Data from: A test for microbiome-mediated rescue via host phenotypic plasticity in Daphnia
Data files
Mar 14, 2025 version files 760.38 MB
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DaphniaMetaData.xlsx
12.28 KB
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DaphniaMetaData123.txt
3.01 KB
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DaphniaMicrobiomeExponentialRateOfPopChange_240616.csv
1.14 KB
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DaphniaMicrobiomemastersheet_240401.csv
7.39 KB
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DaphniaRVals.xlsx
6.70 KB
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DeltaRVals.xlsx
8.91 KB
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FASTQ_Files.zip
760.17 MB
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GP_HarerScript-Daphnia.csv
18.04 KB
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phyloseq-data.zip
135.69 KB
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README.md
6.26 KB
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WU_HarerScript-Daphnia.csv
11.14 KB
Abstract
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.
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
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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
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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
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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
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Treatment: G (green algae non-toxic) and C (cyanobacteria toxic) dietary treatments - r: Reproductive Output
- Delta: Change in the reproductive output