Study area and survey effort
Acoustic recording was conducted in three Indo-Pacific humpback dolphin populations in the South China Sea (SCS) between May 2021 and September 2024 including populations inhabiting the coastal waters of the Pearl River Delta (PRD), Zhanjiang (ZJ), and Sanniang Bay (SNB) (Fig 1). Each of these habitats is geographically isolated, with no communication or gene flow between populations (Lin, Chen, et al., 2024; Lin, Karczmarski, et al., 2024; Tang et al., 2021). Systematic boat-based surveys were conducted in each region under comparable sea conditions, with a Beaufort score of less than 3 and swells below 1 meter, ensuring consistency in data collection. Surveys followed pre-defined routes to standardize the effort across all three areas.
Data collection
Surveys were conducted using small, highly maneuverable outboard engine boats approximately 7 meters in length. Each survey team consisted of at least three trained observers who continuously scanned the surrounding area for dolphins using naked eye. Upon sighting dolphins, the boat slowed down and approached them in a parallel way or with a slight angle from the side or the rear to minimize disturbance.
During each encounter, data were recorded including dolphin behavior, estimated group size, presence or absence of young, and environmental conditions such as water depth, temperature, and the number of nearby vessels within 1 kilometer of dolphins. Groups were defined as one or more dolphins observed in close spatial proximity or social association (Liu et al., 2021). Young, including neonates, calves and unspotted juveniles were identified by their small size and predominantly gray skin pigmentation (Piwetz et al., 2021). Behavioral activity states were attributed based on the definitions from previous studies (Karczmarski & Cockcroft, 1999; Serres et al., 2023), with groups displaying unknown behaviors excluded from further analysis. Habitat types were classified into three categories: open water (OW; > 100m from the shore), nearshore (NS; < 100m from the shore), and boat channel (BC; in a harbor or < 100m from a shipping channel).
Once the boat was within approximately 50 meters of the dolphins, ensuring high-quality acoustic recordings, a SoundTrap acoustic recorder (ST300 HF; frequency response: 20–150 kHz ± 3 dB; sensitivity: -172.8 dB re 1 μPa; Ocean Instruments Inc., Dunedin, New Zealand) was deployed. The recorder, weighted with a 5-kg object, was secured with a rope to the front of the boat and positioned at mid-water depth.
Acoustic data analysis
The acoustic data were stored as 16-bit WAV files. Each recording was thoroughly inspected both aurally and visually using Audition CS6 (Adobe Systems Inc., 2013) and Raven Pro Bioacoustics software (version 1.5; Cornell Laboratory of Ornithology, NY). Spectrograms of whistles were generated in Raven Pro with the following settings: fast Fourier transform (FFT) size of 2048, Hann window with 75% overlap, frequency range of 0–50 kHz, and a time series window of 10 seconds.
Whistles were classified into four categories including ‘Inferior’, ‘fair’, ‘good’ and ‘fine’ depending on their quality according to previous studies (Wang et al., 2013; Yuan et al., 2021). Only ‘good’ and ‘fine’ whistles were included in the present study. Chirps were defined as whistles with durations shorter than 0.25 seconds (Richards et al., 1984 in Jones et al., 2020). Only chirps with clearly defined contours and unambiguous start and end points were included in the analysis.
A chirp train (ChT) was defined as a sequence of at least three individual chirps. Inter-chirp intervals (IChIs) were measured as the time between the end of one chirp and the start of the next. Because whistles separated by <0.25s are usually considered to be part of a single whistle unit and most of IChIs (95.24%) within ChTs were shorter than 0.25s, ChTs were considered as distinct whistles in this study (i.e., versus considering individual chirps). To distinguish between single and multiple ChTs, the largest IChI within a chirp train could not exceed the sum of the two preceding IChIs. Chirps that did not belong to ChTs (hereafter: single chirps) and chirps that were produced within ChTs (hereafter: individual chirps) were categorized into one of six tonal types based on contour shape following Bazúa-Durán & Au (2002): U-shaped (U), convex (C), rising (R), descending (D), flat (F), and sine-shaped (S). For each chirp, 10 acoustic parameters were measured using custom MATLAB scripts for frequency-related parameters, and direct measurement from the spectrograms for other parameters (Table 1). To minimize observer bias, blinded methods were use when all acoustic data were recorded and analyzed.
Table 1 Acoustic parameters used to describe Indo-Pacific humpback dolphin chirps
|
Abbreviation
|
Acoustic parameter
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Description
|
|
Dur
|
Duration (ms)
|
End time - start time
|
|
SF
|
Start frequency (kHz)
|
Frequency at start of whistle contour
|
|
Ft0.25
|
First quartiles frequency (kHz)
|
Frequency at 0.25 of duration
|
|
Ft0.5
|
Middle quartiles frequency (kHz)
|
Frequency at 0.50 of duration
|
|
Ft0.75
|
Third quartiles frequency (kHz)
|
Frequency at 0.75 of duration
|
|
EF
|
End frequency (kHz)
|
Frequency at end of whistle contour
|
|
Fmin
|
Minimum frequency (kHz)
|
Frequency at the lowest point in whistle contour
|
|
Fmax
|
Maximum frequency (kHz)
|
Frequency at the highest point in whistle contour
|
|
FR
|
Frequency range (kHz)
|
Fmax - Fmin
|
|
Fmean
|
Mean frequency (kHz)
|
0.25 (SF + EF +Fmin + Fmax)
|
Statistical analysis
The proportion of single chirps and ChTs among the total number of whistles were calculated. The mean, minimum (Min), maximum (Max), and standard deviation (SD) were calculated for each chirp parameter. To investigate the variability of individual chirps across different ChTs and identify acoustic parameters potentially carrying communication-related information, a coefficient of variation (CV) was calculated for each measured parameter using the following formula:

The normality of the data was tested using Kolmogorov-Smirnov and Shapiro-Wilk tests and the homogeneity of variance was tested using F-tests. The potential difference in chirp duration between single chirps and individual chirps was analyzed using an independent t-test. Differences between the five time-series frequency parameters (SF, Ft0.25, Ft0.5, Ft0.75, and EF) of single chirps and individual chirps were analyzed using a Friedman test. The latter analyses were performed using IBM SPSS 19.0 (SPSS Inc., Chicago, IL, USA).
The following statistical analyses were conducted in R 4.4.1 (Hartig, 2018; Lüdecke et al., 2021R Core Team, 2021). To explore the potential function of ChTs for humpback dolphins, two univariate generalized linear models (GLMs) were fitted using the glm function from the lme4 package (Bates et al., 2015). The response variables were (1) the presence/absence of ChTs (binomial family) and (2) the number of ChTs recorded during an encounter (quasipoisson family). Predictor variables included the location (PRD, ZJ, or SNB), group size, presence/absence of young individuals (calves or juveniles), behavioral state (foraging, socializing, milling, traveling, or resting), habitat type (nearshore, open water, or boat channel), and the number of surrounding vessels. The encounter duration was included as an offset to account for increased ChT detection probability during longer encounters. Model diagnostics, including tests for normality and equal variance of residuals, were performed using the DHARMa package (Hartig, 2018). Model selection was guided by Akaike Information Criterion (AIC) and Bayesian Information Criterion (BIC) values, using the performance package (Lüdecke et al., 2021). Chi-squared tests were used to test the links between the response variables and predictors. When significant effects were detected, post hoc analyses were conducted by re-running the selected model with an appropriate sub-setting. A Bonferroni correction was applied to the post hoc outcomes.