## *Wolbachia*-infected pharaoh ant colonies have higher egg production, metabolic rate, and worker survival ### Reference Information This is the README file for the dataset associated with the paper "*Wolbachia*-infected pharaoh ant colonies have higher egg production, metabolic rate, and worker survival". This file uses Markdown syntax and has a .md extension *** ### General details of this README * **File name:** README(.md) * **Author(s):** Sachin Suresh * **Contributors(s):** Timothy A Linksvayer * **Date created:** 01/30/2023 (mm/dd/yyyy) * **Date modified:** 09/10/2023 (mm/dd/yyyy) *** ### Dataset Version and Release History * **Version number:** 2.0.0 * **Date:** 09/10/2023 (mm/dd/yyyy) * **Identifier:** DOI: 10.5061/dryad.0zpc8672b *** ### Dataset Attribution and Usage * **Dataset Title:** Data for the manuscript '*Wolbachia*-infected pharaoh ant colonies have higher egg production, metabolic rate, and worker survival' * **Dataset collection and contribution:** Rohini Singh * **License:** CC0 1.0 Universal (CC0 1.0) * **Dataset usage:** The authors sincerely request the researchers to reach out for re-using this dataset (https://creativecommons.org/publicdomain/zero/1.0/) * **Dataset citation:** > Rohini Singh, Sachin Suresh, Jennifer H. Fewell, Jon F. Harrison, Timothy A. Linksvayer. 2023. Data for the article '*Wolbachia*-infected pharaoh ant colonies have higher egg production, metabolic rate, and worker survival', https://doi.org/10.5061/dryad.0zpc8672b *** ### Contact Information * Name: Dr. Timothy A. Linksvayer (corresponding author) * Affiliations: Arizona State University; School of Life Sciences * Email: tlinksvayer@gmail.com * Alternate Email: tlinksva@asu.edu #### Alternative Contact * Name: Sachin Suresh (Ph.D. student) * Affiliations: Arizona State University; School of Life Sciences * ORCID ID: https://orcid.org/0000-0002-5245-7008 * Email: ssures53@asu.edu * Alternate Email: sachinddr3@gmail.com *** ### Funding This work was funded by the National Science Foundation (IOS-1452520) awarded to Timothy A. Linksvayer. *** ### Acknowledgments We are grateful to Dr. Juergen Liebig for letting us safely house the ants at Arizona State University, Xuaohui Guo in the Fewell lab and Trevor Fox in the Harrison lab at the Arizona State University for assisting with metabolic rate measurement *** ## Data and File Overview ### Summary Metrics * **File count:** 12 * **Total file size:** 270 KB * **File formats:** .csv, .R ### Table of Contents * 2019-fec-new-queens.csv * met-rate-vid-activity.csv * mr-brood.csv * mr-colony.csv * mr-queens.csv * queen2020-survival.csv * work-surv2019-long.csv * qn\_fc.R * met\_rate.R * met-rate-queens.R * survival-assay.R * fec\_qn\_sachin\_sml.R *** ### Software **Recommended software/tools:** RStudio 2022.12.0; R version 4.2.2 *** ## File Details ### a) 2019-fec-new-queens.csv * **Description:** a comma-delimited file containing queen egg-laying data along with other colony attributes. This file is associated with the experiment which compares the egg-laying rates of queens in wolbachia-infected and -uninfected colonies. * **Format(s):** .csv * **Size:** 18.1 KB * **Dimensions:** 372 rows x 13 columns * **Variables:** * **date:** Date at which the data was collected * **wolbachia:** Refers to *wolbachia* infection status. * **day:** Number of days since the start of experimental protocol * **colonyID:** Unique identifier for the colonies * **q.age.days:** Age of queen(s) in days * **males:** Number of males in the colony * **workers:** Number of workers in the colony * **queens:** Number of queens in the colony * **eggs:** Number of eggs laid by the queens * **yl:** Number of young larvae * **ol:** Number of old larvae * **worker.pp:** Number of worker pre-pupae * **worker.pup:** Number of worker pupae ### b) met-rate-vid-activity.csv * **Description:** a comma-delimited file containing colony-activity data along with other colony attributes. This file is associated with the experiment which compares the metabolic rates of wolbachia-infected and -uninfected colonies. * **Format(s):** .csv * **Size:** 1.88 KB * **Dimensions:** 42 rows x 6 columns * **Variables:** * **year:** Respective year at which the data was collected * **colony:** Unique identifier for the colonies * **wolbachia:** Refers to *wolbachia* infection status. * **total.frames:** Total number of frames in the video analyzed for a colony * **avg.chg.pxl:** Average of the change in pixel value * **sd.chg.pxl:** Standard deviation of the change in pixel value ### c) mr-brood.csv * **Description:** a comma-delimited file containing metabolic rate for brood along with other colony attributes. This file is associated with the experiment which compares the metabolic rates of brood in wolbachia-infected and -uninfected conditions. * **Format(s):** .csv * **Size:** 5.52 KB * **Dimensions:** 23 rows x 30 columns * **Variables:** * **mr.date:** Date at which the data was collected * **colony:** Unique identifier for the colonies * **wolbachia:** Refers to *wolbachia* infection status. * **resp.chamber:** Type of respiratory chamber used * **queen.age:** Age of queen(s) in days * **eggs:** Number of eggs * **young.larvae:** Number of young larvae * **old.larvae:** Number of old larvae * **worker.pupae:** Number of worker pupae * **air.flow:** Rate of air flow (mL/min) * **rq:** respiratory quotient (ratio of carbon dioxide produced to oxygen consumed) (dimensionless number) * **mass.before:** Mass before the experiment (grams) * **mass.after:** Mass after the experiment (grams) * **measure:** Time taken for measurement of CO2 emission (seconds) * **measure.time:** Time taken for measurement of CO2 emission (minutes) * **co2.mean:** Mean CO2 emission from brood (ppm) * **co2. sd:** Standard deviation of the CO2 emission from brood (ppm) * **temp.mean:** Mean temperature of the brood setup (Degree celsius) * **temp. sd:** Standard deviation of the temperature of the brood setup (Degree celsius) * **humid.mean:** Mean humidity of the brood setup (ppm) * **humid. sd:** Standard deviation of the brood humidity (ppm) * **comments:** Comments regarding the experimental conditions * **trash.measure.sec:** Measurement of CO2 emission in trash in seconds * **trash.measure.min:** Measurement of CO2 emission in trash in minutes * **trash.co2.mean:** Mean CO2 emission from trash (ppm) * **trash.co2. sd:** Standard deviation of the CO2 emissions from trash (ppm) * **trash.temp.mean:** Mean temperature of the trash (Degree celsius) * **trash.temp. sd:** Standard deviation of the trash (Degree celsius) * **trash.humid.mean:** Mean humidity of the trash (ppm) * **trash.humid. sd:** Standard deviation of the trash humidity (ppm) ### d) mr-colony.csv * **Description:** a comma-delimited file containing metabolic rate for the whole colony along with other attributes. This file is associated with the experiment which compares the metabolic rates of whole-colonies in wolbachia-infected and -uninfected conditions. * **Format(s):** .csv * **Size:** 13.4 KB * **Dimensions:** 51 rows x 38 columns * **Variables:** * **year:** Respective year at which the data was collected * **mr.date:** Date at which the data was collected * **colony:** Unique identifier for the colonies * **wolbachia:** Refers to *wolbachia* infection status. * **resp.chamber:** Type of respiratory chamber used * **lighting.during.recording:** Whether lighting was used during recording * **humidity:** Refers to whether water tube is present/absent respirometer during measurement (yes/no) * **nest.shape:** Type of nest chamber used * **queen.age:** Age of queen(s) in days * **eggs:** Number of eggs * **young.larvae:** Number of young larvae * **old.larvae:** Number of old larvae * **worker.pupae:** Number of worker pupae * **queens:** Number of queens * **queens:** Number of workers * **air.flow:** Rate of air flow (mL/min) * **rq:** respiratory quotient (ratio of carbon dioxide produced to oxygen consumed)(dimensionless number) * **brood.prp:** Proportion of brood per colony * **mass.before:** Mass before the experiment (grams) * **mass.after:** Mass after the experiment (grams) * **measure:** Time taken for measurement of CO2 emission (seconds) * **measure.time:** Time taken for measurement of CO2 emission (minutes) * **co2.mean:** Mean CO2 emission from colony (ppm) * **co2. sd:** Standard deviation of the CO2 emission from colony (ppm) * **temp.mean:** Mean temperature of the colony (Degree celsius) * **temp. sd:** Standard deviation of the colony temperature (Degree celsius) * **humid.mean:** Mean humidity of the colony (ppm) * **humid. sd:** Standard deviation of the colony humidity (ppm) * **trash.measure.sec:** Measurement of CO2 emission in trash in seconds * **trash.measure.min:** Measurement of CO2 emission in trash in minutes * **trash.co2.mean:** Mean CO2 emission from trash (ppm) * **trash.co2. sd:** Standard deviation of the CO2 emissions from trash (ppm) * **trash.temp.mean:** Mean temperature of the trash (Degree celsius) * **trash.temp. sd:** Standard deviation of the trash (Degree celsius) * **trash.humid.mean:** Mean humidity of the trash (ppm) * **trash.humid. sd:** Standard deviation of the trash humidity (ppm) * **video-activity:** Date of the recorded video activity ### e) mr-queens.csv * **Description:** a comma-delimited file containing metabolic rate for just the queens along with other attributes. This file is associated with the experiment which compares the metabolic rates of queens in wolbachia-infected and -uninfected conditions. * **Format(s):** .csv * **Size:** 5.36 KB * **Dimensions:** 29 rows x 20 columns * **Variables:** * **Date:** Date at which the data was collected * **queens. id:** Unique identifier for the queens * **wolbachia:** Refers to *wolbachia* infection status. * **first.baseline:** Time at which first baseline measurment was taken * **start.settle:** Time at which queens settled down * **end.measure:** End time of measurement * **flow.duration.min:** Flow duration in minutes * **flow.duration. hr:** Flow duration in hours * **last.baseline:** Time at which last baseline measurment was taken * **queens:** Number of queens * **air.flow:** Rate of air flow (mL/min) * **rq:** respiratory quotient (ratio of carbon dioxide produced to oxygen consumed) (dimensionless number) * **mass:** Mass of the queens (grams) * **queen.age:** Age of the queen in days * **temp:** Temperature of the setup (Degree celsius) * **measure:** Time taken for measurement of CO2 emission in seconds * **measure.time:** Time taken for measurement of CO2 emission in minutes * **co2.mean:** Mean CO2 emission from queens (ppm) * **co2. sd:** Standard deviation of the CO2 emission from queens (ppm) * **comments:** Comments regarding the experimental conditions ### f) queen2020-survival.csv * **Description:** a comma-delimited file containing queen survival data along with other colony attributes. This file is associated with the experiment which compares the survival of queens in wolbachia-infected and -uninfected colonies. * **Format(s):** .csv * **Size:** 36.2 KB * **Dimensions:** 612 rows x 15 columns * **Variables:** * **date:** Date at which the data was collected * **colony:** Unique identifier for the colonies * **wolbachia:** Refers to *wolbachia* infection status. * **week:** Week since the start of the observation * **day:** Number of days since the start of experimental protocol * **queen.age:** Age of queen(s) in days * **queens:** Number of queens in the colony * **worker:** Number of workers in the colony * **eggs:** Number of eggs laid by the queens * **young.larvae:** Number of young larvae * **old.larvae:** Number of old larvae * **worker.pre.pup:** Number of worker pre-pupae * **worker.pup:** Number of worker pupae * **queen.pup:** Number of queen pupae * **male.pup:** Number of male pupae * **comments:** Miscellaneous comments ### g) work-surv2019-long.csv * **Description:** a comma-delimited file containing worker survival data along with other colony attributes. This file is associated with the experiment which compares the survival of workers in wolbachia-infected and -uninfected colonies. * **Format(s):** .csv * **Size:** 35.6 KB * **Dimensions:** 1296 rows x 7 columns * **Variables:** * **groupID:** Identifier for the group * **day:** Number of days since the start of experimental protocol * **worker.age:** Age of worker(s) in days * **colony.source:** Identifier of the source colony * **sub.colony:** Sub colony identifier * **wolbachia:** Refers to *wolbachia* infection status. * **worker:** Number of workers ### h) qn\_fc.R * **Description:** an R script for visualization and analysis of queen egg-laying data. This file is associated with the experiment which compares the egg-laying rates of queens in wolbachia-infected and -uninfected colonies. All the commands and codes inside the script are annotated. * **Format(s):** .R * **Size:** 25.3 KB ### i) met\_rate.R * **Description:** an R script for visualization and analysis of metabolic rate data. This file is associated with the experiment which compares the metabolic rates of whole-colonies, workers and brood in wolbachia-infected and -uninfected conditions. All the commands and codes inside the script are annotated. * **Format(s):** .R * **Size:** 45.5 KB ### j) met-rate-queens.R * **Description:** an R script for visualization and analysis of queen metabolic rate data. This file is associated with the experiment which compares the metabolic rates of queens in wolbachia-infected and -uninfected conditions. All the commands and codes inside the script are annotated. * **Format(s):** .R * **Size:** 9.82 KB ### k) survival-assay.R * **Description:** an R script for visualization and analysis of queen and worker survival data. This file is associated with the experiment which compares the survival of queens and workers in wolbachia-infected and -uninfected colonies. All the commands and codes inside the script are annotated. * **Format(s):** .R * **Size:** 60.6 KB ### **l) fec\_qn\_sachin\_sml.R** * **Description:** an R script for visualization and analysis of queen egg-laying data. This file is associated with the experiment which compares the egg-laying rates of queens in wolbachia-infected and -uninfected colonies. All the commands and codes inside the script are annotated. Also, note that this script is a trimmed version of the R-script 'fec\_qn.r' to streamline the analysis and plots * **Format(s):** .R * **Size:** 13 KB *** ## Experiment Details A brief summary of the experiments and results performed in the paper is mentioned below. The data files and scripts associated with the individual studies are also mentioned. ### a) Egg laying by queens **Experiment 1a:** Comparison of egg-laying difference between newly-mated infected and uninfected queens over 50 days. **Result:** Newly-mated *Wolbachia*-infected queens produced more eggs over time than uninfected queens (GLMER: 2 = 7.6, p = 0.005; Fig 1a, main text). * **Raw data:** 2019-fec-new-queens.csv * **R script:** qn\_fc.R **Experiment 1b:** Comparison of egg-laying differences between 20 *Wolbachia*-infected and uninfected queens when the queens were one, three, four, six, and nine months old to quantify differences across the queens' lifespan. \*\*Result: \*\**Wolbachia*-infected colonies have higher metabolic rates depending on the stage of the colony life cycle. * **Raw data:** 2019-fec-new-queens.csv * **R script:** qn\_fc.R, fec\_qn\_sachin\_sml.R ### b) Metabolic Rates of whole colonies, queens, and brood **Experiment 2 :** We compared metabolic rates of (a) infected versus uninfected whole colonies at two different colony life stages: colonies with one-month-old queens and three-month-old queens and (b) different colony members, namely the brood and the queens from colonies with one-month-old queens. **Results:** Metabolic rates differ between infected and uninfected whole-colonies but are dependent on colony life cycle stage and colony component. Metabolic rates did not differ between other infected and uninfected groups early in the colony life cycle (fig 2 and fig s4 in main text). * **Raw data:** met-rate-vid-activity.csv, mr-brood.csv, mr-colony.csv, mr-queens.csv * **R scripts:** met\_rate.R, met-rate-queens.R ### c) Survival of queens and workers **Experiment 3 :** We estimated the effect of Wolbachia infection status on worker survival. **Results:** Wolbachia-infected and uninfected queens had similar group- (Log-rank test, p = 0.8; Fig. 3a in main text) and individual-level survival rates (GLMM, 2 = 0.2, p <0.05; Fig. 3b in main text). Infected workers had higher group-level survival (Log-rank test, p = 0.02; Fig 3c) and individual-level survival (GLMM, 2 = 12, p < 0.001; Fig. 3d in) than uninfected workers (Fig. 3c,d). * **Raw data:** queen2020-survival.csv, work-surv2019-long.csv * **R script:** survival-assay.R *** End of README ***