DOI: 10.5061/dryad.7pvmcvf2w
title: Data from: Ultradian rhythms of activity in a wild subterranean rodent

description: Many animals adapt their activity patterns to the best environmental
 conditions using diel rhythms. African mole-rats (family Bathyergidae) are
 among the mammals that have become models for studying how these rhythms
 can be entrained by different cues (light or temperature) in experimental
 laboratory studies. However, it is unclear whether they exhibit similar
 circadian rhythms in their natural lightless, subterranean environment. In
 this study, we used biologging to investigate the activity rhythms of
 wild, highveld mole-rats. We show that their activity cycle exhibited an
 ultradian rhythm with a length between 4 - 8 hours. On an individual
 level, mole-rats displayed about 5 activity bouts per day, occurring at
 various times during the day and night. On a population level, activity
 peaked in the afternoon, coinciding with the peak in ambient temperature.
 Our research suggests that wild subterranean mammals, which experience
 constant darkness and reduced environmental variation, are unlikely to
 show clear circadian rhythmicity. Instead, activity periods are
 distributed over several bouts throughout the day and night and is likely
 synchronized to daily temperature cycles. We propose that ultradian
 rhythms may be more common than previously thought and discuss how
 physiological processes may generate differences in periodicity between
 laboratory and wild populations.
description: Data was collected using accelerometer devices attached to
 highveld mole-rats (<em>Cryptomys pretoriae</em>).
 Accelerometer devices were set to record at 25hz and were deployed for up
 to 14 days (mean duration 12.95 +/- 2.2 days). Data was downloaded from
 the accelerometer devices using the program X Manager provided by
 Technosmart  (https://www.technosmart.eu/). As a result of the high frequency, accelerometer data files for each individual were over 1GB in size, and even reducing the data to mean values every 2 seconds results in a 1.7GB file with over 11.5 million rows. To allow public sharing of data we have shared the mean overall dynamic body acceleration (ODBA) values in 10 minute windows. Temperature data (soiltemp.csv) was recorded at the study site every 10 minutes with ibuttons buried in the soil and in full sun at 2m high.
description: # Ultradian rhythms of activity in a wild subterranean rodent Kyle T.
 Finn, Otto Brede, Nigel C. Bennett, Markus Zöttl **Data collection
 methods:** Data was collected using accelerometer devices attached to
 highveld mole-rats (Cryptomys pretoriae). Accelerometer devices were set
 to record at 25 Hz and were deployed for up to 14 days (mean duration
 12.95 +/- 2.2 days). Data was downloaded from the accelerometer devices
 using the program X Manager provided by Technosmart
 ([https://www.technosmart.eu/](https://www.technosmart.eu/)). Temperature
 data (soiltemp.csv) was recorded at the study site every 10 minutes with
 ibuttons buried in the soil at 10cm and 30cm. Temperature (degrees C) was
 also recorded in the sun at 2m height. **Data pre-processing:** As a
 result of the high frequency and long recording time of the accelerometer
 data, the raw data files for each individual could exceed 20 million rows
 with a file size of 1.8GB. To allow for public sharing of data we have
 processed the raw accelerometer data for each individual. We first
 calculated overall dynamic body acceleration (ODBA) in 2-second
 windows. Then we took the mean ODBA for each individual in 10-minute
 windows. We combined the results of all individuals into one csv file
 (Highveld_molerat_activity.csv). Example R code used to process the
 accelerometer data is provided in Finn_activity_rhythm_analysis.r on lines
 22-46. **Description of the files:** R script we used for analysis is
 provided in Finn_activity_rhythm_analysis.r  We used R 4.3.0 for analysis.
 The R script relies upon the following packages (version in parenthesis):
 tidyverse (2.0.0), TTR (0.24.4), scales (1.3.0), behavr (0.3.2), ggetho
 (0.3.7), zeitgebr (0.3.5), glmmTMB (1.1.8), lubridate (1.9.3), hms
 (1.1.3), sleepr (0.3.0), patchwork (1.2.0), performance (0.10.9), and
 ggeffects (1.7.0). Data for the analysis is provided in 3 csv files,
 described below. Columns and data descriptions are provided below
 each. Dates are in YYYY-MM-DD format, times are HH:MM:SS. 1.
 Highveld_molerat_activity.csv a. AnimalID - character; the
 individual's unique identification code. The characters before the
 M/F represents the animal's group. The M or F designates male or
 female. And the number after sex is the animal's original capture
 order. b. Timestamp - character; date and time of the 10-minute window for
 activity c. Time - character; just the time from Timestamp d. t - numeric;
 the number of seconds which have passed from midnight on the day the
 device was turned on. Note that the first 24 hours of recording were
 dropped for all individuals (86400 seconds in a day) e. ODBA - numeric;
 mean ODBA within a 10 minute window, calculated from ODBA values in 2
 second intervals. 2. highveld_metadata.csv a. AnimalID - character; the
 individual's unique identification code. Same as for
 Highveld_molerat_activity.csv b. Sex - character; animal's sex c.
 Group - character; animal's group\ d. CaptureDate - character; date
 of capture e. Status - character; animal's reproductive status. N =
 non-reproductive, R = reproductive f. OpenDate - character; date when the
 accelerometer device was activated g. LiftTime - character; time of
 release on OpenDate and start of actual data recording. 3. soiltemp.csv a.
 DateTime - character; date and time when the temperature was recorded. b.
 Temp - numeric; temperature c. Depth - character; depth were temperature
 was recorded: 10cm, 30cm, Air **Version changes:** 26 March 2025: updated
 Highveld_molerat_activity.csv file to fix numbers stored at exponentials,
 removed the row number columns in Highveld_molerat_activity.csv and
 soiltemp.csv.