAST software.
his function simplifies the process necessary for performing AMOVA in R. It gives user the choice of utilizing either the ade4 or the pegas implementation of AMOVA. See ade4::amova() (ade4) and pegas::amova() (pegas) for details on the specific implementation.
I found this:
'Since developing AMOVA, Excoffier has written a program for running such analyses. This program, which runs on Windows, is called Arlequin and is freely available on Excoffier's website. There is also an implementation by Sandrine Pavoine in R language in the ade4 package available on CRAN (Comprehensive R Archive Network). Another implementation is in Info-Gen, which also runs on Windows. The student version is free and fully functional. Native language of the application is Spanish but an English version is also available.
hi
you can use several packages for amova in R .for example "ade4"
you can install this package and library that then use it.
for more information you can see this site:http://pbil.univ-lyon1.fr/ADE-4/ade4-html/amova.html
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