Temporal Variability in Acoustic Behavior of Snapping Shrimp in the East China Sea and Its Correlation With Ocean Environments

The snapping shrimp sound is known to be a major biological noise source of ocean soundscapes in coastal shallow waters of low and mid-latitudes where sunlight reaches. Several studies have been conducted to understand the activity of snapping shrimp through comparison with surrounding environmental factors. In this paper, we report the analysis of the sound produced by snapping shrimp inhabiting an area where sunlight rarely reaches. The acoustic measurements were taken in May 2015 using two 16-channel vertical line arrays (VLAs) moored at a depth of about 100 m, located ∼100 km southwest of Jeju Island, South Korea, as part of the Shallow-water Acoustic Variability Experiment (SAVEX-15). During the experiment, the underwater soundscape was dominated by the broadband impulsive snapping shrimp noise, which is notable considering that snapping shrimp are commonly observed at very shallow depths of tens of meters or less where sunlight can easily reach. To extract snapping events in the ambient noise data, an envelope correlation combined with an amplitude threshold detection algorithm were applied, and then the sea surface-bounced path was filtered out using a kurtosis value of the waveform to avoid double-counting in snap rate estimates. The analysis of the ambient noise data received for 5 consecutive days indicated that the snap rate fluctuated with a strong one-quarter-diurnal variation between 200 and 1,200 snaps per minute, which is distinguished from the periodicity of the snap rate reported in the euphotic zone. The temporal variation in the snap rate is compared with several environmental factors such as water temperature, tidal level, and current speed. It is found that the snap rate has a significant correlation with the current speed, suggesting that snapping shrimp living in the area with little sunlight might change their snapping behavior in response to changes in current speed.

Biological Sound Sources Drive Soundscape Characteristics of Two Australian Marine Parks

Soundscapes represent an intrinsic aspect of a habitat which, particularly in protected areas, should be monitored and managed to mitigate human impacts. Soundscape ecology characterizes acoustic interactions within an environment, integrating biological, anthropogenic, climatological, and geological sound sources. Monitoring soundscapes in marine protected areas is particularly important due to the reliance of many marine species on sound for biological functions, including communication and reproduction. In this study we establish a baseline understanding of underwater soundscapes within two marine National Park Zones (NPZs) along the east coast of Australia: Cod Grounds Marine Park and an NPZ surrounding Pimpernel Rock within Solitary Islands Marine Park. In each of the NPZs, underwater recorders were deployed twice during the austral winter (33–35 days, 2018 and 60–69 days, 2019) and once during the austral summer (35–71 days, 2018–2019). We used the resulting acoustic recordings to determine hourly presence of anthropogenic and biological sounds between 20 Hz and 24 kHz and analyze their contributions to patterns of received sound levels. Sounds from vessels were recorded on most days throughout monitoring but were not found to influence long-term patterns of sound levels over their corresponding frequencies. Biological sources included dolphins, snapping shrimp, fish choruses, humpback whales, and dwarf minke whales. Dolphins, snapping shrimp, and fish choruses were present in all deployments. Median ambient sound levels showed a consistent diel pattern with increased levels resulting from crepuscular fish choruses combined with a higher intensity of snapping shrimp snaps during those times. Singing humpback whales strongly influenced the overall sound levels throughout the winter migration, while dwarf minke whales were consistently detected in the 2019 winter deployment but were only present in 2 h among the earlier deployments. Patterns of acoustic spectra were similar between the two NPZs, and patterns of soundscape measurements were observed to be driven by seasonal differences in biological contributions rather than anthropogenic sound sources, indicating that these NPZs are not yet heavily impacted by anthropogenic noise. These baseline measurements will prove invaluable in long-term monitoring of the biological health of NPZs.

The effects of temperature and pH change on the snapping sound characteristic of Alpheus edwardsii

Aim: The current study undertook manipulative experiments to observe changes in snapping shrimp sound signals in relation to temperature and pH changes. Methodology: Sounds of intertidal snapping shrimp (Alpheus edwardsii) sequentially exposed to different temperature/pH treatments manipulation for a period of 2 week each, were recorded in the laboratory and analysed. The acoustic characteristics of snapping sound signal were examined to relate to the change in temperature, pH and combination of both parameters. Results: Our results showed that there was a significant reduction in the frequency of peak amplitude of snapping sound wave following a two week exposure to a combination of temperature and pH treatments. The frequency of snapping shrimp sound decreased by approximately 30% when exposed to a 2°C increase in temperature and a 0.7 unit decrease in pH, however, elevated temperature alone caused no significant effect on the peak frequency of snapping shrimp sound. Interpretation: The finding suggests that following the prediction values of temperature and pH changes due to climate change in the coming century may implicate the ambient noise at habitats where snapping shrimps dominate.

Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama

Background The formation of the Isthmus of Panama and final closure of the Central American Seaway (CAS) provides an independent calibration point for examining the rate of DNA substitutions. This vicariant event has been widely used to estimate the substitution rate across mitochondrial genomes and to date evolutionary events in other taxonomic groups. Nuclear sequence data is increasingly being used to complement mitochondrial datasets for phylogenetic and evolutionary investigations; these studies would benefit from information regarding the rate and pattern of DNA substitutions derived from the nuclear genome. Results To estimate the genome-wide neutral mutation rate (µ), genotype-by-sequencing (GBS) datasets were generated for three transisthmian species pairs in Alpheus snapping shrimp. A range of bioinformatic filtering parameters were evaluated in order to minimize potential bias in mutation rate estimates that may result from SNP filtering. Using a Bayesian coalescent approach (G-PhoCS) applied to 44,960 GBS loci, we estimated µ to be 2.64E−9 substitutions/site/year, when calibrated with the closure of the CAS at 3 Ma. Post-divergence gene flow was detected in one species pair. Failure to account for this post-split migration inflates our substitution rate estimates, emphasizing the importance of demographic methods that can accommodate gene flow. Conclusions Results from our study, both parameter estimates and bioinformatic explorations, have broad-ranging implications for phylogeographic studies in other non-model taxa using reduced representation datasets. Our best estimate of µ that accounts for coalescent and demographic processes is remarkably similar to experimentally derived mutation rates in model arthropod systems. These results contradicted recent suggestions that the closure of the Isthmus was completed much earlier (around 10 Ma), as mutation rates based on an early calibration resulted in uncharacteristically low genomic mutation rates. Also, stricter filtering parameters resulted in biased datasets that generated lower mutation rate estimates and influenced demographic parameters, serving as a cautionary tale for the adherence to conservative bioinformatic strategies when generating reduced-representation datasets at the species level. To our knowledge this is the first use of transisthmian species pairs to calibrate the rate of molecular evolution from GBS data.