Development of a Seafloor Community Classification for the New Zealand Region Using a Gradient Forest Approach

To support ongoing marine spatial planning in New Zealand, a numerical environmental classification using Gradient Forest models was developed using a broad suite of biotic and high-resolution environmental predictor variables. Gradient Forest modeling uses species distribution data to control the selection, weighting and transformation of environmental predictors to maximise their correlation with species compositional turnover. A total of 630,997 records (39,766 unique locations) of 1,716 taxa living on or near the seafloor were used to inform the transformation of 20 gridded environmental variables to represent spatial patterns of compositional turnover in four biotic groups and the overall seafloor community. Compositional turnover of the overall community was classified using a hierarchical procedure to define groups at different levels of classification detail. The 75-group level classification was assessed as representing the highest number of groups that captured the majority of the variation across the New Zealand marine environment. We refer to this classification as the New Zealand “Seafloor Community Classification” (SCC). Associated uncertainty estimates of compositional turnover for each of the biotic groups and overall community were also produced, and an added measure of uncertainty – coverage of the environmental space – was developed to further highlight geographic areas where predictions may be less certain owing to low sampling effort. Environmental differences among the deep-water New Zealand SCC groups were relatively muted, but greater environmental differences were evident among groups at intermediate depths in line with well-defined oceanographic patterns observed in New Zealand’s oceans. Environmental differences became even more pronounced at shallow depths, where variation in more localised environmental conditions such as productivity, seafloor topography, seabed disturbance and tidal currents were important differentiating factors. Environmental similarities in New Zealand SCC groups were mirrored by their biological compositions. The New Zealand SCC is a significant advance on previous numerical classifications and includes a substantially wider range of biological and environmental data than has been attempted previously. The classification is critically appraised and considerations for use in spatial management are discussed.

Feasibility Study on Biomonitoring of Microplastics in Fish Gastrointestinal Tracts

Monitoring the occurrence and trends of microplastic contamination in the marine environment is key to establish microplastic (MP) data baselines, to work out policy mitigation measures, and to assess the effectiveness of waste regulations. To establish MP contamination baselines in the marine environment, marine biota species can be selected as monitoring matrices to track plastic pollution in the environment. The aim of this work was to evaluate the feasibility of biomonitoring MPs in fish gastrointestinal tract (GIT). A selection of suitable fish species was performed, based on species distribution, sampling effort, commercial value of species, sustainable development of fish populations, migration behaviour, and scientific evidence for occurrence of MPs in the fish GIT. Sampling and MP extraction protocols were developed and validated on fish GIT samples acquired in the Southern North Sea. The fish species selection protocol enabled the selection of ubiquitous distributed and non-endangered fish species relevant for MP monitoring in the North Sea. The fish GIT sampling protocol considered background contamination measures and sampling fillet as procedural blanks. Advantages and disadvantages of onboard dissection were discussed. The MPs extraction protocol was based on matrix digestion, density separation, and Nile red staining of particles followed by fluorescent microscopy observation. The confirmation of MPs identification and the analysis of the polymer composition was done using micro-Fourier transform infrared (μFTIR) spectroscopy. The MP analysis indicated a low number of MPs in the fish GIT. The mean number of particles per single fish GIT was 0.48 ± 0.81 (Nile red staining observations) to 0.26 ± 0.64 (corrected for background contamination). A power analysis (sampling effort) indicated that to detect significant differences, in a balanced-ANOVA type of analysis, between species and/or sampling areas, the sample size would require a minimum of 109 up to 370 individual fish. The feasibility of MP biomonitoring in fish GIT was assessed by a SWOT-analysis, which indicated that fish GIT is a suitable matrix for biomonitoring of MPs, but that the large number of samples needed to identify significant differences can be a major drawback. A potential implementation strategy for MP biomonitoring within Europe was suggested.

Daily Variation in Sampled Densities of Ixodes scapularis and Amblyomma americanum (Acari: Ixodidae) Nymphs at a Single Site—Implications for Assessing Acarological Risk

The public health challenge posed by tick-borne disease (TBD) has increased efforts to characterize the spatial and temporal distribution of ticks and associated pathogens to better focus tick control strategies and personal protection measures. We describe variability in nymphal Ixodes scapularis Say and Amblyomma americanum (L.) density derived from daily drag sampling at a single location in New Jersey over 4 yr and explore how observed differences in daily collections might affect the estimation of acarological risk. We found significant variability in the density of host-seeking nymphs that could suggest substantially different rates of human-tick encounters depending on sampling date, habitat, and ambient weather conditions. The spatial and temporal variability in the distribution of 2 sympatric tick species with different host preferences and questing strategies, suggests that to produce results that are comparable among sites across the area sampled, surveillance efforts may be limited to shorter collection seasons, fewer sites or less sampling effort (fewer plots or fewer visits) per site, and a geographic scope that minimizes the potential temporal and spatial biases indicated here. Our results illustrate that evaluation of models of tick distribution or relative acarological risk based on surveillance data requires a full description of the diversity of habitats sampled and the conditions under which sampling is performed. The array of factors that affect tick host-seeking and that could bias interpretation of sampling results emphasizes the need to standardize sampling protocols and for more caution when interpreting tick sampling data collected over large temporal and spatial scales.

Mammal virus diversity estimates are unstable due to accelerating discovery effort

Host-virus association data underpin research into the distribution and eco-evolutionary correlates of viral diversity and zoonotic risk across host species. However, current knowledge of the wildlife virome is inherently constrained by historical discovery effort, and there are concerns that the reliability of ecological inference from host-virus data may be undermined by taxonomic and geographical sampling biases. Here, we evaluate whether current estimates of host-level viral diversity in wild mammals are stable enough to be considered biologically meaningful, by analysing a comprehensive dataset of discovery dates of 6571 unique mammal host-virus associations between 1930 and 2018. We show that virus discovery rates in mammal hosts are either constant or accelerating, with little evidence of declines towards viral richness asymptotes, even in highly sampled hosts. Consequently, inference of relative viral richness across host species has been unstable over time, particularly in bats, where intensified surveillance since the early 2000s caused a rapid rearrangement of species' ranked viral richness. Our results illustrate that comparative inference of host-level virus diversity across mammals is highly sensitive to even short-term changes in sampling effort. We advise caution to avoid overinterpreting patterns in current data, since it is feasible that an analysis conducted today could draw quite different conclusions than one conducted only a decade ago.

Silvopastoral and conventional management of extensive livestock and the diversity of bats in fragments of tropical dry forest in Córdoba, Colombia

The establishment of extensive livestock systems in the Colombian Caribbean Region has historically generated a strong loss of the tropical dry forest (TDF) with negative effects on biodiversity. Currently, the implementation of silvopastoral systems (SPS) has been proposed with strategy to curb the loss of biodiversity caused by the conventional management system (CS). The objective was to evaluate the effect of SPS and CS of extensive livestock on the assemblage of bats associated with fragments of TDF. During a continuous year and a sampling effort of 30,240 h-net/night, the structure and composition of bat assemblage between SPS and CS were compared. 2788 bats belonging to six families, 23 genera, and 39 species were captured. The Phyllostomidae family presented the highest species richness (S = 30), with the greatest abundance in the Stenodermatinae subfamily (n = 1543). Bat assemblage in the SPS fragments was more equitable; and the relative abundance per species, per genera, and per foraging guilds was also significantly higher. The capture success showed significant variations between the climatic seasons (dry and rainy). The rate of species turnover was higher in the CS fragments. The species Artibeus planirostris, Artibeus lituratus, Carollia perspicillata, Carollia castanea, Phyllostomus discolor, Dermanura phaeotis, Uroderma convexum, Glossophaga soricina, C. brevicauda, and Sturnira lilium accounted for 92% of the captures. In conclusion, frugivorous bats were more abundant in the SPS, type of extensive livestock management that can generate greater temporal stability of bat assemblage. This research provides the first scientific evidence of the positive effect of silvopastoral management on the diversity of bats in tropical dry forest areas of the Colombian Caribbean region.

[Transiting species, phenologies and their trends]

[In order to contribute to the knowledge of the spatio-temporal progression of post-nuptial migration of birds across the Italian Alps, we present in detail the results of the analysis carried out for 69 species (4 non-Passeriformes; 65 Passeriformes) of the 191 ringed within the Progetto Alpi. Data were collected in 40 ringing stations located in different habitats and at different altitudes (mountain passes, slopes and valley floors) and active in the post-breeding migratory period (1 August - 30 November). Among these, those (n=15) with continuous activity (at least one month) and known sampling effort (daily capture effort described as product of net area in square meters by operating time in hours) were selected. Data from the 6 stations that operated continuously over the years (2001-2017) and with standardised capture effort were used for trend analyses. Species covered refer to those with more than 100 birds ringed within the first eight hours after sunrise (excluding local retraps). Species accounts contain detailed data from datasets from all stations participating in the Alps Project (1997-2017)]. [Article in Italian]

Temporal trends in abundance and phenology of migratory birds across the Italian Alps during a 20-year period

Introduction: Bird migration across mountainous regions has been studied usually at single sites due to the difficulty in employing and support a multi-site sampling effort. This may affect inference on migration whose scale is larger that a single site. The Progetto Alpi has been monitoring post-breeding bird migration through the Italian Alps with a network of several ringing stations since 1997. Until 2017, 666,471 ringing data of 191 different species were collected. Methods: Phenology of bird migration in terms of date of capture and the related elevational distribution during the sampling season (August-November) were analysed for 69 species. For a subset of 45 species the inter-annual variation in phenology along with trends in the number of ringed birds and in the ratio between the number of juveniles and adults ringed, were also analysed. Results: Migration through the Italian Alps occurred differently between species, with heterogeneity across species in the median date of capture and their elevational distribution. No linear trends in phenology were detected. For four species an annual linear increase of the ringed individuals was detected, while for other four species an annual linear decrease of the captures was detected. For two species, an increase of the ratio between the number of the juveniles and the number of adults ringed was detected. Conclusions: The long-term standardized monitoring of post-breeding migration allowed us to consolidate and increase knowledge of bird migration through Italian southern Alps. The information gathered allowed us to define the temporal and elevation distribution of passerine birds crossing the mountainous area, and to test interannual trends in the number of captures. The main purpose of this work was to report on the information collected in twenty years of field activity, providing a contribution to the understanding this complex phenomenon. Further investigations and more in-depth analyses are necessary to understand how environmental factors and species-specific eco-physiological traits interact and affect migratory strategies of passerine birds in the Italian Alpine region.

Taxonomic and geographic bias in 50 years of research on the behaviour and ecology of galagids

Identifying knowledge gaps and taxonomic and geographic bias in the literature is invaluable for guiding research towards a more representative understanding of animal groups. Galagids are nocturnal African primates and, for many species, detailed information on their behaviour and ecology is unavailable. To identify gaps and bias in the literature we reviewed published peer-reviewed research articles on galagid behaviour and ecology over a 50-year period from January 1971 to December 2020. Using the Web of Science and Google Scholar databases, we identified 758 articles, assessed 339 full texts for eligibility and included 211 in the review. Species of Otolemur have been extensively researched in comparison to other genera (78.2% of studies; Euoticus: 13.3% of studies; Galago: 66.4% of studies; Galagoides: 20.9% of studies; Paragalago: 22.3% of studies; Sciurocheirus: 15.2% of studies). The most common category of research was physiology (55.0% of studies), followed by behavioural ecology (47.4% of studies), and fewer studies were on genetics and taxonomy (16.1% of studies) and habitat and distribution (14.2% of studies). Text mining revealed that the word ‘behaviour’ was the most common word used in abstracts and keywords, and few words were related to ecology. Negative binomial regression revealed that mean body mass and geographic range size were significant positive predictors of the total number of scientific outputs on each species. Research on wild populations was carried out in only 24 (60%) of the 40 countries galagids are thought to inhabit. Studies were undertaken in locations with lower mean annual temperatures and higher human population densities over warmer and less populated areas. We encourage a more equal sampling effort both taxonomically and geographically that in particular addresses the paucity of research on smaller species and those with restricted ranges. Research on in situ populations, especially in warmer and remote areas, is urgently needed, particularly in West, Central and some Southern African countries.

Subsampling to Enhance Efficiency in Input Uncertainty Quantification

Quantifying the impact of input estimation errors in data-driven stochastic simulation often encounters substantial computational challenges due to the entanglement of Monte Carlo and input data noises. In this paper, we propose a subsampling framework to bypass this computational bottleneck, by leveraging the form of the output variance and its estimation error in terms of data size and sampling effort. Compared with standard subsampling in the literature, our motivation is distinctly to reduce the sampling complexity of the two-layer bootstrap required in simulation uncertainty quantification. Compared with standard bootstraps, our subsampling approach provably and experimentally leads to more accurate variance and confidence interval estimations under the same amount of simulation budget.

Mosquito Communities Vary across Landscape and Vertical Strata in Indian River County, Florida

Mosquito and arbovirus surveillance is essential to the protection of public health. A majority of surveys are undertaken at ground level. However, mosquitoes shelter, breed, and quest for hosts across vertical strata, thus limiting our ability to fully describe mosquito and arboviral communities. To elucidate patterns of mosquito vertical stratification, canopy traps were constructed to sample mosquitoes at heights of 1.5, 5.0, and 8.7 m across three different landscape types in a Florida coastal conservation area. We assessed trapping efforts using individual-based rarefaction and extrapolation. The effects of height, landscape, site location, and sampling date on mosquito community composition were parsed out using permutational ANOVA on a Hellinger-transformed Bray–Curtis dissimilarity abundance matrix. Lastly, a generalized linear mixed effects model (GLMM) was used to explore species-specific vertical patterns. We observed differences in sampling effort and community composition structure across various heights and landscapes. Our GLMM revealed significant effects of trap height for Aedes taeniorhynchus, Anopheles crucians, Anopheles quadrimaculatus, and Culex coronator, but not for Culex nigripalpus, the ultra-dominant species present in this area. Together these data provide evidence that height and landscape significantly affect mosquito community structures and highlight a need to develop sampling regimes to target specific vector and nuisance species at their preferred height and across different landscape types.