Overview

This repository contains data and analysis scripts related to our behavioral and reproductive trait studies. The dataset includes raw data from various experiments and corresponding R scripts that perform linear models and linear mixed effects models on the data.

Files

Elevated Plus Maze (EPM) Data and Scripts

1. EPM_Exp_1.csv
   • Description: Contains the raw data from the Experiment 1 elevated plus maze test.
   • Variables:
     1. Subject: A unique identifier assigned to each animal tested.
     2. Treatment: Experimental group designation.
     3. Distance_moved: Total distance the subject moved (in cm) during the EPM trial.
     4. NUM_Closed_arm (Number of Closed Arm Entries): The number of times the subject entered either of the two closed arms.
     5. DUR_Closed_arm (Duration in Closed Arms): Total time (in seconds) spent in the closed arms during the trial.
     6. NUM_Open_arm (Number of Open Arm Entries): The number of times the subject entered either of the two open arms.
     7. DUR_Open_arm (Duration in Open Arms): Total time (in seconds) spent in the open arms during the trial.
     8. Prcnt_open_arm (Percent Time in Open Arms): The percentage of the total trial time spent in the open arms.
     9. Age_at_EPM: The age of the subject in days at the time of EPM testing. ‘NA’ indicates age was unknown.
2. EPM_Exp_2.csv
   • Description: Contains the raw data from the Experiment 2 elevated plus maze test.
   • Variables:
     1. Subject: A unique identifier assigned to each animal tested.
     2. Treatment: Experimental group designation. ‘PSNF’ indicates pup-sensitized nonfathers.
     3. Trial: Indicates test number on EthoVision software.
     4. Male_age_at_testing: The age of the subject in days at the time of the EPM testing.
     5. NUM_Closed_arms (Number of Closed Arm Entries): The number of times the subject entered either of the two closed arms.
     6. DUR_Closed_arms (Duration in Closed Arms): Total time (in seconds) spent in the closed arms during the trial.
     7. LAT_Closed_arms (Latency to Enter Closed Arms): Time (in seconds) from the start of the trial to the subject's first entry into a closed arm.
     8. NUM_Opened_arms (Number of Open Arm Entries): The number of times the subject entered either of the two open arms.
     9. DUR_Open_arms (Duration in Open Arms): Total time (in seconds) spent in the open arms during the trial.
     10. LAT_Open_arms (Latency to Enter Open Arms): Time (in seconds) from trial start to the subject's first entry into an open arm.
     11. Total_time: Total duration of the trial in seconds.
     12. Distance_moved: Total distance the subject moved (in cm) during the EPM trial.
     13. Percent_open_arms_w_center (% Time in Open Arms Including Center): The percentage of the trial spent in the open arms including any time the animal spent in the center platform of the maze (which connects the arms).
     14. Percent_open_arms_wo_center (% Time in Open Arms Excluding Center): The percentage of time spent in the open arms excluding time spent in the center zone.
3. EPM_LM_G.R
   • Description: R script that contains the code used to perform linear models on the elevated plus maze data for Experiments 1 and 2.

Novel Object Recognition (NOR) Data and Scripts

1. NOR_Exp_1.csv
   • Description: Contains the raw data from the Experiment 1 novel object recognition test.
   • Variables:
     1. Subject: A unique identifier assigned to each animal tested.
     2. Treatment: Experimental group designation.
     3. Age_at_NOR: The age of the subject in days at the time of NOR testing. ‘NA’ indicates age was unknown.
     4. Marble_time (Time with Familiar Object): The total amount of time (in seconds) the subject spent interacting with the familiar marble.
     5. Block_time (Time with Novel Object): The total amount of time (in seconds) the subject spent interacting with the novel block.
     6. Prcnt_novel_object (Percent Time with Novel Object): The percentage of total object interaction time spent investigating the novel object. Calculated as (Block_time) / (Marble_time + Block_time) ​× 100.
     7. Difference_score: A measure of preference calculated as Block_time minus Marble_time.
2. NOR_Exp_2.csv
   • Description: Contains the raw data from the Experiment 2 novel object recognition test.
   • Variables:
     1. Treatment: Experimental group designation. ‘PSNF’ indicates pup-sensitized nonfathers.
     2. Subject: A unique identifier assigned to each animal tested.
     3. Difference_score: A measure of preference calculated as Block_time minus Marble_time.
     4. Percent_novel_object (Percent Time with Novel Object): The percentage of total object interaction time spent investigating the novel object. Calculated as (Block_time) / (Marble_time + Block_time) ​× 100.
     5. Block_time (Time with Novel Object): The total amount of time (in seconds) the subject spent interacting with the novel block.
     6. Marble_time (Time with Familiar Object): The total amount of time (in seconds) the subject spent interacting with the familiar marble.
     7. Male_age_at_testing: The age of the subject in days at the time of NOR testing.
     8. Female_mating_history: The number of males to which a female was paired.
3. NOR_LM_G.R
   • Description: R script that contains the code used to perform linear models on the novel object recognition data for Experiments 1 and 2.

Reproductive Trait Data and Scripts

1. Testes_weight_Sperm_count_Exp_1.csv
   • Description: Contains the raw average testes weight and sperm count data from Experiment 1.
   • Variables:
     1. ID: A unique identifier assigned to each individual subject.
     2. Treatment: Experimental group designation. ‘NF’ indicates nonfathers.
     3. Age: The age of the subject in days.
     4. BW (Body Weight): The body weight of the subject at the time of dissection, measured in milligrams.
     5. Relative_testes_weight: Mean testes  weight (in mg) normalized to body weight.
     6. Sperm_count: Number of sperm collected from the epididymis.
     7. Mean_testes_weight: The average weight (in mg) of a single testis calculated by dividing the combined weight of both testes by two.
2. Sperm_count_Exp_2.csv
   • Description: Contains the raw sperm count data from Experiment 2.
   • Variables:
     1. ID: A unique identifier assigned to each individual subject.
     2. Treatment: Experimental group designation. ‘NF’ indicates nonfathers and ‘PSNF’ indicates pup-sensitized nonfathers.
     3. BW (Body Weight): The body weight of the subject at the time of dissection, measured in milligrams.
     4. Age: The age of the subject in days.
     5. Sperm_Count: Number of sperm collected from the epididymis. Cells are left empty if we were unable to collect sperm from subject.
3. Testes_weight_Exp_2.csv
   • Description: Contains the raw average testes weight data from Experiment 2.
   • Variables:
     1. ID: A unique identifier assigned to each individual subject.
     2. Treatment: Experimental group designation. ‘NF’ indicates nonfathers and ‘PSNF’ indicates pup-sensitized nonfathers.
     3. BW (Body Weight): The body weight of the subject at the time of dissection, measured in milligrams.
     4. Age: The age of the subject in days.
     5. Mean_testes_weight: The average weight of a single testis calculated by dividing the combined weight of both testes by two.
4. Testes_weight_Sperm_count_Exp_2.csv
   • Description: Contains the raw average testes weight and sperm count data from Experiment 2.
   • Variables:
     1. ID: A unique identifier assigned to each individual subject.
     2. Treatment: Experimental group designation. ‘NF’ indicates nonfathers and ‘PSNF’ indicates pup-sensitized nonfathers.
     3. Sperm_Count: Number of sperm collected from the epididymis. Cells are left empty if we were unable to collect sperm from subject.
     4. Mean_testes_weight: The average weight (in mg) of a single testis calculated by dividing the combined weight of both testes by two.
5. Repro_LM_G.R
   • Description: R script that contains the code used to perform linear models on the reproduction data for Experiments 1 and 2.

Pup-Exposure and Caregiving Behavior Data and Scripts

1. Pup_exposure.csv
   • Description: Contains the raw data on pup-exposure behavior.
   • Variables:
     1. Subject: A unique identifier assigned to each animal tested.
     2. Treatment: Experimental group designation.
     3. PND (Postnatal Day): The age of the pups used in the assay, in days.
     4. Male_age_at_testing: The age of the male subject at the time of the test, in days.
     5. NUM_pups_sired: The number of offspring the subject had sired at the time of testing. This value is therefore NA for pup-sensitized nonfathers.
     6. DUR_Exploration_near: Total time (in seconds) spent exploring near the pup enclosure.
     7. NUM_Exploration_near: Total number of bouts of exploration near the pup enclosure.
     8. DUR_Exploration_away: Total time (in seconds) spent exploring areas away from the pup enclosure.
     9. NUM_Exploration_away: Total number of bouts of exploration away from the pup enclosure.
     10. DUR_Pup_directed: Total time (in seconds) engaged in direct pup interactions (e.g., sniffing, licking, touching directed at pups).
     11. NUM_Pup_directed: Total number of bouts of pup-directed interaction.
     12. DUR_Latency_pup_directed: Time (in seconds) from the start of the test until the male first engaged in a pup-directed behavior.
     13. NUM_Latency_pup_directed: Number of latency periods scored prior to first pup-directed interaction.
     14. DUR_Grooming: Total time (in seconds) spent auto-grooming.
     15. NUM_Grooming: Total number of auto-grooming bouts.
     16. DUR_Resting: Total time (in seconds) spent resting or inactive.
     17. NUM_Resting: Number of distinct resting bouts during the test.
     18. DUR_Jump/backflips: Total time (in seconds) spent engaging in jumping or backflipping. All NA because this is a point behavior.
     19. NUM_Jump/backflips: Number of bouts of jumping or backflipping behaviors.
2. Caregiving.csv
   • Description: Contains the raw data on caregiving behavior.
   • Variables:
     1. Subject: A unique identifier assigned to each animal tested.
     2. Treatment: Experimental group designation.
     3. PND (Postnatal Day): The age of the pups used in the assay, in days.
     4. Male_age_at_testing: Age of the male (in days) at the time of the caregiving assay.
     5. Pup_1_time: Total time (in seconds) tested with the first pup.
     6. Earliest_latency: Latency (in seconds) to the first occurrence of any caregiving-related behavior.
     7. Parental_behavior_latency: Latency (in seconds) to the first instance of huddling, grooming, or retrieving.
     8. Huddle_latency: Latency (in seconds) to first occurrence of huddling behavior.
     9. Huddling: Total duration (in seconds) spent huddling over the pup.
     10. NUM_Huddling: Number of huddling bouts.
     11. Groom_latency: Latency (in seconds) to first occurrence of grooming behavior directed at the pup.
     12. Grooming: Total duration (in seconds) spent grooming the pup.
     13. NUM_Grooming: Number of pup grooming bouts.
     14. Huddling_grooming: Combined total duration (in seconds) of huddling and grooming behaviors.
     15. Sniff_latency: Latency (in seconds) to first sniff of the pup.
     16. Sniffing: Total time (in seconds) spent sniffing the pup.
     17. NUM_Sniffing: Number of discrete sniffing bouts.
     18. Retrieve_latency_1: Latency (in seconds) to first pup retrieval.
     19. Retrieve_latency_1_fixed: Latency (in seconds) to first pup retrieval corrected if retrieval did not take place. NA indicates male did not retrieve pup.  
     20. Retrieving_1: Total duration (in seconds) spent retrieving the pup.
     21. NUM_Retrieving_1: Number of pup retrievals.
     22. Pup_interaction: Total duration (in seconds) of any pup-directed interaction (e.g., sniffing, grooming, huddling, retrieving).
     23. Nest_building: Total time (in seconds) spent manipulating nesting material.
     24. NUM_Nest_building: Number of nest-building bouts.
     25. General_activity: Total time (in seconds) spent in general movement or exploration, not directed toward the pup.
     26. NUM_General_activity: Number of bouts of general (non-caregiving) activity.
     27. Resting: Total time (in seconds) spent inactive during the trial.
     28. General_resting: Combined total duration (in seconds) of general activity and resting behaviors.
     29. Pup_2_Time: Total time (in seconds) tested with the second pup introduced later in the assay.
     30. Retrieve_latency_2: Latency (in seconds) to retrieve the second pup.
     31. Retrieve_latency_2_fixed: Latency (in seconds) to retrieve the second pup corrected if retrieval did not take place. NA indicates male did not retrieve pup.  
     32. NUM_Lack_of_retrieve_2: Count of failure to retrieve pup 2 (e.g., 1 = did not retrieve).
     33. Investigate_latency_2: Latency (in seconds) to first investigation of pup 2.
     34. NUM_Lack_of_investigate_2: Count of failure to investigate pup 2 (e.g., 1 = did not investigate).
3. Pup_exposure_LM_G.R
   • Description: R script that contains the code used to perform linear mixed effects models on the pup-exposure data.
4. Caregiving_LM_G.R
   • Description: R script that contains the code used to perform linear mixed effects models on the caregiving data.

Usage

1. Data Files:
   • The raw data files can be loaded into R.
2. Script Files:
   • The analysis scripts can be run in an R environment. Ensure that you set the working directory to the location of the data files or provide the correct path to the data files within the scripts.
   • The scripts will perform the specified modeling on the provided data and output results including model summaries. 

Contact

For any questions or further information, please contact Maria Colt at mcolt@umd.edu.