Search

Animals produce a wide array of sounds with highly variable acoustic structures. It is possible to understand the causes and consequences of this variation across taxa with phylogenetic comparative analyses. Acoustic and evolutionary analyses are rapidly increasing in sophistication such that choosing appropriate acoustic and evolutionary approaches is increasingly difficult. However, the correct choice of analysis can have profound effects on output and evolutionary inferences. Here, we identify and address some of the challenges for this growing field by providing a roadmap for quantifying and comparing sound in a phylogenetic context for researchers with a broad range of scientific backgrounds. Sound, as a continuous, multidimensional trait can be particularly challenging to measure because it can be hard to identify variables that can be compared across taxa and it is also no small feat to process and analyse the resulting high-dimensional acoustic data using approaches that are appropriate for subsequent evolutionary analysis. Additionally, terminological inconsistencies and the role of learning in the development of acoustic traits need to be considered. Phylogenetic comparative analyses also have their own sets of caveats to consider. We provide a set of recommendations for delimiting acoustic signals into discrete, comparable acoustic units. We also present a three-stage workflow for extracting relevant acoustic data, including options for multivariate analyses and dimensionality reduction that is compatible with phylogenetic comparative analysis. We then summarize available phylogenetic comparative approaches and how they have been used in comparative bioacoustics, and address the limitations of comparative analyses with behavioural data. Lastly, we recommend how to apply these methods to acoustic data across a range of study systems. In this way, we provide an integrated framework to aid in quantitative analysis of cross-taxa variation in animal sounds for comparative phylogenetic analysis. In addition, we advocate the standardization of acoustic terminology across disciplines and taxa, adoption of automated methods for acoustic feature extraction, and establishment of strong data archival practices for acoustic recordings and data analyses. Combining such practices with our proposed workflow will greatly advance the reproducibility, biological interpretation, and longevity of comparative bioacoustic studies.

Evaluating changes in the collective behavior of a population can be an indirect method for inferring organismal responses to changing environmental conditions. Apex predators, such as the sperm whale (Physeter macrocephalus), can provide valuable insights into the ecosystem processes of the deep sea, where little direct observation can be made. Sperm whales are often difficult to observe at sea, as they inhabit deep, offshore waters and spend most of their lives beneath the surface. However, sperm whales are extremely amenable to passive acoustic monitoring, as their vocalizations are well-studied, highly distinguishable, produced regularly, and can be detected at relatively long ranges (>10 km). Sperm whales produce distinct clicks in two behavioral contexts (social interaction or foraging/prey capture); thus, we can use acoustic detection of these vocalizations to infer patterns of large-scale, collective behavior, which is similar to studying calling frogs or insects indicating their reproductive phenology. We recorded behaviorally-specific sperm whale vocalizations at three sites in the Northern Gulf of Mexico in July 2010 and 2011. We used these recordings to construct population-level time budgets, an empirical collective metric of behavior, based on the ratio of hours in a day with social clicks to the hours in a day with foraging clicks, and represented this as an “acoustic activity index.” Our index showed significant differences in the proportions of social and foraging behavior across the range of sperm whales in the Northern Gulf of Mexico, and the proportion of social activity increased by more than a factor of two from 2010 to 2011. These differences support previous evidence of differential habitat use by sperm whales in the Gulf of Mexico, and suggest possible changes in environmental conditions between years. Thus, the acoustic activity index may provide a powerful way to evaluate changes in behavior and link them to changing ecological conditions. This novel application of bioacoustics to constructing time budgets and creating a behaviorally-based index at the population scale can serve as an indicator of ecological change, and greatly enhance our ability to understand the behavior and ecology of many acoustically active species.

Many fish species produce sounds as a part of their reproductive behavior. Using passive acoustic recording approaches, these sounds can be used to document temporal and spatial patterns of reproductive activity of fish populations. We conducted an 11-month passive acoustic survey at three different locations off the coasts of Georgia (40 km north of Grays Reef National Marine Sanctuary) and North Carolina (Onslow Bay) to understand the spawning phenology of two species of acoustically active fishes: black drum (Pogonias cromis) and toadfish (Opsanus sp.). Due to the depth of the recording locations, we could not confirm whether the toadfish calls were produced by O. tau, or another Opsanus species. Both taxa have readily identifiable, distinct sounds. Chorusing sounds from both species were detected at all three Georgia sites and at two of the three North Carolina locations; chorusing duration of both species was greater in Georgia. The onset and duration of chorusing activity for both species was correlated with water temperature. The abundance of calls of these two species from field recordings further demonstrates the value of long-term passive acoustic surveys for understanding the reproductive seasonality of acoustically active fish species.

As part of the Deepwater Horizon Oil Spill Natural Resource Damage Assessment in the Gulf of Mexico, we conducted a large passive acoustic survey across the eastern Gulf continental shelf edge to assess impacts to sperm whale population. In the months immediately after the spill, sperm whale occurrence was significantly higher in areas closest to the spill. Over the following seasons in 2010-2011, we documented cyclical patterns of decreased and increased occurrence suggesting that this population exhibits a seasonal occurrence pattern in the region, with seasonal movements to other regions, and not likely directly influenced by the oil spill. Unfortunately, a lack of adequately scaled, pre-spill data on sperm whales, along with limitations on the survey duration constrain our ability to infer spill-related changes in sperm whale occurrence. However, our study establishes post-disaster baseline data for continued monitoring, and an expanded study design could provide a model for continued monitoring.

Ornaments used in courtship often vary wildly among species, reflecting the evolutionary interplay between mate preference functions and the constraints imposed by natural selection. Consequently, understanding the evolutionary dynamics responsible for ornament diversification has been a longstanding challenge in evolutionary biology. However, comparing radically different ornaments across species, as well as different classes of ornaments within species, is a profound challenge to understanding diversification of sexual signals. Using novel methods and a unique natural history dataset, we explore evolutionary patterns of ornament evolution in a group—the birds-of-paradise—exhibiting dramatic phenotypic diversification widely assumed to be driven by sexual selection. Rather than the tradeoff between ornament types originally envisioned by Darwin and Wallace, we found positive correlations among cross-modal (visual/acoustic) signals indicating functional integration of ornamental traits into a composite unit—the “courtship phenotype.” Furthermore, given the broad theoretical and empirical support for the idea that systemic robustness—functional overlap and interdependency—promotes evolutionary innovation, we posit that birds-of-paradise have radiated extensively through ornamental phenotype space as a consequence of the robustness in the courtship phenotype that we document at a phylogenetic scale. We suggest that the degree of robustness in courtship phenotypes among taxa can provide new insights into the relative influence of sexual and natural selection on phenotypic radiations., Author summary Animals frequently vary widely in ornamentation, even among closely related species. Understanding the patterns that underlie this variation is a significant challenge, requiring comparisons among drastically different traits—like comparing apples to oranges. Here, we use novel analytical approaches to quantify variation in ornamental diversity and richness across the wildly divergent birds-of-paradise, a textbook example of how sexual selection can profoundly shape organismal phenotypes. We find that color and acoustic complexity, along with behavior and acoustic complexity, are positively correlated across evolutionary timescales. Positive links among ornament classes suggests that selection is acting on correlated suites of traits—a composite courtship phenotype—and this integration may be partially responsible for the extreme variation in signal form that we see in birds-of-paradise.

The distribution and seasonal patterns of the North Atlantic right whale, Eubalaena glacialis, inform management decisions that mitigate anthropogenic threats. Based on data from visual surveys, much of the population migrates between winter calving grounds in coastal waters adjacent to the southeast USA and summer feeding and nursery grounds adjacent to the northeast USA. However, little is known about right whale occurrence along the mid-Atlantic US migratory corridor. A better understanding of right whale occurrence in this region is needed prior to off- shore wind energy development activities, which may increase mortality risks and chronic impacts on the population. We conducted an 11 mo passive acoustic survey along coastal North Carolina and Georgia near several wind energy areas to document the acoustic occurrence of right whales in the southern region of the mid-Atlantic US coast. Right whales were acoustically detected across all seasons, with peak seasonal presence occurring during autumn in the Georgia site and during winter in the North Carolina site. A secondary peak in presence also occurred dur- ing June and July in the Georgia site, when right whales were not expected to be in the area. Given the nearly year-round presence of right whales in the survey areas, these results may war- rant an evaluation of current management protocols in order to provide adequate protection to the population in the face of offshore energy development activities.

Species' conservation relies on understanding their seasonal habitats and migration routes. North Atlantic right whales (Eubalaena glacialis), listed as endangered under the U.S. Endangered Species Act, migrate from the southeastern U.S. coast to Cape Cod Bay, Massachusetts, a federally designated critical habitat, from February through May to feed. The whales then continue north across the Gulf of Maine to northern waters (e.g., Bay of Fundy). To enter Cape Cod Bay, right whales must traverse an area of dense shipping and fishing activity in Massachusetts Bay, where there are no mandatory regulations for the protection of right whales or management of their habitat. We used passive acoustic recordings of right whales collected in Massachusetts Bay from May 2007 through October 2010 to determine the annual spatial and temporal distribution of the whales and their calling activity. We detected right whales in the bay throughout the year, in contrast to results from visual surveys. Right whales were detected on at least 24% of days in each month, with the exception of June 2007, in which there were no detections. Averaged over all years, right whale calls were most abundant from February through May. During this period, calls were most frequent between 17:00 and 20:00 local time; no diel pattern was apparent in other months. The spatial distribution of the approximate locations of calling whales suggests they may use Massachusetts Bay as a conduit to Cape Cod Bay in the spring and as they move between the Gulf of Maine and waters to the south in September through December. Although it is unclear how dependent right whales are on the bay, the discovery of their widespread presence in Massachusetts Bay throughout the year suggests this region may need to be managed to reduce the probability of collisions with ships and entanglement in fishing gear.

Male fin whales, Balaenoptera physalus, produce a song consisting of 20 Hz notes at regularly spaced time intervals. Previous studies identified regional differences in fin whale internote intervals (INI), but seasonal changes within populations have not been closely examined. To understand the patterns of fin whale song in the western North Atlantic, the seasonal abundance and acoustic features of fin whale song are measured from two years of archival passive acoustic recordings at two representative locations: Massachusetts Bay and New York Bight. Fin whale 20 Hz notes are detected on 99% of recorded days. In both regions, INI varies significantly throughout the year as two distinct periods: a “short-INI” season in September–January (9.6 s) and a “long-INI” season in March–May (15.1 s). February and June–August are transitional-INI months, with higher variability. Note abundance decreases with increasing INI, where note abundance is significantly lower in April–August than in September–January. Short-INI and high note abundance correspond to the fin whale reproductive season. The temporal variability of INI may be a mechanism by which fin whale individuals encode and communicate a variety of behaviorally relevant information.

Species' conservation relies on understanding their seasonal habitats and migration routes. North Atlantic right whales (Eubalaena glacialis), listed as endangered under the U.S. Endangered Species Act, migrate from the southeastern U.S. coast to Cape Cod Bay, Massachusetts, a federally designated critical habitat, from February through May to feed. The whales then continue north across the Gulf of Maine to northern waters (e.g., Bay of Fundy). To enter Cape Cod Bay, right whales must traverse an area of dense shipping and fishing activity in Massachusetts Bay, where there are no mandatory regulations for the protection of right whales or management of their habitat. We used passive acoustic recordings of right whales collected in Massachusetts Bay from May 2007 through October 2010 to determine the annual spatial and temporal distribution of the whales and their calling activity. We detected right whales in the bay throughout the year, in contrast to results from visual surveys. Right whales were detected on at least 24% of days in each month, with the exception of June 2007, in which there were no detections. Averaged over all years, right whale calls were most abundant from February through May. During this period, calls were most frequent between 17:00 and 20:00 local time; no diel pattern was apparent in other months. The spatial distribution of the approximate locations of calling whales suggests they may use Massachusetts Bay as a conduit to Cape Cod Bay in the spring and as they move between the Gulf of Maine and waters to the south in September through December. Although it is unclear how dependent right whales are on the bay, the discovery of their widespread presence in Massachusetts Bay throughout the year suggests this region may need to be managed to reduce the probability of collisions with ships and entanglement in fishing gear.

The possible effects of anthropogenic noise on the marine environment is becoming an important topic in the oceanic community. The exploration for fossil-fuel or alternative energy and the construction of facilities to support these endeavors often requires sizable construction efforts; which usually require permitting to study the impact of noise on the environment. Of particular interest is the variety of data products used to influence environmental impact reports and the processing time required to generate these data from large amounts of passive acoustic recordings. This paper outlines work being done by the Bioacoustics Research Program at Cornell University and the Lab of Ornithology, (BRP) for developing MATLAB tools in support of environmental compliance reporting. Due to the success of acoustic monitoring, understanding acoustic signatures is now becoming part of environmental impact assessment and required compliance for permitting. BRP has leveraged various existing tools and capabilities which result in integrated special purpose software tools within a MATLAB toolbox called SEDNA1. SEDNA incorporates various tools to measure acute and chronic noise levels, detect and classify marine mammal vocalizations, and compute various metrics such as receive levels, signal excess, masking and communication space. This work will summarize the high performance computing strategy used in the SEDNA Toolbox along with the capability to integrate various layers of data within a modeling framework that incorporates ambient noise, vessel and animal data. Finally, the work will demonstrate the power of this approach through animated data visualization, showing animal, vessel and ambient noise integrated over relatively large temporal and spatial scales.

Using multiple acoustic sensors in an array for estimating sound source location relies on time synchrony among the devices. When independent time synchrony methods—such as GPS time stamps—are unavailable, the precision of the time base in individual sensors becomes one of the main sources of error in synchrony, and consequently increases the uncertainty of location estimates. Quartz crystal oscillators, on which many acoustic sensors base sampling rate timing, have a vibration frequency that varies with temperature f(T). Each oscillator exhibits a different frequency-temperature relationship, leading to sensor-dependent sample rate drift. Our Marine Autonomous Recording Units (MARUs) use such oscillators for their sample rate timing, and they experience variations in temperature of at least 20°C between preparation in air and deployment underwater, leading to sample rate drift over their deployments. By characterizing each MARU’s oscillator f(T) function, and measuring the temperature of the MARU during ...

Large whales communicate primarily in the low (