# A Collection of Best Practices for the Collection and Analysis of Bioacoustic Data
## 4 Ecosystem Biodiversity  
A third area of inquiry that is benefiting from advances in bioacoustic methods, related to the prior two, concerns sampling of species richness. In particular, the development of acoustic biodiversity indices that tally species richness [105; 106; 107] is allowing for relatively rapid assessment and monitoring of ecosystem biodiversity. Researchers can link acoustic parameters such as spectral amplitude, amplitude variability, and number of frequency bands with biotic parameters such as species diversity and abundance or number of distinct vocalizations. This approach allows for the quick tracking of changes in species community composition related to factors such as seasonality [108], anthropogenic noise [107], invasive species [105], habitat loss, or climate change [109]. As with studies of species identification and population structure (above), it is helpful in acoustic studies of ecosystem biodiversity to consider the type and location of one's recording platform, and to ensure that methods used to process data are appropriate for the sample at hand. If, for example, when generating spectrograms, FFT size is too large in relation to the recording sampling rate, some temporal resolution will be lost, given the necessary trade-offs in sound analysis between time and frequency resolution [110]. Additionally, data collected should capture temporal, ecosystem, behavioral, or geographic variability as appropriate to the study question. If the study aims to compare multiple ecosystems, data collection and processing methods should be consistent across all target regions. A caveat that is particularly relevant for the study of ecosystem biodiversity is that by default, many acoustic biodiversity indices will integrate over all types of acoustic signals detected. If, however, a given species produces distinct signals in different behavioral states, these different signals may not be attributed to a single species and the resulting estimate of species diversity may be artificially elevated. In addition, many recordings include extraneous sounds, both biological (of other species) and ambient, which if not correctly classified could further inflate estimates of species diversity. For these reasons, verification of the vocal repertoires of individual species, only possible through direct field observations (see above) or captive studies, are critical for valid application of bioacoustic data for species richness and abundance calculations. A related challenge is to account for variation in probabilities of signal detection, given that some types of sounds will be harder to detect than others [111]. The behavioral and environmental parameters that impact detection probabilities are unknown for the signals of many species; they include the likelihood of occurrence of different types of vocalizations; vocal frequency, duration, and amplitude; the rate at which different signals attenuate; and the dynamic local environment effects on sound propagation. An accurate assessment of acoustic biodiversity in any ecosystem, and more specifically the confidence we can place on indices generated from acoustic data, will rely on our ability to reliably detect those species that are present. In a study of avian biodiversity in a temperate woodland, [PERSON] et al. [69] generated estimates of biodiversity using acoustic as well as traditional methods and determined whether results from the two sets of methods matched. [PERSON] et al. also asked whether the acoustic indices could be used to track daily biodiversity variation. Towards these ends, the researchers collected acoustic recordings at three woodland sites over two three-hour periods at dawn and dusk for 73 consecutive days. Acoustic recorders were positioned at least 300 m from each other to avoid overlap in recordings, each at a height of 2 m with microphones pointed horizontally.