BioSoundSCape

Based in the Cape Region of South Africa, the BioSoundSCape research project seeks to develop a novel, generalizable and species agnostic approach to measure animal diversity over large areas and through time using a combination of acoustics and advanced remote sensing technology. BioSoundscape is funded by the U.S. National Aeronautics and Space Administration (NASA) and is part of a larger biodiversity science program called  BioSCape , which is an international collaboration between NASA and the South Africa National Space Agency (SANSA) to study biodiversity in South Africa’s Greater Cape Floristic Region (GCFR).

"Our innovative acoustics and remote sensing approach to estimating animal diversity at regional scales will be a useful tool for monitoring, conservation and management of biodiversity.

This study focuses on bird and frog species that emit sounds. The GCFR is a key region for South Africa’s birds of conservation interest. There are a number of endemic and near-endemic species, particularly among nectarivores, like the Cape Sugarbird (Promerops cafer), Southern Double-collared Sunbird (Cinnyris chalybea) and the Orange-breasted Sunbird (Anthobaphes violacea).

"Monitoring birds in the Cape Fold Mountains is hard, with rugged terrain and unpredictable climate. The use of autonomous recording units and remote sensing will give conservationists a better handle on what is happening in this important site for biodiversity."

The GCFR has a unique set of amphibian species with a very high level of endemism (62%) and four genera restricted to this region. Amphibians are vulnerable to environmental change with dramatic population declines widespread over the globe and may be considered sentinels of environmental health. In the GCFR, many endemic frog species are tightly coupled to environmental factors and this, combined with their generally low vagility, should provide useful insights when assessed in relation to remotely-sensed habitat diversity. Although many of frog species call during the day, similar to birds, our ability to record soundscapes through 24 hours and over multiple days can capture more bird and frog diversity than possible with single 10-minute point counts at a given site.

"We have a good understanding of the taxonomy of frogs of the fynbos but our understanding of their biology and behaviour is lacking. BioSoundSCape will provide many insights at the local and landscape level into amphibian acoustic habits."

Starting in July, 2023, we will deploy low-cost, autonomous recording units (AudioMoths) at GCFR sample sites spanning a range of land cover types, fire history and anthropogenic disturbance gradients. We will also collect coincident in situ bird and frog point count measurements conducted by local volunteer ecologists with experience in species identification. Collaborators at  BirdLife South Africa ,  CapeNature ,  SANBI , and  Stellenbosch University  will help facilitate deployment and retrieval of sound recorders and point counts.

"Nature’s soundscapes provide a rich musical record of our biodiversity, and this project explores the possibilities of unlocking their potential for species monitoring, particularly over the long-term.”

 “In addition to potential biodiversity conservation outcomes, this project will engage local birdwatchers and land managers in on-the-ground data collection as field volunteers.”

We treat sound recordings as spectrograms, which are time vs. frequency 2D image representations of sounds. From spectrograms, we use a suite of acoustic indices that emphasize biotic sounds over non-biotic sounds. We will explore an innovative, but relatively untested means of automatically deriving acoustic features for ecological monitoring that was recently proposed by  Sethi et al. (2020) . In this approach, spectrograms are processed through a convolutional neural network (CNN) named VGGish, which was trained using a large-scale dataset of manually annotated audio events from YouTube videos.

"BioSoundScape is undoubtedly one of only a handful of projects around the world that target biodiversity surveys at multiple scales with data from a variety of technologies, and that involves a large team of collaborators across multiple institutions in two continents."

Below are some example soundscapes from our pilot-phase deployments.

Remote sensing is the process of gathering information about an object, area or phenomenon from a distance, without coming into direct contact with it. This can be done through the use of sensors on satellites or airborne platforms, such as aircraft or drones. These sensors measure different aspects of the environment, such as vegetation spectral reflectance and structural properties.

As part of the BioSCape campaign, in October-November 2023 NASA deployed four instruments attached to Gulfstream III and V aircraft. BioSoundSCape will use two of these sensors, the Airborne Visible/Infrared Imaging Spectrometer Next Generation (AVIRIS-NG) imaging spectrometer and the Land, Vegetation, and Ice Sensor (LVIS) wide-swath imaging laser altimeter.

Images from AVIRIS NG provide detailed information on the reflectance of light from the earth's surface at wavelengths from 400 nm (blue light) to 2500 nm (shortwave infrared light). These data can be used to identify different vegetation types, as well as the presence of plant chemicals, such as water, nitrogen and chlorophyll.

“BioSoundSCape will give us new insights on how to combine spectral information from remote sensing with bioacoustic measurements for biodiversity monitoring at unprecedented spatial and temporal scales. This could also tell us how birds use different habitat and vegetation types in South Africa.”

The LVIS sensor provides information on the physical structure of vegetation, such as the height, density, and spatial arrangement of trees and other plants. This information can be used to create 3D maps of vegetation cover, which can characterize animal habitat. Structural measurements can also be used to identify areas that have been impacted by human activities or disturbance, such as fire.

“Through Biosoundcape's fusion of cutting-edge remotely sensed habitat characterization and scalable animal observations, we hope to unlock secrets of plant-animal interactions and drive biodiversity preservation forward.”

We will first test the hypothesis that bird and frog species richness is positively related to acoustic diversity, as measured by features from deep learning (e.g., VGGish described above). Next, coincident AVIRIS-NG imaging spectroscopy and LVIS laser data from the NASA BioSCape airborne campaign will be used to characterize plant spectral and structural habitat diversity, respectively. Our approach then integrates measures of acoustic, spectral, and structural diversity to investigate the strength and shape of the animal-habitat diversity relationship across vegetation types and gradients of natural and anthropogenic disturbance.

"BioSCape is an amazing opportunity to see if remotely sensed hyperspectral and 3-dimension data can inform conservationists about biodiversity as measured by acoustic data. This should be super useful for monitoring biodiversity change over time in the hyper-diverse Fynbos biome."

Q1. How is acoustic diversity related to animal diversity (birds and amphibians)?

Q2. What are the relationships among measures of acoustic, spectral and structural diversity and how do they change across spatial scales and vegetation types?

Q3. How do anthropogenic and natural disturbance affect acoustic diversity and habitat quality?

Here is a webinar conversation with Dr. Matthew Clark about bioacoustics research leading to BioSoundSCape and how the project links with the larger BioSCape project.

Researchers & Collaborators

Dr.  Matthew Clark ,  Sonoma State University , California USA (PI, matthew.clark@sonoma.edu)  Dr. António Ferraz , NASA  Jet Propulsion Lab/Univ. of California, Los Angeles USA  Dr. Alan Lee ,  BirdLife South Africa   Dr. John Measey ,  Stellenbosch University , South Africa Dr. Ryan Pavlick,  NASA Jet Propulsion Lab , USA Ernst Retief,  BirdLife Africa  Dr. Hanneline Robinson-Smit,  BirdLife South Africa   Dr. Leo Salas ,  Point Blue Conservation Science , USA  Dr. Fabian Schneider ,  NASA Jet Propulsion Lab , USA  Dr. Colleen Seymour ,  South African National Biodiversity Institute (SANBI)  Rose Snyder,  Point Blue Conservation Science , USA Dr. Andrew Turner,  CapeNature , South Africa

Storymap credits: John Murray (design, maps), Athena Everson (soundscape videos), Talia Gutman (soundscape videos), Matthew Clark (design, content)