The species-specific character of sounds in the animal kingdom has been extensively documented, yet research on fishes has predominantly focused on a limited number of species, overlooking the potential of acoustic signals to reflect broader taxonomic ranks. In this study, we analyzed acoustic data of hand-held sounds from 388 specimens spanning 5 genera and 33 species within the family Holocentridae, with the objective of evaluating the use of sound characteristics for taxonomic discrimination across various levels (subfamily, genus, species). Sounds could be indicative of grouping. Taxa discriminability depends on taxonomic level; the higher the taxonomic level, the better the discrimination of taxa based on sounds. Analogous to the role of morphological traits in taxonomic delineation, this research corroborates the utility of acoustic features in identifying fish taxa across multiple hierarchical levels. Remarkably, certain holocentrid species have evolved complex sound patterns characterized by unique temporal arrangements where pulses are not continuous but emitted in blocks, facilitating the exploitation of the acoustic space.
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.
more » « less- Award ID(s):
- 1755132
- PAR ID:
- 10449270
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Biological Reviews
- Volume:
- 96
- Issue:
- 4
- ISSN:
- 1464-7931
- Format(s):
- Medium: X Size: p. 1135-1159
- Size(s):
- p. 1135-1159
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
Abstract -
Coral reefs comprise some of the most biodiverse habitats on the planet. These ecosystems face a range of stressors, making quantifying community assemblages and potential changes vital to effective management. To understand short- and long-term changes in biodiversity and detect early warning signals of decline, new methods for quantifying biodiversity at scale are necessary. Acoustic monitoring techniques have proven useful in observing species activities and biodiversity on coral reefs through aggregate approaches (i.e. energy as a proxy). However, few studies have ground-truthed these acoustic analyses with human-based observations. In this study, we sought to expand these passive acoustic methods by investigating biological sounds and fish call rates on a healthy reef, providing a unique set of human-confirmed, labeled acoustic observations. We analyzed acoustic data from Tektite Reef, St. John, US Virgin Islands, over a 2 mo period. A subset of acoustic files was manually inspected to identify recurring biotic sounds and quantify reef activity throughout the day. We found a high variety of acoustic signals in this soundscape. General patterns of call rates across time conformed to expectations, with dusk and dawn showing important and significantly elevated peaks in soniferous fish activity. The data reflected high variability in call rates across days and lunar phases. Call rates did not correspond to sound pressure levels, suggesting that certain call types may drive crepuscular trends in sound levels while lower-level critical calls, likely key for estimating biodiversity and behavior, may be missed by gross sound level analyses.more » « less
-
Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. To circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. We successfully sequenced the genomes of 15 AM fungal species for which genome data was not previously available. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. We evaluated the phylogenetic placement of Glomeromycota in relation to its sister phyla (Mucoromycota and Mortierellomycota), and found no support to reject a polytomy. Finally, we explored the phylogenetic relationships within Glomeromycota. Our results support family level classification from previous phylogenetic studies, and the polyphyly of the order Glomerales with Claroideoglomeraceae as the sister group to Glomeraceae and Diversisporales.more » « less
-
more » « less
Abstract Vocalization is a common means of communication across vertebrates, but the evolutionary origins of the neural circuits controlling these behaviors are not clear. Peripheral mechanisms of sound production vary widely: fish produce sounds with a swimbladder or pectoral fins; amphibians, reptiles, and mammalians vocalize using a larynx; birds vocalize with a syrinx. Despite the diversity of vocal effectors across taxa, there are many similarities in the neural circuits underlying the control of these organs. Do similarities in vocal circuit structure and function indicate that vocal behaviors first arose in a single common ancestor, or have similar neural circuits arisen independently multiple times during evolution? In this review, we describe the hindbrain circuits that are involved in vocal production across vertebrates. Given that vocalization depends on respiration in most tetrapods, it is not surprising that vocal and respiratory hindbrain circuits across distantly related species are anatomically intermingled and functionally linked. Such vocal‐respiratory circuit integration supports the hypothesis that vocal evolution involved the expansion and functional diversification of breathing circuits. Recent phylogenetic analyses, however, suggest vocal behaviors arose independently in all major tetrapod clades, indicating that similarities in vocal control circuits are the result of repeated co‐options of respiratory circuits in each lineage. It is currently unknown whether vocal circuits across taxa are made up of homologous neurons, or whether vocal neurons in each lineage arose from developmentally and evolutionarily distinct progenitors. Integrative comparative studies of vocal neurons across brain regions and taxa will be required to distinguish between these two scenarios.
-
Warning signals are well known in the visual system, but rare in other modalities. Some moths produce ultrasonic sounds to warn bats of noxious taste or to mimic unpalatable models. Here, we report results from a long-term study across the globe, assaying moth response to playback of bat echolocation. We tested 252 genera, spanning most families of large-bodied moths, and document anti-bat ultrasound production in 52 genera, with eight subfamily origins described. Based on acoustic analysis of ultrasonic emissions and palatability experiments with bats, it seems that acoustic warning and mimicry are the raison d'être for sound production in most moths. However, some moths use high-duty-cycle ultrasound capable of jamming bat sonar. In fact, we find preliminary evidence of independent origins of sonar jamming in at least six subfamilies. Palatability data indicate that jamming and warning are not mutually exclusive strategies. To explore the possible organization of anti-bat warning sounds into acoustic mimicry rings, we intensively studied a community of moths in Ecuador and, using machine-learning approaches, found five distinct acoustic clusters. While these data represent an early understanding of acoustic aposematism and mimicry across this megadiverse insect order, it is likely that ultrasonically signaling moths comprise one of the largest mimicry complexes on earth.more » « less
