Dear Sean, 

thank you for your answer and papers.

The goal is to compare the microhabitat diversities at two different types of sampling sites and to analyse the relationsips between microhabitat diversity and species diversity (surface dwelling invertebrates). 

The main problem is that there are many sites with the same microhabitat richness but in different ratio (they cover different area at individual sampling sites). We we do not want to miss this information. Types of microhabitat at these (relatively little diversified monotonous) sites are characterised by different types of vegetation (+ bare soil).

I already read some papers, Simpson or the inverse of Simpson´s could be apllied, I think. Maybe we will try analyse it using different data sets (the total areas of vegetation types (e.g. Ricklefs & Lovette 1999); number of different habitats present within the (e. g. Hendrickx et al. 2007); the number of trap stations in the ´i-th´ habitat (e. g. Fox & Fox 2000).

Thank you again!

Diversity index, shanon index, jackard index are good

Dear Peter, 

As Sean said, it depends. You can choose the proper indices according to your data set, sampling method or sampling frequency etc. There are lots of indices, especially used for benthic macroinvertebrate studies. I attached a file about these indices (and a link just in case, it is same)

And also, you can use multivariate analysis like CCA (Canonical correspondence analysis). Maybe, this will be much helpful. 

If you have any further question, don't hesitate to contect me. 

Best regards, 

Gencer

Article Applications of various diversity indices to benthic macroin...

Hi Nina,

thank you very much. Sure, we will do also ordination. And maybe we will ask for help someone who is  more experienced in GLMM.

-best, Peter

I would also suggest some ordination technique that allows you to incorporate your species abundance and environmental similarities in the same analysis. One such approach is Non-metric Multi-dimensional scaling (NMS or NMDS). In this you can have one data matrix with your species abundance for each site and in a second matrix you will have your environmental (micro-habitat) variables. This way you can investigate which components of the environment contribute to the differences/similarities in the vegetation communities.

This, and many additional ordination options, is described quite well in McCune & Grace. 2002. Analysis of Ecological Communities. MjM Software. Oregon, USA.

Dear Richard, thank you for your suggestion!

The Gini-Simpson Index or the Shannon Entropy may work. Even better, use 2^entropy as the "effective number of microhabitat types. Hypothesis testing may be an issue, and I recommend bootstrap methods. Check these papers:

SimpsonE H (1949) Measurementofdiversity. Nature 163:688

14. Jost L, Baños T (2006) Entropy and diversity. Oikos 113:373–375

Thank you very much!

The are also alpha, beta and gamma diversities that you can try to apply. 

Tuomisto, H. (2010) A diversity of beta diversities: straightening up a concept gone awry. Part 2. Quantifying beta diversity and related phenomena. Ecography, 33, 23-45. doi:10.1111/j.1600-0587.2009.06148.x