Question

A student analyses 2 microbial communities associated with two Michigan lakes.  After looking at various diversity metrics he finds some contradicting results.

a) Shannon Index:  community A > community B;  Faith PD: community A same as community B. What can help explain these results?

b) Next he compares how similar these communities are to the ones present in Minnesota.

He uses Jaccard, Unweighted (uw) Unifrac and Bray-Cutis. What can help explain these results as different methods give different results shown?

Jaccard: Community A MI more similar to community X MN

uwUnifrac Community A MI more similar to community X MN

B-C:       Community B MI more similar to community X MN

Answer 1

Shannon index for calculating the index diversity and is an alpha richness parameter. This index also analyzes the number of times each taxon appears in the phylogenetic history. Shannon index works on the principle that species are more divergent and not more diverse during comparison. This index analyzes the quantitative diversity in the index for analyzing the similarity between different species. This measure was used for measuring the diversity of the different species in Michigan with the species present in Minnesota. In Faith Phylogenetic Distance History, there is calculation of the sum of the total branches that leads to the total branches analysis for the different species communities. In this experiment, the sum of distance of the community A and community B on the phlyogenetic branch was the same. Jaccard index measures the beta diversity. Beta diversity measures the extent of differences or variations between different communities. Unweighted UniFrac measures the divergence among the different communities. Unweighted Unifrac measures the distance between the two communities by calculating the distance in the branch that leads to one of the two community descendants in a phylogenetic tree. Bray-Curtis analysis is used for calculating the dissimilarity between the different sequences. The Bray-Curtis analysis is not able to analyze and satisfy the triangle inequality distance principle therefore the comparison of the two species through this value will be different from the Jaccard and the Unifrac community values. This analysis does not analyze the volume and area of an object but is based on only the size and shape of an object. Therefore Bray-curtis analysis is only a relative analysis and is not a true analysis. Thus the comparison is giving different comparison analysis of the Michigan and Minnessota species diversity interpretation data.