A test for microbiome-mediated rescue via host phenotypic plasticity in Daphnia

Phenotypic plasticity is a primary mechanism by which organismal phenotypes shift in response to the environment. Host-associated microbiomes often exhibit considerable shifts in response to environmental variation and these shifts could facilitate host phenotypic plasticity, adaptation, or rescue populations from extinction. However, it is unclear how much shifts in microbiome composition contribute to host phenotypic plasticity, limiting our knowledge of the underlying mechanisms of plasticity and, ultimately, the fate of populations inhabiting changing environments. In this study, we examined phenotypic responses and microbiome composition in 20 genetically distinct Daphnia magna clones exposed to non-toxic and toxic diets containing Microcystis, a cosmopolitan cyanobacteria and common stressor for Daphnia. Daphnia exhibited significant plasticity in survival, reproduction, and population growth rates in response to Microcystis exposure. However, th..., , , # A test for microbiome-mediated rescue via host phenotypic plasticity in Daphnia

[https://doi.org/10.5061/dryad.pc866t1zv](https://doi.org/10.5061/dryad.pc866t1zv)

The dataset includes the R code and .csv files necessary to reproduce the statistical analyses and figures in the manuscript \"A test of microbiome-mediated rescue via host phenotypic plasticity in Daphnia\".

**Description of the data and file structure**

To process raw FASTQ files (81), read in the commands seen in QIIME2-Commands.txt. To process all the outputs, R-code is provided in \"Daphnia_Microbiome_R_Code_Submission.R\" and \"DaphniaMicrobiomeAnalysis_240401_Non_GenomicWork.R\". Processed QIIME2 input-data is called \"feature-table.txt\", \"taxonomy.tsv\", and \"tree.nwk\" and located inside phyloseq-data.zip, while the rest of the input data such as metadata, custom PCA data for Härer script, and r values are labeled in their respective .csv, .xlsx, and .txt files. 

### Files and variables

#### File: DaphniaMetaData123.tx...,