A framework for the quantification of soundscape diversity using Hill numbers

1. Soundscape studies are increasingly common to capture landscape-scale ecological patterns. Yet, several aspects of soundscape diversity quantification remain unexplored. Although some processes influencing acoustic niche usage may operate in the 24h 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 functional ecology. 2. Our workflow quantifies the functional diversity of sound in the 24-hour acoustic trait space. We put forward an entity, the Operational Sound Unit (OSU), which groups sounds by their shared functional properties. Using OSUs as our unit of diversity measurement, 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; (iii) soundscape evenness. We demonstrate the use of these metrics by (a) simulating soundscapes to assess if the indices possess a set of desirable behaviours; and (b) quantifying the soundscape richness and evenness along a gradient in species richness to illustrate how these metrics can be used to shed unique insights into patterns of acoustic niche usage. 3. 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 soniferous species. This suggests that the acoustic niche space is more filled where taxonomic richness is higher. Moreover, species-poor acoustic communities have a higher proportion of rare sounds and use the acoustic space less effectively. As the correlation between the soundscape and taxonomic richness is strong (>0.8) and holds at low sampling intensities, soundscape richness could serve as a proxy for taxonomic richness. 4. Quantifying the soundscape diversity through the lens of functional ecology using the analytical framework of Hill numbers generates novel insights into acoustic niche usage at a landscape scale and provides a useful proxy for taxonomic richness measurement.

A rapid prototyping approach for intensive field courses to build scientific and professional skills

This paper reports on the design and evaluation of Field Studies in Functional Ecology (FSFE), a two-week intensive residential field course that engages students to master core content in functional ecology alongside skills that facilitate their transition from ‘student’ to ‘scientist’. This paper provides an overview of the course structure, showing how the constituent elements have been designed and refined over successive iterations of the course. We detail how FSFE students are guided first to develop their own research questions (Field Problems), and then through a structured reflective approach of rapid prototyping and iterative refinement of each stage of the research process. Using extensive evaluation data, we show how, coached by experts within a cognitive apprenticeship framework, FSFE students develop a coherent and nuanced understanding of how to approach and execute ecological studies. The sophisticated knowledge and skills as ecology researchers that they develop during the course is highlighted through high quality presentations and peer-reviewed publications in a student-led journal. We illustrate how field course elements can be used to provide cognitive, affective and reflective tools that allow students to gain maximum value from their educational journey, and the confidence to consider research in their future careers.

Sharing cities with avian scavengers: sustainable development in social-ecological systems

Correlations in the timings of vulture collapse and rapid urbanisation in South Asia have affected the benefit trade-offs concerning conservation-breeding for vulture restoration. We show how the loss of vultures 30 years ago has led to the extinction of experience amongst people in South Asia who are co-adapted to various animal species within shared landscapes. We conducted ethnography, involving avian scavengers (vultures, kites and crows) in Delhi, to unpack how salience and charisma for avian scavenger’s link with socio-cultural legends. Perceptions about avian scavengers were based on birds’ appearance, behaviour, and ecosystem services. Anthropomorphisation mediated human-animal co-adaptation and drove ritual feeding of commensals that opportunistically consume garbage. Conflated with ethnoecology, such human-constructed niches supported enormous animal populations in the region and drove mutual tolerance. Prior evaluations of scavengers’ niche from biophysical perspectives alone have, therefore, overlooked links between vultures and animal husbandry practices. It undermined competitive release on commensals that have responded by an increase in numbers and distribution, by taking advantage of ritual feeding and people’s affiliative attitudes. The absence of vultures limits the availability of spaces where animal husbandry can be practised. Conversely, expanding built-up spaces, overhead wires, fake news, and interference from competing scavengers will be impediments to vulture restoration. Conservation policies should examine immediate and long-term objectives of solid waste disposal, considering the odds against the attainment of former functional ecology by vultures. We conclude that wildlife restoration in urbanising tropical landscapes is a moving target, necessitating policies sensitive to progressive loss and/or changes in associative heritage due to shifting economic and cultural practices.

Sharing cities with avian scavengers: sustainable development in social-ecological systems

Correlations in the timings of vulture collapse and rapid urbanisation in South Asia have affected the benefit trade-offs concerning conservation-breeding for vulture restoration. We show how the loss of vultures 30 years ago has led to the extinction of experience amongst people in South Asia who are co-adapted to various animal species within shared landscapes. We conducted ethnography that focused on avian scavengers (vultures, kites and crows) in Delhi to unpack how salience and charisma for avian scavengers link with socio-cultural legends. Perceptions about avian scavengers were based on birds’ appearance, behaviour, and ecosystem services. Anthropomorphisation mediated human-animal co-adaptation and drove ritual feeding of commensals that opportunistically consume garbage. Conflated with ethnoecology, such human-constructed niches supported enormous animal populations in the region and drove mutual tolerance. Prior evaluations of scavengers’ niche from biophysical perspectives alone have, therefore, overlooked links between vultures and animal husbandry practices. It undermined competitive release on commensals that have responded by an increase in numbers and distribution, by taking advantage of ritual feeding and people’s affiliative attitudes. The absence of vultures limits the availability of spaces where animal husbandry can be practised. Conversely, expanding built-up spaces, overhead wires, fake news, and interference from competing scavengers will be impediments to vulture restoration. Conservation policies should examine immediate and long-term objectives of solid waste disposal, considering the odds against the attainment of the yesteryear functional ecology of vultures in South Asia. We conclude that wildlife restoration in urbanising tropical landscapes is a moving target, necessitating policies sensitive to progressive loss and/or changes in associative heritage due to shifting economic and cultural practices.

Recurrent urinary tract infection and estrogen shape the taxonomic ecology and functional potential of the postmenopausal urobiome

Community-acquired urinary tract infection (UTI) is among the most common bacterial infections observed in humans. Postmenopausal women are a rapidly growing and underserved demographic group who are severely affected by rUTI with a >50% recurrence rate. In this population, rUTI can persist for years, reducing quality of life and imposing a significant healthcare burden. rUTI is most often treated by long-term antibiotic therapy, but development of antibiotic resistance and allergy leave physicians with fewer treatment options. The female urobiome has been identified as a key component of the urogenital environment. However, structural and functional changes in the urobiome underlying rUTI susceptibility in postmenopausal women are not well understood. Here, we used strictly curated, controlled cross-sectional human cohorts of postmenopausal women, urobiome whole genome (shotgun) metagenomic sequencing (WGMS), advanced urine culturing techniques, extensive biobanking of >900 patient-derived urinary bacterial and fungal isolates, and mass spectrometry-based estrogen profiling to survey the urobiome in rUTI patients during infection relapse and remission as well as healthy comparators with no lifetime history of UTI. Our results suggest that a history of rUTI strongly shapes the taxonomic and functional ecology of the urobiome. We also find a putative protective commensal population, consisting of species known to convey protection against bacterial vaginosis such as Lactobacillus crispatus, within the urobiome of women who do not experience UTI. Integration of clinical metadata detected an almost exclusive enrichment of putative protective species belonging to the genus, Lactobacillus, in women taking estrogen hormone therapy (EHT). We further show that the urobiome taxonomic ecology is shaped by EHT, with strong enrichments of putatively protective lactobacilli, such as L. crispatus and L. vaginalis. Integrating quantitative metabolite profiling of urinary estrogens with WGMS, we observed robust associations between urobiome taxa, such as Bifidobacterium breve and L. crispatus, and urinary estrogen conjugate concentrations, suggesting that EHT strongly alters the taxonomic composition of the female urobiome. We have further used functional metagenomic profiling and patient-derived isolate phenotyping to identify microbial metabolic pathways, antimicrobial resistance genes (ARGs), and clinically relevant antimicrobial resistance phenotypes enriched between disease-states. Our data suggest distinct metabolic and ARG signatures of the urobiome associated with current rUTI status and history. Taken together, our data suggests that rUTI history and estrogen use strongly shape the functional and taxonomic composition of the urobiome in postmenopausal women.

Which peer reviewers voluntarily reveal their identity to authors? Insights into the consequences of open-identities peer review

Identifying reviewers is argued to improve the quality and fairness of peer review, but is generally disfavoured by reviewers. To gain some insight into the factors that influence when reviewers are willing to have their identity revealed, I examined which reviewers voluntarily reveal their identities to authors at the journal Functional Ecology , at which reviewer identities are confidential unless reviewers sign their comments to authors. I found that 5.6% of reviewers signed their comments to authors. This proportion increased slightly over time, from 4.4% in 2003–2005 to 6.7% in 2013–2015. Male reviewers were 1.8 times more likely to sign their comments to authors than were female reviewers, and this difference persisted over time. Few reviewers signed all of their reviews; reviewers were more likely to sign their reviews when their rating of the manuscript was more positive, and papers that had at least one signed review were more likely to be invited for revision. Signed reviews were, on average, longer and recommended more references to authors. My analyses cannot distinguish cause and effect for the patterns observed, but my results suggest that ‘open-identities’ review, in which reviewers are not permitted to be anonymous, will probably reduce the degree to which reviewers are critical in their assessment of manuscripts and will differentially affect recruitment of male and female reviewers, negatively affecting the diversity of reviewers recruited by journals.

Vulture loss and urbanisation correlations form blind spots for conservation and development

Correlations in the timings of vulture collapse and rapid urbanisation in South Asia have affected the benefit trade-offs concerning conservation-breeding for vulture restoration. We show how the loss of vultures 30 years ago has led to the extinction of experience amongst people in South Asia who are co-adapted to various animal species within shared landscapes. We conducted ethnography, involving avian scavengers (vultures, kites and crows) in Delhi, to unpack how salience and charisma for avian scavenger’s link with socio-cultural legends. Perceptions about avian scavengers were based on birds’ appearance, behaviour, and ecosystem services. Anthropomorphisation mediated human-animal co-adaptation and drove ritual feeding of commensals that opportunistically consume garbage. Conflated with ethnoecology, such human-constructed niches supported enormous animal populations in the region and drove mutual tolerance. Prior evaluations of scavengers’ niche from biophysical perspectives alone have, therefore, overlooked prior links between vultures and animal husbandry practices. It undermined competitive release on commensals that have responded by an increase in numbers and distribution, by taking advantage of ritual feeding and people’s affiliative attitudes. The absence of vultures limits the availability of spaces where animal husbandry can be practised. Conversely, expanding built-up spaces, overhead wires, fake news, and interference from competing scavengers will be impediments to vulture restoration. Conservation policies should examine immediate and long-term objectives of solid waste disposal, considering the odds against the attainment of former functional ecology by vultures. We conclude that wildlife restoration in urbanising tropical landscapes is a moving target, necessitating policies sensitive to progressive loss and/or changes in associative heritage due to shifting economic and cultural practices.

Thigmomorphogenic responses of epiphytic bromeliads to mechanically induced stress

Vascular epiphytes represent almost 10% of all terrestrial plant diversity. Despite the extensive research on the functional ecology and challenges of epiphytic growth, there is still very little known on how exposure to mechanically induced stress affects the growth and development of epiphytes. Therefore, this study investigated the effect of such mechanical stress on the growth and biomass allocation of epiphytic bromeliads. Juvenile plants of two species were subjected to two types of mechanical stress in the greenhouse—permanent displacement and temporary, recurring mechanical flexing. ANOVAs were used to test possible treatment effects on growth, root–shoot ratio, root diameter, and root area distribution ratio. Contrary to previous studies on herbaceous plants, these bromeliads showed little to no change in root and shoot properties in either species. The root–shoot ratio increased in disturbed Guzmania lingulata plants, but not in Vriesea sp. Treatment effects on growth were inconsistent: a stress effect on growth was significant only in the first 2 months of the experiment in G. lingulata, whilst none of the stress treatments negatively affected growth in Vriesea sp. All disturbed plants showed some degree of curvature on their stems and leaves against the area of stress to obtain an upright position. This was probably related to the maintenance of a functional tank. This study provides quantitative and qualitative data to understand thigmomorphogenic responses of bromeliads to mechanical stress. Future studies could include field surveys to quantify on-site mechanical stresses and the corresponding morphological changes in vascular epiphytes.