https://doi.org/10.5061/dryad.k6djh9wfc

Description of the data and file structure

This repository is associated with Cristini, D., Kelly, J. B., Mahler, P., Schleheck, D., Lerner, H., & Becks, L. (2025). Seasonal genotypic and phenotypic differentiation of a cosmopolitan freshwater diatom.

The data are collected in five different folders: Lake_data.zip, Genotypic_data.zip, Trait_data.zip, IXM_protocols.zip and 18S_rDNA_data.zip.

Lake_data.zip:

The folder contains the data collected in the field (Lake Constance) and reported in Figure 1 of the manuscript.

• "Temperature.csv": the file contains the temperature values collected in Lake Constance during the sampling season and used to represent the temperature profiles reported in Figure 1a;
• "Phyto_biov+DeltaT.csv": the file contains the temperature and phytoplankton data used to estimate the relationship between thermal stratification (delta_T) and phytoplankton development, as presented in Figure 1b;
• "Rel_biov_phyto.csv": the file contains information on the species, taxonomic group, biovolume, relative biovolume and biovolume percentage relative to the phytoplankton. The data are represented in Figure 1c;
• "Nutrients.csv": the file contains the nutrient (PO4-P, NO3 and SiO2-Si) concentrations measured during the sampling season and reported in Figure 1d.

Genotypic_data.zip:

The folder contains the files providing genotypic information for 33 Asterionella formosa isolates. Specifically:

• "Af90_varsites_all.fasta": fasta file with the aligned variant sites comprising Fst outliers. The data were used to construct the phylogenomic tree of the Asterionella formosa isolates;
• "Af90_varsites_noout.fasta": fasta file with the aligned variant sites without Fst outliers. The file was used to estimate pairwise FST values, Jost's D and Hedrick's G′ST to obtain information on population differentiation and gene flow between clades. This fasta file was also used to identify hybridization and the genetic population structure of the A. formosa isolates;
• "Aformosa_final_annotations.gff3": The A. formosa genome annotation file was used for functional annotation. A detailed description of how we obtained the annotation is reported in the Methods section of the paper.

Phenotypic_data.zip:

The folder contains the data obtained from the phenotypic assays conducted with the A. formosa genotypes in the laboratory. The folder contains R codes as well.

• "Fitness_mean_rep.csv" contains the experimental data generated in the laboratory to estimate the fitness of our different isolates in different environments. "Fitness_code.txt" is the R code we used to obtain the fitness values;
• "GR_mean_rep.csv": The file contains the growth data generated in the laboratory and used to calculate the maximum growth rates and carrying capacity for each of our seven genotypes tested. The "GR_code.txt" is the relative R code;
• "PO4_mean_rep.csv" and "Si_mean_rep.csv": The files contain the growth data obtained from laboratory experiments in which phosphorus and silica concentrations were manipulated to estimate nutrient half-saturation constants for each of the seven Asterionella genotypes tested. "P-K_code.txt" and "SI-K_code.txt" are the R codes used to estimate the nutrient half-saturation constants;
• "Sinkrate_experiment.xlsx" contains the sinking rate of A. formosa obtained in the laboratory;
• "Temp_mean.csv" contains the growth data generated in the laboratory to calculate the temperature optima of the isolates. "Temp_code.txt" is the relative R code used to calculate the thermal optimum;
• "Data_PCA.csv" contains all the phenotypic data of the isolates used to conduct the PCA analysis reported in Figure 5. The R code for the PCA analysis is contained in "PCA_code.txt".

IXM_protocols.zip:

To determine Asterionella formosa cell density in the laboratory assays, we used a high-content microscope (ImageXpress® Micro 4 High-Content Imaging System, IXM), which allowed us to acquire images of the algae using a Cy5 filter set (algal autofluorescence, 642 nm) under a 5× magnification. Image acquisition was performed using the protocol provided "Acquisition_protocol_Aformosa_counting.HTS".

The images were subsequently analyzed using the software “MetaXpress® High Content Image Acquisition and Analysis” to obtain cell counts. Image analysis was conducted using the protocol contained in the file "Custume module_counting.HTS".

18S_rDNA_data.zip:

The folder contains the 18S rDNA gene amplicon sequences generated from total DNA of phytoplankton (5–180 μm size class; n = 3) collected in Lake Constance during the sampling season. These data were used to assess the relative abundance of Chytridiomycota and are presented in Figure 2.