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Line transect surveys are widely used in Neotropical rainforests to estimate the population abundance of medium- and large-sized vertebrates. The use of indices such as encounter rate has been criticized because the probability of animal detection may fluctuate due to the heterogeneity of environmental conditions among sites. In addition, the morphological and behavioral characteristics (biological traits) of species affect their detectability. In this study, we compared the extent to which environmental conditions and species' biological traits bias abundance estimates in terra firme rainforests in French Guiana. The selected environmental conditions included both physical conditions and forest structure covariates, while the selected biological traits included the morphological and behavioral characteristics of species. We used the distance sampling method to model the detection probability as an explicit function of environmental conditions and biological traits and implemented a model selection process to determine the relative importance of each group of covariates. Biological traits contributed to the variability of animal detectability more than environmental conditions, which had only a marginal effect. Detectability was best for large animals with uniform or disruptive markings that live in groups in the canopy top. Detectability was worst for small, solitary, terrestrial animals with mottled markings. In the terra firme rainforests that represent ~80% of the Amazonia and Guianas regions, our findings support the use of relative indices such as the encounter rate to compare population abundance between sites in species-specific studies. Even though terra firme rainforests may appear similar between regions of Amazonia and the Guianas, comparability must be ensured, especially in forests disturbed by human activity. The detection probability can be used as an indicator of species' vulnerability to hunting and, thus, to the risk of local extinction. Only a few biological trait covariates are required to correctly estimate the detectability of the majority of medium- and large-sized vertebrates. Thus, a biological trait model could be useful in predicting the detection probabilities of rare, uncommon, or localized species for which few data are available to fit the detection function., (© 2017 by the Ecological Society of America.)

Estimating relative abundance is critical for informing conservation and management efforts and for making inferences about the effects of environmental change on populations. Freshwater fisheries span large geographic regions, occupy diverse habitats and consist of varying species assemblages. Monitoring schemes used to sample these diverse populations often result in populations being sampled at different times and under different environmental conditions. Varying sampling conditions can bias estimates of abundance when compared across time, location and species, and properly accounting for these biases is critical for making inferences. We develop a joint species distribution model (JSDM) that accounts for varying sampling conditions due to the environment and time of sampling when estimating relative abundance. The novelty of our JSDM is that we explicitly model sampling effort as the product of known quantities based on time and gear type and an unknown functional relationship to capture seasonal variation in species life history. We use the model to study relative abundance of six freshwater fish species across the state of Minnesota, USA. Our model enables estimates of relative abundance to be compared both within and across species and lakes, and captures the inconsistent sampling present in the data. We discuss how gear type, water temperature and day of the year impact catchability for each species at the lake level and throughout a year. We compare our estimates of relative abundance to those obtained from a model that assumes constant catchability to highlight important differences within and across lakes and species. Synthesis and applications: Our method illustrates that assumptions relating indices of abundance to observed catch data can greatly impact model inferences derived from JSDMs. Specifically, not accounting for varying sampling conditions can bias inference of relative abundance, restricting our ability to detect responses to management interventions and environmental change. While our focus is on freshwater fisheries, this model architecture can be adopted to other systems where catchability may vary as a function of space, time and species.

This study was conducted in Van province, which is located in the eastern region of Türkiye. The study area is located in the Irano-Anatolian hotspot region, divided to the east and west by the Anatolian diagonal. Here, we demonstrate the diversity, distribution, and seasonality of horseflies. Malaise and water traps were used to collect adult horseflies. A total of 1026 specimens were collected and 52 species identified. Chrysops divaricatus Loew, 1858; Haematopota csikii Szilady, 1922; Haematopota pallidula (Krober, 1922) and Haematopota turkestanica (Krober, 1922) were recorded for the first time from Türkiye. The distribution and seasonality of the species were presented.

Abstract Conservation areas encompassing elevation gradients are biodiversity hotspots because they contain a wide range of habitat types in a relatively small space. Studies of biodiversity patterns along elevation gradients, mostly on small mammal or bird species, have documented a peak in diversity at mid elevations. Here, we report on a field study of medium and large mammals to examine the impact of elevation, habitat type, and gross primary productivity on community structure. Species richness was observed using a camera trap transect with 219 sites situated across different habitat types from 2329 to 4657 m above the sea level on the western slope of Mt Kenya, the second highest mountain in Africa. We found that the lowest elevation natural habitats had the highest species richness and relative abundance and that both metrics decreased steadily as elevation increased, paralleling changes in gross primary productivity, and supporting the energy richness hypothesis. We found no evidence for the mid‐domain effect on species diversity. The lowest elevation degraded Agro‐Forestry lands adjacent to the National Park had high activity of domestic animals and reduced diversity and abundance of native species. The biggest difference in community structure was between protected and unprotected areas, followed by more subtle stepwise differences between habitats at different elevations. Large carnivore species remained relatively consistent but dominant herbivore species shifted along the elevation gradient. There was some habitat specialization and turnover in species, such that the elevation gradient predicts a high diversity of species, demonstrating the high conservation return for protecting mountain ecosystems for biodiversity conservation.

Abstract Exploring how interactions between species evenness and dominant species identity affect litter decomposition processes is vital to understanding the relationship between biodiversity and ecosystem functioning in the context of global changes. We carried out a 127‐day litter decomposition experiment under controlled conditions, with interactions of four species evenness types (high, medium, low and single species) and three dominant species identity (Leymus chinensis, Serratula centauroides, Artemisia capillaris). After collecting the remaining litter, we estimated how evenness and dominant species identity affected litter mass loss rate, carbon (C) loss rate, nitrogen (N) loss rate and remaining litter C/N directly or indirectly, and assessed relative mixture effects (RMEs) on litter mass loss. The main results are shown as follows. (1) By generalized linear models, litter mass loss rate was significantly affected by evenness after 69‐day decomposition; N loss rate was affected by dominant species identity after 69‐day decomposition, with treatment dominated by Serratula centauroides being at least 9.26% higher than that dominated by any of other species; and remaining litter C/N was affected by the interactions between evenness and dominant species identity after 30‐, 69‐ and 127‐day decomposition. (2) Twenty‐three out of 27 RMEs were additive, and dominant species identity showed a significant effect on RMEs after 127‐day decomposition. (3) By confirmatory path analyses, litter mass loss rate was affected by dominant species identity directly after 127‐day decomposition, and by both species evenness and dominant species identity indirectly which was mediated by initial litter functional dispersion (FDis) after 30‐ and 69‐day decomposition; remaining litter C/N was affected by evenness indirectly which was mediated by initial litter FDis after 127‐day decomposition. These findings highlight the importance of evenness and dominant species identity on litter decomposition. The study provides insights into communities during retrogressive successions in semi‐arid grasslands in the context of global changes.

Abstract Background Diatoms are present in all waters and are highly sensitive to pollution gradients. Therefore, they are ideal bioindicators for water quality assessment. Current indices used in these applications are based on identifying diatom species and counting their abundances using traditional light microscopy. Several molecular techniques have been developed to help automate different steps of this process, but obtaining reliable estimates of diatom community composition and species abundance remains challenging. Results Here, we evaluated a recently developed quantification method based on Genotyping by Sequencing (GBS) for the first time in diatoms to estimate the relative abundances within a species complex. For this purpose, a reference database comprised of thousands of genomic DNA clusters was generated from cultures of Nitzschia palea. The sequencing reads from calibration and mock samples were mapped against this database for parallel quantification. We sequenced 25 mock diatom communities containing up to five taxa per sample in different abundances. Taxon abundances in these communities were also quantified by a diatom expert using manual counting of cells on light microscopic slides. The relative abundances of strains across mock samples were over- or under-estimated by the manual counting method, and a majority of mock samples had stronger correlations using GBS. Moreover, one previously recognized putative hybrid had the largest number of false positive detections demonstrating the limitation of the manual counting method when morphologically similar and/or phylogenetically close taxa are analyzed. Conclusions Our results suggest that GBS is a reliable method to estimate the relative abundances of the N. palea taxa analyzed in this study and outperformed traditional light microscopy in terms of accuracy. GBS provides increased taxonomic resolution compared to currently available quantitative molecular approaches, and it is more scalable in the number of species that can be analyzed in a single run. Hence, this is a significant step forward in developing automated, high-throughput molecular methods specifically designed for the quantification of [diatom] communities for freshwater quality assessments.

Abstract Recent literature has shown citizen science data that include reported counts, such as observations from the eBird database, can be used to model the relative abundance of selected species. The objective of our study was to extend on both the methodology and the range of species considered by previous research on relative abundance modeling; we selected the Floridian peninsula as our geographical area of interest. We confirmed that, much like for other bird species and geographical areas, modeling such data with a classic Poisson generalized linear model was not appropriate due to overdispersion. Moreover, assuming linearity for the effects of all environmental and observer effort covariates on relative abundance was shown to be overly simplistic. These concerns led us to consider a variety of potentially suitable modeling techniques; the quasi‐Poisson generalized additive model displayed the best combination of flexibility, strong predictive performance, and ease of interpretation. Expanding on previous research for eBird data, we chose to explicitly incorporate spatial dependence into the modeling task by performing hierarchical generalized additive modeling with a spatial conditional autoregressive structure for random effects. This practice allows us to account for spatial factors not represented by model covariates, such as species dispersal patterns or colonial breeding habits. After conducting appropriate testing procedures and fitting spatially explicit models, we found that our data contain moderate spatial dependence and that spatially explicit models have overall superior predictive performance to models that do not account for spatial dependence. Upon closer inspection, spatially explicit models perform especially well compared with their nonspatial counterparts in identifying situations with low abundance, with a negligible trade‐off in prediction accuracy for situations with high abundance. We conclude that quasi‐Poisson hierarchical generalized additive models with spatial random effects provide the best representation of the relative abundance of bird populations. Moreover, our spatially explicit models are more realistic based on domain knowledge when regarding the impact of environmental covariates, which is important when considering conservation implications and future projections.

Abstract Determining what factors influence the distribution and abundance of wildlife populations is crucial for implementing effective conservation and management actions. Yet, for species with dynamic seasonal, sex‐, and age‐specific spatial ecology, like the diamondback terrapin (Malaclemys terrapin; DBT), doing so can be challenging. Moreover, environmental factors that influence the distribution and abundance of DBT in their northernmost range have not been quantitatively characterized. We investigated proximity to nesting habitat as one potential driver of spatiotemporal variation in abundance in a three‐step analytical approach. First, we used a scale selection resource selection function (RSF) approach based on landcover data from the National Landcover Database (NLCD) to identify the scale at which DBT are selecting for (or avoiding) landcover types to nest. Next, we used RSF to predict areas of suitable nesting habitat and created an index of nest suitability (NSI). Finally, analyzing visual count data using a generalized linear mixed model (GLMM), we investigate spatiotemporal drivers of relative abundance, with a specific focus on whether similar factors affect offshore abundance and onshore nest site selection. We found the scale of selection for developed and saltmarsh land use classes to be 550 and 600 m and open water land use classes to be 100. Selection was positive for nesting areas proximal to saltmarsh habitat and negative for developed and open water. Expected relative abundance was best explained by the interaction between NSI and day of season, where expected relative abundance was greater within high NSI areas during the nesting season (2.20 individuals, CI: 1.19–3.93) compared to areas of low NSI (1.84 individuals, CI: 1.10–3.10). Our results provide evidence that inferred spatial patterns of suitable nesting habitats explain spatiotemporal patterns of terrapin movement and abundance.

In Ethiopia, most of the studies on mammals have focused on single species and protected areas. This survey investigated the impacts of habitats and seasons on the medium and large-sized mammals’ diversity and distribution in a human-dominated landscape. This survey was conducted using 36 systematically distributed transect lines within stratified habitat types. A total of 685 records belonging to 21 species, six orders, and 13 families were identified, including globally vulnerable Panthera leo, Panthera pardus, and Hippopotamus amphibious. Overall, Papio anubis and Chlorocebus aethiops were the dominant species recorded in the area. Except for three species, all species encountered in the three habitats are subsets of the species recorded in the grassland. The species record frequency was highest in the forest. The dry season characterized by a higher frequency of records but by lower species richness than the wet season. In general, the study area is potential for mammalian species conservation in Ethiopia.

The correct interpretation of relative abundance indices provided by different sampling methods is essential to correctly estimate population size. Although multiple indices and models have been proposed, their ability to estimate relative abundances and their performance in models explaining abundance trends remains unclear. We used the red fox (Vulpes vulpes) as a model species to compare the relationship and derived models of relative abundance between three indices of relative abundance: RAI (number of captures/total occasions); NI (number of photo-identified individuals) obtained by camera-trapping, and NSE (number of segments with scats) obtained by the scat census sampling method. In addition, we modelled the relationship between a set of habitat predictors and fox relative abundance for each of the three estimated relative abundance indices. We compared the relative abundance models explained for each index against N-mixture models that estimate abundance controlled for variation in detection. Results showed a positive correlation between the RAI and NI indices, while both indices showed a negative relationship with the NSE index. Relative abundance models and N-Mixture models showed a different selection of predictors to explain abundance trends. NSE and RAI indices selected predictors that could explain variability in fox detection rather than fox abundance. In contrast, the NI index and N-Mixture models selected the same predictors to explain fox abundance. Our results suggest the use of the NI index for abundance models without the need to control for variation in detection. Relative abundance indices based on scats and captures per occasion are suboptimal indices for species abundance studies due to possible bias caused by animal behaviour. If count-based methods on captures per occasion (RAI) are selected, we suggest using session-based data processing to incorporate detectability variation in N-mixture models.

Abstract Understanding the ecological and evolutionary factors that influence species rarity has important theoretical and applied implications, yet the reasons why some species are rare while others are common remain unresolved. As a novel exploration of scientific knowledge, we used network analysis conceptually to visualize the foci of a comprehensive base of >800 studies on plant species rarity within the context of ecology and evolution. In doing so, we highlight existing research strengths that could substantiate novel syntheses and gaps that could inspire new research. Our results reveal strong integrated foci on population dynamics with other ecological concepts. In contrast, despite the potential for ecological and evolutionary processes to interact, few studies explored the interplay of environmental factors and microevolutionary patterns. The cellular and molecular biology, physiology, and plasticity of rare plant species within both ecological and evolutionary contexts similarly provide avenues for impactful future investigations.

Abstract We evaluated the richness, diversity, and composition of the medium and large mammal community in the Loka Abaya National Park (LANP), southern Ethiopia, and how these parameters differ among four habitat types: wooded grassland, riverine forest, hilly scrubland and wetland, and between seasons. We recorded a total of 2,573 individual animals of 28 medium and large mammal species in the park. This included three globally threatened species: the endangered African wild dog (Lycaon pictus), the vulnerable Leopard (Panthera pardus), and Hippopotamus (Hippopothamus amphibius). Season had little effect on species richness, diversity, and composition both across and within habitat types. However, species richness across seasons was significantly different among the four habitat types, in the declining order of the following: wooded grassland > riverine forest > hilly scrubland > wetland. The strongest similarity in species composition, both across and within seasons, was found between wooded grassland and riverine forest. In terms of relative abundance, mammal assemblage of the wooded grassland and wetland habitats had more evenly distributed number of species with different relative abundance categories. Overall, Anubis Baboon (Papio anubis), Grivet Monkey (Chlorocebus aethiops), and Greater Kudu (Tragelephus strepsiceros) were the three most abundant species across habitat types. In conclusion, findings of our study reveal that LANP plays an important role in Ethiopia's mammal conservation. Our findings will serve as baseline information for managers of the park to make effective conservation decisions and as a baseline for researchers wishing to conduct related ecological studies.

Abstract Co‐occurrence of closely related species is often explained through resource partitioning, where key morphological or life‐history traits evolve under strong divergent selection. In bumble bees (genus Bombus), differences in tongue lengths, nest sites, and several life‐history traits are the principal factors in resource partitioning. However, the buff‐tailed and white‐tailed bumble bee (Bombus terrestris and B. lucorum respectively) are very similar in morphology and life history, but their ranges nevertheless partly overlap, raising the question how they are ecologically divergent. What little is known about the environmental factors determining their distributions stems from studies in Central and Western Europe, but even less information is available about their distributions in Eastern Europe, where different subspecies occur. Here, we aimed to disentangle the broad habitat requirements and associated distributions of these species in Romania and Bulgaria. First, we genetically identified sampled individuals from many sites across the study area. We then not only computed species distributions based on presence‐only data, but also expanded on these models using relative abundance data. We found that B. terrestris is a more generalist species than previously thought, but that B. lucorum is restricted to forested areas with colder and wetter climates, which in our study area are primarily found at higher elevations. Both vegetation parameters such as annual mean Leaf Area Index and canopy height, as well as climatic conditions, were important in explaining their distributions. Although our models based on presence‐only data suggest a large overlap in their respective distributions, results on their relative abundance suggest that the two species replace one another across an environmental gradient correlated to elevation. The inclusion of abundance enhances our understanding of the distribution of these species, supporting the emerging recognition of the importance of abundance data in species distribution modeling.

An observation on avian species composition, density, and diversity was carried out at three selected water bodies of Khanapur Taluka, Belagavi District, for a period of 11 months in 2014. During the study, a total of 28 species belonging to 12 families from five orders were recorded. Of these, Ciconiiformes was represented by seven families followed by Coraciiformes by two families while Anseriformes, Charadriiformes and Gruiformes were represented by one family each. Among the three water bodies studied, maximum species composition (26 species) was recorded from Nandgad pond which also hosts Lesser Adjutant Stork and Wooly-necked Stork categorized as ‘Vulnerable’ and Painted Stork, River Tern and Oriental White Ibis as ‘Near Threatened’ by the IUCN Red List. Bidi Minor Irrigation Tank stands second with 17 species while the minimum was recorded at Hebbal Minor Irrigation Tank with 11 species. Based on our observation, a smaller habitat with habitat heterogeneity can attract more assemblages of avifauna and also result in increased species richness and diversity.

Abstract The interactions between plants and insects play an important role in ecosystems. Climate change and cropping patterns can affect herbivorous pest insect dynamics. Understanding the reasons for population fluctuations can help improve integrated pest management strategies. Here, a 25‐year dataset on climate, cropping planting structure, and the population dynamics of cotton bollworms (Helicoverpa armigera) from Bachu County, south Xinjiang, China, was analyzed to assess the effects of changes in climate and crop planting structure on the population dynamics of H. armigera. The three generations of H. armigera showed increasing trends in population size with climate warming, especially in the third generation. The relative abundances of the first and second generations decreased, but that of the third generation increased. Rising temperature and precipitation produced different impacts on the development of different generations. The population numbers of H. armigera increased with the increase in the non‐Bacillus thuringiensis (Bt) cotton‐planted area. Asynchrony of abrupt changes existed among climate change, crop flowering dates, and the phenology of H. armigera moths. The asynchronous responses in crop flowering dates and phenology of H. armigera to climate warming would expand in the future. The primary factors affecting the first, second, and third generations of moths were Tmean in June, the last appearance date of the second generation of moths, and the duration of the third generation of moths, respectively. To reduce the harm to crops caused by H. armigera, Bt cotton should be widely planted.

Altitude can drive the distribution of living organisms through effects on both soil properties and plant-fungi interactions. We examined how altitude influenced soil fungal communities (including three ecological groups), directly and indirectly through variation in soil properties and/or plant communities, by sampling along an altitudinal gradient from 1300 to 4200 m a.s.l. in an alpine meadow in Western China. We found that soil properties (r = 0.401; P = 0.001) and plant communities (r = 0.332; P = 0.001) significantly affected soil fungal community composition. Soil nitrogen content, altitude and nitrate nitrogen content were the best predictors of saprophytic, symbiotic and biotrophic fungi, respectively. Altitude increased the relative abundance (standard coefficient = 0.385) and richness (standard coefficient = 0.689) of soil saprophytic fungi by promoting soil nitrogen content (standard coefficient = 0.574). Altitude directly increased soil symbiotic fungi (standard coefficient = 0.811), while nitrate nitrogen content promoted the richness and abundance of plant fungal pathogens. Our results shed light on drivers of soil fungi community composition and the distribution of different ecological groups along an altitudinal gradient in an alpine meadow.

Rodents have long plagued forestry production in China, particularly in desert areas in northwestern China, where prevention and monitoring techniques are lacking. Predators are important in regulating rodent populations, and determining how to maximise the role of predators in the comprehensive management of rodent pests is one of the most important issues in rodent control. To accurately understand the activities and vegetation damage patterns of the great gerbil (Rhombomys opimus) in a desert forest area, as well as the activities of its predators, we set up infrared cameras in the Sal Hu Song desert forest region of Altay city, Xinjiang Uygur Autonomous Region, China, in December 2016 and conducted one year of field monitoring of R. opimus and its predators. A total of 2407 independent and valid photographs of R. opimus and its predators were collected. By calculating the relative abundance index, we analysed the activity rhythms of R. opimus and its predators and calculated the correlations of their activity rhythms. The relative abundance of R. opimus was 237.75 in Sal Hu Song, and the predators were mainly the long-legged buzzard (Buteo rufinus) at 94.50, marbled polecat (Vormela peregusna) at 45.74, and red fox (Vulpes vulpes) at 44.26. R. opimus is a typical diurnal animal, with activity peaks occurring between 10:00 and 12:00 and between 17:00 and 19:00, and its activities were mainly movement and foraging. Over the year, R. opimus had two peak activity periods, March and September–October. The peak activity periods of V. peregusna were March and September, while the peak activity period of V. vulpes was February–March. The peak activity period of B. rufinus was June. Among these three predators, the activity rhythms of V. peregusna had the highest correlation with those of R. opimus. This study will contribute to monitoring and managing pest animals in these desert areas.

While urbanization is clearly contributing to biodiversity loss, certain wildlife assemblages can paradoxically be diverse and abundant in moderately developed areas. One hypothesis to explain this phenomenon is that abundant anthropogenic resources for wildlife (i.e., food and shelter) outweigh the costs associated with urbanization. To test this hypothesis, we used camera traps to measure mammal species richness, diversity, and relative abundance (i.e., detection rate) in 58 residential yards in Raleigh, North Carolina, focusing on six types of features that might be used as resources: animal feeding, vegetable gardens, compost piles, chicken coops, brushpiles, and water sources. We also placed cameras at random control sites within each yard and sampled forests in nearby suburban and rural areas for comparison. We fit mixed-effects Poisson models to determine whether yard features, yard-scale characteristics, or landscape-scale landcover predicted mammal relative abundance for eight species. We also tested if the relative abundance of native canid predators in yards was related to the number of prey (rodents and lagomorphs). Species richness, diversity, and relative abundance of most mammal species was higher in yards and suburban forests than in rural forests. Within a yard, purposeful feeding had the strongest effect on animal relative abundance, with eastern gray squirrels (Sciurus carolinensis) being the most common (32.3 squirrels/day at feeders; 0.55 at control sites; 0.29 in suburban forests; and 0.10 in rural forests). We observed species using (e.g., eating) most yard features, although canids were less likely than other taxa to use resources in yards. The presence of a yard feature did not strongly affect the abundance of species at the control site in the yard, suggesting the influence of these features was highly localized. The relative abundance of predators had a positive association with prey relative abundance, and predators were less common in yards with fences. These results demonstrate that there is high use of anthropogenic resources, especially supplemental feeding by urban wildlife, and this increase in prey species may then attract predators, which supports the hypothesis that use of supplemental food resources explains the abundance of urban wildlife.

Aquatic and semiaquatic Hemiptera bugs play significant ecological roles, and they are important indicators and pest control agents. Little information is currently available concerning its populations in southern Assam. This study assessed hemipterans in four sites of Sonebeel, the largest wetland in Assam (3458.12 ha at full storage level), situated in Karimganj District. The major inflow and outflow of the wetland are the rivers Singla and Kachua, respectively (the Kachua drains into the Kushiyara River). Samples were trapped with pond nets and were seasonally recorded. This study recorded a total of 28 species of aquatic and semiaquatic hemipterans belonging to 20 genera under nine families. Population, geographical and environmental data (e.g., rainfall) were used to assess the relative abundance of species, species richness and different diversity indices, and species distribution.

Abstract Background Permafrost degradation may develop thermokarst landforms, which substantially change physico–chemical characteristics in the soil as well as the soil carbon stock. However, little is known about changes of bacterial community among the microfeatures within thermokarst area. Results We investigated bacterial communities using the Illumina sequencing method and examined their relationships with soil parameters in a thermokarst feature on the northern Qinghai-Tibetan Plateau. We categorized the ground surface into three different micro-relief patches based on the type and extent of permafrost collapse (control, collapsing and subsided areas). Permafrost collapse significantly decreased the soil carbon density and moisture content in the upper 10 cm samples in the collapsing areas. The highest loading factors for the first principal component (PC) extracted from the soil parameters were soil carbon and nitrogen contents, while soil moisture content and C:N ratios were the highest loading factors for the second PC. The relative abundance of Acidobacteria decreased with depth. Bacterial diversity in subsided areas was higher than that in control areas. Conclusions Bacterial community structure was significantly affected by pH and depth. The relative abundance of Gemmatimonadetes and Firmicutes were significantly correlated with the first and second PCs extracted from multiple soil parameters, suggesting these phyla could be used as indicators for the soil parameters in the thermokarst terrain.

Freshwater fish fauna of Nandur-Madhmeshwar wetland was studied during the period 2010–2012. A total of 39 species of freshwater fish belonging to 14 families and 30 genera were recorded. Out of the 39 species, 21 species are reported for the first time from this wetland, which includes Mystus malabaricus, an endemic species of the Western Ghats. The fish fauna of the wetland is threatened due to invasive alien species as well as anthropogenic activities such as overfishing, sand mining, siltation, and organic and inorganic pollution. As a result, urgent implementations of stringent conservation measures are essential.

The North American rock pool mosquito, Aedes atropalpus, has reportedly decreased in abundance following the introduction of Ae. japonicus japonicus to the USA, but the specific mechanisms responsible for the reduction remain unclear. Thus, there is a need for field studies to improve our knowledge of natural rock pool systems where both species co-occur. We sampled rock pool invertebrates over a 12-month period along the Chattooga River at a high-elevation site (728 m) near Cashiers, NC, and at a lower-elevation site (361 m) near Clayton, GA. We identified 12 orders of macroinvertebrates representing at least 19 families and 5 mosquito species. Aedes j. japonicus was present year-round at both sites. We observed overwintering Ae. j. japonicus larvae in pools with water temperatures as cold as 3°C and detected apparent winter egg hatching in water below 10°C. Aedes atropalpus was rarely encountered at the high-elevation site but was highly abundant in the summer months at the low-elevation site. Late-stage Ae. j. japonicus larvae inhabited pools in March 2019 when Ae. atropalpus first appeared in the same pools, creating the potential for asymmetrical stage-specific interactions. Our observations provide evidence of overwintering and early hatching of Ae. j. japonicus in the southeastern climate. Further study of the importance of stage-dependent competition and winter egg hatching of diapausing Ae. j. japonicus eggs is warranted. [ABSTRACT FROM AUTHOR]

Background. Analysis of species count data in ecology often requires normalization to an identical sample size. Rarefying (random subsampling without replacement), which is the current standard method for normalization, has been widely criticized for its poor reproducibility and potential distortion of the community structure. In the context of microbiome count data, researchers explicitly advised against the use of rarefying. Here we introduce a normalization method for species count data called scaling with ranked subsampling (SRS) and demonstrate its suitability for the analysis of microbial communities. Methods. SRS consists of two steps. In the scaling step, the counts for all species or operational taxonomic units (OTUs) are divided by a scaling factor chosen in such a way that the sum of scaled counts equals the selected total number of counts Cmin. The relative frequencies of all OTUs remain unchanged. In the subsequent ranked subsampling step, non-integer count values are converted into integers by an algorithm that minimizes subsampling error with regard to the population structure (relative frequencies of species or OTUs) while keeping the total number of counts equal Cmin. SRS and rarefying were compared by normalizing a test library representing a soil bacterial community. Common parameters of biodiversity and population structure (Shannon index H', species richness, species composition, and relative abundances of OTUs) were determined for libraries normalized to different size by rarefying as well as SRS with 10,000 replications each. An implementation of SRS in R is available for download (https://doi.org/10.20387/BONARES-2657-1NP3). Results. SRS showed greater reproducibility and preserved OTU frequencies and alpha diversity better than rarefying. The variance in Shannon diversity increased with the reduction of the library size after rarefying but remained zero for SRS. Relative abundances of OTUs strongly varied among libraries generated by rarefying, whereas libraries normalized by SRS showed only negligible variation. Bray--Curtis index of dissimilarity among replicates of the same library normalized by rarefying revealed a large variation in species composition, which reached complete dissimilarity (not a single OTU shared) among some libraries rarefied to a small size. The dissimilarity among replicated libraries normalized by SRS remained negligibly low at each library size. The variance in dissimilarity increased with the decreasing library size after rarefying, whereas it remained either zero or negligibly low after SRS. Conclusions. Normalization of OTU or species counts by scaling with ranked subsampling preserves the original community structure by minimizing subsampling errors. We therefore propose SRS for the normalization of biological count data. [ABSTRACT FROM AUTHOR]

Because birds are frequently detected by sound, autonomous audio recorders (called automated recording units or ARUs) are now an established tool in addition to in-person observations for monitoring the status and trends of bird populations. ARUs have been evaluated and applied during breeding seasons, and to monitor the nocturnal flight calls of migrating birds. However, birds behave differently during migration than during the breeding season. Here we present a method for using ARUs to monitor land birds during the migration period in remote habitats. We conducted in-person point counts next to continuously recording ARUs, and compared estimates of the number of species detected and focal species relative abundance from point counts and ARUs. We used a desk-based audio bird survey method for processing audio recordings, which does not require automated species identification algorithms. We tested two methods of using extended duration ARU recording: surveying consecutive minutes and surveying randomly selected minutes. Desk-based surveys using randomly selected minutes from extended duration ARU recordings performed similarly to point counts, and better than desk-based surveys using consecutive minutes from ARU recordings. Surveying randomly selected minutes from ARUs provided estimates of relative abundance that were strongly correlated with estimates from point counts and successfully showed the increase in abundance associated with migration timing. Randomly selected minutes also provided estimates of the number of species present that were comparable to estimates from point counts. Our results suggest that ARUs are an effective way to track migration timing and intensity in remote or seasonally inaccessible habitat during spring migration. Additional testing is needed to determine the efficacy of our methods during fall migration, and at more southerly latitudes. We recommend that desk-based surveys use randomly sampled minutes from extended duration ARU recordings, rather than using consecutive minutes from recordings. Our methods can be immediately applied by researchers with the skills to conduct point counts, with no additional expertise necessary in automated species identification algorithms.

Secondary forests are extensive in the tropics. Currently, these plant communities are the available habitats for wildlife and in the future they will possibly be some of the most wide-spread ecosystems world-wide. To understand the potential role of secondary forests for wildlife conservation, three ungulate species were studied: Mazama temama, Odocoileus virginianus and Pecari tajacu. We analyzed their relative abundance and habitat use at two spatial scales: (1) Local, where three different successional stages of tropical deciduous forest were compared, and (2) Landscape, where available habitats were compared in terms of landscape composition (proportion of forests, pastures and croplands within 113 ha). To determine the most important habitat-related environmental factors influencing the Sign Encounter Rate (SER) of the three ungulate species, 11 physical, anthropogenic and vegetation variables were simultaneously analyzed through model selection using Akaike’s Information Criterion. We found, that P. tajacu and O. virginianus mainly used early successional stages, while M. temama used all successional stages in similar proportions. The latter species, however, used early vegetation stages only when they were located in landscapes mainly covered by forest (97%). P. tajacu and O. virginianus also selected landscapes covered essentially by forests, although they required smaller percentages of forest (86%). All ungulate species avoided landscape fragments covered by pastures. For all three species, landscape composition and human activities were the variables that best explained SER. We concluded that landscape is the fundamental scale for ungulate management, and that secondary forests are potentially important landscape elements for ungulate conservation.

Orthopterans are convenient indicators for threatened grassland ecosystems. Many sampling methods are known; among them, sweep netting is the most common. This study compares sweep netting with less common pan trapping and quantifies differences in species representation and sex ratio between the two sampling techniques. Sampling took place in the submontane grassland in the northeastern part of the Czech Republic (Central Europe) during July, August, and September 2010. Both sweep netting and pan trapping were used concurrently in 11 meadows. Sampled orthopteran adults were determined to the species level and their sex was noted. Both methods recorded the same pool of 14 species. A chi-squared test showed significant differences in representation of 7 out of 8 analyzed species in sweep-net and pan-trap samples. Sex ratios also noticeably differed. Possible causes of the differences are discussed. This study showed that pan trapping is a solid alternative to sweep netting. [ABSTRACT FROM AUTHOR]

Global declines in chondrichthyan populations necessitate evidence‑based planning for their conservation. False Bay, in south‑west South Africa, has a high diversity of marine biota, with Atlantic and Indian Ocean influences, but its chondrichthyan fauna is poorly described ecologically. False Bay has a long fishing history and supports various harvesting methods, including shark‑directed fishing. This is the first baited remote underwater video system (BRUVs) survey of the relative abundance, diversity and seasonal distribution of chondrichthyans in False Bay. Nineteen species from 11 families were recorded across 185 sites at between 4 and 49 m depth. Diversity was greatest in summer, on reefs and in shallow water. Endemic scyliorhinids, especially Haploblepharus edwardsii, dominated everywhere, in summer and winter. Habitat and season were key predictors of species composition, and a significant interaction between depth and season indicated migration patterns for Mustelus mustelus. By avoiding the selectivity associated with catch records, BRUVs data are superior to fishery‑dependent catch‑per‑unit‑effort data to monitor chondrichthyan diversity and abundance. Baited remote underwater video systems access greater depths and more habitats than previously surveyed in False Bay and avoid taxonomic lumping typical of catch records in the region, making them more efficient than other methods of surveying chondrichthyan diversity. [ABSTRACT FROM AUTHOR]

Grassland birds are highly imperiled because of historical habitat loss and ongoing conversion of grasslands to agricultural and urban land uses. Therefore, prioritizing and further justifying conservation action in remaining grasslands is critical to protecting what remains. Grassland bird conservation has focused on identifying and protecting large grassland complexes referred to as Grassland Bird Conservation Areas (GBCAs). We identified and classified GBCAs in a region highly impacted by both agricultural and urban land conversion using previously developed methods. Then, we extended the analysis to include estimated relative abundance of five grassland focal species in each GBCA. Models of relative abundance were built using eight years of monitoring data collected by citizen scientists. Finally, we quantified the value of ecosystem services provided by each GBCA. There were nearly 55,000 ha of grassland habitats in the Chicago Metropolitan Region that met GBCA criteria, 33% (18,415 ha) of which were protected. Proportion of abundance in protected versus unprotected areas was similar for Bobolink (Dolichonyx oryzivorus; 46%), Grasshopper Sparrow (Ammodramus savannarum; 52%), and Sedge Wren (Cistothorus platensis; 48%), whereas, Henslow's Sparrow (Ammodramus henslowii; 75%) had a higher proportion of relative abundance in protected GBCAs and Eastern Meadowlark (Sturnella magna) had lower proportions (37%). GBCAs provisioned just under $900 million annually in ecosystem services, 73% of which is because of flood control. Outputs of this comprehensive approach will inform grassland bird conservation by providing detailed information about the value for birds and people of grassland habitats.