Genotype specific and microbiome effects of hypoxia in the model organism Daphnia magna

Genotype specific and microbiome effects of hypoxia in the model organism Daphnia magna: data and script https://doi.org/10.1111/jeb.14233 Description of the data and file structure The data contains multiple files: an R script ("script_microbiome_JEB_forpublication.Rmd"): all analyses and the creation of the figures can be found here one csv file containing the body size data ("BAP_2022_BodySize.csv")***information for the body size data columns*Clone: the genotype of the recipient clone (categorical variable with two levels: F and KNO)*MaternalLine: each recipient clone was split into three maternal lines (categorical variable: 1, 2, and 3)*Donor: the genotype of the donor clone (F or KNO) as well as the treatment (exposed to hypoxia or not; H or N) (categorical variable with four levels: FH, FN, KNOH, KNON)*DonorClone: the genotype of the donor clone (categorical variable with two levels: F, KNO)*DonorTreatment: the treatment that the donor clone went through (hypoxic or normoxic: H or N)*Individual: the replicate within the experimental treatments (categorical variable with 5 levels: 1, 2, 3, 4, and 5)Day: the day when the body size was measured (categorical variable with three levels: day 3, day 7, and day 10)BodySize: the body size (in micrometer) of the measured Daphnia (numerical variable)* one csv file containing the survival data ("BAP_2022_Survival.csv)***information for the survival data columns*NR: the order of measurements*Clone: the genotype of the recipient clone (categorical variable with two levels: F and KNO)*Maternal.line: each recipient clone was split into three maternal lines (categorical variable: 1, 2, and 3)*Donor: the genotype of the donor clone (F or KNO) as well as the treatment (exposed to hypoxia or not; H or N) (categorical variable with four levels: FH, FN, KNOH, KNON)*DonorClone: the genotype of the donor clone (categorical variable with two levels: F, KNO)*DonorBlootstelling: the treatment that the donor clone went through (hypoxic or normoxic: H or N)*Replica: the replicate within the experimental treatments (categorical variable with 4 levels: 1, 2, 3, and 4)*Individual: the specific individual within a replica*Status: whether the data was censored or not (categorical variable; 0 or 1)*Time: the number of days the Daphnia survivedCloneMaternalLine: a combination of the genotype of the clone and its maternal lineRep: a combination of the genotype of the clone, its maternal line, and the replica* two phyloseq objects to use in R ("ps_Daphnia.Rdata" and "ps_Daphnia_control.Rdata") The sequences from the microbiome data are stored in NCBI, under BioProject ID accession number PRJNA934852. All analyses were performed in R (v. 4.2.2) with phyloseq v. 1.42.0, vegan v. 2.6-4, pairwiseAdonis v. 0.4.1, picante v. 1.8.2, survminer v. 0.4.9, survival v. 3.5-0, emmeans v. 1.8.4-1, glmmTMB v. 1.1.5, fitdistrplus v. 1.1-8, bestNormalize v. 1.8.3, VennDiagram v. 1.7.3, ggplot2 v. 3.4.0, ggpubr v. 0.5.0, dplyr v. 1.0.10, and stringr v. 1.5.0.