# Biodiversity¶

When analyzing metabarcoding data we are typically interested in the diversity within samples as well as the diversity between samples.

Question 17.

The following questions can be answered using the `Try our examples`

:`Mammalian gut`

data set.

## \(\alpha\)-diversity analysis¶

Lets proceed with the `Alpha diversity analyses`

.
Familiarize yourself with the different `diversity measures`

by hoovering over the `?`

.
Apply the alpha diversity analyses at the species level using those measures that were also introduced in the lecture.

Warning

MicrobiomeAnalyst does not have an option to test whether data is normally distributed. As you know from the course Data verzamelen en analyseren, using a parametric test, like an ANOVA, requires that your data (technically the residuals) are normally distributed. Non-parametric tests like the Kruskall-Wallis test can also be used if the data is not normally distributed. Make sure you apply an appropriate test for all analyses.

Question 18.

`statistical method`

to apply and why.Recall your hypotheses from question 3.

Question 20.

## \(\beta\)-diversity analysis¶

Lets proceed with the `Beta diversity analyses`

and perform the Principle Coordinate Analysis (PCoA).
Start with the Bray-Curtis index of the species abundances and the (non-parametric) PERMANOVA statistical test.

Recall your hypotheses from question 3.

Question 21.

Repeat the analyses but now using the Jaccard index.

Question 22.