Data from: Phenotypic variation across the first steps of experimentally evolved multicellularity.

This BBC_2026__README.txt file was generated on 2026-01-31 by Beatriz Baselga Cervera GENERAL INFORMATION 1. Title of Dataset and code: Data from: Phenotypic variation across the first steps of experimentally evolved multicellularity. 2. Author Information Corresponding Investigator Name: Dr Beatriz Baselga-Cervera Institution: University of Minnesota Twin cities, Minnesota, US. Email: bbaselga@umn.edu; beabaselga@gmail.com Co-investigator 1 Name: Dr Noah Gettle Institution: Wellcome Sanger Institute, Hinxton, UK Email: noah.gettle@sanger.ac.uk Co-investigator 2 Name: Dr Michael Travisano Institution: University of Minnesota Twin cities, Minnesota, US. Email:travisan@umn.edu 4.Data collector: Dr Beatriz Baselga-Cervera 5. Date of data collection: 2021-2022 6. Geographic location of data collection: Saint Paul, US 5. Funding sources that supported the collection of the data: Fundación Alfonso Martín Escudero, Madrid, Spain. 6. Recommended citation for this dataset: Baselga-Cervera et al. (2026), Data from: Phenotypic variation across the first steps of experimentally evolved multicellularity. Zenodo. Data set. DATA & FILE OVERVIEW 1. Description of dataset In this study, we study the genotype to phenotype map that provides the basis for the diverse morphologies and unique adaptations observed in nascent multicellularity carried over from their unicellular ancestors under high and low nutrient availability conditions. We carried out a NetLogo agent-based model simulation of the multicellular snowflake yeast growth. Populations characterization was conducted with a Coulter Counter multisize 4 and FlowCam 3. The populations studied were the genetically uniform diploid wild-type Saccharomyces cerevisiae Y55 strain clones, C1W8.1 and C1W8.2 multicellular evolved strains, constructed ACE2 gene knockouts, and strains containing the missense mutation (ACE2 c.1934 A>T). The population data represent the six independent isolates per strain in two different media, YPD and SD. 2. File list: NetLogo Agent Base model: File 1 name: Snowflake 3d.nlogo3d File 1 Description: Netlogo code for the 3D model. File name: Netlogo_model_Rawdata.xlsx File 2 Description: Data obtained from the Netlogo model. Coulter Counter size distribution data of all the populations: File 3 name: Counter_Counter_Raw_data.xls File 3 description: Data from Saccharomyces cerevisiae Y55 strain clones, C1W8.1 and C1W8.2 multicellular evolved strains, constructed ACE2 gene knockouts, and strains containing the missense mutation (ACE2 c.1934 A>T) in YPD and SD at 24h growth. File 4 name: Coulter_Counter_Raw_data_heterozygous_contructions File 4 description: Size distributions of the heterozygous construct knockout (ACE2/ace2Δ) and homozygous missense (ACE2/ace2Δ) in YPD and SD at 24h growth. FlowCam image data: File 5 name: FlowCamPicturesData.zip File 5 description: Pictures generated by the FlowCam. File 6 name: Flow_Cam_Raw data.xls File 6 desciption: FlowCam data from Saccharomyces cerevisiae Y55 strain clones, C1W8.1 and C1W8.2 multicellular evolved strains, constructed ACE2 gene knockouts, and strains containing the missense mutation (ACE2 c.1934 A>T) in YPD and SD at 24h growth. Data generated statistically: File 7 name: bootstrapped_means.csv File 7 description: bootstrapped means from the Coulter Counter data to calculate the relative contributions to phenotypic variation. File 8 name: bootstrapped_vars.csv File 8 description: bootstrapped variance from the Coulter Counter data to calculate the phenotypic noise. File 9 name: overlapPairs_values.xlsx File 9 description: overlapping indexes (η) of the KDE distributions were computed using the R-package ‘overlapping’ from the Coulter Counter data. R codes for data generated statistically: File 10 name: R_code_bootstrapping.docx File 10 description: R code to obtain bootstrapped means and variance from the Counter_Counter_Raw_data.xls data to calculate the relative contributions to phenotypic variation. File 11 name: R_code_Overlap_KDE_distributions_from _the_Coulter_Counter_data File 11 description: R code to obtain overlapping indexes (η) of the Kernel density estimations (KDE) distributions from Counter_Counter_Raw_data.xls R codes for figures: File 12 name: R_code_Fig2.docx File 12 description: R code for Figure 2 panels B and C. Panels are created from Netlogo_model_Rawdata.xlsx. File 13 name: R_code_Fig3.docx File 13 description: R code for Figure 3 panels A to E. Panels are created from Counter_Counter_Raw_data.xls File 14 name: R_code_Fig4.docx File 14 description: R code for Figure 4, data from Counter_Counter_Raw_data.xls File 15 name: R_code_FigS1.docx File 15 description: R code for Figure S1. Raw data from Coulter_Counter_Raw_data_heterozygous_contructions.xlsx File 16 name: R_code_FigS2.docx File 16 description: R code for Figure S2. Raw data from Counter_Counter_Raw_data.xls File 17 name: R_code_FigS3.docx File 17 description: R code for Figure S3. Raw data from Counter_Counter_Raw_data.xls File 18 name: Figure 5 Graphs File 18 description: Excel document with data and Figure 5 Graph METHODOLOGICAL INFORMATION Strains: ancestral wildtype (Y55 strains), C1W8.1 and C1W8.2 multicellular derived strains isolated after 60 days of selection in YPD media, constructed ACE2 gene knockouts, and strains containing the ACE2 missense mutation (ACE2 c.1934 A>T). Media: Growth media used in this study were Yeast Peptone Dextrose media (YPD; 1% (v/w) yeast extract, 2% (v/w) peptone, 2% (v/w) D-glucose, pH 5.8) and Standard minimal (SD; Yeast nitrogen base with amino acids (YNB w/AA) 6.7 g L-1, 0.5% (v/w) D-glucose). Phenotypic characterization of the different strains was conducted in a Coulter Counter Multisizer 4 and FlowCam® 3.0 Fluid Imaging Technologies. Replicate populations of different individual isolates per strain were analyzed to obtain the population distributions in both YPD and SD media. Agent Base Model data was generated in Netlogo (https://ccl.northwestern.edu/netlogo/). 3. Detailed description NetLogo Agent Base model: File 1 name: Netlogo Snowflake 3D.nlogo3d o File 1 Description: Netlogo code for the 3D model. o File name: Data_NETLOGO_model.csv o File 2 Description: Data obtained from the Netlogo model. § Page 1: Agent Base Model data generated with Netlogo. Column 1: run number Column 2: size-of-turtle(cells) Column 3: [step] Column 4: count cells Column 5: ticks(division cycles) Column 6:distance-turtle(cells) Column 7: cell-cluster-radius Column 8: max-distance-between-turtles Column 9: x Column 10: y Column 11: x Column 12: Bradius (bounding radius) Column 13: Bvolum (bounding volume) Column 14: BSA (bounding Surface Area ratio) Coulter Counter size distribution data of all the populations: File 3 name: Counter_Counter_Raw_data.xls File 3 description: Data from Saccharomyces cerevisiae Y55 strain clones, C1W8.1 and C1W8.2 multicellular evolved strains, constructed ACE2 gene knockouts, and strains containing the missense mutation (ACE2 c.1934 A>T) in YPD and SD at 24h growth. § Page 1: Coulter Coulter data runs at 24h Column 1: Volume (um3) Column 2: Diameter (um2) Column 3: ace2Δ _k_1_SD. Homozygous ACE2 knockout construct (ace2Δ /ace2Δ) isolate one is SD media. Column 4: ace2Δ _k_1_YPD. Homozygous ACE2 knockout construct (ace2Δ /ace2Δ) isolate one is YPD media. Column 5: ace2Δ _k_2_SD. Homozygous ACE2 knockout construct (ace2Δ /ace2Δ) isolate two is SD media. Column 6: ace2Δ _k_2_YPD. Homozygous ACE2 knockout construct (ace2Δ /ace2Δ) isolate two is YPD media. Column 7: ace2Δ _k_3_SD. Homozygous ACE2 knockout construct (ace2Δ /ace2Δ) isolate three is SD media. Column 8: ace2Δ _k_3_YPD. Homozygous ACE2 knockout construct (ace2Δ /ace2Δ) isolate three is YPD media. Column 9: ace2Δ _k_4_SD. Homozygous ACE2 knockout construct (ace2Δ /ace2Δ) isolate four is SD media. Column 10: ace2Δ _k_4_YPD. Homozygous ACE2 knockout construct (ace2Δ /ace2Δ) isolate four is YPD media. Column 11: ace2Δ _k_5_SD. Homozygous ACE2 knockout construct (ace2Δ /ace2Δ) isolate five is SD media. Column 12: ace2Δ _k_5_YPD. Homozygous ACE2 knockout construct (ace2Δ /ace2Δ) isolate one is YPD media. Column 13: ace2Δ _k_6_SD. Homozygous ACE2 knockout construct (ace2Δ /ace2Δ) isolate five is SD media. Column 14: ace2Δ _k_6_YPD. Homozygous ACE2 knockout construct (ace2Δ /ace2Δ) isolate five is YPD media. Column 15: ace2Δ _m_1_SD. Homozygous ACE2 missense construct (ace2Δ /ace2Δ) isolate one is SD media. Column 16: ace2Δ _m_1_YPD. Homozygous ACE2 knockout construct (ace2Δ /ace2Δ) isolate one is YPD media. Column 17: ace2Δ _m_2_SD. Homozygous ACE2 missense construct (ace2Δ /ace2Δ) isolate two is SD media. Column