Yes, you can use any DI to reflects how many different types (such as species) there are in a dataset (a community), and simultaneously takes into account how evenly the basic entities (such as individuals) are distributed among those types. The Shannon-wiener index value increases with biodiversity. In contrast, the Simpson index measures the relative abundance of species, with a higher value indicating high dominance/low biodiversity. So use either, but explain the merits/disadvantages :) 

Hi,

Before starting the calculations of beta diversity, please have a look at the attached papers from Anderson et al. and Baselga et al. I also added the betapart package description to calculate beta diversity in R.

Best regards,

Koenraad

Thank you very much.

I would like to use beta diversity across all the sites. Can I use beta diversity for group level taxonomy of meiofauna such as nematoda, harpacticoida, polychaeta, oligochaeta, tanaidacea, etc.