Sampling strategy matters: eDNA-based assessment and extrapolation of myxozoan diversity in a model stream system

Determining true species diversity is particularly challenging for parasitic organisms. Environmental DNA (eDNA) metabarcoding has revolutionized diversity studies by increasing both efficiency and precision. This approach is especially relevant for parasitic species, like myxozoans that spend part of their life cycle outside their hosts, often during hostswitching stages. However, the adequacy of sampling depth and methodology in capturing total diversity often remains uncertain. To address this, we used a small stream as a model system and collected 60 small-volume aquatic sediment samples. Using an eDNA metabarcoding approach with myxozoan-specific primers, including newly designed primers for Malacosporea and the Paramyxidium group, we identified 30 myxozoan OTUs. These were predominantly from the Myxobolus clade but represented a broad spectrum of freshwater myxozoans, including Malacosporea. Rarefaction and extrapolation analyses estimated the potential maximum myxozoan diversity ..., , , # Data from: Sampling strategy matters: eDNA-based assessment and extrapolation of myxozoan diversity in a model stream system

Dataset DOI: [10.5061/dryad.ffbg79d4z](10.5061/dryad.ffbg79d4z)

## Description of the data and file structure

In this repository, we provide the data and necessary information for our paper titled “Sampling strategy matters: eDNA-based assessment and extrapolation of myxozoan diversity in a model stream system”. We include resulting myxozoan OTUs, OTU table and R-code we used to produce all analyses in this paper.

### Files and variables

#### File: R-code_Lisnerova_et_al_OIKOS_2.zip

**Description:**  This R script reproduces the statistical analyses and figures presented in the manuscript:

Lisnerová, M. et al. (2025) published in Oikos.

##### Files

- `R-code_Lisnerova_et_al_OIKOS.R` – main script with all analyses and figure generation and details

- `community_presence.csv: `The table shows the presence/absence matrix of species across samples. Each r...,