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FIGURE 15 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 15. Spectrograms and oscillograms showing intra-specific call variation in two treefrog species from Madagascar, exemplifying the need to account for the possibility of different call / note types and of strong influence of motivation when taxonomically interpreting bioacoustical differences. (A) Males of Boophis at Antsatramidola, Madagascar, were emitting two very different types of calls, one of which might represent a territorial call. However, we never heard the two calls from the same individuals and therefore in the field were convinced of the presence of two morphologically cryptic species. Subsequent genetic study revealed that the individuals were all conspecific with B. tampoka and emitting two different call types (Köhler et al. 2007; Vences et al. 2011). (B) Boophis ankaratra emits long series of notes. Typical note repetition rate is reflected by the call from Manjakatompo, emitted by a male in the presence of several other calling males. At Itremo, during a dry evening, only few specimens were sporadically calling and obviously were in a state of low sexual motivation; despite a slightly higher temperature, note repetition rate was much lower at this occasion. Spectrograms produced with CoolEdit Pro at Hanning window function, 256 bands resolution.
FIGURE 21 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 21. Spectrograms and oscillograms showing frog advertisement calls with components at frequencies higher than usually reported, partly reaching into the ultrasound spectrum. In these four frog species, the dominant frequency is below 10 kHz but harmonics are visible at much higher frequency. Eleutherodactylus iberia (from Bahia de Taco, Cuba) and Stumpffia sp. [Ca6 Vieites et al. 2009] (from Andasibe, Madagascar) are miniaturized frogs with <11 mm snout-vent length (SVL) whereas Eleutherodactylus [Ca4 Rodríguez et al. 2010b] and Platypelis barbouri are small sized frogs around 20 mm SVL. Note that frequency of the spectrograms goes up to 40 kHz. Eleutherodactylus [Ca4] has almost no frequency components in the ultrasound spectrum, yet frequency reaches distinctly above 10 kHz, much higher than usually reported for frogs. Recordings were made with ultrasound microphone Ultramic200k (Dodotronic, Italy). Graphics produced with the R package Seewave (Sueur et al. 2008a). All spectrograms produced at Hanning window function, 1024 bands resolution. Format of candidate species names follows Padial et al. (2010).
FIGURE 7 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 7. Concordance and discordance among call centered and note centered approaches to name sound units in anuran vocalizations. The upper two schematic spectrograms show examples where both approaches lead to the same categorization of sounds. (A) A single tonal sound is repeated after regular silent intervals of longer duration than the sounds. There is no defined duration of the series of sounds; if undisturbed, calling could go on for minutes or hours. In both approaches, one sound unit would be a call, and the note-centered approach would define each call consisting of a single note. (B) Series of rapidly repeated sounds, each composed of a series of bursts of sound energy. Because these bursts are <10 ms in duration they are defined as pulses. The call-centered approach does not define each major subunit as call because the silent intervals between them are much shorter than the units themselves; thus, both approaches agree in defining the units as notes. (C) This species emits clearly defined and stereotyped series of sounds, each series being separated by variable intervals from the next series. The note-centered approach defines one coherent entity of sound emission as a call; hence, each sound series unit is a call, and the subunits are notes. In contrast, the call-centered approach defines each sound unit as a call (and each series as a call series) because it is separated from other such units by a long silent interval. (D) This species emits two distinct kinds of pulsatile sound units, of which one is much longer than the other. Because the combination of sounds is emitted as coherent entity, in the note centered approach the entire sound emission is a call and the sound units are notes of two types, of which one is arranged in a series. In the call-centered approach, each sound unit is a call because they are separated by long silent intervals from the next unit. Two call types can be distinguished and one of these is arranged in a call series.
FIGURE 4 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 4. Comparative spectrograms of a call of Dryophytes andersonii, all drawn with Hanning window function, showing the effect of different FFT resolution on the graphic representation of calls. Each spectrogram shows the identical 300 ms section of a recording. Note that with higher FFT settings, the spectral detail of the call representation increases. At lower FFT settings, the temporal pattern of the call is more clearly recognizable. Call recording taken from Elliot et al. (2009). Graphics produced with the R package Seewave (Sueur et al. 2008a).
FIGURE 1 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 1. Inspiratory calling of Bombina bombina (above) and expiratory calling in Pelophylax kl. esculentus (below). Oscillograms show one call and small photos show state of vocal sac at the respective time indicated. Video and sound recorded with a Nikon D750 and processed in Windows Movie Maker software; oscillograms drawn in CoolEdit Pro 2.0 software. Recording of Bombina made at Schorfheide-Chorin Reserve, Germany on 24 May 2015; recording of Pelophylax made at Riddagshausen Reserve, Braunschweig, Germany, on 2 June 2015.
FIGURE 20 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 20. Results of a spectrogram cross-correlation analysis (FFT = 1024, window = Hanning, overlap = 90%) comparing one call of Bombina bombina at Schorfheide-Chorin Reserve, Germany, recorded with four different combinations: Tascam DR05 digital recorder with Sennheiser K6/ME66 microphone (Tascam); Edirol R09 recorder with built-in microphone (Edirol); Sony D6C analog tape recorder (fitted with a type II cassette tape) with Audio Technica ATR6250 external microphone (Sony); and Apple iPhone 6 with built-in microphone (iPhone). Values in the cells represent pairwise pixel-bypixel similarity values between spectrograms, produced from the respective recordings of the same individual call.
FIGURE 6 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 6. Hierarchy of main units and subunits proposed for the description of anuran vocalizations. Call, note and pulse are primary units (in gray boxes). Call is the fundamental unit which might consist of a single note or several notes. In call descriptions, units can consist only of subunits in top-down direction of decreasing hierarchy. Pulses are defined here as the smallest, undividable unit.
FIGURE 19 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 19. Comparison of the recording performance of four different recorder/microphone combinations on a set of nine advertisement calls of one individual of Bombina bombina at Schorfheide-Chorin Reserve, Germany. All recordings were made simultaneously at the same recording distance, and same calls were thus compared. Call variables were automatically assessed using SoundRuler software (see text for details on the methods employed). Recording equipment as follows: Tascam DR-05 digital recorder/Sennheiser K6+ME66 microphone; Edirol R09 recorder with built-in microphone; Macintosh iPhone 6 with built-in microphone and recording software; Sony D6C cassette tape recorder with Audiotechnica external microphone (recordings digitized with CoolEdit Pro software at sampling rate of 44.1 kHz). Rise time is the time from the start of a call to the point where it reaches the maximum amplitude. Shape-on is the ratio between the rise time and the total duration of a call. Other call properties as defined in the text. Boxplots show median (middle line), first and third quartiles (upper and lower box limits), and non-outlier range (whiskers).
FIGURE 13 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 13. Comparative spectrograms and oscillograms exemplifying the effect of hybridization on the call structure of anurans. The two tree frogs Phyllomedusa distincta (diploid) and P. tetraploidea (tetraploid) co-occur and hybridize in Ribeirão Branco, south of São Paulo state, Brazil, producing triploid hybrids (3n = 39) (Haddad et al. 1994; Gruber et al. 2013). Their advertisement calls are of similar structure and indistinguishable to the human ear, but have subtle quantitative differences (Student's t-Test = 11.06; p <0.0001): 6–11 notes (7.8 ± 1.02; n = 31 calls from 3 males) in P. distincta, 8–17 notes (12.8 ± 2.4; n = 58 calls from 8 males) in P. tetraploidea (4n). An intermediate range of 6–16 notes (9.7 ± 1.9; n = 78 calls from 9 males) is found in triploid hybrids (3n). Recordings obtained in the hybridization zone (Ribeirão Branco, São Paulo, Brazil) using a Nagra E tape recorder and a Sennheiser ME80 microphone, at air temperatures varying from 14.5 to 21 o C. All recorded specimens were karyotyped to confirm their identities. Spectrograms made with the R package Seewave (Sueur et al. 2008a) with Hanning window function at 512 bands FFT resolution.
FIGURE 10 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 10. Individual, intraspecific and interspecific call trait variation in Leptodactylus spp. exemplified by the trait call duration. (A) Individual variation in call duration during one night in individual A (one nightly calling activity phase of ca. 1 hrs of calling; N = 4,401 calls; 18 November 2014; 29.1 to 29.4 °C); (B) Intraspecific variation: comparison of call durations of three individuals during each one night of calling (individual A: see above; individual B: n = 22,472 calls, ca. 5:20 hrs of calling, 27 November 2014, 23.0 to 23.4 °C; individual C: n = 15,561, 2:50 hrs of calling, 14 November 2014, 22.7 to 23.4 °C); (C) Interspecific variation: comparison of Kernel density estimates of call durations of three sympatric species (L. syphax: same three individuals as above, n = 38,434 calls; L. mystacinus: one individual, ca. 3:20 hrs of calling, n = 49,573, 24 January 2012, 25.1 to 25.9 °C; L. vastus, one individual, ca. 1:10 hrs of calling, n = 3,649 calls, 16 November 2014, 25.2 to 26.4 °C). All recordings were done at the Research Station 'Chiquitos', Bolivia, with Song Meters SM2 (Wildlife Acoustics) respectively Olympus DM-550 recorders (sampling frequency 22.05 kHz; 16-bit resolution), and afterwards analyzed with software Raven Pro, version 1.4 (Bioacoustics Research Program 2011) using implemented amplitude detectors; statistics were done with R; only calls with high amplitude were considered (i.e., less intense 'initial calls' of a series were excluded; M. Jansen, unpublished data).
FIGURE 17 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 17. Interpretation of advertisement call differences: (A) Example showing spectrograms and oscillograms with distinct qualitative call differences of two frogs in sympatry (syntopy), providing evidence for species-level divergence, despite a comparatively low level of genetic divergence (Köhler et al. 2010). (B) Example showing distinct and constant quantitative call differences of two frogs in sympatry (syntopy), providing clear indication of species-level divergence, corroborated by high genetic divergence (Vences et al. 2010b). Spectrograms produced with CoolEdit Pro at Hanning window function, 256 bands resolution.
FIGURE 18 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 18. Interpretation of advertisement call differences: (A) Spectrograms and oscillograms of calls of two allopatric frog species without any significant differences (evidence for species-level divergence by molecular genetics and tadpole morphology; Vences et al. 2010a). (B) Moderate structural call differences of two allopatric populations currently assigned to the same species. The calls of Blommersia wittei from Sambava and Andrakata are composed of clicking notes of a metallic sound, whereas at Nosy Be, Benavony, and Montagne d'Ambre, notes contain pulses and calls exhibit less distinct inter-note intervals. Spectrograms produced with CoolEdit Pro at Hanning window function, 256 bands resolution.
FIGURE 16 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 16. Spectrograms illustrating qualitative call differences between closely related species (all mantellid frogs from Madagascar). All spectrograms show only a section of a longer series of notes. Gephyromantis eiselti and G. thelenae form a clade together with a third species (Kaffenberger et al. 2011). While G. eiselti emits series of tonal notes, G. thelenae emits much slower series of much longer pulsed notes at similar temperatures. Boophis majori and B. narinsi are sister species (Wollenberg et al. 2011) and differ extremely in note duration and note repetition rate (short clicks vs. long pulsatile sounds). In both cases, the species in each pair occur in syntopy and are extremely similar to each other in adult morphology. Despite distinct qualitative call differences, genetic divergences between each of the two species pairs are remarkably low (p-distances 2.2–3.3% in a fragment of the mitochondrial 16S rRNA gene; Wollenberg & Harvey 2010; Vences et al. 2012a). In such extreme cases of bioacoustical divergence, and if the presence of different call types or recording artifacts can be excluded, bioacoustical data provide conclusive evidence for species level divergence. Recordings from Vences et al. (2006, 2012a); spectrograms made with the R package Seewave (Sueur et al. 2008a) at Hanning windowing function, 512 bands resolution.
FIGURE 9 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 9. Example illustrating the need to consider homology aspects in terminoloy of anuran vocalizations. The calls shown are from four related species of mantellid frogs in the nominal subgenus of the genus Gephyromantis. The four species emit vocalizations consisting of a series of sound units (each corresponding to one expiration), with a defined number of units per series. All spectrograms are to scale; for G. boulengeri, an entire series is shown whereas the remaining spectrograms show parts of a series. In a note-centered terminology, one entire series would be a call, and each sound unit a note. In a call-centered terminology, in G. boulengeri, a series might be defined as one call (because no intervals of full silence occur between sound units), while in G. enki, each sound unit would be a call (separated by wide intervals of silence from the next call) and the series would be a call series. Either definition might be appropriate when looking at a single species, but in a comparative taxonomic study, it is of utmost importance to compare homologous bioacoustical entities and to apply the same name to them; hence, in a call centered approach, also the vocalization of G. boulengeri would need to be dubbed a call series. Spectrograms made with the R package Seewave (Sueur et al. 2008a) at Hanning windowing function, 512 bands resolution. Note that we here refer to homology from the perspective of sound production (one unit corresponding to one expiration) and not from the perspective of signal content of the respective sound unit.
FIGURE 12 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 12. Nightly variation of dominant frequency (A) and call duration (B) in one individual of Leptodactylus syphax. One nocturnal activity phase of ca. 2 hrs of calling (n = 8,106 calls; 29.9 to 31.8 °C). Recording was obtained on 17 November 2014 at the Research Station 'Chiquitos', Bolivia, with a Song Meter SM2 (Wildlife Acoustics; sampling frequency 22,050 Hz; 16- bit resolution), and afterwards analyzed with software Raven Pro, version 1.4 (Bioacoustics Research Program 2011) using implemented amplitude detectors; statistics were done with R; only calls with high amplitude were considered (i.e., less intense 'introductory calls' of a series were excluded). Red lines show smoothed data (Local Polynomial Regression Fitting with span=0.05; M. Jansen & A. Masurowa, unpubl. data).
FIGURE 23 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 23. Spectrograms and oscillograms of calls of the same individual of Bombina bombina recorded at different saturations of the recording levels and different recording distances (Tascam DR-05 digital recorder and a Sennheiser K6/ ME66 microphone; water temperature 22.1 °C; 24 May 2015 at Schorfheide-Chorin Reserve, Germany). Calls were successively recorded from the same individual within a short time period of ca. 30 minutes and each spectrogram thus shows a different call. The upper left spectrogram is from a recording with recording levels in the field deliberately set on oversaturation. The other three spectrograms were analyzed with equalized levels. Note that the number of harmonics is highest in the oversaturated recording, but also depends on recording distance, with the highest-frequency harmonics disappearing with increasing distance. Sounds of birds and insects are visible on the recordings that were not filtered to allow objective comparison. All spectrograms made with the R package Seewave (Sueur et al. 2008a), with settings: Hanning window function, 1024 bands resolution, overlap = 90%.
FIGURE 14 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 14. Variation of two call traits within the Madagascar-Comoroan anuran family Mantellidae. (A) Correlation of dominant frequency and maximum male snout-vent length in 155 mantellid species. (B) Variation of note duration (mean, minimum and maximum values) among 171 species of mantellids, ordered by mean note duration (5–20 measurements per species). On Y-axis values are arranged along a logarithmic scale for graphical reasons (but scale shows original values in milliseconds, not log-transformed values). Notes defined following a note-centered scheme (cf. Fig. 7).
Products developed through the "What About Model Data?, Determining Best Practices for Preservation and Replicability, EarthCube Research Coordination Network" project
This dataset includes products developed through the "What About Model Data? Determining Best Practices for Preservation and Replicability, EarthCube Research Coordination Network (RCN)" project. Products include: 1) a rubric worksheet to assist researchers in deciding what simulation output needs to be preserved in a trusted, community repository to communicate knowledge and satisfy publisher and funder requirements, 2) instructions on how to use the rubric worksheet, which include reference use cases, and 3) outputs and presentations from the three project workshops.
Artifact for "Efficient Construction of Practical Python Call Graphs with Entity Knowledge Base"
<p>This is the artifact for the paper entitled "Efficient Construction of Practical Python Call Graphs with Entity Knowledge Base"</p>
Data for PASP paper: Optimal photometry of point sources: Joint source flux and background determination on array detectors - from theory to practical implementation
<p>High-resolution figures for paper "Optimal photometry of point sources: Joint source flux and background determination on array detectors - from theory to practical implementation", accepted for publication in The Publications of the Astronomical Society of the Pacific (PASP).</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.