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Taxonomic diversity can be measured using a variety of statistical models. Alpha diversity represents the species diversity (richness, evenness, compositional complexity) within experimental samples and treatment a group (e.g. an experiment group) and beta diversity (next section) examines diversity between groups.
'Diversity' is based on the amplicon sequence variants (ASV) detected by DADA2 per sample.
Alpha diversity was estimated In this section we can estimate alpha diversity using Shannon’s index, Simpson's index, Chao1 richness and observed ASVs. Statistical differences between treatment groups for each of the diversity indices was calculated using pairwise Kruskal-Wallis. Species richness is also plotted as rarefaction curves.Multiple diversity indices Different diversity indices were used because each have different strengths and weaknesses and are better contextually - i.e. depending on the structure and nature of your dataset. For example, Shannon’s index is more sensitive to sample size and influenced by rare ASVs. Simpson's index is less sensitive to sample size and or rare ASVs, but is influenced by dominance/abundance of ASVs. The multiple methods are included in this report so the researcher can decide which is most appropriate for their experimental design.
A good overview of most of these methods can be seen in this paper:
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