Species abundances and richness are central parameters in ecology and crucial for describing diversity and composition across environments. Understanding how they vary in natural environments is critical for informed conservation decisions, especially in the face of anthropogenic pressures, such as deforestation and climate change. We evaluate the influence of landscape and local habitat variables on the richness and abundances of lizards in the Caatinga, the largest continuous block of seasonally dry tropical forests. We sampled seven lizard communities for three months using visual encounters along transects. We recorded landscape and microhabitat variables and evaluated their influence on lizard species richness, diversity, and occurrence using model selection. Ten lizard species were recorded, with Tropidurus semitaeniatus, Ameivula ocellifera, and Tropidurus hispidus being the most abundant. Topographic complexity and the number of rocky outcrops positively affect species richness and diversity by promoting environmental heterogeneity and hence increasing refuges, shelters, and thermoregulation sites. Different microhabitat and landscape variables were important predictors of the occurrences of individual lizard species. The quantity of rocks significantly increased the likelihood of Tropidurus semitaeniatus occurrence, while litter negatively affected Tropidurus hispidus, and fallen logs increased the probability of Ameiva ameiva occurrence. We argue that preserving topographically complex regions is essential for maintaining the diversity of lizards in the Caatinga biome.

In order to evaluate the seasonal responses of periphytic protozoan fauna to the antibiotic nitrofurazone at sensitive concentration, a 1-year baseline survey was carried out in Chinese coastal waters of the Yellow Sea. To assess the nitrofurazone (NFZ)-induced toxicokinetics in different season, the test protozoan samples were collected using microscope slides and exposed to the sensitive NFZ concentration of 8 mg ml−1. Differences in species composition and typical species were observed in the test organism fauna in the control and treatment among four seasons. However, the community patterns were significantly shifted under the sensitive concentration, with a part of stressed test samples significantly departed from a respected taxonomic pattern. Therefore, it is suggested that periphytic protozoan fauna may be significantly changed at the same sensitive concentration in both the species composition and community pattern, although there were significant differences in tolerant species among four seasons in marine environments.

Understanding the processes that allow phylogenetically related plant species coexist is important to understand the ecological and evolutionary processes that structure biological communities. In this study, we investigated how the species Erythroxylum simonis, Erythroxylum pauferrense and Erythroxylum citrifolium share ecological niche dimensions according to the abiotic characteristics of their environments of occurrence. To this end, in ten pre-established plots in an Atlantic Forest remnant in northeastern Brazil, we carried out a population survey of the three species and characterised their abiotic niche by measuring light availability, humidity and the physical–chemical properties of the soil. We used generalised linear models to test whether abiotic variables influence species abundance. Our results indicate that the three species coexist along the different environmental gradients, with some level of niche overlap. The species E. simonis is the best competitor, showing generalist behaviour and the highest abundance in all environmental gradients. We emphasise that the adult populations of the species have adapted to various environmental and ecological challenges. Thus, the results reported are influenced by their ability to perform well in terms of physiology, growth and survival in their early-life stages.

Parasite species interactions, host biology traits, and external environmental factors can drive co-occurrence patterns between parasite species. We investigated co-occurrence patterns between three ectoparasite species (mite (Neotrombicula harperi), and fleas (Orchopeas caedens and Ceratophyllus vison)) of North American red squirrels (Tamiasciurus hudsonicus). We evaluated (1) whether ectoparasites of red squirrels exhibit non-random co-occurrence patterns, and (2) the contribution of host and external environmental factors to parasite co-occurrence. Bayesian ordination and regression analysis (boral) revealed random associations between parasite species pairs when accounting for host and external environmental factors. However, the mite N. harperi exhibited a negative association with the flea O. caedens and positive association with the flea C. vison linked to temporal patterns of occurrence. Our data suggests that parasites of the investigated population of red squirrels tend to form associations based on temporal trends in infestation rather than species interactions. Further experimentation should investigate the role of additional factors on parasite co-occurrence patterns, such as temperature, precipitation, and humidity.

Although mesopelagic fish dominate the oceanic ecosystem, they remain one of the least investigated components. From the vertically stratified sample collections, we investigated community structure, vertical distribution and diel/ontogenetic vertical migration covering four seasons for larval and juvenile/adult mesopelagic fish at the time-series station K2 in the Western Subarctic Gyre of the North Pacific. We collected 10 and 20 species of larval and juvenile/adult fish, respectively. Among the larval fish community, Leuroglossus schmidti was the most abundant; total abundances except L. schmidti were low throughout the year; species richness of myctophids were low. Among the 20 species of juvenile/adult fish, larvae of only six species were collected; thus, most mesopelagic fish species do not use the Western Subarctic Gyre as their nursery. In the juvenile/adult fish community, Stenobrachius leucopsarus and Stenobrachius nannochir were abundant. Species diversity and total abundance in the warm seasons (summer and autumn) were higher than in the cold seasons (winter and spring). The decreasing of species diversity and total abundance during the cold seasons was probably affected by horizontal migrations of fish for reproduction toward the southern transition or subarctic slope areas. Stenobrachius leucopsarus was distributed at shallow depths with opportunistic diel vertical migration (DVM); in contrast Stenobrachius nannochir occurred at greater depths, without DVM. The distribution depths of S. leucopsarus during day and those of S. nannochir changed seasonally and synchronously; shallowest in autumn, deepest in spring.

Few studies have investigated the ecological interactions between wild species of Suidae and their parasites, leaving our knowledge concerning this host–parasite system fragmented. In the present study, we applied network studies to analyse community nestedness in helminth assemblages of common warthogs, Phacochoerus africanus (Gmelin) (Suidae). Helminth data were compiled from 95 warthogs, including young and adult males and females, from 2 different conservation areas in Mpumalanga and Limpopo Provinces, South Africa, collected monthly over a period of 1 year each. The aim was to study the effect of host sex, age and season of sampling on the structure of helminth infracommunities harboured by the warthogs and to search for non-random structural patterns in the warthog–helminth interaction networks. Furthermore, we investigated the influence of a warthog's age, sex and season of sampling on beta diversity and dark diversity of their helminth infracommunities. Lastly, we asked whether the effects of host sex, age and sampling season on helminth communities differed between the 2 localities. We found that helminth communities of warthogs were nested and host–parasite interactions were influenced by all 3 factors as well as combinations thereof. However, the resulting patterns differed at the 2 localities, indicating that local environmental processes are important drivers of community structure.

We investigate structural features and processes associated with the onset of systemic conflict using an approach which integrates complex systems theory with network modeling and analysis. We present a signed network model of cooperation and conflict dynamics in the context of international relations between states. The model evolves ties between nodes under the influence of a structural balance force and a dyad-specific force. Model simulations exhibit a sharp bifurcation from peace to systemic war as structural balance pressures increase, a bistable regime in which both peace and war stable equilibria exist, and a hysteretic reverse bifurcation from war to peace. We show how the analytical expression we derive for the peace-to-war bifurcation condition implies that polarized network structure increases susceptibility to systemic war. We develop a framework for identifying patterns of relationship perturbations that are most destabilizing and apply it to the network of European great powers before World War I. We also show that the model exhibits critical slowing down, in which perturbations to the peace equilibrium take longer to decay as the system draws closer to the bifurcation. We discuss how our results relate to international relations theories on the causes and catalysts of systemic war.

This paper investigates properties of the class of graphs based on exchangeable point processes. We provide asymptotic expressions for the number of edges, number of nodes, and degree distributions, identifying four regimes: (i) a dense regime, (ii) a sparse, almost dense regime, (iii) a sparse regime with power-law behaviour, and (iv) an almost extremely sparse regime. We show that, under mild assumptions, both the global and local clustering coefficients converge to constants which may or may not be the same. We also derive a central limit theorem for subgraph counts and for the number of nodes. Finally, we propose a class of models within this framework where one can separately control the latent structure and the global sparsity/power-law properties of the graph.

Estuarine ecosystem conditions actively influence the early life stage of fishes. This study reports how environmental factors influenced the ichthyoplankton in a tropical estuary within an Environmental Protection Area by comparing the structure and composition of fish eggs and larval assemblages. A total of 1672 fish larvae and 486 fish eggs were collected. Higher densities of larvae were recorded for Engraulidae, Characidae, Clupeidae, Gerreidae, Mugilidae and Atherinopsidae, and higher egg densities of the families Mugilidae, Clupeidae and Engraulidae were found. The spatio-temporal variations were determined by the environmental predictors salinity, pH, dissolved oxygen and temperature, with salinity influenced by precipitation as one of the main predictors of the distribution of ichthyoplankton. During the rainy season, greater densities of eggs were recorded in the upper and intermediate zones, mainly Characidae and Engraulidae; in the dry season, in the lower zone, there was a greater density of larvae, particularly Atherinopsidae and Mugilidae. The information provided in the present study contributes to our knowledge of nursery habitat requirements for the initial development of marine migrant and resident species in tropical estuaries.

The introduction of Pacific oysters to the sedimentary south-eastern North Sea coast and their establishment on intertidal native blue mussel beds has caused the development of mixed reefs of mussels and oysters with extensive tidepools. Tidepools have been intensively studied at rocky shores where they show community structures, which usually differ from that of the surrounding emerging substrates. Tidepools at sedimentary coasts, however, have received less attention. We compared the community structure and species interactions inside and outside tidepools in oyster reefs by determining densities of snails, barnacles and amphipods. Snail densities were similar in and outside tidepools. Barnacle coverage on bivalve shells, however, was lower inside tidepools, which may be caused by higher predation pressure and increased snail grazing under permanently submerged conditions, as was revealed by field and laboratory experiments. Additionally, we studied the occurrence of copepod and trematode parasites in blue mussels inside and outside tidepools. Prevalence and intensity of parasitic copepods was higher in mussels inside tidepools. Trematode parasites, by contrast, showed a lower intensity in mussels inside tidepools. This can be explained by high amphipod densities found inside tidepools because trematode larvae represent a food source of amphipods. Our study suggests that the community structure of oyster reefs within tidepools is not a submerged equivalent to that of intertidal reefs. As their counterparts at rocky shores, they show their own species distribution patterns with particular species interactions and only provide refuge for specific species such as parasitic copepods.

Random intersection graphs model networks with communities, assuming an underlying bipartite structure of communities and individuals, where these communities may overlap. We generalize the model, allowing for arbitrary community structures within the communities. In our new model, communities may overlap, and they have their own internal structure described by arbitrary finite community graphs. Our model turns out to be tractable. We analyze the overlapping structure of the communities, show local weak convergence (including convergence of subgraph counts), and derive the asymptotic degree distribution and the local clustering coefficient.

Oceanic islands and seamounts are considered biodiversity hotspots. Here, we present a taxonomy and community analyses of hyperiid amphipods collected near oceanic islands and over seamounts of the Juan Fernández Archipelago and Desventuradas Archipelago in the South-east Pacific. Both archipelagos are separated by about 800 km over the meridional gradient, suggesting the existence of different hyperiid communities because of apparent geographic isolation and distinctive oceanographic characteristics between regions. To test this hypothesis, zooplankton samples were collected from 19 stations during the CIMAR 22 ‘Oceanic Island’ cruise in October–November 2016. In total, 56 species of hyperiids were found, of which Phrosina semilunata, Lestrigonus schizogeneios, Hyperietta stephenseni, Hyperioides longipes, Phronimella elongata and Primno latreillei were the most abundant and recurrent species. The species richness (S), Shannon–Wiener diversity (H’) and dominance (D) of both the archipelagos were not significantly different. Additionally, except for a small group of rare species, the species composition was similar in both areas. Most species showed greater abundances than those observed in the coastal upwelling zone off Chile, whereas shared species between regions suggested the presence of a single biogeographic unit comprising the coastal transition zone and oceanic area off Chile within which both archipelagos are included. Correlation analysis indicated that salinity was the best predictor for the community structure, which provides evidence that the contributions of previously described water masses of the South-east Pacific may influence the spatial distribution and composition of the hyperiid community.

There is great heterogeneity in parasite communities among hosts, understanding the nature and drivers of such variations is still a great scientific quest. Here, we analyse the variation in parasite communities by addressing the following questions: (i) What is the beta-diversity component (nestedness or turnover) that most contributes to beta diversity in parasite communities among anuran species? (ii) Does the beta diversity of parasite communities follow a non-random pattern? (iii) Is the dissimilarity in composition of parasite communities related to the phylogenetic or functional dissimilarity among hosts? We found that turnover in parasite assemblages was the main component of beta diversity, but the variation observed both in the total beta diversity and in its components did not differ from the respective null models. The dissimilarity among parasite communities was not related to the phylogenetic species variability or functional dissimilarity among anuran species for most localities. In short, our findings may indicate a process of resource tracking by the parasite species, in which the resource may not necessarily be conserved phylogenetically in their hosts.

Discovering community structure in complex networks is a mature field since a tremendous number of community detection methods have been introduced in the literature. Nevertheless, it is still very challenging for practitioners to determine which method would be suitable to get insights into the structural information of the networks they study. Many recent efforts have been devoted to investigating various quality scores of the community structure, but the problem of distinguishing between different types of communities is still open. In this paper, we propose a comparative, extensive, and empirical study to investigate what types of communities many state-of-the-art and well-known community detection methods are producing. Specifically, we provide comprehensive analyses on computation time, community size distribution, a comparative evaluation of methods according to their optimization schemes as well as a comparison of their partitioning strategy through validation metrics. We process our analyses on a very large corpus of hundreds of networks from five different network categories and propose ways to classify community detection methods, helping a potential user to navigate the complex landscape of community detection.

Macroalgae play important ecological roles, including as hosts for a wide range of epifauna. However, the diversity relationships between macroalgae and epifauna are poorly understood for most tropical host species and algal morphologies. This study aims to characterize and analyse the diversity of invertebrates present amongst macroalgae with three distinct morphologies (three-dimensional, filamentous and foliose) across different tropical intertidal sites in Singapore. Morphological and DNA barcoding tools were employed for epifaunal species identification, and ordination statistics and multiple linear regression were used to test the effects of algal morphology, species and site on community structure and diversity of epiphytic invertebrates. Overall, epifaunal communities were distinct among sites and algal morphologies, and diversity was affected significantly by algal morphology. In particular, filamentous macroalgae hosted the highest abundance of epifauna dominated mainly by amphipods, which were able to take advantage of the high surface area to volume ratio in filamentous algal mats as a consequence of their thinner forms. Foliose species showed a significantly negative effect on invertebrate diversity. Our findings highlight the diverse associations between intertidal macroalgae and invertebrates with high turnover between algal morphology and sites that contribute to the high biodiversity of tropical shores. Future studies should consider the effects of the host habitat, seasonality and more algal species on epifaunal diversity.

The response of soil microbial communities to soil quality changes is a sensitive indicator of soil ecosystem health. The current work investigated soil microbial communities under different fertilization treatments in a 31-year experiment using the phospholipid fatty acid (PLFA) profile method. The experiment consisted of five fertilization treatments: without fertilizer input (CK), chemical fertilizer alone (MF), rice (Oryza sativa L.) straw residue and chemical fertilizer (RF), low manure rate and chemical fertilizer (LOM), and high manure rate and chemical fertilizer (HOM). Soil samples were collected from the plough layer and results indicated that the content of PLFAs were increased in all fertilization treatments compared with the control. The iC15:0 fatty acids increased significantly in MF treatment but decreased in RF, LOM and HOM, while aC15:0 fatty acids increased in these three treatments. Principal component (PC) analysis was conducted to determine factors defining soil microbial community structure using the 21 PLFAs detected in all treatments: the first and second PCs explained 89.8% of the total variance. All unsaturated and cyclopropyl PLFAs except C12:0 and C15:0 were highly weighted on the first PC. The first and second PC also explained 87.1% of the total variance among all fertilization treatments. There was no difference in the first and second PC between RF and HOM treatments. The results indicated that long-term combined application of straw residue or organic manure with chemical fertilizer practices improved soil microbial community structure more than the mineral fertilizer treatment in double-cropped paddy fields in Southern China.

In recent decades, parasite community ecology has produced hundreds of studies on an ever-growing number of host species, and developed into an active sub-discipline of parasitology. However, this growth has been characterized by a lack of standards in the practices used by researchers, with many common approaches being flawed, unjustified or misleading. Here, in the hope of promoting advances in the study of parasite community ecology, I identify some of the most common errors or weaknesses in past studies, and propose ten simple rules for best practice in the field. They cover issues including, among others, taxonomic resolution, proper and justifiable analytical methods, higher-level replication, controlling for sampling effort or species richness, accounting for spatial distances, using experimental approaches, and placing raw data in the public domain. While knowledge of parasite communities has expanded in breadth, with more and more host species being studied, true progress has been very limited with respect to our understanding of fundamental general processes shaping these communities. It is hoped that the guidelines presented here can direct researchers away from the entrenched use of certain approaches flawed in design, analysis or interpretation, by offering a more rigorous and standardized set of practices, and, hopefully, a way forward.