Using acoustic indices in ecology : guidance on study design, analyses and interpretation

TBL was supported by Leverhulme Trust, research grant number RPG-2020-160; the Lorentz Centre, Leiden, The Netherlands; and UKAN+. AE and OM were supported by UKAN+.The rise of passive acoustic monitoring and the rapid growth in large audio datasets is driving the development of analysis methods that allow ecological inferences to be drawn from acoustic data. Acoustic indices are currently one of the most widely applied tools in ecoacoustics. These numerical summaries of the sound energy contained in digital audio recordings are relatively straightforward and fast to calculate but can be challenging to interpret. Misapplication and misinterpretation have produced conflicting results and led some to question their value. To encourage better use of acoustic indices, we provide nine points of guidance to support good study design, analysis and interpretation. We offer practical recommendations for the use of acoustic indices in the study of both whole soundscapes and individual taxa and species, and point to emerging trends in ecoacoustic analysis. In particular, we highlight the critical importance of understanding the links between soundscape patterns and acoustic indices. Acoustic indices can offer insights into the state of organisms, populations, and ecosystems, complementing other ecological research techniques. Judicious selection, appropriate application and thorough interpretation of existing indices is vital to bolster robust developments in ecoacoustics for biodiversity monitoring, conservation and future research.Publisher PDFPeer reviewe

The phage gene wmk is a candidate for male killing by a bacterial endosymbiont

Wolbachia are the most widespread maternally-transmitted bacteria in the animal kingdom. Their global spread in arthropods and varied impacts on animal physiology, evolution, and vector control are in part due to parasitic drive systems that enhance the fitness of infected females, the transmitting sex of Wolbachia. Male killing is one common drive mechanism wherein the sons of infected females are selectively killed. Despite decades of research, the gene(s) underlying Wolbachia-induced male killing remain unknown. Here using comparative genomic, transgenic, and cytological approaches in fruit flies, we identify a candidate gene in the eukaryotic association module of Wolbachia prophage WO, termed WO-mediated killing (wmk), which transgenically causes male-specific lethality during early embryogenesis and cytological defects typical of the pathology of male killing. The discovery of wmk establishes new hypotheses for the potential role of phage genes in sex-specific lethality, including the control of arthropod pests and vectors

Pooled HIV-1 Viral Load Testing Using Dried Blood Spots to Reduce the Cost of Monitoring Antiretroviral Treatment in a Resource-Limited Setting

: Rollout of routine HIV-1 viral load monitoring is hampered by high costs and logistical difficulties associated with sample collection and transport. New strategies are needed to overcome these constraints. Dried blood spots from finger pricks have been shown to be more practical than the use of plasma specimens, and pooling strategies using plasma specimens have been demonstrated to be an efficient method to reduce costs. This study found that combination of finger-prick dried blood spots and a pooling strategy is a feasible and efficient option to reduce costs, while maintaining accuracy in the context of a district hospital in Malawi

Using scRNA-seq to identify transcriptional variation in the malaria parasite ookinete stage

The crossing of the mosquito midgut epithelium by the malaria parasite motile ookinete form represents the most extreme population bottleneck in the parasite life cycle and is a prime target for transmission blocking strategies. However, we have little understanding of the clonal variation that exists in a population of ookinetes in the vector, partially because the parasites are difficult to access and are found in low numbers. Within a vector, variation may result as a response to specific environmental cues or may exist independent of those cues as a potential bet-hedging strategy. Here we use single-cell RNA-seq to profile transcriptional variation in Plasmodium berghei ookinetes across different vector species, and between and within individual midguts. We then compare our results to low-input transcriptomes from individual Anopheles coluzzii midguts infected with the human malaria parasite Plasmodium falciparum. Although the vast majority of transcriptional changes in ookinetes are driven by development, we have identified candidate genes that may be responding to environmental cues or are clonally variant within a population. Our results illustrate the value of single-cell and low-input technologies in understanding clonal variation of parasite populations

The Malaria Cell Atlas: single parasite transcriptomes across the complete Plasmodium life cycle

Malaria parasites adopt a remarkable variety of morphological life stages as they transition through multiple mammalian host and mosquito vector environments. We profiled the single-cell transcriptomes of thousands of individual parasites, deriving the first high-resolution transcriptional atlas of the entire life cycle. We then used our atlas to precisely define developmental stages of single cells from three different human malaria parasite species, including parasites isolated directly from infected individuals. The Malaria Cell Atlas provides both a comprehensive view of gene usage in a eukaryotic parasite and an open-access reference dataset for the study of malaria parasites

Accuracy and repeatability of wrist joint angles in boxing using an electromagnetic tracking system

© 2019, The Author(s). The hand-wrist region is reported as the most common injury site in boxing. Boxers are at risk due to the amount of wrist motions when impacting training equipment or their opponents, yet we know relatively little about these motions. This paper describes a new method for quantifying wrist motion in boxing using an electromagnetic tracking system. Surrogate testing procedure utilising a polyamide hand and forearm shape, and in vivo testing procedure utilising 29 elite boxers, were used to assess the accuracy and repeatability of the system. 2D kinematic analysis was used to calculate wrist angles using photogrammetry, whilst the data from the electromagnetic tracking system was processed with visual 3D software. The electromagnetic tracking system agreed with the video-based system (paired t tests) in both the surrogate ( 0.9). In the punch testing, for both repeated jab and hook shots, the electromagnetic tracking system showed good reliability (ICCs > 0.8) and substantial reliability (ICCs > 0.6) for flexion–extension and radial-ulnar deviation angles, respectively. The results indicate that wrist kinematics during punching activities can be measured using an electromagnetic tracking system

Designing interactive newsprint

The possibility of linking paper to digital information is enhanced by recent developments in printed electronics. In this article we report the design and evaluation of a local newspaper augmented with capacitive touch regions and an embedded Bluetooth chip working with an adjunct device. These allowed the interactive playback of associated audio and the registration of manual voting actions on the web. Design conventions inherited from paper and the web were explored by showing four different versions of an interactive newspaper to 16 community residents. The diverse responses of residents are described, outlining the potential of the approach for local journalism and recommendations for the design of interactive newsprint

Benthos

Currently, > 4,000 Arctic macro- and megabenthic species are known, representing the majority of Arctic marine faunal diversity. This estimate is expected to increase. • Benthic invertebrates are food to shes, marine mammals, seabirds and humans, and are commercially harvested. • Traditional Knowledge (TK) emphasizes the link between the benthic species and their predators, such as walrus, and their signi cance to culture. • Decadal changes in benthos biodiversity are observed in some well-studied regions, such as the Barents Sea and Chukchi Sea. • Drivers related to climate-change such as warming, ice decline and acidification are affecting the benthic community on a pan-Arctic scale, while drivers such as trawling, river/glacier discharge and invasive species have signficant impact on regional or local scales. • Increasing numbers of species are moving into, or shifting, their distributions in Arctic waters. These species will outcompete, prey on or offer less nutritious value as prey for Arctic species. • Current monitoring efforts have focused on macro- and megabenthic species, but have been confined to the Chukchi Sea and the Barents Sea. Efforts are increasing in waters of Greenland, Iceland, the Canadian Arctic, and in the Norwegian Sea. All other Arctic Marine Areas are lacking long-term benthic monitoring. • As a first step towards an international collaborative monitoring framework, we recommend to develop a time- and cost-effective, long-term and standardized monitoring of megabenthic communities in all Arctic regions with regular annual groundfish assessment surveys. Expanding monitoring on micro-, meio- and macrobenthic groups is encouraged

Listening to tropical forest soils

Acoustic monitoring has proven to be an effective tool for monitoring biotic soundscapes in the marine, terrestrial, and aquatic realms. Recently it has been suggested that it could also be an effective method for monitoring soil soundscapes, but has been used in very few studies, primarily in temperate and polar regions. We present the first study of soil soundscapes using passive acoustic monitoring in tropical forests, using a novel analytical pipeline allowing for the use of in-situ recording of soundscapes with minimal soil disturbance. We found significant differences in acoustic index values between burnt and unburnt forests and the first indications of a diel cycle in soil soundscapes. These promising results and methodological advances highlight the potential of passive acoustic monitoring for large-scale and long-term monitoring of soil biodiversity. We use the results to discuss research priorities, including relating soil biophony to community structure and ecosystem function, and the use of appropriate hardware and analytical techniques

Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes

The genomes of malaria parasites contain many genes of unknown function. To assist drug development through the identification of essential genes and pathways, we have measured competitive growth rates in mice of 2,578 barcoded Plasmodium berghei knockout mutants, representing >50% of the genome, and created a phenotype database. At a single stage of its complex life cycle, P. berghei requires two-thirds of genes for optimal growth, the highest proportion reported from any organism and a probable consequence of functional optimization necessitated by genomic reductions during the evolution of parasitism. In contrast, extreme functional redundancy has evolved among expanded gene families operating at the parasite-host interface. The level of genetic redundancy in a single-celled organism may thus reflect the degree of environmental variation it experiences. In the case of Plasmodium parasites, this helps rationalize both the relative successes of drugs and the greater difficulty of making an effective vaccine