Bioacoustic Analysis Research Articles

Species delimitation in the White-faced Cuckoo-dove (Turacoena manadensis) based on bioacoustic data

The White-faced Cuckoo-dove (Turacoena manadensis) is a poorly-known Wallacean endemic with a limited distribution on Sulawesi and its satellites, including the Togian, Banggai and Sula archipelagoes. In 1900, populations from the Sula archipelago were awarded subspecies status T. manadensis sulaensis based on smaller size and minor differences in plumage; however, this distinction has not been corroborated subsequently, and T. manadensis is considered by most modern sources to be monotypic across its range. We conducted vocal analysis of the cuckoo-doves’ main song using recordings collected from across the taxon’s natural range. Descriptive information on the songs was obtained from the recordings using bioacoustic analysis software, after which several statistical methods were used to investigate differences in vocalizations among populations. We report deep bioacoustic divergences in vocal trait pattern from across the cuckoo-doves’ range, with birds from Peleng and Taliabu in the east having a different vocal trait pattern from birds from Sulawesi, Buton, and Togian in the west. These patterns agree with changes in landmass that accompanied the sea level fluctuations caused by Pleistocene glacial cycles, and indicate that eastern and western cuckoo-dove populations are at the level of different biological species. We propose that the eastern taxon be elevated to species level as T. sulaensis. Given the rampant degree of habitat destruction in its limited range, this taxonomic change will have important implications on the conservation status of T. sulaensis.

Visualizing sound: counting wolves by using a spectral view of the chorus howling.

IntroductionMonitoring large carnivores is a central issue in conservation biology. The wolf (Canis lupus) is the most studied large carnivore in the world. After a massive decline and several local extinctions, mostly due to direct persecutions, wolves are now recolonizing many areas of their historical natural range. One of the main monitoring techniques is the howling survey, which is based on the wolves’ tendency to use vocalisations to mark territory ownership in response to howls of unknown individuals. In most cases wolf howling sessions are useful for the localisation of the pack, but they provide only an aural estimation of the chorus size.We tested and present a new bioacoustic approach to estimate chorus size by recording wolves’ replies and visualising choruses through spectrograms and spectral envelopes. To test the methodology, we compared: a) the values detected by visual inspections with the true chorus size to test for accuracy; b) the bioacoustic estimations of a sample of free-ranging wolves’ replies developed by different operators to test for precision of the method; c) the aural field estimation of chorus size of a sample of free-ranging wolves’ replies with the sonogram analysis of the same recordings to test for difference between methods.ResultsVisual inspection of the chorus by spectrogram and spectrum proved to be useful in determining the number of concurrent voices in a wolf chorus. Estimations of chorus size were highly correlated with the number of wolves counted in a pack, and 92 % of 29 known chorus sizes were recognized by means of bioacoustic analysis. On the basis of spectrographic evidence, it was also possible to identify up to seven concurrent vocalisations in a chorus of nine wolves. Spectral analysis of 37 free ranging wolves’ replies showed a high correlation between the chorus size estimations of the different operators (92.8 %), but a low correlation with the aural estimation (59.2 %).ConclusionsWolf howling monitoring technique could be improved by recording wolves’ replies and by using bioacoustic tools such as spectrograms and spectral envelopes to determine the size of the wolf chorus. Compared with other monitoring techniques (i.e., genetic analysis), bioacoustic analysis requires widely available informatic tools (i.e., sound recording set of devices and sound analysis software) and a low budget. Information obtained by means of chorus analysis can also be combined with that provided by other techniques.Moreover, howls can be recorded and stored in audio file format with a good resolution (i.e. in “Wave” format), thus representing a useful tool for future listening and investigations, which can be countlessly employed without risks of time deterioration.Electronic supplementary materialThe online version of this article (doi:10.1186/s12983-015-0114-0) contains supplementary material, which is available to authorized users.

What does Da Vinci have to do with it?

It may seem unusual to suggest a relationship between Leonardo Da Vinci (1452–1519) and the study of avian communication, as he is perhaps better known for his attempts at developing a theory of human flight based on the principles of avian flight. His approach, however, was that “from the study of structure comes the knowledge of function.” Here, I present how an understanding of the structure of the various vocalizations produced by chickadees may lend to an understanding of the function of these vocalizations. Chickadees are an excellent model system for this type of research given that they produce various calls that are comprised of individual units that may function in different ways. We have conducted several bioacoustics analyses in the search for similarities and differences among call structures, as well as attempted to delineate the bioacoustical markers that would provide meaningful information to listeners. Further, I will discuss what constitutes human “language” and how the calls of chickadees may satisfy the criteria for a non-human language. With this in mind, we use various field and laboratory techniques in an attempt to understand the structure of vocalizations which may in turn convey information regarding the function of the vocalizations.

Scaled mining of environmental acoustic data from temperate to tropical forests, from ocean to tropical rivers: A convolutional feature learning approach

Scaled passive acoustic monitoring has recently been developed to assess changes in biodiversity. It is applied to monitor changes in fauna composition associated with anthropogenic impacts and to improve the management of species and habitat conservation. Under the auspices of the “Scaled Acoustic BIODiversity” SABIOD project (CNRS MI/GDR MADICS/JASON UTLN), interdisciplinary teams collaborate to develop new joint machine learning and signal processing bioacoustic analyses. Currently, terabytes of sounds are recorded monthly using the innovative open SABIOD autonomous sensor arrays, positioned within forests or deep in the ocean. The challenges associated with tropical biodiversity as the variety of sound sources and the complexity of acoustic paths are being addressed by optimizing strategies that couple features learning, convolutional neural net, and advanced passive acoustic localization/filtering. Applications are many, including the classification of one thousand Amazon bird species, whale song classification, automatic indexing forest soundscapes, passive acoustic 3D tracking of bats and cetaceans with our patented system, and offshore cetacean monitoring. We discuss the main difficulties encountered and summarize the promising steps and strategies that we intend to pursue in the future coupling scaled CNN with Deep Scattering Spectrum. Demo/details: http://sabiod.univ-tln.fr.

Seemingly simple songs: Black-capped chickadee song revisited

Our lab has been studying songbird communication from an integrative perspective for over 13 years. A significant part of this program involves conducting bioacoustic analyses of vocalizations that are critical to survival. Initially, black-capped chickadees and their chick-a-deecall were our main research focus. In more recent years, we have turned our attention back to the fee-bee song, intensely studied by Weisman, Ratcliffe, and colleagues. Our re-examination of the fee-bee song revealed several, previously unreported features of this seemingly acoustically simple vocalization. We showed that songs contain regionalized cues for dominance status, and that females respond differentially to dominant song playback irrespective of their geographic origin. Moreover, females themselves produce a fee-bee song not previously reported in the literature. Female song is acoustically distinct from male song, and we have used operant conditioning experiments to identify features that can be used to identify sex of the singer. Finally, we have begun to explore neural response to different vocalizations, including song, and found that responses vary by singer, listener, and vocalization type. Our current efforts are aimed at unraveling the acoustic basis of communication in this nearly ubiquitous North American species.

Two New Species of Liuixalus (Rhacophoridae, Anura): Evidence from Morphological and Molecular Analyses.

Due to small body sizes, superficial similarities in morphologies, and obscure activity behaviors, the phylogeny and taxonomy of species in the genus Liuixalus were very troublesome. Some species might comprise a complex of cryptic species. To investigate the species of group, we constructed the matrilineal genealogy of the genus using 16s rRNA mitochondrial DNA sequences. Analyses recovered six well supported matrilines that involved L. romeri, L. ocellatus, L. hainanus, L. calcarius, Liuixalus shiwandashan sp. nov. and Liuixalus jinxiuensis sp. nov., though the historical relationships among them remained unresolved. Currently, Liuixalus included 4 species, distributed eastwards from northern Vietnam to Hong Kong, China. Based on genealogical and morphological distinctiveness, we described Liuixalus jinxiuensis sp. nov. from the type locality Mt. Dayao, Jinxiu, China and Liuixalus shiwandashan sp. nov. from the type locality Mt. Shiwanda, China. A combination of morphological measurements, genetic, bioacoustic and osteological analysis was served to diagnose the new taxa.

Advertisement and release calls of Phyllomedusa ayeaye (Anura: Hylidae) with comments on the social context of emission

Male calls play different roles in anuran social organization, such as spacing, territoriality and female attraction. However, calls and associated behaviors remain poorly described for many anuran species. Here we describe the advertisement and release calls of the tree frog Phyllomedusa ayeaye (Lutz, 1966) and report on the social context of emissions and a physical combat. Approximately 35 minutes of digital recordings were obtained from 34 hours of observations at one breeding site in the state of Minas Gerais, southeastern Brazil. Bioacoustic analysis showed that males emitted two types of advertisement calls: 1) simple call (a sequence of short pulsed notes) and 2) composite call (a sequence of short pulsed notes followed by a long pulsed note). Composite calls were emitted more frequently during more intense chorus activity, with various active males at the breeding site. The release call was also composed by short pulsed notes, with a wider spectrum of frequencies and emitted more rapidly than the advertisement calls. Our results suggest that the composite call of P. ayeaye may represent a mixed advertisement call. Long notes might be the aggressive part directed to males, whereas short notes directed to females. Our description of call types, their functions, and male physical interactions will be useful for studies investigating the systematics and behavior of Phyllomedusa species.

Gnominthus gen. nov., a new genus of crickets endemic to Papua New Guinea with novel acoustic and behavioral diversity (Insecta, Orthoptera, Gryllidae, Eneopterinae)

The present study describes Gnominthus, a new genus of Eneopterinae crickets from New Guinea Island (Papua New Guinea), which belongs to the tribe Lebinthini. Descriptions focus on general morphology, male and female genitalia, and forewing venation. Bioacoustical analyses of the calling song and the description of the mating behavior are also provided. The novelties found here increase the idea hypothesized before that the Lebinthini may represent a very diverse group in terms of shapes, behaviors and acoustic signals.

Calling Activity and Vocal Repertoire ofHypsiboas prasinus(Anura, Hylidae), a Treefrog from the Atlantic Forest of Brazil

Abstract: Vocalizations are important for female attraction and territory delimitation in prolonged breeding anurans. Males of Hypsiboas prasinus display year-round nocturnal calling activity, using herbaceous and bushy vegetation along the margins of ponds as calling sites. We monitored the temporal pattern of calling activity from July 2011 to June 2012, and vocalizations were recorded for bioacoustical analysis. We quantified the physical parameters for four of the five types of vocalizations found in this species: an introductory advertisement call (Type A call), a chorus advertisement call (Type B call), a resuming activity advertisement call (Type C call), and an agonistic call. Calling activity was spread throughout the annual cycle and there was no correlation between air temperature and calling activity. This finding indicates that the calling pattern is controlled predominantly by behavior and not physiology. During the cold dry season, some individuals were observed to shift their calling site...

The Sri Lankan torrent toads (Bufonidae: Adenominae: Adenomus): species boundaries assessed using multiple criteria.

The bufonid genus Adenomus, an endemic of the montane and lowland rainforests of central and south-western Sri Lanka, has been considered to comprise of three species, viz. A. kelaartii, A. dasi and A. kandianus, the last of which has been recently highlighted as "the world's rarest toad". We conducted a survey across the known range of Adenomus and used multiple criteria to delineate species boundaries within the genus. These include: a molecular phylogeny based on a 16S ribosomal RNA gene fragment; an examination of the external morphology of adults and larvae, and the skeletal morphology of adults; a bioacoustic analysis; and ecological niche modelling. We show that Adenomus is monophyletic and that it comprises only two species: A. kelaartii and A. kandianus, with A. dasi being a junior synonym of the latter. For the two valid species of Adenomus, we provide detailed osteological descriptions; clarify the distribution patterns; and provide genetic data to facilitate their scientific conservation management.

The enigmatic Black Tinamou: Do distribution, climate, and vocalizations reveal more than one species?

The Black Tinamou (Tinamus osgoodi) is a rare species with 2 recognized subspecies distributed locally. This is one of the most poorly known tinamous; few sound recordings exist, and few behavioral or sighting records are found in the literature or in ornithological databases. We compiled all the information on its geographic distribution and climate to provide a greater understanding of its current distribution. We also compiled all available sound recordings of the species in order to perform bioacoustic analyses to evaluate differences between subspecies. The 2 subspecies seem to be isolated by an ample distance, and each inhabits an area with a distinct climate. We also found some differences between their vocalizations. Future work should consider reevaluating the taxonomic status of the 2 subspecies. Conservation status of the resulting taxa must be reassessed, although more information on their ecology and natural history is needed.

Comparison of autonomous and manual recording methods for discrimination of individually distinctive Ovenbird songs

Many animals produce individually distinctive vocalizations with increased outputs during the breeding season. Many animals, including birds, can recognize other individuals based on the distinctive features of their songs and researchers can use bioacoustics tools to discriminate among individuals. Typically, bioacoustics analyses use recordings made with highly directional microphones that are free of background noise and spectral overlap. However, recent technological advances in automated recording have made it possible to record remotely and cover larger areas simultaneously. We tested whether spectrogram cross-correlation can be used to discriminate among songs of 19 individual Ovenbirds (Seiurus aurocapillus). We used two microphone types: directional (Sennheiser MKH-70) and omnidirectional (SMX-II) microphones. Because birds may vary in their distance from the SMX-II microphones, songs were selected as either high-quality (close to the recorder) or low-quality (further away from the recorder). We found that all recording types could be used to discriminate the songs of individual male Ovenbirds from other males in the population. Discrimination among directional recordings was significantly better than among omnidirectional recordings, and high-quality recordings could be used to discriminate among individuals significantly better than low-quality recordings. Taken together, our results suggest that automated omnidirectional recording could be valuable for future behavioural research allowing individuals to be followed over an entire breeding season. In addition, acoustic surveys of communities could provide information about abundance as well as presence and/or absence of species.

Taxonomy of “Mouse-colored Tapaculos” (II): An endangered new species from the montane Atlantic Forest of southern Bahia, Brazil (Passeriformes: Rhinocryptidae:Scytalopus)

ABSTRACT An isolated population of tapaculos attributed to Scytalopus speluncae has been known from the mountains of southeastern Bahia state, Brazil, since the early 1990s, and a second isolated population was discovered in 1999. Morphological and bioacoustic analyses of 11 specimens and several tape recordings indicated that these populations represent a new species, in agreement with a previous molecular phylogenetic study. This species is unambiguously distinguished from its closest relatives by 4 suites of characters: (1) morphometrics–body proportions, (2) plumage color, (3) vocalizations, and (4) genetics. Using each of these character sets, separately or in combination, one can distinguish with 100% confidence the new species from its sister lineages. The new species is known from only 5 localities distributed in 2 distinct mountain ranges, 1 on the eastern slopes of the Planalto da Conquista, between the municipalities of Boa Nova and Iguai, and another in the Serra das Lontras, ∼100 km to the so...

A review of Northern Peruvian glassfrogs (Centrolenidae), with the description of four new remarkable species.

Peru is well known for amphibian diversity and endemism, yet there have been relatively few field studies of glassfrog (Centrolenidae) diversity in this country. Research in Colombia and Ecuador indicates that centrolenid diversity is higher in the northern Andes. However, part of this trend appears to be due to sampling effort. We conducted fieldwork throughout northern Peru, and based on phylogenetic analysis of DNA sequences, combined with bioacoustic and morphological analyses of new and available material we now recognize 33 species from the country (versus 30 species prior to this work). Field surveys led to the discovery of four remarkable species: Centrolene charapita new species is a large, ornamented glassfrog that appears to be sister to Ce. geckoideum; Chimerella corleone new species represents the second-known member of the genus Chimerella; Cochranella guayasamini new species is the second-known member of the genus with humeral spines; and Hyalinobatrachium anachoretus new species occurs in the cloud forest of the east-Andean versant in Peru. In addition to the new species described here, we provide new country records, new localities including range extensions of up to 875 km, information on diagnostic characters and phylogenetic relationships, call and larval descriptions, and observations on natural history for several Peruvian centrolenids. Our results also revealed several taxonomic problems concerning species of the genus Rulyrana, and we conclude that R. croceopodes and R. tangarana are junior synonyms of R. saxiscandens. By implication of our phylogenetic analyses, we recognize the following new combinations: Espadarana audax new combination, Espadarana durrelorum new combination, and Espadarana fernandoi new combination.

The anuran calling repertoire in the light of social context

Frogs are immediately associated to their conspic- uous vocalizations emitted during the breeding season. There- fore, many scientists were inspired to study their acoustic communication. Nowadays, many types of calls are described and we felt the need of reviewing the terminology currently and historically applied. As a result, we proposed the classifi- cation of anuran vocalization into three major categories: reproductive, aggressive, and defensive calls. These catego- ries are subdivided according to the social context of emission mostly reflecting also acoustic differences among call types. Some call types are here proposed to be synonymies of the mostly used and inclusive terms. We also suggest terminologies for basic bioacoustical analyses, mostly applied incalldescriptions. Furthermore,we present cases of complex calls, including call gradation. Finally, based on novel data (such as anunusual caseof juvenile vocalizations), wediscuss situations in which it is difficult to classify call types, reflecting the need of experimental studies.

Snow buntings sing individually distinctive songs and show inter-annual variation in song structure

Birds use song to communicate with conspecifics, and song can influence both intra-sexual competition and inter-sexual mate choice. Some birds produce repertoires consisting of hundreds of songs while others produce a single song type. For species with a single-song repertoire, there are varying levels of inter-individual variation which can be the result of environmental, genetic, and physiological factors. Male Snow Buntings (Plectrophenax nivalis) typically produce a single song type, and while syllable sharing occurs between individuals, many researchers have anecdotally noted the individuality of each male's song. To investigate this long-held assertion, we performed a detailed bioacoustic analysis of male Snow Buntings recorded in the Canadian Arctic. We use canonical discriminant analysis to provide quantitative evidence confirming that male Snow Buntings sing individually distinctive songs. Furthermore, we present the first evidence that some Snow Buntings exhibit inter-annual variation in song structure; while songs remain consistent within each year, two males changed their song type between years. Inter-individual variation in song content can have important behavioral implications, because it facilitates individual recognition and can affect individual fitness.

A comparative analysis of the acoustic structure of separation calls of Mongolian wild horses (Equus ferus przewalskii) and domestic horses (Equus caballus)

Abstract In equines, calls given by foals or mothers when they are seeking contact with each other or by stallions seeking contact with other group members could be classified as affiliative or separation calls when a reunion follows the vocalizations. To investigate how domestication can affect the characteristics of vocalizations produced by equines, separation calls produced by Przewalski's (Przw) horses and Mongolian domestic horses (MDH) living in the same habitat were recorded, spectrally analyzed, and compared. Species-specific acoustic differences were found in the separation vocalizations of mares and foals. In particular, the second and third formants of the calls emitted by Przw mothers were significantly higher in frequency than those emitted by Mongolian domestic mothers, whereas the same acoustical variables were significantly lower in Przw foals than Mongolian domestic foals. Second and third formants have a significant effect on discriminating separation calls emitted by mares and foals from these different equine species. With the exception of the duration of the call, no significant species-specific differences in acoustic parameters were observed in separation calls emitted by stallions. Bioacoustic analysis can discriminate 2 different species that can be affected by their environment, evolution, and social organization.

Morphology, Molecular Genetics, and Bioacoustics Support Two New Sympatric Xenophrys Toads (Amphibia: Anura: Megophryidae) in Southeast China

Given their recent worldwide declines and extinctions, characterization of species-level diversity is of critical importance for large-scale biodiversity assessments and conservation of amphibians. This task is made difficult by the existence of cryptic species complexes, species groups comprising closely related and morphologically analogous species. The combination of morphology, genetic, and bioacoustic analyses permits robust and accurate species identification. Using these methods, we discovered two undescribed Xenophrys species, namely Xenophrys lini sp. nov. and Xenophrys cheni sp. nov. from the middle range of Luoxiao Mountains, southeast China. These two new species can be reliably distinguished from other known congeners by morphological and morphometric differences, distinctness in male advertisement calls, and substantial genetic distances (>3.6%) based on the mitochondrial 16s and 12s rRNA genes. The two new species, together with X. jinggangensis, are sympatric in the middle range of Luoxiao Mountains but may be isolated altitudinally and ecologically. Our study provides a first step to help resolve previously unrecognized cryptic biodiversity and provides insights into the understanding of Xenophrys diversification in the mountain complexes of southeast China.

Acoustic feature extraction and classification in Ishmael

Ishmael is a user-friendly bioacoustic analysis tool for Windows. It includes displays of sound waveforms and spectrograms, recording capability for real-time input, several methods for acoustic localization, beamforming, several methods for automatic call detection, and a sound annotation facility. Ishmael is intended for users wishing to analyze large volumes of data quickly and easily. Ishmael’s capabilities for classification now include a feature-extraction module that implements noise-resistant acoustic characterizations based on Fristrup’s AcouStat system (Fristrup, Woods Hole Tech. Rept. WHOI-92-04, 1992). These features can be used as input to classifier(s) connected to Ishmael and implemented in Matlab. Examples of cetacean (odontocete and mysticete) sound feature extraction and classification will be shown.

Re-evaluating the taxonomic status of Chiromantis in Thailand using multiple lines of evidence (Amphibia: Anura: Rhacophoridae).

Because of general phenotypic similarities and distribution of species across two continents, the genus Chiromantis has proven somewhat enigmatic. Among Indochinese species, the validity of C. hansenae has been questioned by some who consider it a junior synonym of C. vittatus. We employ three lines of evidence to elucidate the taxonomic status and phylogenetic relationships of four congeneric species of Chiromantis frogs from Thailand. Results of molecular, morphological, and bioacoustic data analyses support at least four evolutionarily distinct and monophyletic clades: C. doriae, C. nongkhorensis, C. vittatus and C. hansenae. Genetic divergence between C. vittatus and C. hansenae is > 10%, significantly greater than C. doriae and C nongkhorensis (4.5%). Our results support the taxonomic validity of C. hansenae and suggest that there may be more diversity within C. hansenae and C. vittatus than is currently recognized.