LifeCLEF Bird Identification Task 2017

International audienceThe LifeCLEF challenge BirdCLEF offers a large-scale proving ground for system-oriented evaluation of bird species identification based on audio recordings of their sounds. One of its strengths is that it uses data collected through Xeno-canto, the worldwide community of bird sound recordists. This ensures that BirdCLEF is close to the conditions of real-world application, in particular with regard to the number of species in the training set (1500). The main novelty of the 2017 edition of BirdCLEF was the inclusion of soundscape recordings containing time-coded bird species annotations in addition to the usual Xeno-canto recordings that focus on a single foreground species. This paper reports an overview of the systems developed by the five participating research groups, the methodology of the evaluation of their performance, and an analysis and discussion of the results obtained

Can soundscape indices be used to reflect biodiversity in an Ecuadorian Andean tropical montane habitat?

The measurement of biodiversity presents a challenging task for conservationists. Traditional ecological descriptors such as species richness, Shannon and Simpson diversities have long been relied on by ecologists to provide an indication of biodiversity, however, the generation of these indices requires manual assessments of local fauna through methods which can often be expensive, time consuming and invasive. Analysis of the Soundscape, the collection of sounds generated by organisms (biophony), humans (anthrophony) and non-biological sounds such as wind and water (geophony), presents new potential for biodiversity sampling. To date, a range of indices have been developed that aim to provide a value relating to acoustic characteristics of an environment, based on the spectral and temporal properties within sound recordings. Several studies have yielded promising results when using the acoustic indices for biodiversity assessments in temperate, and to some extent, tropical habitats. We here aimed to further the current understanding of soundscape indices by investigating how they behave in a tropical habitat of high avifaunal diversity. Point count data for bird species was collected from the Santa Lucia Cloud Forest Reserve, NW Ecuador (0°17'30"N, 78°40'30"W), during Summer 2014, while acoustic recordings were taken simultaneously using a handheld audio recorder. We first analysed the change in bird species composition and diversity along two environmental gradients of habitat disturbance and altitude, and investigated how the acoustic indices behaved along these same gradients. We then explored whether the acoustic indices can be used to estimate biodiversity based on their correlation with traditional ecological indices. From the point count data we found a high turnover in species composition across sample sites. Mean species richness was found to negatively correlate with increasing altitude (p=1.485e-05) and was found to be significantly lower in sites of primary forest than in both secondary forest and silvopasture (p=0.0165). Although each of the acoustic indices showed varying levels of change across the environmental gradients, we found that only four of the eight acoustic indices, the Normalized Difference Soundscape Index (NDSI, p=0.048), spectral entropy Hs, p=0.033), temporal entropy (Ht, p=0.031), and total entropy (H, p=0.031), were found to significantly correlate with species composition. We found that spectral entropy (Hs) and total entropy (H) were the only acoustic indices to significantly correlate with ecological indices, however since the total entropy (H) is developed as a product of the spectral entropy (Hs) we suggest that only the H index should be utilised for biodiversity measurements. We found that while the acoustic indices have the potential to characterise certain features of a habitat or to assist in analysing bird species composition, their use for biodiversity assessment is limited. We would suggest that more work to develop and understand the indices is needed before we can reliably make use of them for measuring biodiversity

Avian communities and ecoacoustics in a tropical human-modified landscape

Large areas of the tropics have been cleared of forest and converted to agriculture. The consequent human-modified landscapes (HMLs) comprise a heterogenous mix of habitats; forest fragments and riparian strips are embedded in a matrix of cattle pasture, non-native timber plantations, and urban centres. These habitat changes can have dramatic consequences for wildlife, leading to range shifts and extirpations. In turn, this can influence the integrity of ecosystem services such as frugivory and seed dispersal. Understanding how habitat conversion affects natural ecosystems is critical to inform conservation interventions, but requires long-term biodiversity monitoring and detailed knowledge of species-level responses to HMLs. The research presented in this thesis was conducted in the Emparador HML, in central Republic of Panama. In Chapter 2, we show that the regional avian community is shaped by extent of forest cover across the landscape, and to a lesser degree, extent of forest fragmentation and distance to core forest. Effects of forest cover and fragmentation were examined at local (10 ha) and landscape (500 ha) scales. Species-level responses to these factors varied widely; while abundance of many species increased with greater local-scale forest cover, greater landscape-scale forest cover was often associated with declines. Generalist species that readily persist in HMLs still responded positively to local-scale forest cover, suggesting that even smaller forest fragments in these landscapes are important for maintaining diverse avian assemblages. Critically, we found that species’ responses were not associated with particular traits such as dietary composition or forest dependence, highlighting that species may often exhibit idiosyncratic responses to landscape structure. Chapters 3 and 4 address the wider issue of long-term monitoring, and the potential for data collection over large spatiotemporal scales using remote audio recorders. Ecoacoustics, the study of environmental sound is a relatively new discipline, and as such there is still considerable uncertainty surrounding best-practice for collecting and processing recordings. One of the most straightforward means of utilising audio recordings for environmental monitoring is via acoustic indices. These are objective measures of sound based on features such as pitch and amplitude. To date, attempts to use these indices have been hindered by inconsistent or inappropriate methodologies. In Chapter 3, we determine how many recordings are required to comprehensively capture a soundscape, the acoustic energy of a location. Furthermore, we demonstrate that there are habitat-specific patterns in acoustic indices values, suggesting that these indices reflect differences in vegetation structure and wildlife. We develop this further in Chapter 4, where we show that avian species richness and abundance are clearly linked to patterns in acoustic indices values. Critically, these patterns were coherent among habitat types emphasising their potential for monitoring. Acoustic indices sensitive to the frequencies occupied by bird song have the greatest potential for monitoring an avian community. The results from these two chapters suggest that acoustic indices can be effective tools for monitoring biodiversity, with values reflecting consistent differences across habitats, and among avian assemblages. Audio recordings are a source of permanent, verifiable evidence that can be collected at much greater spatiotemporal scales than traditional biodiversity monitoring data. As the use of audio recorders grows, it is important to compare their efficacy with standard methods of data collection. In Chapter 5, we contrast data derived from audio recordings with that gathered using standard point count methods, and consider whether recorders are a feasible means of surveying antbirds (Thamnophilidae), a disturbance-sensitive avian taxon. Both approaches revealed species’ responses to landscape structure, with qualitatively similar patterns in response to forest cover and vegetation quality. We show that common species can be readily monitored using audio recorders, with greater levels of detectability compared with point counts. However, rarer species were more likely to be detected using point counts. The work presented in this thesis helps to explain the patterns seen in avian responses to Neotropical HMLs. In particular we emphasise the importance of forest cover for maintaining bird assemblages in these landscapes. We demonstrate the utility of audio recorders for data collection, and highlight their potential for future biodiversity monitoring. In the face of human population growth, and ongoing habitat disturbance and agricultural intensification, conservation efforts are essential to avoid widespread species extinctions and ecosystem collapse. Interventions must take place in HMLs, to bolster ecosystem services, provide buffer zones for protected areas, and improve connectivity in the wider landscape

Population and Migratory Ecology of Canada Warblers (Cardellina canadensis) in the Central Appalachian Mountains, West Virginia, USA

Nearctic-Neotropical migrant birds experience a wide range of environmental conditions throughout their annual cycle; thus, it is particularly challenging to evaluate the spatial factors that may influence population growth. The Canada Warbler (Cardellina canadensis) faces substantial range-wide population declines, but little study has been conducted regarding elements occurring across the entire year that drive demographic rates. The aims of this research are (1) determine the relationship between Canada Warbler population demographic rates and environmental conditions along an elevation gradient in the central Appalachian Mountains and (2) ascertain the nonbreeding season location and migratory routes used by the central Appalachian population, which is near the southern extent of the entire breeding range. Research occurred from 2019 – 2021 at six study sites ranging in elevation from 526 – 1282m spanning an approximate 130km north-south gradient within the Monongahela National Forest, West Virginia, USA. To determine the relationship between demographic rates and environment, I assessed adult annual survival and daily nest survival. I uniquely color-banded 203 adult male Canada Warblers in 2019 and 2020, and resighted marked birds in 2020 and 2021. I modeled survival in response to predictor variables including elevation, rhododendron coverage, available stream length, topographic position, and aspect. I implemented a spatial Cormack-Jolly-Seber model with Bayesian methods and compared models using DIC criteria. To determine nest survival, I located nests and monitored their outcomes using motion-sensitive game cameras. I modeled daily nest survival as a function of elevation, rhododendron coverage, other shrub coverage, topographic position, and aspect using Bayesian methods and compared models using DIC. I found that elevation was the best predictor of adult survival, which increased from 0.573 (95% credible intervals (CI) = 0.333 – 0.820) at 555 m to 0.702 (95% CI = 0.493 – 0.871) at 1255 m, although the slope coefficient of the elevation effect overlapped 0. I located 12 nests in 2021, of which 9 fledged successfully. The intercept-only model was the best predictor of daily survival, which, exponentiated over the 19-day nesting period, resulted in a posterior mean nest survival of 0.604 (95% CI = 0.527 – 0.696). To elucidate the migration ecology of the population, I deployed 32 light-level geolocator tags on adult males in 2020 and retrieved tags in 2021. I recovered 13 (40.1%) geolocators, of which 10 provided data on post-breeding (fall) migration routes and nonbreeding season sites, and nine provided data on pre-breeding (spring) migration routes. The nonbreeding sites were clustered nonrandomly in Colombia, indicative of potential population connectivity. Post-breeding migration was largely overland through Mexico and Central America, with potential trans-Gulf flights by some birds. Pre-breeding migration routes by each individual were significantly (t = -4.75, df = 8, p = 0.001) further east than the post-breeding route, based on the minimum (westernmost) longitude recorded during migration (mean difference = 232km), consistent with a pattern of anticlockwise loop migration. Overall, my research documented critically lacking information on region-specific relationships between demographic rates and environmental conditions and provides the first insight into the migratory ecology of a population of Canada Warblers near the southern extent of their breeding range. My results fill crucial ecological knowledge gaps for an imperiled species and serve as a foundation for full annual cycle demographic modeling

Methodology for ecosystem change assessing using ecoacoustics analysis

RESUMEN: La ecoacústica se ha convertido en un área de creciente interés para el monitoreo de ecosistemas. Entre las principales ventajas que presenta sobre las técnicas tradicionales se encuentran su bajo costo, poca afectación al entorno y simplicidad; además de que la distribución de varias grabadoras hace posible la recolección de más información. Sin embargo, para estudios de largo plazo, la cantidad de datos hace que la inspección manual de las grabaciones sea una tarea tediosa y por consiguiente el análisis sea limitado. Como alternativa a la inspección manual, una serie de índices han sido propuestos para resumir la información acústica de las grabaciones. No obstante, estos índices han sido aplicados principalmente a estudios de biodiversidad y su relación con el estado del ecosistema no es claro aún. En este trabajo se confió en la robustez del ANOVA frente a datos que no se distribuyen normalmente para proponer una metodología de selección de los mejores índices o descriptores acústicos para una aplicación específica y usarlos para modelar los patrones del paisaje acústico del ecosistema con modelos ocultos de Markov y emisiones por mezclas Gaussianas (GMMHMM). Además, el conjunto de descriptores que entran al modelo incluye por defecto un indicador de biodiversidad para cada banda de 1kHz. Esta metodología fue aplicada a dos casos colombianos con tipos de ecosistema definidos. En el primer caso, una serie de grabaciones de bosque, rastrojo y pastizal fueron colectados por más de un año en el este de Antioquia. La segunda aplicación buscaba encontrar patrones de paisaje acústico de las transformaciones de bosque seco en dos regiones del caribe colombiano. El modelo identificó seis y tres patrones acústicos para la primera y segunda base de datos respectivamente. En la primera aplicación, se encontraron sonidos continuos, alta intensidad biofónica y ocupación de varias bandas en los patrones asociados a bosque, mientras que en los rastrojos se presentó más entropía, que se relaciona con alta presencia geofónica, lo que limita la actividad biofónica. Finalmente los paisajes acústicos de pastizal alternaron entre periodos de alta geofonía y alta complejidad frecuencial, haciéndolo un ecosistema intermedio en el sentido acústico. La adaptación del modelo para clasificación resultó en la identificación del 81% de las muestras de bosque, 96,6 % de las muestras de rastrojo y 51,2 % de las muestras de pastizal. Los resultados de clasificación para la segunda aplicación no fueron altos, con 68% para las muestras de baja transformación, 58,9% para la transformación media y 31,8% para la transformación alta. No obstante, las matrices de confusión indicaron que las muestras de entrenamiento no fueron suficientes, y que debería proporcionarse mayor muestreo para obtener mejores resultados. Dado que GMMHMM es un modelo secuencial, también presentó la configuración temporal de los patrones acústicos dadas sus probabilidades de transición. Esta característica nos permitió destacar la importancia de la conservación, cuando encontramos que los estados más estables e inaccesibles fueron asociados a los ecosistemas más diversos acústicamente.ABSTRACT: Ecoacoustics has become a field of growing interest for ecosystem monitoring. Its main advantages over traditional methods include cost effectiveness, non-invasiveness and simplicity; besides the distribution of many recorder units makes possible the recollection of more information. However, for long term studies, the quantity of collected data makes the manual inspection of recordings a cumbersome task, leading to reduced analysis. As an alternative to manual inspection, a series of indices have been proposed to summarize the acoustical information in recordings. Nonetheless, these indices have been applied mainly to biodiversity studies and their connection to ecosystem state is still not clear. In this work we trusted ANOVA robustness for non-normal data for proposing a methodology that selected the best acoustical indices or features for a specific application and used them to model the ecosystem soundscape patterns with hidden Markov models and Gaussian mixture emissions (GMMHMM). Additionally, the set of input features included by default a biodiversity indicator per 1kHz band. This methodology was applied to two Colombian cases with defined ecosystem types. In the first case, a series of forest, stubble and pasture recordings were collected for over a year in the east of Antioquia. The second application aimed to find the soundscape patterns of dry forests transformations in two regions of the Colombian Caribbean. The model identified six and three soundscape patterns for the first and second dataset respectively. In the first application, continuous sounds, high biophonic intensity and multiple occupied frequency bands were found in the patterns associated to forest sites; on the other hand, stubble sites presented more general entropy, which we related to high geophonic presence, preventing biophonic activity. Lastly, pasture soundscapes alternated between periods of high geophony and high frequency complexity, making it an intermediate ecosystem in the acoustical sense. The adaptation of the model for classification resulted in the identification of 81% of the forest samples, 96.6% of the stubble samples and 51.2% of the pasture samples. The classification results for the second application were not as high, with 68% for the low transformation samples, 58.8% for the medium transformation and 31.8% for the high transformation. Nonetheless, the confusion matrices indicated that the training samples were not enough, and more sampling should be provided for attaining better results. Given that GMMHMM is a sequential model, it also presented the temporal configuration of the acoustical patterns by their transition probabilities. This feature allowed us to emphasize the importance of conservation, when we found that the most stable and inaccessible states were associated to the most acoustically diverse ecosystems

Explosive breeding in tropical anurans: Environmental triggers, community composition and acoustic structure

Background: Anurans largely rely on acoustic communication for sexual selection and reproduction. While multiple studies have focused on the calling activity patterns of prolonged breeding assemblages, species that concentrate their reproduction in short-time windows, explosive breeders, are still largely unknown, probably because of their ephemeral nature. In tropical regions, multiple species of explosive breeders may simultaneously aggregate leading to massive, mixed and dynamic choruses. To understand the environmental triggers, the phenology and composition of these choruses, we collected acoustic and environmental data at five ponds in French Guiana during a rainy season, assessing acoustic communities before and during explosive breeding events. Results: We detected in each pond two explosive breeding events, lasting between 24 and 70 h. The rainfall during the previous 48 h was the most important factor predicting the emergence of these events. During explosive breeding events, we identified a temporal factor that clearly distinguished pre- A nd mid-explosive communities. A common pool of explosive breeders co-occurred in most of the events, namely Chiasmocleis shudikarensis, Trachycephalus coriaceus and Ceratophrys cornuta. Nevertheless, the species composition was remarkably variable between ponds and for each pond between the first and the second events. The acoustic structure of explosive breeding communities had outlying levels of amplitude and unexpected low acoustic diversity, significantly lower than the communities preceding explosive breeding events. Conclusions: Explosive breeding communities were tightly linked with specific rainfall patterns. With climate change increasing rainfall variability in tropical regions, such communities may experience significant shifts in their timing, distribution and composition. In structurally similar habitats, located in the same region without obvious barriers, our results highlight the variation in composition across explosive breeding events. The characteristic acoustic structure of explosive breeding events stands out from the circadian acoustic environment being easily detected at long distance, probably reflecting behavioural singularities and conveying heterospecific information announcing the availability of short-lived breeding sites. Our data provides a baseline against which future changes, possibly linked to climate change, can be measured, contributing to a better understanding on the causes, patterns and consequences of these unique assemblagesThis research was supported by the Labex CEBA (Centre d’Étude de la Biodiversité Amazonienne), which provided fnancial and logistic support for the data collection. JSU was supported by COLCIENCIAS (Doctoral Scholarship of the Colombian government, 2014 call #646). DLL was supported by a Global Marie S. Curie fellowship (European Commission, program H2020, EAVESTROP–661408), a postdoctoral grant Atracción de Talento Investigador (Comunidad de Madrid, CAM, Spain, 2016-T2/AMB-1722), and acknowledges funding provided by the Ministerio de Economía, Industria y Competitividad (CGL2017-88764-R, MINECO/AEI/FEDER, Spain). None of the funders had any role in the design, analysis, interpretation of results or writing the manuscrip

Effect of tourist disturbance upon bird diversity and activity in Chicaque Natural Park, Colombia

El turismo y ecoturismo están creciendo en popularidad dentro del mercado nacional e internacional. A pesar de que estas actividades promueven el desarrollo económico, se sabe poco del efecto que tienen estas actividades sobre la diversidad local en zonas trópicas. Para comprobar si el turismo ejerce un efecto sobre la diversidad y actividad vocal de las aves, se combinó la observación de individuos con el uso de registros auditivos de 10 minutos para evaluar dos tipos de senderos; con alta frecuencia de uso y con baja frecuencia de uso por turistas en el Parque Natural Chicaque donde se realizan actividades de turismo natural y ecoturismo. Se construyó una base de datos para comprar diversidad (# de aves registradas) y actividad vocal (numero de sonidos producidos por aves durante 10 minutos) en 7 puntos de cada uno de los senderos seleccionados, cada punto con características vegetales y en alturas similares. Se encontraron diferencias entre el numero de especies en los dos tipos de senderos, sin embargo, la actividad vocal no se vio afectada por el tipo de sendero. Los senderos de alta frecuencia de uso tuvieron menor numero de especies de aves mientras los de menor frecuencia registraron mayor numero de especies. Las especies más ruidosas y frecuentadas fueron aves de sotobosque que viven entre chusque y matorrales densos, por lo que se sugiere que al ser difíciles de detectar perciben menor riesgo cuando son aproximadas por un posible depredador o turista, por lo tanto no cesan de cantar.Tourism, as well as ecotourism has become increasingly popular for both, international and national visitors. Although these activities promote economic development, there are few studies that attempt to shed some light upon the impact that nature based tourism has on local diversity in the tropics, and in the behavior of wild animals. The aim of this study is to test if trails frequently visited by tourists differs in bird diversity and vocal activity compared to those trails less frequently visited by tourists. To do so, sound recordings were made while simultaneously identifying any birds sighted in Chicaque Natural Park, a private entity situated in a cloud forest at north-eastern Andes mountains, in Colombia, where people go to experience recreational, nature based tourism. A database was constructed to compare diversity (number of bird species) and vocal activity (number of vocalizations per 10 minutes recordings) between two descending trails; the main path and other the secondary paths. I found differences between the number of species in main and secondary trails, however, visitors did not apparently impact song rate. Vocal species live in the understory behind a wall of vegetation, these secretive habits probably prevent them from being disturbed, and just keep singing in the wild.Biólogo (a)Pregrad

Bora loans in Resígaro: Massive morphological and little lexical borrowing in a moribund Arawakan language

This study analyzes the influence of Bora (Boran) on Resígaro (Arawakan), two languages of the Colombian-Peruvian Amazon region, using a newly discovered Resígaro wordlist from the 1930s (Manuel María de Mataró no date), another wordlist from the late 1920s (Rivet & Wavrin 1951), and another from the early 1970s (Allin 1976:382-458). It shows that despite heavy structural and morphological influence (Aikhenvald 2001:182-190) Resígaro has borrowed relatively few lexical items, around 5% in all three sources. It also shows that the borrowing of entire sets of grammatical morphemes, including classifiers, number markers, and bound grammatical roots that is observable in contemporary Resígaro (Seifart 2011) goes back to at least the early 20th century. This suggests that this remarkable case of massive morphological borrowing is not merely an effect of language decay, linked to the current language endangerment situation of Resígaro, with only two surviving speakers

Good practice guidelines for long-term ecoacoustic monitoring in the UK: with a particular focus on terrestrial biodiversity at the human-audible frequency range

Passive acoustic monitoring has great potential as a cost-effective method for long-term biodiversity monitoring. However, to maximise its efficacy, standardisation of survey protocols is necessary to ensure data are comparable and permit reliable inferences. The aim of these guidelines is to outline a basic long-term acoustic monitoring protocol that can be adapted to suit a range of projects according to specific objectives and size