Bioacoustics

Bioacoustics

  • Christophe Eggert added an answer:
    Do female midwife toads call back?

    I am currently trying to assess the population size of a non-native species here in England, the midwife toad (Alytes obstetricans). So far I have only found what I think are males (as they call) but I have noticed a difference in the kind of calls that are made by the toads.When I have looked at the calls using sonogram analysis software two different calls are distinguished. I was wondering if one could be from a male and the other from a female.

    I have attached a sonogram which shows a short section of one of my recordings. Am I right in thinking that individual A is a male and individual B is a female returning his call?

    Christophe Eggert · Fauna Consult

    In Alytes obstectricans Heinzmann describes six functionnally different calls in males and two types in females. The two were a mating call and a distress call.

    Heinzmann U. 1970. Untersuchungen zur Bio-Akustik un Okologie der Geburtshelferkröte, Alytes o. obstetricans (Laur.). Oecologia. 5. 19-55

  • Carlos B. Araújo added an answer:
    Are there "must have" books on bioacoustics which you can recommend?

    I wondered if there are any books that provide information you would have loved to have as a beginner?! That give a good basis (Background knowledge, Methods, dos and don'ts) so you can avoid unnecessary mistakes in data collection, analysis etc.

    Thank you!

    Carlos B. Araújo · Universidade Federal da Paraíba

    Soundscape Ecology: Principles, Patterns, Methods and Applications; of Almo Farina (2014) is certainly a must have for beginners.

  • Corrie Schoeman added an answer:
    Does the activity of non-echolocating bats can be affected by extreme human-induced noise?

    I am curious about the idea if it is possible that non-echolocating bat species may be affected by extreme noise. Since most of the studies published deals with echolocating species. Thanks in advance! 

    Corrie Schoeman · University of KwaZulu-Natal

    Recently, we suggested that Eidolon dupreanum may use an incipient echolocation system (using laryngeal sound rather than wing clap sound as shown in the Boonman et al. 2014 paper) to navigate dark caves. So it seems likely that non-echolocation bats may be significantly affected by loud noise.

    Schoeman & Goodman 2012. Acta Chiropterologica 14: 409-416

  • Luis Henrique Soares Alves added an answer:
    I'm revising the Pseudopaludicola genus based on its bioacoustics. Could someone help me with recorded calls?
    Advertisement call of Pseudopaludicola species.
    Luis Henrique Soares Alves · Federal University of Juiz de Fora

    Boa tarde!

    Me passe seus questionamentos por email lhsalves@hotmail.com. Descrevendo metodologia e objetivo para ver o que posso fazer.

    Abraços!

  • Carlos B. Araújo added an answer:
    Can anyone study richess of song complexes of any species of Passeriformes NUMERICALLY?

    I study the riches of song complexes (dialects, sub-dialects etc) of Chaffinch (Fringilla coelebs) in Ukraine. But I did not found studies of numerical separation of these complexes and numerical description of their riches.

    Carlos B. Araújo · Universidade Federal da Paraíba

    You may use Shannon entropy measurements to calculate note disorder within the song. Please take o look in:

    SILVA, M. L. ; VIELLIARD, Jacques Marie Edme ; PIQUEIRA, J. R. C. 2000. Using shannon entropy on measuring the individual variability in the Rufous-bellied Thrush Turdus rufiventris vocal communication. Journal of Theoretical Biology, 207(1): 57-64, 

  • Eugenia Yablonovska-Grishchenko added an answer:
    Does anyone know this kind of great tit vocalization? May be a contact call?

    I’m recording great tit vocalizations around the nest during breeding. Males can use songs, alarm calls or this kind of call that I am not sure to identify (see the attached files).

    Eugenia Yablonovska-Grishchenko · National Taras Shevchenko University of Kyiv

    I identify the sound in file C5_F17_incub_out as some alarme call. This signal tits use to the address of man intruding into hteirs territory. I register this call in Kaniv Nature Reserve many times.

  • Eugenia Yablonovska-Grishchenko added an answer:
    What do you think about acoustical monitoring of owls with commercial recorders such as Olympus DM650?

    We (some Czech and Slovak ornithologists) use commercial recorders for owl monitoring (in a weatherproof box placed on the tree).

    I am looking for other people who use this method or similar. 

    Eugenia Yablonovska-Grishchenko · National Taras Shevchenko University of Kyiv

    I use Olympus LS11 for recordings of owls for individual discerning of Strix aluco. Its parameters are similar. Results are good: records at distanse 500-700 m are good-read at sonogram.

  • Gianni Pavan added an answer:
    Is it possible to estimate SPL (dB) of bird calls from .wav file (audio recording)?
    I am working on avian acoustic adaptations in urban habitats. I use Avisoft SAS LabPro and Raven Pro1.4 software. These software do give amplitude levels of sound but are exceptionally too high in comparison to measurement made by Sound Level Meter SVAN 957. What measurement setting should I do in the software for getting accurate SPL( dB) from the .wav files?
    Gianni Pavan · University of Pavia

    if you use 1/4" omnidirectional microphones you can use a sound calibrator that fits on the microphone capsule. They usually produce 94dBSPL at 1kHz. Record the calibration tone at the beginning of each recording, or at least after any level adjustment. This way you always have a reference tone in your recordings to make measures of Received Level. Then you can assess Source Level if you have a good estimate of the distance form the source. The method is great if you have suitable microphones; it works perfectly with autonomous recorders designed to capture sounds at 360°, e.g. for soundscape recording.

    However the method can't apply if you use generic microphones, cardioids, supercardioids, or parabolas. In such a case you can use a speaker with a fixed tone; in open field (not in a room!) you can set your microphone and recorder, and use to a Sound Level Meter to measure the level you receive at the microphone and take a note of the level you're recording. Don't expect great accuracy as sound propagation is often complex and received levels may vary. Once you have a good measure for a given setup and recording level ..... don't make changes and do your recording .... If you can lock your configuration (microphone, cable, recording gain and recording level) you can go on for a while ..... but periodically it is recommended to verify the calibration.

  • Paul Crump added an answer:
    How do you calculate the number of true negatives using an automated acoustic classifier?

    I’m working on an automated frog call detection problem. I’m trying to determine a good way to estimate the number of true negatives within a given sample. The true and false positives, and the false negative are easy, but to perform some of the more sophisticated analyses, one needs a value for the true negatives. True negatives in this context can be defined as the sample space within which the automated classifier could have made an incorrect classification, but did not.


    My thought was to sum the time taken up by the true and false positives then add the time taken by the false negatives (determined by multiplying the number of false negatives by the mean time of a true positive). Then subtract that value from the overall time, leaving the time that was “at risk” of incorrect classification. Then divide the remaining time by the mean time of a false negative (with the logic that if it did make a hit, it would have been incorrect) to get the number of true negatives.


    The problem with this method is that it does not work when there are lots of calls, frequently the summed time exceeds the recording time, which makes sense. I am going to explore the use of the median, but I was curious if anyone else has gone down this particular path with any degree of success?


    Cheers,

    Paul

    Paul Crump · University of New Brunswick - Saint John

    Thank you Ronald and Benedikt for your suggestions.

  • Patrícia F Monticelli added an answer:
    Bioacoustics and saline environment, is there any study about?

    I am trying to understand signal evolution in terrestrial mammals in an environment such as neotropical beach (south of Brazil, municipality of Florianópolis,Santa Catarina), humid, saline, windy versus a rural more savana like environment. I know the classical studies of Richards and Willey, Aubin and Jouventin, but I could not find any study relating saline or humidity degrees with signal funtional structure. Any possible help? Any comparison made about bird species living in coastal versus savanna environment?    

    Patrícia F Monticelli · University of São Paulo

    Dear Hervé Glotin.

    Lets follow each other here in research gate! I am preparing papers yet, that shall discuss this. Did you mean researching together?

  • Olesya Anatolyevna Astakhova added an answer:
    In clades that duet, why does one species or subclade lose their duet?

    And more broadly, are there some good cases of bioacoustic signals being lost where the reason for the loss is well-studied?

    Olesya Anatolyevna Astakhova · Lomonosov Moscow State University

    The crane (screaming birds) developed duets between female and male. In passerine birds developed song duets between males.

  • Alberto Behar added an answer:
    Decibelimeter model for bioacoustic research?

    I am looking for a decibelimeter for bioacoustic research that is not as expensive as a Brüel & Kjær and that has an enough quality. Any tips?

    Alberto Behar · Ryerson University

    Larson Davis SLM are of comparable quality to B&K and the price is much lower.

    Strongly recommended!

  • Nicolas Cusseau added an answer:
    What is the best available probe/way to measure particle motion (velocity/acceleration) of an underwater sound?

    I am looking for a way to estimate particle acceleration of an underwater sound produced by aquatic animals, per e.g. Something easy to use in the field and reliable. Like a vector sensor or an underwater geophone?

    Nicolas Cusseau · Eurogiciel

    If I model the acceleration as a = v*2*pi*f (where f is the centroid frequency), then my main concern is no longer the bounds on the velocities estimated. It is the frequency estimation because I assume the diver or the fish is introducing "micro"-Doppler effect.

    Have a look at a fish school on ADCP data to be convinced ;).

    I know that AVS is the new trend sponsored at ECUA but could someone point us to a good scientific paper (that should be the point on ResearchGate) with directivity index, gain  and bounds on the frequency-dependent DOA estimated instead of commercial articles about the Hydroflown?

  • Marie A Roch added an answer:
    Which is the best software for marine soundscape analysis?
    I am new to the soundscape analysis field. I am looking for a software that would allow me to analyse different metrics, from the basics (amplitude of a certain frequency band) to the advanced such as counting of specific signals (snapping shrimps snaps and fish vocalizations) and diversity indexes. I have limited experience with R and no experience at all with Matlab but I am willing to invest time in it if it is really worth it.
    Marie A Roch · San Diego State University

    Dear Tullio,

    There is no magic bullet that will let you detect every type of signal.  For general data exploration, I'd suggest the following software packages:  xbat (Matlab program written by Harold Figueroa from Cornell - nicely done, no longer supported and documentation is supposed to be a bit on the slim side),. Cornell's Raven, Osprey (Matlab program written by Dave Mellinger at Oregon State that has some nice annotation features), or Triton (Matlab program written primarily by Sean Wiggins at Scripps Institution of Oceanography that is designed for very large datasets and has a nice compressed spectrogram function [some of the other packages have this as well]).  There are other packages out there as well.  For detecting calls, it really depends upon your soundscape and the calls you are interested in as to how easy that is to do.  The Teager energy detector was used by Kandia and Stylianou (2006) for detecting odontocete echolocation clicks and should work well for snapping shrimp; we developed it independently and while we never published as Kandia & Stylianou beat us to the punch our description can be seen in some our papers (look at Soldevilla et al. 2008 or Roch et al. 2011).  

    I haven't done work on fish calls, but I would expect that for pulsed calls you would want to key in on some aspect of the frequency range and pulse rate. 

    If you just want a general signal detector, you could look at the work of Erbe and King (2008), they designed a signal detector that is very easy to implement and can do a pretty nice job.

    Best of luck in your research - Marie

    Erbe, C., and King, A. R. (2008). "Automatic detection of marine mammals using information entropy," J. Acous. Soc. Am. 124(5), 2833-2840.

    Kandia, V., and Stylianou, Y. (2006). "Detection of sperm whale clicks based on the Teager-Kaiser energy operator," Appl. Acous. 67(11-12), 1144-1163.

    Roch, M. A., Klinck, H., Baumann-Pickering, S., Mellinger, D. K., Qui, S., Soldevilla, M. S., and Hildebrand, J. A. (2011). "Classification of echolocation clicks from odontocetes in the Southern California Bight," J. Acous. Soc. Am. 129(1), 467-475.

    Soldevilla, M. S., Henderson, E. E., Campbell, G. S., Wiggins, S. M., Hildebrand, J. A., and Roch, M. A. (2008). "Classification of Risso's and Pacific white-sided dolphins using spectral properties of echolocation clicks," J. Acous. Soc. Am. 124(1), 609-624.

  • Gianni Pavan added an answer:
    Which acoustic software do you use for simulations (underwater or outdoor propagation)?
    I usually deal with outdoor noise propagation (noise impact assessments). I use software like Cadna, Soundplan and Predictor. I'm Interested in bioacoustics (I don't do this for a job) I'd like to know if specific software (free and not) exists to study the noise effects on animals. Sometimes reading noise reports that deal with impacts on animals I noticed that usually a dB(A) is used. Is it correct that a human filter scale can study the noise effects on animals?
    Gianni Pavan · University of Pavia

    Propagation plays an important role and in the marine environment it is really complex.

    The best available free software is ActUp, not easy but powerful:

    https://cmst.curtin.edu.au/products/actoolbox.cfm

  • Laura Kloepper added an answer:
    Is there any clue in song sonogram or spectrogram to understand which structure is producing the sound?
    I'm working with sound emission of Netrosoma (Orthoptera) from Mexico, together with Paolo Fontana. We are trying to understand which body parts are involved in sound emission since some spp are without stridulatory file.
    Laura Kloepper · Brown University
    I agree with Charles Henry about anatomical validation. In our lab we have modified a GoPro action camera (which records at 240 frames per second and fantastic resolution) with macro lenses and have been getting incredible "high speed" video of echolocating bats for a fraction of typical high speed camera costs. Contact me directly if you'd like more information on this setup--all the components are available commercially from various companies.
  • Scott R. Veirs added an answer:
    What is the best sound production software to produce sounds from scratch?
    What is the best software to produce sounds from scratch with sequences/pulses of different frequencies and intensities, for a playback study?
    Scott R. Veirs · Beam Reach Marine Science & Sustainability School
    I vote for (and use) opensource, free, platform-independent Audacity -- http://audacity.sourceforge.net/
  • Brandon Peterson added an answer:
    What is the lowest frequency of acoustic waves able to be generated in a liquid interface?
    Biomedical use of ultrasonic acoustic waves usually use frequencies in the MHz or sometimes in the kHz ranges. I am working on a project that requires much lower frequencies, and would like to know the experiences of anybody using instruments currently available to produce these low frequencies.
    Brandon Peterson · University of Groningen
    Dear all,

    No worries about "mis"information. I appreciate the forum of discussion, as multiple viewpoints always tend to generate better science than formulating an experiment based on a sole idea. As a microbiologist, waves are outside my area of expertise, so I have learned a lot already from the discussion above.

    Many thanks for all the responses.
  • Jun-Xian Shen added an answer:
    Are there italian studies on the effects of noise on animals?
    I m interested on the effects of noise on animals, in particular in studies made in Italy
    Jun-Xian Shen · Chinese Academy of Sciences
    Yes. I am still interested the studies on the effects of noise on animals, especially frogs in China. One new paper is just published on JCP A, 2014.
  • Christina Perazio added an answer:
    How to determine the pulse repetition rate of dolphin burst-pulse sounds?
    I am trying to categorize burst-pulse sounds of dolphins within a data set, and am having trouble figuring out how to determine the pulse repetition rate of a sound. Raven (Cornell software) does not seem to have any instructions on how to do it in their software, but is this something another software can do? Can you count the number of pulses visually? Do I need a code, for example in Matlab? Any help would be greatly appreciated!
    Christina Perazio · University of Southern Mississippi
    Thank you very much. I agree-the sound classification based on 'sound names' gets confusing with different authors referring to similar sounds with varying names, or very different sounds with similar names. I wanted to be more precise by using sound categories, so I have used the inter pulse interval to create classes for sounds as you suggest. I am looking into the soundruler software, since it seems to be very useful, but am having difficulty getting it to work on my mac, but I will contact the company. Thank you again!
  • Javier Almunia added an answer:
    Do wild dolphins experience age-related hearing loss, i.e. presbycusis, as is common in humans?
    Humans aren’t the only ones who lose their hearing as they grow older. Scientists report that wild Indo-Pacific humpback dolphins (Sousa chinensis), which can live 40-plus years, also have trouble picking up sounds as they age.
    http://news.sciencemag.org/biology/2013/10/scienceshot-could-you-repeat-click
    http://jeb.biologists.org/content/216/22/iii.full
    Javier Almunia · Loro Parque Fundación
    The National Marine Mammal Foundation has a research program on aging in dolphins (http://nmmf.org/aging/#more-209)

    And they have published results on the hearing loss with age, also early onset of hearing loss on males
    http://scitation.aip.org/content/asa/journal/jasa/120/6/10.1121/1.2357993
  • Ciro Alberto Sánchez added an answer:
    Does anyone have a protocol on how to calibrate a portable audio recorder?
    I am working on underwater environmental recordings made with an hydrophone (Hi Tech HTI 96 min) and a portable recorder (sony PCM M10). I would like to convert my relative negative dB values in SPL dB re 1 uPa. So far I know that I need to feed a pure sine wave in the recorder with a signal generator, read voltage with an oscilloscope, make a recording and then put these readings together with a software like Avisoft or Raven. I have access to the instruments and the software but I find it really hard to obtain detailed info about the practicality of this process. Does anyone have experience with this calibration and maybe have a protocol? I would be immensely grateful because this thing is driving me crazy.
    Ciro Alberto Sánchez · Instituto Nacional de Metrologia
    Tullio,

    You can research on CEM, Spanish Center of Metrology web site: www.cem.es
  • Gowtham Chitimireddy added an answer:
    Where can I find indications regarding the application of Directive 2008/56/EC in Italy?
    I am interested especially in the noise section.
    Gowtham Chitimireddy · Indian Institute of Technology (Banaras Hindu University) Varanasi
    even though it sound's ridiculous these details are considered confidential. so, the only place you can find solution for this in EC office in belgium
  • J. Patrick Kelley added an answer:
    Is anybody using CoolEdit for the analysis of underwater field recordings?
    I've recorded several tracks in wav format (96KHz, 24 bit, which is the maximum "resolution" allowed by my recorder), but when I open these tracks in CoolEdit and I try to zoom in the recordings, a weird thing happens (Ive already used this program and this is the first time I' ve this problem): the spectrogram is grainy...seems like a picture taken at a very low resolution in which you can detect pixels. Does anybody know how to solve this problem?
    J. Patrick Kelley · University of New Hampshire
    So, did the old version of CoolEdit have a maximum allowable sample rate?
  • Ingrid Kaatz added an answer:
    What is the best digital recorder to record sounds produced by bottlenose dolphins (Tursiops truncatus)?
    I am starting Master and I'll study about bottlenose dolphins' bioacoustic. I need to buy a new recorder and I'd like know what is the best.
    Ingrid Kaatz
    OOPS
    learning how to attach pdfs!
    Here is the bioacoustic tech paper I noted above!

About Bioacoustics

Bioacoustics refers to the investigation of sound production, dispersion through elastic media, and reception in animals, including humans. This involves neurophysiological and anatomical basis of sound production and detection, and relation of acoustic signals to the medium they disperse through. The findings give us some evidence about the evolution of acoustic mechanisms, and from that, the evolution of animals that employ them.

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