Data and code from: Life under leaves: Substrate-borne vibrations provide a window into the behavior and ecology of two miniaturized geckos
Data files
Dec 08, 2025 version files 7.54 GB
-
Datasets.zip
24.18 KB
-
README.md
7.40 KB
-
Vibrational_Recordings.zip
7.54 GB
Abstract
Traditional sampling methods have limited our understanding of the behavioral ecology of leaf litter fauna. Substrate-borne vibrations provide a window that addresses this shortcoming. Under natural conditions, we implemented a passive monitoring system that measures vibrations produced by two miniaturized Puerto Rican geckos: Sphaerodactylus grandisquamis in the mesic karst forest and Sphaerodactylus townsendi in the coastal dry forest. The dichotomy between habitats allowed us to test the hypothesis that microclimate conditions drive divergence in thermoregulatory behavior. For each species in its native habitat, thirty individuals were monitored inside a field enclosure, excluding other vibration sources. We measured vibrations at two strata depths (i.e., surface and bottom) to characterize behavioral responses to diel cycle, microclimate, and predatory bird calls. Vibrational data revealed contrasting activity patterns across strata. Mesic S. grandisquamis showed continuous daytime activity at all strata levels, regardless of microclimate. Dry forest S. townsendi featured a biphasic activity pattern, peaking midday and at dusk, and increased activity in deeper litter strata during hot and dry conditions (i.e., midday). Analysis at fine temporal scales for S. grandisquamis revealed a reduction in surface activity after the onset of bird calls from three species that pose a predation risk. Our results demonstrate interspecific differences in thermoregulatory behavior that likely increase the fitness of each species in their respective habitats. Furthermore, vibrational monitoring strongly suggests Sphaerodactylus exploit their niche in a three-dimensional manner, mirroring habitat use patterns of arboreal fauna and highlighting the importance of incorporating multiple strata levels when studying leaf litter microhabitats.
https://doi.org/10.5061/dryad.mcvdnck8v
Description of the data and file structure
The vibrational dataset represents field recordings for 1) Sphaerodactylus grandisquamis in the mesic karst forest at Mata de Plátano and 2) Sphaerodactylus townsendi in the coastal dry forest at Cabezas de San Juan, along with concurrent microclimate data from the leaf litter. Processing of vibrational data was conducted in MATLAB, and analyses were performed in R.
Files and variables
Container: Vibrational_Recordings.zip
Files: 34 segments of acoustic data across 4 sensor types. File names (“07.XX_YY_YY_Z”) are organised by date (“07.XX_” = 07/XX) followed by time of day (“YY_YY_” = YY:YY), then sensor type (“Z”).
Description: Time-synchronised recordings of airborne sound (i.e., air) and vibrations (i.e., surface, bottom, and ground sensors) from the passive monitoring system. For Mata de Platano, 17 segments of S. grandisquamis activity (i.e., acoustic energy) were recorded from July 6-10, 2022, and one segment of the control enclosure was recorded on July 11. For Cabezas de San Juan, 16 segments of S. townsendi activity were recorded from July 14-19, 2022, and one segment of the control enclosure was recorded on July 20.
Container: Datasets.zip
Note for spreadsheets: NA = data not available
File: Bird_calls.csv
Description: S. grandisquamis activity at Mata de Platano during matched controls and post-onset of calls, each corresponding to a 20-second time interval for each of 68 calls from three predatory bird species: the Puerto Rican lizard-cuckoo (Coccyzus vieilloti), the gray kingbird (Tyrannus dominicensis), and the red-legged thrush (Turdus plumbeus).
Variables:
1) Call_number: 68 salient bird calls, ordered chronologically.
2) Recording: Reference recording segment which contains the bird call.
3) Site: Location where data was collected.
4) Year: Year of recording.
5) Month: Month of recording.
6) Day: Day of recording.
7) Hour: Hour of recording.
8) Minute: Minute of recording.
9) Species: Bird species identity for the call.
10) Songtype: Song type of the call.
11) MatchedControl_Start_sec: Time in seconds of the start of the 20-second time interval corresponding to the matched controls.
12) MatchedControl_End_sec: Time in seconds of the end of the 20-second time interval corresponding to the matched controls.
13) PostOnsetCall_Start_sec: Time in seconds of the start of the 20-second time interval corresponding to the post-onset of calls.
14) PostOnsetCall_End_sec: Time in seconds of the end of the 20-second time interval corresponding to the post-onset of calls.
15) Surface__MatchedControl_AcousticEnergy: S. grandisquamis activity (i.e., acoustic energy) at the surface level during matched controls. Values are the result of calculations in MATLAB.
16) Bottom__MatchedControl_AcousticEnergy: S. grandisquamis activity (i.e., acoustic energy) at the bottom level during matched controls. Values are the result of calculations in MATLAB.
17) Surface__PostOnsetCall_AcousticEnergy: S. grandisquamis activity (i.e., acoustic energy) at the surface level during post-onset of calls. Values are the result of calculations in MATLAB.
18) Bottom__PostOnsetCall_AcousticEnergy: S. grandisquamis activity (i.e., acoustic energy) at the bottom level during post-onset of calls. Values are the result of calculations in MATLAB.
19) Comments_MatchedControl: Summary of audible species and noise level during matched control time intervals.
20) Comments_PostOnsetCall: Summary of audible species and noise level during post-onset of calls.
File: Microclimate.csv
Description: Microclimate (i.e., temperature (°C) and relative humidity) at Cabezas de San Juan, as measured by iButtons.
Variables:
1) Site: Location where data was collected.
2) Date: Date of measurements.
3) Time: Start time of measured time interval.
4) Time_day: Time of day, starting post-sunrise on the first day of measurements in each habitat.
5) Sunrise: Time of sunrise on day of measurements.
6) Time_after_sunrise_hours: Time in hours post-sunrise.
7) Enclosure_Relative_Humidity_Bottom: Relative humidity from the iButton positioned at the bottom of the enclosure.
8) Enclosure_Temp_Bottom: Temperature (°C) from the iButton positioned at the bottom of the enclosure.
9) Outside_Temp_Air: Temperature (°C) from the iButton positioned 25 centimeters in the air above the enclosure.
10) Outside_Temp_Surface: Temperature (°C) from the iButton positioned at the surface of unmanipulated leaf litter in the environment.
11) Diel: Two-level categorical variable indicating daylight hours (i.e., day) or nighttime (i.e., night).
File: Vibrations.csv
Description: Sphaerodactylus activity (i.e., acoustic energy) at the surface and bottom sensors across the recorded time period at Mata de Platano for S. grandisquamis and Cabezas de San Juan for S. townsendi.
Variables:
1) Serial: Serial number for quantified time intervals.
2) Site: Location where data was collected.
3) File: Reference recording segment for vibrations.
4) Date: Date of recording.
5) Segment: Time of day of recording (i.e., morning, afternoon, evening).
6) File_segment: Date and letter numbering of recording per day (i.e., a, b, c, d, e).
7) 15min_segment: Ordinal numbering of recording for a given day.
8) Time_after_sunrise_hours: Time in hours post-sunrise at the middle time stamp of the 15-minute interval.
9) Vibs_surface: Sphaerodactylus activity (i.e., acoustic energy) at the surface of leaf litter.
10) Vibs_bottom: Sphaerodactylus activity (i.e., acoustic energy) at the bottom of leaf litter.
11) Comparison: Two-level categorical variable indicated enclosures without Sphaerodactylus (i.e., control) and enclosures with Sphaerodactylus (i.e., experimental) during the same 1.5 hour time period in each habitat.
Code/software
Container: Code.zip
File: Vibrational_Summations_and_Bird_calls.mlx
Description: The following analyses were performed in MATLAB (v.2024a; MathWorks Inc., 2024).
1) Summation of Sphaerodactylus activity (S. grandisquamis & S. townsendi) within 15-minute time intervals (activity at surface and bottom).
2) Summation of S. grandisquamis activity within 20-second time intervals (matched controls vs. post-onset of bird calls).
3) Randomization tests and visualizations for the behavioural response of S. grandisquamis to bird calls.
File: Sphaero_Vibrations.Rmd
Description: The following analyses and visualizations were performed in R (v.2024.12.0+467; R Core Team, 2024).
1) Microclimate differences between Mata de Platano & Cabezas de San Juan.
2) Models of Sphaerodactylus activity and strata depth as a function of microclimate.
3) Comparison of measured activity between enclosures with Sphaerodactylus (i.e., experimental) and without Sphaerodactylus (i.e., control).
4) Comparison of S. grandisquamis activity during matched controls and post-onset of bird calls.
The vibrational dataset represents field recordings for 1) Sphaerodactylus grandisquamis in the mesic karst forest at Mata de Plátano and 2) Sphaerodactylus townsendi in the coastal dry forest at Cabezas de San Juan, along with concurrent microclimate data from the leaf litter. Processing of vibrational data was conducted in MATLAB, and analyses were performed in R. All data and scripts are provided.