Many animals emit vocal sounds which, independently from the sounds’ function, contain some individually distinctive signature. Thus the automatic recognition of individuals by sound is a potentially powerful tool for zoology and ecology research and practical monitoring. Here, we present a general automatic identification method that can work across multiple animal species with various levels of complexity in their communication systems. We further introduce new analysis techniques based on dataset manipulations that can evaluate the robustness and generality of a classifier. By using these techniques, we confirmed the presence of experimental confounds in situations resembling those from past studies. We introduce data manipulations that can reduce the impact of these confounds, compatible with any classifier. We suggest that assessment of confounds should become a standard part of future studies to ensure they do not report over-optimistic results. We provide annotated recordings used for analyses along with this study and we call for dataset sharing to be a common practice to enhance the development of methods and comparisons of results.

Animals use acoustic signals for communication, implying that the properties of these signals can be under strong selection. The acoustic adaptation hypothesis predicts that species in dense habitats emit lower‐frequency sounds than those in open areas because low‐frequency sounds propagate further in dense vegetation than high‐frequency sounds. Signal frequency may also be under sexual selection because it correlates with body size and lower‐frequency sounds are perceived as more intimidating. Here, we evaluate these hypotheses by analysing variation in peak song frequency across 5,085 passerine species (Passeriformes). A phylogenetically informed analysis revealed that song frequency decreases with increasing body mass and with male‐biased sexual size dimorphism. However, we found no support for the predicted relationship between frequency and habitat. Our results suggest that the global variation in passerine song frequency is mostly driven by natural and sexual selection causing evolutionary shifts in body size rather than by habitat‐related selection on sound propagation.

1. In field ecological and behavioural studies, it is often necessary to identify specific individuals. In birds, colour rings are frequently used to mark individuals; however, rings are often difficult to observe, especially in small species and dense habitats. Acoustic-based monitoring detecting individuals by their characteristic vocalization is a potentially suitable alternative, but this approach is challenging in species with complex songs. 2. On the example of the Tree Pipit (Anthus trivialis), a small migratory passerine often singing in flight or from perches obscured by foliage, we demonstrate that acoustic monitoring based on the syllable repertoire can be very efficient tool for individual recognition. During a 3-year study, we obtained over 500 recordings from males from one study population (a number of them returning after winter). Males banded with colour rings were repeatedly recorded throughout the seasons, and syllable repertoires were determined from spectrograms for each recording. 3. The repertoire of each unambiguously identified male was distinct and stable within as well as between seasons; and males with similar syllable repertoires differed in syntax. Based on the congruence between identification based solely on spectrogram assessment, and that based on observation of colour rings, we inferred that reliable identification of singing males (including non-ringed ones) was possible in the studied population from assessing a repertoire and song syntax of <5-min recording (containing 20-30 songs). The acoustic-based data: (i) increased the overall estimated number of territorial males at the study locality (from 49 ringed to 61), and improved the estimates of the period of their presence; (ii) revealed dynamic within-season changes in territory occupancy that would otherwise be missed; and (iii) allowed identification of returning birds (including nonringed ones and those actively avoiding approaching humans). 4. Our results suggest that some commonly used methods may substantially underestimate return rates of migratory bird species. Individual acoustic monitoring should be applicable on various bird species with complex song and stable repertoires, and may be particularly useful for those living in dense habitat or sensitive to handling.

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Bird song plays an important role in the establishment and maintenance of prezygotic reproductive barriers. When two closely related species come into secondary contact, song convergence caused by acquisition of heterospecific songs into the birds’ repertoires is often observed. The proximate mechanisms responsible for such mixed singing, and its effect on the speciation process, are poorly understood. We used a combination of genetic and bioacoustic analyses to test whether mixed singing observed in the secondary contact zone of two passerine birds, the Thrush Nightingale (Luscinia luscinia) and the Common Nightingale (L. megarhynchos), is caused by introgressive hybridization. We analysed song recordings of both species from allopatric and sympatric populations together with genotype data from one mitochondrial and seven nuclear loci. Semi-automated comparisons of our recordings with an extensive catalogue of Common Nightingale song types confirmed that most of the analysed sympatric Thrush Nightingale males were ‘mixed singers’ that use heterospecific song types in their repertoires. None of these ‘mixed singers’ possessed any alleles introgressed from the Common Nightingale, suggesting that they were not backcross hybrids. We also analysed songs of five individuals with intermediate phenotype, which were identified as F1 hybrids between the Thrush Nightingale female and the Common Nightingale male by genetic analysis. Songs of three of these hybrids corresponded to the paternal species (Common Nightingale) but the remaining two sung a mixed song. Our results suggest that although hybridization might increase the tendency for learning songs from both parental species, interspecific cultural transmission is the major proximate mechanism explaining the occurrence of mixed singers among the sympatric Thrush Nightingales. We also provide evidence that mixed singing does not substantially increase the rate of interspecific hybridization and discuss the possible adaptive value of this phenomenon in nightingales.