Analysis of Molecular Variance (AMOVA) with vegan and BiodiversityR, including a graphical method to identify potential migrants

Over a decade ago, while working on a manual for statistical analysis of dominant markers (this manual was partially inspired by a previous manual on the statistical analysis of biodiversity and community ecology data), I had explored the similarities between (i) Analysis of Molecular Variance (AMOVA) that was originally developed by Excoffier et al. 1992 ( See here for a recent expansion of the framework to autopolyploids ) and (ii) Ordination methods and Multivariate Analysis of Variance Using Distance Matrices in the field of community ecology (I provide references for these in subsequent sections). Whereas the manual is now more than a decade old (although many methods are still relevant; those interested could compare with this recent Review of Best Practices Population Genetic Analysis), in my opinion it remains valid to still highlight the connections between AMOVA and several methods of community ecology that are directly available via the vegan and BiodiversityR packages.

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