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Here we detail the use of an R package, 'EcoCountHelper', and an associated analytical pipeline aimed at making generalized linear mixed-effects model (GLMM)-based analysis of ecological count data more accessible. We recommend a GLMM-based analysis workflow that allows the user to (1) employ selection of distributional forms (Poisson vs negative binomial) and zero-inflation (ZIP and ZINB, respectively) using AIC and variance-mean plots, (2) examine models for goodness-of-fit using simulated residual diagnostics, (3) interpret model results via easy to understand outputs of changes in predicted responses, and (4) compare the magnitude of predictor variable effects via effects plots. Our package uses a series of easy-to-use functions that can accept both wide- and long-form multi-taxa count data without the need for programming experience. To demonstrate the utility of this approach, we use our package to model acoustic bat activity data relative to multiple landscape characteristics in a protected area (Grand Teton National Park), which is threatened by encroaching disease--white nose syndrome. Global threats to bat conservation such as disease and deforestation have prompted extensive research to better understand bat ecology. Notwithstanding these efforts, managers operating on lands crucial to the persistence of bat populations are often equipped with too little information regarding local bat activity to make informed land-management decisions. In our case study in the Tetons, we found that an increased prevalence of porous buildings increases activity levels of Eptesicus fuscus and Myotis volans; Myotis lucifugus activity decreases as distance to water increases; and Myotis volans activity increases with the amount of forested area. By using GLMMs in tandem with 'EcoCountHelper', managers without advanced programmatic or statistical expertise can assess the effects of landscape characteristics on wildlife in a statistically-robust framework. [ABSTRACT FROM AUTHOR]

Anthropogenic noise and its effects on acoustic communication have received considerable attention in recent decades. Yet, the natural acoustic environment's influence on communication and its role in shaping acoustic signals remains unclear. We used large-scale playbacks of ocean surf in coastal areas and whitewater river noise in riparian areas to investigate how natural sounds influences song structure in six songbird species. We recorded individuals defending territories in a variety of acoustic conditions across 19 study sites in California and 18 sites in Idaho. Acoustic characteristics across the sites included naturally quiet 'control' sites, 'positive control' sites that were adjacent to the ocean or a whitewater river and thus were naturally noisy, 'phantom' playback sites that were exposed to continuous broadcast of low-frequency ocean surf or whitewater noise, and 'shifted' playback sites with continuous broadcast of ocean surf or whitewater noise shifted up in frequency. We predicted that spectral and temporal song structure would generally correlate with background sound amplitude and that signal features would differ across site types based on the spectral profile of the acoustic environment. We found that the ways in which song structure varied with background acoustics were quite variable from species to species. For instance, in Idaho both the frequency bandwidth and duration of lazuli bunting (Passerina amoena) and song sparrow (Melospiza melodia) songs decreased with elevated background noise, but these song features were unrelated to background noise in the warbling vireo (Vireo gilvus), which tended to increase both the minimum and maximum frequency of songs with background noise amplitude. In California, the bandwidth of the trill of white-crowned sparrow (Zonotrichia leucophrys) song decreased with background noise amplitude, matching results of previous studies involving both natural and anthropogenic noise. In contrast, wrentit (Chamaea fasciata) song bandwidth was positively related to the amplitude of background noise. Although responses were quite heterogeneous, song features of all six species varied with amplitude and/or frequency of background noise. Collectively, these results provide strong evidence that natural soundscapes have long influenced vocal behavior. More broadly, the evolved behavioral responses to the long-standing challenges presented by natural sources of noise likely explain the many responses observed for species communicating in difficult signal conditions presented by human-made noise. [ABSTRACT FROM AUTHOR]

As linear mixed-effects models (LMMs) have become a widespread tool in ecology, the need to guide the use of such tools is increasingly important. One common guideline is that one needs at least five levels of the grouping variable associated with a random effect. Having so few levels makes the estimation of the variance of random effects terms (such as ecological sites, individuals, or populations) difficult, but it need not muddy one's ability to estimate fixed effects terms--which are often of primary interest in ecology. Here, I simulate datasets and fit simple models to show that having few random effects levels does not strongly influence the parameter estimates or uncertainty around those estimates for fixed effects terms--at least in the case presented here. Instead, the coverage probability of fixed effects estimates is sample size dependent. LMMs including low-level random effects terms may come at the expense of increased singular fits, but this did not appear to influence coverage probability or RMSE, except in low sample size (N = 30) scenarios. Thus, it may be acceptable to use fewer than five levels of random effects if one is not interested in making inferences about the random effects terms (i.e. when they are 'nuisance' parameters used to group non-independent data), but further work is needed to explore alternative scenarios. Given the widespread accessibility of LMMs in ecology and evolution, future simulation studies and further assessments of these statistical methods are necessary to understand the consequences both of violating and of routinely following simple guidelines. [ABSTRACT FROM AUTHOR]

The present study aimed to investigate the diet of African manatees in Cameroon to better inform conservation decisions within protected areas. A large knowledge gap on diet and seasonal changes in forage availability limits the ability to develop informed local management plans for the African manatee in much of its range. This research took place in the Sanaga River Watershed, which includes two protected areas in the Littoral Region of Cameroon: the Douala-Edea National Park and the Lake Ossa Wildlife Reserve. We analyzed 113 manatee fecal samples and surveyed shoreline emergent and submerged vegetation within the Sanaga River Watershed. We used microhistological analyses to determine the relative contribution of each plant species to African manatee diets and compared across locations and across seasons (wet vs. dry season). We found that the shoreline vegetation is diverse with over 160 plant species, unevenly distributed across space and season, and dominated by emergent vegetation mostly represented by the antelope grass (Echinochloa pyramidalis). We recorded a total of 36 plant species from fecal samples with a spatial and temporal distribution mostly reflecting that of the corresponding shoreline vegetation. African manatees appear to be primarily opportunistically feeding on available vegetation across the seasons and habitat. This work documents the current, but changing, state of plant availability in the Sanaga River Watershed and reports the African manatee diet in Cameroon for the first time. This information can play a critical role in successfully managing the species and these protected areas. If we wish to protect the African manatee and the aquatic ecosystems within the Sanaga River Watershed, we must understand how forage availability changes over time, especially as its waters become nutrient enriched, eutrophic, and exposed to invasive species of plants in a changing world. [ABSTRACT FROM AUTHOR]

Novel anthropogenic noise has received considerable attention in behavioural ecology, but the natural acoustic environment has largely been ignored as a niche axis.Using arrays of speakers, we experimentally broadcasted whitewater river noise continuously for three summers, and monitored spider abundance and behaviour across 15 sites, to test our hypothesis that river noise is an important structuring force as a niche axis.We find substantial evidence that orb‐weaving spiders (Araneidae and Tetragnathidae) are more abundant in high sound level environments, but are not affected by background noise spectrum.We explore multiple possible mechanisms underlying these patterns, such as loss of vertebrate predators and increased prey capture, and assess spider web‐building behaviour and body condition in noise. Continued research on the natural and anthropogenic acoustic environment will likely reveal a web of connections hidden within this neglected ecological niche axis. A free Plain Language Summary can be found within the Supporting Information of this article. [ABSTRACT FROM AUTHOR]

Burgeoning urbanization, development and human activities have led to reduced opportunities for nature experience in quiet acoustic environments. Increasing noise affects both humans and wildlife alike.We experimentally altered human‐caused sound levels in a paired study using informational signs that encouraged quiet behaviours in week‐on, week‐off blocks on the trail system of Muir Woods National Monument, California, USA to test if the soundscape influences both wildlife and human experiences.Using continuous measurements from acoustic recording units (n = 13) spatially distributed within the park, we found signs significantly lowered sound levels by approximately 1.2 decibels (A‐weighted), thereby increasing listening area by 24% and bird availability by approximately 5.8% for every 1 decibel decrease.Visitor‐intercept surveys (n = 537) revealed that our mitigation increased the number of birds perceived by visitors, rankings of soundscape pleasantness, and importantly, preferences for soundscape management.By lowering human‐caused sound levels, we created an acoustic environment equivalent to a ~21% reduction in visitors. The positive feedback cycle we describe may lead to increased conservation support in a time when the extinction of nature experience looms. A free Plain Language Summary can be found within the Supporting Information of this article. A free Plain Language Summary can be found within the Supporting Information of this article. [ABSTRACT FROM AUTHOR]

Background: Previous research has shown diverse vertical space use by various taxa, highlighting the importance of forest vertical structure. Yet, we know little about vertical space use of tropical forests, and we often fail to explore how this three-dimensional space use changes over time. Methods: Here we use canopy tower systems in French Guiana and passive acoustic monitoring to measure Neotropical bat activity above and below the forest canopy throughout nine nights. We use a Bayesian generalized linear mixed effect model and kernel density estimates to demonstrate patterns in space-use over time. Results:We found that different bats use both canopy and understory space differently and that these patterns change throughout the night. Overall, bats were more active above the canopy (including Cormura brevirostris, Molossus molossus, Peropteryx kappleri and Peropteryx macrotis), but multiple species or acoustic complexes (when species identification was impossible) were more active in the understory (such as Centronycteris maximiliani, Myotis riparius, Pteronotus alitonus and Pteronotus rubiginosus). We also found that most bats showed temporally-changing preferences in hourly activity. Some species were less active (e.g., P. kappleri and P. macrotis), whereas others were more active (Pteronotus gymnonotus, C. brevirostris, and M. molossus) on nights with higher moon illuminance. Discussion: Here we show that Neotropical bats use habitat above the forest canopy and within the forest understory differently throughout the night. While bats generally were more active above the forest canopy, we show that individual groups of bats use space differently over the course of a night, and some prefer the understory. This work highlights the need to consider diel cycles in studies of space use, as animals use different habitats during different periods of the day. [ABSTRACT FROM AUTHOR]

Anthropogenic noise is a widespread pollutant that has received considerable recent attention. While alarming effects on wildlife have been documented, we have limited understanding of the perceptual mechanisms of noise disturbance, which are required to understand potential mitigation measures. Likewise, individual differences in response to noise (especially via perceptual mechanisms) are likely widespread, but lacking in empirical data. Here we use the echolocating bat Phyllostomus discolor, a trained discrimination task, and experimental noise playback to explicitly test perceptual mechanisms of noise disturbance. We demonstrate high individual variability in response to noise treatments and evidence for multiple perceptual mechanisms. Additionally, we highlight that only some individuals were able to cope with noise, while others were not. We tested for changes in echolocation call duration, amplitude, and peak frequency as possible ways of coping with noise. Although all bats strongly increased call amplitude and showed additional minor changes in call duration and frequency, these changes could not explain the differences in coping and non-coping individuals. Our understanding of noise disturbance needs to become more mechanistic and individualistic as research knowledge is transformed into policy changes and conservation action. [ABSTRACT FROM AUTHOR]

Artificial light at night is rapidly changing the sensory world. While evidence is accumulating for how insects are affected, it is not clear how this impacts higher trophic levels that feed on insect communities. Spiders are important insect predators that have recently been shown to have increased abundance in urban areas, but have shown mixed responses to artificial light. On a single bridge with alternating artificially lit and unlit sections, I measured changes in the orb-weaving spider Larinioides sclopetarius (Araneidae) web abundance, web-building behavior, prey-capture, and body condition. In artificially lit conditions, spiders caught more prey with smaller webs, and had higher body conditions. However, there were fewer spiders with active webs in those lit areas. This suggests that either spiders were not taking advantage of an ecological insect trap, perhaps due to an increased risk of becoming prey themselves, or were satiated, and thus not as active within these habitats. The results from this natural experiment may have important consequences for both insects and spiders in urban areas under artificial lighting conditions. [ABSTRACT FROM AUTHOR]

Global water scarcity necessitates creative, yet practical, solutions to meet ever-growing demand. Green infrastructure is increasingly used in this context to provide water in environmentally friendly and sustainable ways. In this study, we focused on reclaimed wastewater from a joint gray and green infrastructure system employed by the Loxahatchee River District in Florida. The water system consists of a series of treatment stages for which we assessed 12 years of monitoring data. We measured water quality after secondary (gray) treatment, then in onsite lakes, offsite lakes, landscape irrigation (via sprinklers), and ultimately in downstream canals. Our findings show gray infrastructure designed for secondary treatment, integrated with green infrastructure, achieved nutrient concentrations nearly equivalent to advanced wastewater treatment systems. For example, we observed a dramatic decline in mean nitrogen concentration from 19.42 mg L -1 after secondary treatment to 5.26 mg L -1 after spending an average of 30 days in the onsite lakes. Nitrogen concentration continued to decline as reclaimed water moved from onsite lakes to offsite lakes (3.87 mg L -1 ) and irrigation sprinklers (3.27 mg L -1 ). Phosphorus concentrations exhibited a similar pattern. These decreasing nutrient concentrations led to relatively low nutrient loading rates and occurred while consuming substantially less energy and producing fewer greenhouse gas emissions than traditional gray infrastructure-at lower cost and higher efficiency. There was no evidence of eutrophication in canals downstream of the residential landscape whose sole source of irrigation water was reclaimed water. This study provides a long-term example of how circularity in water use can be used to work toward sustainable development goals., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

The biological sciences community is increasingly recognizing the value of open, reproducible and transparent research practices for science and society at large. Despite this recognition, many researchers fail to share their data and code publicly. This pattern may arise from knowledge barriers about how to archive data and code, concerns about its reuse, and misaligned career incentives. Here, we define, categorize and discuss barriers to data and code sharing that are relevant to many research fields. We explore how real and perceived barriers might be overcome or reframed in the light of the benefits relative to costs. By elucidating these barriers and the contexts in which they arise, we can take steps to mitigate them and align our actions with the goals of open science, both as individual scientists and as a scientific community.