DOI: 10.5061/dryad.pc866t1zv
title: Data from: A test for microbiome-mediated rescue via host phenotypic plasticity in Daphnia

description: 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, the effects
 of Microcystis exposure on the Daphnia
 microbiome were limited, with the primary effect being differences in
 abundance observed across five bacterial families. Moreover, there was no
 significant correlation between the magnitude of microbiome shifts and
 host phenotypic plasticity. Our results suggest that microbiome
 composition played a negligible role in driving host phenotypic plasticity
 or microbiome-mediated rescue.
description: # 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.txt **Description:** FASTQ associated metadata in .txt format. Used in Daphnia_Microbiome_R_Code_Submission.R to combine QIIME2 output data with the appropriate groupings within metadata.  #### File: DaphniaMetaData.xlsx **Description:** FASTQ associated metadata in .xlsx format. Used in Daphnia_Microbiome_R_Code_Submission.R to combine QIIME2 output data with the appropriate groupings within metadata.  #### File: DaphniaMicrobiomemastersheet\_240401.csv **Description:** Daphnia phenotypic data master sheet. Used in DaphniaMicrobiomeAnalysis_240401_Non_GenomicWork.R to see the effects of treatment on various phenotypic outputs.  ##### Variables * clone: 20 Genotypes * Replicate: 3 Replicates of each unique genotype * Treatment: G (green algae | non-toxic) and C (cyanobacteria | toxic) dietary treatments * survival_day0: Phenotypic Output * survival_day7: Phenotypic Output * survival_day14: Phenotypic Output * survival_day21: Phenotypic Output * neonates_day0: Phenotypic Output * neonates_day7: Phenotypic Output * neonates_day14: Phenotypic Output * neonates_day21: Phenotypic Output * neonates_total: Phenotypic Output * neonates_divided_allmoms: Phenotypic Output * Fbroods: Phenotypic Output * Tbroods: Phenotypic Output #### File: DaphniaRVals.xlsx **Description:** *Daphnia* r values. Calculations of Daphnia reproductive output given genotype, and treatment diet. Used in Daphnia_Microbiome_R_Code_Submission.R. #### File: WU\_HarerScript-Daphnia.csv **Description:** Weighted Unifrac Harer data input. Used in Daphnia_Microbiome_R_Code_Submission.R to calculate the magnitude and angle of microbial change within Euclidian space.  ##### Variables * id: Arbitrary numbers * Clone: 20 Unique Genotypes * Treatment: G (green algae | non-toxic) and C (cyanobacteria | toxic) dietary treatments * Group: Paired grouping of the same clone by different treatments, e.g 1G-1C, 2G-2C * PC1: Principal Component Eigenvector * PC2: Principal Component Eigenvector * PC3: Principal Component Eigenvector * PC4: Principal Component Eigenvector * PC5: Principal Component Eigenvector * PC6: Principal Component Eigenvector * PC7: Principal Component Eigenvector * PC8: Principal Component Eigenvector * PC9: Principal Component Eigenvector * PC10: Principal Component Eigenvector * PC11: Principal Component Eigenvector * PC12: Principal Component Eigenvector * PC13: Principal Component Eigenvector * PC14: Principal Component Eigenvector * PC15: Principal Component Eigenvector * PC16: Principal Component Eigenvector * PC17:  Principal Component Eigenvector * PC18:  Principal Component Eigenvector * PC19:  Principal Component Eigenvector * PC20: Principal Component Eigenvector * PC21: Principal Component Eigenvector #### File: GP\_HarerScript-Daphnia.csv **Description:** Bray-Curtis Harer data input. Used in Daphnia_Microbiome_R_Code_Submission.R to calculate the magnitude and angle of microbial change within Euclidian space.  ##### Variables * Id: Arbitrary numbers * Clone: 20 Unique Genotypes * Treatment: G (green algae | non-toxic) and C (cyanobacteria | toxic) dietary treatments * Group: Paired grouping of the same clone by different treatments, e.g 1G-1C, 2G-2C * PC1: Principal Component Eigenvector * PC2: Principal Component Eigenvector * PC3: Principal Component Eigenvector * PC4: Principal Component Eigenvector * PC5: Principal Component Eigenvector * PC6: Principal Component Eigenvector * PC7: Principal Component Eigenvector * PC8: Principal Component Eigenvector * PC9: Principal Component Eigenvector * PC10: Principal Component Eigenvector * PC11: Principal Component Eigenvector * PC12: Principal Component Eigenvector * PC13: Principal Component Eigenvector * PC14: Principal Component Eigenvector * PC15: Principal Component Eigenvector * PC16: Principal Component Eigenvector * PC17: Principal Component Eigenvector * PC18: Principal Component Eigenvector * PC19: Principal Component Eigenvector * PC20: Principal Component Eigenvector * PC21: Principal Component Eigenvector * PC22: Principal Component Eigenvector * PC23: Principal Component Eigenvector * PC24: Principal Component Eigenvector * PC25: Principal Component Eigenvector * PC26: Principal Component Eigenvector * PC27: Principal Component Eigenvector * PC28: Principal Component Eigenvector * PC29: Principal Component Eigenvector * PC30: Principal Component Eigenvector * PC31: Principal Component Eigenvector * PC32: Principal Component Eigenvector * PC33: Principal Component Eigenvector * PC34: Principal Component Eigenvector * PC35: Principal Component Eigenvector #### File: DeltaRVals.xlsx **Description:** Delta r values. Calculated from DaphniaRVals.xlsx - used in Daphnia_Microbiome_R_Code_Submission.R to assess the difference in change between clone x treatment interaction on phenotype.  #### File: DaphniaMicrobiomeExponentialRateOfPopChange\_240616.csv **Description:** Exponential Rate of Population Change data. ##### Variables * clone: 20 Unique Genotypes * Treatment: G (green algae | non-toxic) and C (cyanobacteria | toxic) dietary treatments * r: Reproductive Output * Delta: Change in the reproductive output