Applications and advances in acoustic monitoring for infectious disease epidemiology

Emerging infectious diseases continue to pose a significant burden on global public health, and there is a critical need to better understand transmission dynamics arising at the interface of human activity and wildlife habitats. Passive acoustic monitoring (PAM), more typically applied to questions of biodiversity and conservation, provides an opportunity to collect and analyse audio data in relative real time and at low cost. Acoustic methods are increasingly accessible, with the expansion of cloud-based computing, low-cost hardware, and machine learning approaches. Paired with purposeful experimental design, acoustic data can complement existing surveillance methods and provide a novel toolkit to investigate the key biological parameters and ecological interactions that underpin infectious disease epidemiology

Impacts of a large hydroelectric dam on the Madeira River (Brazil) on floodplain avifauna

Hydroelectric dams represent an important threat to seasonally flooded environments in the Amazon basin. We aimed to evaluate how a dam in the Madeira River, one of the largest tributaries of the Amazonas River, affected floodplain avifauna. Bird occurrence was recorded through simultaneous passive acoustic monitoring in early successional vegetation and floodplain forest downstream from the dam and upstream in sites impacted by permanent flooding after dam reservoir filling. Species were identified through manual inspection and semi-automated classification of the recordings. To assess the similarity in vegetation between downstream and upstream sites, we used Landsat TM/ETM+ composite images from before (2009-2011) and after (2016-2018) reservoir filling. Downstream and upstream floodplain forest sites were similar before, but not after dam construction. Early successional vegetation sites were already different before dam construction. We recorded 195 bird species. While species richness did not differ between upstream and downstream sites, species composition differed significantly. Ten species were indicators of early successional vegetation upstream, and four downstream. Ten species were indicators of floodplain forest upstream, and 31 downstream. Seven of 24 floodplain specialist species were detected by the semi-automated classification only upstream. While we found some bird species characteristic of early successional vegetation in the upstream sites, we did not find most species characteristic of tall floodplain forest. Predominantly carnivorous, insectivorous, and nectarivorous species appear to have been replaced by generalist and widely distributed species.</p

A framework for quantifying soundscape diversity using Hill numbers

Soundscape studies are increasingly used to capture landscape-scale ecological patterns. Yet, several aspects of soundscape diversity remain unexplored. Although some processes influencing acoustic niche usage may operate in the 24-hr temporal domain, most acoustic indices only capture the diversity of sounds co-occurring in sound files at a specific time of day. Moreover, many indices do not consider the relationship between the spectral and temporal traits of sounds simultaneously. To provide novel insights into landscape-scale patterns of acoustic niche usage at broader temporal scales, we present a workflow to quantify soundscape diversity through the lens of trait-based ecology. Our workflow quantifies the diversity of sound in the 24-hr acoustic trait space. We introduce the Operational Sound Unit (OSU), a unit of diversity measurement that groups sounds by their shared acoustic properties. Using OSUs and building on the framework of Hill numbers, we propose three metrics that capture different aspects of acoustic trait space usage: (i) soundscape richness, (ii) soundscape diversity and (iii) soundscape evenness. We demonstrate the use of these metrics by (a) simulating soundscapes to assess whether the indices possess a set of desirable behaviours and (b) quantifying soundscape richness and evenness along a gradient in species richness. We demonstrate that (a) the indices outlined herein have desirable behaviours and (b) the soundscape richness and evenness are positively correlated with the richness of sound-producing species. This suggests that more acoustic niche space is occupied when the species richness is higher. Additionally, species-poor acoustic communities have a higher proportion of rare sounds and use the acoustic space less evenly. Our workflow generates novel insights into acoustic niche usage at a landscape scale and provides a useful tool for biodiversity monitoring. Moreover, Hill numbers can also be used to measure the taxonomic, functional and phylogenetic diversity. Using a common framework for diversity measurement gives metrics a common behaviour, interpretation and standardised unit, thus ensuring comparisons between soundscape diversity and other metrics represent real-world ecological patterns rather than mathematical artefacts stemming from different formulae

It\u27s Time to Listen: There is Much to be Learned from the Sounds of Tropical Ecosystems

Knowledge that can be gained from acoustic data collection in tropical ecosystems is low‐hanging fruit. There is every reason to record and with every day, there are fewer excuses not to do it. In recent years, the cost of acoustic recorders has decreased substantially (some can be purchased for under US$50, e.g., Hill et al. 2018) and the technology needed to store and analyze acoustic data is continuously improving (e.g., Corrada Bravo et al. 2017, Xie et al. 2017). Soundscape recordings provide a permanent record of a site at a given time and contain a wealth of invaluable and irreplaceable information. Although challenges remain, failure to collect acoustic data now in tropical ecosystems would represent a failure to future generations of tropical researchers and the citizens that benefit from ecological research. In this commentary, we (1) argue for the need to increase acoustic monitoring in tropical systems; (2) describe the types of research questions and conservation issues that can be addressed with passive acoustic monitoring (PAM) using both short‐ and long‐term data in terrestrial and freshwater habitats; and (3) present an initial plan for establishing a global repository of tropical recordings

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Quantificação de um critério de conservação: raridade de aves de terra firme em uma floresta na Amazônia Central

The distinction between rare and common species is fundamental in research and management decisions. Nevertheless the definition of these categories often relies on a mix of sampling methods, biological processes and subjective impressions. Most studies that used field sampling techniques to count landbirds failed to present measures of precision and do not account to imperfect detectability, in that way this counts are based in a fraction of true population. We tested if classifications of bird rarity based on ornithologist s perceptions are the same when we estimated occupancy accounting for imperfect detection. We selected ten species pairs whose members are related phylogenetically and one member is reported to be rarer than the other. On three different occasions 760 ha of primary terra-firme forest was sampled by 10 observers with point counts. Playback and autonomous recorder was used as complementary approach. All observers were trained and evaluated using memory-improvement software. It wasn t possible refute the hypothesis that rarer species occur in higher proportion of places as common species because only five pairs showed a clear difference in rarity and all were in the direction predicted by existing literature. Only two of these, Dendrocolaptes picumnus and Cyphorhinus arada, are genuinely rarer species and occupy less than 50% of sampling points. Although published rarity classifications never mistook a genuinely rarer species to be more common than its pair,ours results gather clear evidence that distinction between rare and common species must be based in quantitative measures that account for detection probabilities and that presents measures of precision. Because species rarity figures so prominently in landbird conservation, it is essential that researches and managers attempt to provide reliable information. Thus, in research and management that depend on correct rarity classification, we recommend the use of quantitative methods with calculated confidence intervals and that dealing with imperfect detections.A distinção entre quais espécies são raras e quais são comuns é fundamental tanto em pesquisa como em conservação. Entretanto a definição das categorias de raridade é frequentemente resultante de uma combinação entre a realidade biológica, processos relacionados à amostragem e percepções subjetivas. A maioria de trabalhos sobre populações de aves não apresentam medidas de precisão associadas as estimativas de parâmetros populacionais e não consideram que as espécies são detectadas de forma imperfeita e portanto essas estimativas são baseadas em uma fração da verdadeira população. Nesse contexto testamos se as categorias de raridade baseadas nas percepções dos ornitólogos se sustentam quando é estimada a ocorrência das espécies considerando uma detectabilidade imperfeita. Foram selecionados dez pares de espécies em que os membros são filogeneticamente aparentados e um é hipoteticamente mais raro que outro. Em três ocasiões diferentes ao longo de um ano dez observadores amostraram as espécies-alvo em uma área de 760 ha de mata primária de terra firme, utilizando a técnica de pontos de escuta. As técnicas de playback e gravações autônomas também foram utilizadas como abordagens complementares. Os observadores foram previamente treinados em identificação de aves e avaliados através de um programa computacional livre que trabalha com técnicas de memorização. Não foi possível refutar a hipótese de que as espécies raras tem ocorrência tal alta quanto as espécies consideradas comuns pois, existem somente, evidências óbvias de diferenças de raridade em cinco pares de espécie e dessas, apenas Dendrocolaptes picumnus e Cyphorhinus arada ocorrem em menos de 50% dos pontos amostrais. Embora as categorias de raridade advindas da percepção dos ornitológos não tenham classificado uma espécie realmente rara como sendo comum fica claro que a categorização de uma espécie deve se basear em uma medida quantitativa associada a uma medida de precisão. Nossos resultados indicam que nem sempre uma espécie mais rara é mais díficil de detectar, entretanto fatores relacionados à amostragem podem influenciar a probabilidade de detecção diferentemente para cada espécie. Essas medidas quantitativas da raridades das espécies são informações consistentes e essenciais para o sucesso de qualquer ação de manejo. Assim tanto em pesquisa quanto em manejo que dependem de uma correta classificação de raridade, nós recomendamos o uso de métodos quantitativos que forneçam o grau de confiabilidade e que lidem com a detectabilidade imperfeita das espécies

Lowland extirpation of anuran populations on a tropical mountain

Background Climate change and infectious diseases threaten animal and plant species, even in natural and protected areas. To cope with these changes, species may acclimate, adapt, move or decline. Here, we test for shifts in anuran distributions in the Luquillo Mountains (LM), a tropical montane forest in Puerto Rico by comparing species distributions from historical (1931–1989)and current data (2015/2016). Methods Historical data, which included different methodologies, were gathered through the Global Biodiversity Information Facility (GBIF) and published literature, and the current data were collected using acoustic recorders along three elevational transects. Results In the recordings, we detected the 12 native frog species known to occur in LM. Over a span of ∼25 years, two species have become extinct and four species suffered extirpation in lowland areas. As a consequence, low elevation areas in the LM (<300 m) have lost at least six anuran species. Discussion We hypothesize that these extirpations are due to the effects of climate change and infectious diseases, which are restricting many species to higher elevations and a much smaller area. Land use change is not responsible for these changes because LM has been a protected reserve for the past 80 years. However, previous studies indicate that (1) climate change has increased temperatures in Puerto Rico, and (2) Batrachochytrium dendrobatidis (Bd) was found in 10 native species and early detection of Bd coincides with anurans declines in the LM. Our study confirms the general impressions of amphibian population extirpations at low elevations, and corroborates the levels of threat assigned by IUCN