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On the Phenology of Protists: Recurrent patterns reveal seasonal variation of protistan (Rhizaria: Cercozoa, Endomyxa) communities in tree canopies

Welcome to the On the Phenology of Protists repository!

This repository is a collection of several scripts and mini-tutorials guiding you through the methods of metabarcoding analyses which were performed in the paper by Walden et al., 2021. The data and methods are mainly based on the paper by Jauss & Walden et al., 2020 and the corresponding Github repository FromForestSoilToCanopy .

The raw data can be downloaded here, plots and figures were generated with the final OTU Table (not provided) and annotation files accessible in the folder 00_Data.

Table of Content

Relevant scripts and tutorials can be found in the corresponding markdown files, which are linked and highlighted for each category.

00 Data

This folder contains the final OTU table, taxonomic and functional annotation, sample metadata as well as supplementary material of this study.

01 Sequencing Results and Taxonomic and Funtional Annotation

The visualisation of the taxonomy then includes plotting the sequence similarity to reference sequences and a diagram showing the total taxonomic composition per microhabitat and sampling period and the total functional trait composition per microhabitat and sampling period

02 Seasonal variation and spatial structuring

In this section we were looking for differentially abundundant OTUs per sampling season per sampling season in order to find seasonal patterns within detected protistan OTUs. In addition we provide the script for a Variation Partitioning Analysis between the season, microhabitats and tree species.

03 Determination of Alpha Diversity

Here we deal with the methods of plotting rarefaction curves for earch sampling period and of course how to plot different alpha diversity indices in a combined boxplot.

04 Exploring Beta Diversity

One of the most straightforward methods of visualising beta diversity on the base of Bray-Curtis-Distances is an NMDS plot, the script is provided here. But we also perform and plot a Principle Coordinate Analysis to investigate differences between the foliar communites of different sampling periods, aswell as a Redundancy Analysis.

05 Shared OTUs between Sampling Periods

This section deals with the visualisation of shared OTUs of all investigated sampling periods.

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