Amandine Gasc

Acoustic Indices for Biodiversity Assessment and Landscape Investigation

Jérôme Sueur1), Almo Farina2), Amandine Gasc1,3), Nadia Pieretti2), Sandrine Pavoine3,4) 1) Muséum national d’Histoire naturelle, Département Systématique et Évolution, UMR 7205-CNRS ISYEB, 45 rue Buffon, Paris, France. sueur@mnhn.fr 2) Department of Basic Sciences and Foundations, Urbino University, Urbino, Italy 3) Muséum national d’Histoire naturelle, Département Ecologie et Gestion de la Biodiversité, UMR 7204 CNRS-UPMC CESCO, 55-61 rue Buffon, 75005 Paris, France 4) Mathematical Ecology Research Group, Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK

Biodiversity Sampling Using a Global Acoustic Approach: Contrasting Sites with Microendemics in New Caledonia

New Caledonia is a Pacific island with a unique biodiversity showing an extreme microendemism. Many species distributions observed on this island are extremely restricted, localized to mountains or rivers making biodiversity evaluation and conservation a difficult task. A rapid biodiversity assessment method based on acoustics was recently proposed. This method could help to document the unique spatial structure observed in New Caledonia. Here, this method was applied in an attempt to reveal differences among three mountain sites (Mandjélia, Koghis and Aoupinié) with similar ecological features and species richness level, but with high beta diversity according to different microendemic assemblages. In each site, several local acoustic communities were sampled with audio recorders. An automatic acoustic sampling was run on these three sites for a period of 82 successive days. Acoustic properties of animal communities were analysed without any species identification. A frequency spectral complexity index (NP) was used as an estimate of the level of acoustic activity and a frequency spectral dissimilarity index (Df) assessed acoustic differences between pairs of recordings. As expected, the index NP did not reveal significant differences in the acoustic activity level between the three sites. However, the acoustic variability estimated by the index Df, could first be explained by changes in the acoustic communities along the 24-hour cycle and second by acoustic dissimilarities between the three sites. The results support the hypothesis that global acoustic analyses can detect acoustic differences between sites with similar species richness and similar ecological context, but with different species assemblages. This study also demonstrates that global acoustic methods applied at broad spatial and temporal scales could help to assess local biodiversity in the challenging context of microendemism. The method could be deployed over large areas, and could help to compare different sites and determine conservation priorities.

Temporal and spatial variability of animal sound within a neotropical forest

article i nfo Soundscape ecology aims to use biological, geophysical and anthropogenic sound to understand natural-human landscape dynamics. The analysis of natural soundscapes with no human noise is a prerequisite to understand and quantify the effects of human activity on animal ecology linked to sound. Preserved tropical forests are the lo- cation of unique, highly diverse, and animal sound. However, although the acoustic behavior of several tropical spe- cies has been examined, very few analyses have attempted tropical sounds at a spatial scale able to incorporate landscape characters. Here we analyze the acoustic structure of a neotropical forest landscape in French Guiana. We used a four dimensional synchronous acoustic sampling (three spatial dimensions and the temporal dimen- sion) by deploying an array of 24 microphones in the understory and canopy of the Nouragues Nature Reserve dur- ing a 43 day period and we undertook a detailed signal analysis to detect spatial and temporal animal acoustic heterogeneity. We identified a clear pattern of acoustic activity with four distinct periods of activity that differed by their spectral characteristics indicating acoustic heterogeneity along the 24-hour cycle but periodicity at a longer time scale. We revealed acoustic divergences between the understory and the canopy layers in terms of amplitude level and frequency content. We highlighted vertical (understory/canopy) and horizontal acoustic heterogeneities with a more diverse (frequency) patch in the north of the study area sampled and a more active (intensity) patch in the southeast of the study area. Our results show that the soundscape of a tropical forest, in the absence of human disturbance, is subtly structured in time and is heterogeneous in space. This structure is probably linked to endogenous factors that rule out the acoustic time activity of animal species, to the vertical stratification of singing communities or guilds, to horizontal variations in the distributions of species and to veg- etation spatial heterogeneity. Our study emphasizes that tropical soundscapes need to be recorded and analyzed in considerable spatial and temporal detail to understand their dynamics without the presence of human pro- duced noise. Our analysis also suggests that tropical forests are unique places for acoustic diversity, supporting the need for preservation from all perturbations including anthropic noise.

Invasive predators deplete genetic diversity of island lizards.

Invasive species can dramatically impact natural populations, especially those living on islands. Though numerous examples illustrate the ecological impact of invasive predators, no study has examined the genetic consequences for native populations subject to invasion. Here we capitalize on a natural experiment in which a long-term study of the brown anole lizard (Anolis sagrei) was interrupted by rat invasion. An island population that was devastated by rats recovered numerically following rat extermination. However, population genetic analyses at six microsatellite loci suggested a possible loss of genetic diversity due to invasion when compared to an uninvaded island studied over the same time frame. Our results provide partial support for the hypothesis that invasive predators can impact the genetic diversity of resident island populations.

First description of underwater acoustic diversity in three temperate ponds

The past decade has produced an increased ecological interest in sonic environments, or soundscapes. However, despite this rise in interest and technological improvements that allow for long-term acoustic surveys in various environments, some habitats’ soundscapes remain to be explored. Ponds, and more generally freshwater habitats, are one of these acoustically unexplored environments. Here we undertook the first long term acoustic monitoring of three temperate ponds in France. By aural and visual inspection of a selection of recordings, we identified 48 different sound types, and according to the rarefaction curves we calculated, more sound types are likely present in one of the three ponds. The richness of sound types varied significantly across ponds. Surprisingly, there was no pond-to-pond daily consistency of sound type richness variation; each pond had its own daily patterns of activity. We also explored the possibility of using six acoustic diversity indices to conduct rapid biodiversity assessments in temperate ponds. We found that all indices were sensitive to the background noise as estimated through correlations with the signal-to-noise ratio (SNR). However, we determined that the AR index could be a good candidate to measure acoustic diversities using partial correlations with the SNR as a control variable. Yet, research is still required to automatically compute the SNR in order to apply this index on a large data set of recordings. The results showed that these three temperate ponds host a high level of acoustic diversity in which the soundscapes were variable not only between but also within the ponds. The sources producing this diversity of sounds and the drivers of difference in daily song type richness variation both require further investigation. Such research would yield insights into the biodiversity and ecology of temperate ponds.

Future directions for soundscape ecology: The importance of ornithological contributions

ABSTRACT Building upon the rich legacies of bioacoustics and animal communication, soundscape ecology represents a new perspective through which ecologists can use the acoustic properties of ecosystems to understand the complex interactions of organisms, geophysical dynamics, and human activities. In this paper, we focus on the potential benefits of a soundscape approach for enhancing ornithological research and of ornithological perspectives for advancing the nascent field of soundscape ecology. We first summarize 4 major grounding principles of soundscape ecology in relation to avian ecology, evolution, and behavior. We then propose 3 research objectives that we envision as future directions for soundscape ecology: development of (1) soundscape metrics and interpretation, (2) understanding of soundscape drivers, and (3) soundscape-based disturbance indicators. Ornithological contributions can help advance the field of soundscape ecology to obtain these research objectives across various spatial, temporal, and organizational scales. Detailed ornithological knowledge can aid in the improvement of soundscape databases, interpretation of soundscape metrics, and validation of soundscape theories. Such contributions should also invite input from other taxonomic-group specialists, further enriching soundscape ecology. Reciprocally, soundscape approaches can enrich ornithology by offering an acoustic-based theoretical framework grounded in a broad ecological context, hosting soundscape collections from diverse ecosystems, and advancing acoustic methodologies. This paper is intended to stimulate further discussion and collaboration between ornithologists, soundscape ecologists, and any researchers studying sound in an ecological context in order to enhance research in these important domains of ecology.

Screening large audio datasets to determine the time and space distribution of Screaming Piha birds in a tropical forest

Acoustic monitoring has proved to be an efficient approach to monitor wildlife, notably in environments with limited visibility, such as tropical rainforests. Today, recording equipment allows acoustic data to be gathered in remote areas at wide spatial and temporal scales. The resulting datasets are large and the use of automated processing systems to extract relevant information can greatly facilitate their analysis. Here, we have developed signal processing techniques to reveal the spatio-temporal dynamics of an emblematic bird voice of the neotropical forest: the song of the Screaming Piha (Lipaugus vociferans). Using recordings made in a French Guianan lowland forest, with an array of 24 microphones in a three dimensional space, we implemented a detection system based on spectrogram cross-correlation to trace the vocalisations of L. vociferans. We tuned the detection system based on the percentage area under the Receiver Operating Characteristic curve, finding a maximum of 95.88%. To strictly minimise false positives, we set the operating point to have 34.9% true positives and 0% false positives. We detected a total of 12,735 songs attributed to the study bird during 25 study days. We found that spatial patterns of lower activity corresponded to a zone having smaller trees and more tree gaps — a known liana forest patch — suggesting that Screaming Piha birds tend to avoid non-mature primary forests. The sampling sites near the creeks had more detections than the sites further away, suggesting that the lek mating arenas might be distributed strategically to be near to a source of water. We also found a marked temporal pattern. The lek was active during the whole day, from sunrise to sunset, with two peaks of activity shifted by more than 2 h from the dawn and dusk chorus. The approach described here can be tested using other conspicuous and stereotyped sounds that occur within a heterogeneous and noisy background. To decipher the complex interacting sounds of the tropical forest, these focal studies on specific acoustic elements should be complemented with community or soundscape analysis, to demonstrate the human impact on the ecosystem and to provide guidelines for natural resource management.

Data storage and sharing for the long tail of science

Research data infrastructure such as storage must now accommodate new requirements resulting from trends in research data management that require researchers to store their data for the long term and make it available to other researchers. We propose Data Depot, a system and service that provides capabilities for shared space within a group, shared applications, flexible access patterns and ease of transfer at Purdue University. We evaluate Depot as a solution for storing and sharing multi-terabytes of data produced in the long tail of science with a use case in soundscape ecology studies from the Human-Environment Modeling and Analysis Laboratory. We observe that with the capabilities enabled by Data Depot, researchers can easily deploy fine-grained data access control, manage data transfer and sharing, as well as integrate their workflows into a High Performance Computing environment.

Dyadic behavioural interactions in cockroaches (Blaberidae): ecomorphological and evolutionary implications

Few studies have assessed the relative importance of morphological, ecological and phylogenetic factors in the evolution of social behaviour. We examine the role of these factors in social evolution among blaberid cockroaches. We first analyse and compare behavioural interactions in 13 species. We then ask how the nature of these interactions relates to body shape, phylogeny and habitat. We showed that, although these cockroaches display diverse behavioural interactions, a structure in these data exists with some species clustering together. We found that similarity in social interactions was related to species body shape, but not to ecology or phylogenetic relationships. We suggest that body shape plays an important role in the evolution of social behaviour and that this factor should be investigated further in future analyses.

A new technique for analysing interacting factors affecting biodiversity patterns: crossed-DPCoA.

We developed an approach for analysing the effects of two crossed factors A and B on the functional, taxonomic or phylogenetic composition of communities. The methodology, known as crossed-DPCoA, defines a space where species, communities and the levels of the two factors are organised as a set of points. In this space, the Euclidean distance between two species-specific points is a measure of the (functional, taxonomic or phylogenetic) dissimilarity. The communities are positioned at the centroid of their constitutive species; and the levels of two factors at the centroid of the communities associated with them. We develop two versions for crossed-DPCoA, the first one moves the levels of factor B to the centre of the space and analyses the axes of highest variance in the coordinates of the levels of factor A. It is related to previous ordination approaches such as partial canonical correspondence analysis and partial non-symmetrical correspondence analysis. The second version projects all points on the orthogonal complement of the space generated by the principal axes of factor B. This second version should be preferred when there is an a priori suspicion that factor A and B are associated. We apply the two versions of crossed-DPCoA to analyse the phylogenetic composition of Central European and Mediterranean bird communities. Applying crossed-DPCoA on bird communities supports the hypothesis that allopatric speciation processes during the Quaternary occurred in open and patchily distributed landscapes, while the lack of geographic barriers to dispersal among forest habitats may explain the homogeneity of forest bird communities over the whole western Palaearctic. Generalizing several ordination analyses commonly used in ecology, crossed-DPCoA provides an approach for analysing the effects of crossed factors on functional, taxonomic and phylogenetic diversity, environmental and geographic structure of species niches, and more broadly the role of genetics on population structures.