Because conducting experimental coinfections is intractable in most parasite systems, inferences about the presence and strength of interspecific interactions in parasite communities are often made from analyses of field data. It is unclear whether methods used to test for competition are able to detect competition in field-collected datasets. Data from a study of the intestinal helminth communities of creek chub (Semotilus atromaculatus) were used to explore the potential of commonly available methods to detect negative interactions among parasite species in species-poor, low-intensity communities. Model communities were built in the absence of competition and then modified by four modes of competition. Both parametric and null model approaches were utilized to analyze modelled parasite communities to determine the conditions under which competitive interactions were discerned. Correlations had low Type I error rates but did not reliably detect competition, when present, at a statistically significant level. Results from logistical regressions were similar but showed improved statistical power. Results from null model approaches varied. Envelope analyses had near ideal properties when parasite prevalence was high but had high Type I error rates in low prevalence communities. Co-occurrence analyses demonstrated promising results with certain co-occurrence metrics and randomization algorithms, but also had many more cases of failure to detect competition when present and/or reject competition when it was absent. No analytical approach was clearly superior, and the variability observed in the present investigation mirrors similar efforts, suggesting that clear guidelines for detecting competition in parasite communities with observational data will be elusive.

The microzooplankton community structure (species abundance, biomass, diversity) was investigated at a coastal marine station on the South-West Atlantic Ocean (34°23′S–53°45′W, Uruguay). This is a hydrographically complex site within the Subtropical Convergence zone of the SW Atlantic where knowledge of the microzooplankton is particularly scant. The main goal was to perform a first characterization of that community and evaluate its association to environmental drivers along an annual cycle. Oceanographic variables (temperature, salinity, irradiance, nutrients, chlorophyll-a) and ciliates (aloricate and loricate), and dinoflagellates were recorded monthly from July 2019 to June 2020. Over 100 microzooplankton taxa belonging to approximately 30 families and 40 genera were identified, including several subtropical and subantarctic species. Community structure followed wide transitions at the seasonal scale – particularly between summer and winter as subtropical taxa alternated with euryhaline taxa from colder subantarctic waters. The core environmental variables (temperature, salinity and dissolved inorganic nitrogen [DIN]) explained overall variance in microzooplankton community assembly. During summer, high temperatures (20.3, 16.3–22.4°C) and low nutrients (DIN: 3.5, 0.7–6.7 μM; PO4: 1.0, 0.8–1.5 μM) benefited the development of aloricate ciliates. A nutrient pulse in winter posed favourable stoichiometric conditions and the numerical abundance was dominated by dinoflagellates and loricate ciliates in the following months, while diversity remained highest (taxonomic richness: 36 [22–46]; Shannon–Wiener index: 2.5 [1.9–2.8]). Results suggested that the microzooplankton community at the study site is mainly structured by hydrographic variability linked to the seasonal replacement of offshore water masses that differed in thermohaline properties and nutrient levels, and local processes.

The proliferation of disturbance-adapted species in human-modified landscapes may change the structure of plant communities, but the response of biodiversity to human disturbances remains poorly understood. We examine the proliferation of the palm, Syagrus coronata, in disturbed forest stands and its impacts on the structure of vascular epiphyte assemblages in a human-modified landscape of Brazilian Caatinga dry forest. First, we compared S. coronata density between old-growth and regenerating forest stands. We then surveyed vascular epiphytes on 680 phorophytes (S. coronata and non-palm/control species) across five habitat types with different disturbance levels. There was an eight-fold increase in S. coronata density in regenerating areas compared with in old-growth forest. Syagrus coronota supported richer epiphyte assemblages at local (i.e. per palm) and landscape (i.e. pooling all palms) scale than control phorophytes, supporting more than 11 times the number of species of control phorophytes at both scales. Epiphyte assemblages were more abundant, species-rich and dominated by abiotically dispersed species in forest sites with intermediate disturbance levels (regenerating forest stands). More than simply operating as an exclusive phorophyte for more than 90% of the epiphyte species we recorded here, S. coronata favours epiphyte persistence and structures their assemblages across human-modified landscapes of the Caatinga forest.

Studies integrating variation in species composition among sites are useful in understanding the impacts of land-use changes on the spatial distribution of biodiversity. However, the failure to recognize the distinction between beta diversity components, dissimilarity due to species replacement (i.e. turnover) and dissimilarity due to species loss from site to site (i.e. nestedness), can lead to inappropriate use of some indices. Here, we evaluated how the spatial distribution of anuran beta diversity components, turnover and nestedness, is associated with local and landscape descriptors in a tropical agricultural landscape with a recent history of agriculture expansion in south-eastern Brazil. Overall, 27 anuran species were found in the region with average ± SD species richness in each pool of 9.5 ± 3.5 species, ranging from 4 to 15 species. We observed that species turnover was the major component for anuran dissimilarity among pools, indicating that anuran species occurring in species-poor pools are not subsets of anuran species occurring in species-rich pools. Local variables and geographic distance were not important descriptors explaining the variation of anuran beta diversity. In contrast, the distance of the pools to the nearest forest fragment explained 16% of the variance in total beta diversity, 5% of the nestedness component and 2% of spatial turnover. Our results show that pools distributed across farmland landscapes are harbouring different anuran species composition, and together, these pools are contributing to the regional diversity of anurans in this region which is considered one of the most deforested and fragmented within Brazil.

Understanding why ecological communities contain the species they do is a long-standing question in ecology. Two common mechanisms that affect the species found within communities are dispersal limitation and environmental filtering. Correctly identifying the relative influences of these mechanisms has important consequences for our understanding of community assembly. Here variable selection was used to identify the environmental variables that best predict tropical forest primate community similarity in four biogeographic regions: the Neotropics, Afrotropics, Madagascar and the island of Borneo in South-East Asia. The environmental variables included net primary productivity and altitude, as well as multiple temperature, precipitation and topsoil variables. Using the best environmental variables in each region, Mantel and partial Mantel tests were used to reanalyse data from a previously published study. The proportion of variance explained increased for each region. Despite increases, much of the variation remained unexplained for all regions (R2: Africa = 0.45, South America = 0.16, Madagascar = 0.28, Borneo = 0.10), likely due to different evolutionary and biogeographic histories within each region. Nonetheless, substantial variation among regions in the environmental variables that best predicted primate community similarity were documented. For example, none of the 14 environmental variables was included for all four regions, yet each variable was included for at least one region. Contrary to prior results, environmental filtering was an important assembly mechanism for primate communities in tropical forests worldwide. Geographic distance more strongly predicted African and South American communities whereas environmental distance more strongly predicted Malagasy and Bornean communities. These results suggest that dispersal limitation structures primate communities more strongly than environmental filtering in Africa and in South America whereas environmental filtering structures primate communities more strongly than dispersal limitation in Madagascar and Borneo. For communities defined by genera, environmental distance more strongly predicted primate communities than geographic distance in all four regions, which suggests that environmental filtering is a more influential assembly mechanism at the genus level. Therefore, a more nuanced consideration of environmental variables affects conclusions about the influences of environmental filtering and dispersal limitation on primate community structure.

A comprehensive assessment of the effect of disturbances on tropical and subtropical forests is needed to better understand their impacts on forest structure and diversity. Although taxonomic and functional diversity measures have been successfully adopted in this context, phylogenetic diversity metrics are still poorly explored. We compared the phylogenetic structure of the seed rain and regenerating seedling community in patches of an old-growth Atlantic Forest remnant dominated or not by a ruderal bamboo species, Guadua tagoara. We sampled those patches before and after illegal harvesting of the palm Euterpe edulis thus assessing if the harvesting led to changes in the phylogenetic structure of the seed rain and the regenerating community in both patches. Bamboo-dominated patches showed a significantly higher presence of species in the seed rain that were more distantly related to each other in the phylogeny than expected by chance compared with patches without bamboos, but this difference disappeared after palm-heart harvesting. Contrary to what we expected, we did not find significant changes in the phylogenetic structure of seedlings before or after palm-heart harvesting. The phylogenetic structure at the tips of the phylogeny was random overall. The maintenance of a higher presence of far relatives in the phylogeny of the seedling community suggests, assuming trait conservatism, that despite bamboo dominance and palm-heart harvesting, functional diversity is being preserved at least in the early regenerating stages and in the time frame of the study. However, higher presence of pioneer taxa after palm-heart harvest indicates that this disturbance may lead old-growth areas to earlier successional stages.

The northern New England region includes the states of Vermont, New Hampshire, and Maine and encompasses a large degree of climate and edaphic variation across a relatively small spatial area, making it ideal for studying climate change impacts on agricultural weed communities. We sampled weed seedbanks and measured soil physical and chemical characteristics on 77 organic farms across the region and analyzed the relationships between weed community parameters and select geographic, climatic, and edaphic variables using multivariate procedures. Temperature-related variables (latitude, longitude, mean maximum and minimum temperature) were the strongest and most consistent correlates with weed seedbank composition. Edaphic variables were, for the most part, relatively weaker and inconsistent correlates with weed seedbanks. Our analyses also indicate that a number of agriculturally important weed species are associated with specific U.S. Department of Agriculture plant hardiness zones, implying that future changes in climate factors that result in geographic shifts in these zones will likely be accompanied by changes in the composition of weed communities and therefore new management challenges for farmers.

Parasites of the genera Plasmodium and Haemoproteus (Apicomplexa: Haemosporida) are a diverse group of pathogens that infect birds nearly worldwide. Despite their ubiquity, the ecological and evolutionary factors that shape the diversity and distribution of these protozoan parasites among avian communities and geographic regions are poorly understood. Based on a survey throughout the Neotropics of the haemosporidian parasites infecting manakins (Pipridae), a family of Passerine birds endemic to this region, we asked whether host relatedness, ecological similarity and geographic proximity structure parasite turnover between manakin species and local manakin assemblages. We used molecular methods to screen 1343 individuals of 30 manakin species for the presence of parasites. We found no significant correlations between manakin parasite lineage turnover and both manakin species turnover and geographic distance. Climate differences, species turnover in the larger bird community and parasite lineage turnover in non-manakin hosts did not correlate with manakin parasite lineage turnover. We also found no evidence that manakin parasite lineage turnover among host species correlates with range overlap and genetic divergence among hosts. Our analyses indicate that host switching (turnover among host species) and dispersal (turnover among locations) of haemosporidian parasites in manakins are not constrained at this scale.

Sown-grass margin strips, historically established to limit pesticide drift and soil erosion, are now also promoted for enhancing floral diversity and associated ecosystem services. To better understand weed community assembly in grass margin strips, we performed floral surveys in 75 sown-grass margin strips in two regions in France and characterized each species using information from trait databases. We hypothesized that traits of dominant species would differ between newly sown-grass margin strips and older strips. Weed species were separated into functional groups based on their traits using multiple correspondence analysis and hierarchical ascendant classification. Functional group trajectories were investigated in sown-grass margin strips that differed in age using a space-for-time substitution approach. We found that geophyte, competitor, and monocotyledon species were more frequent and abundant in grass margin strips than therophyte, ruderal, and dicotyledon species. Results also showed that floral diversity was greatest in grass margin strips of intermediate age. Our findings have implications for optimizing diversity and ecosystem services on land enrolled in conservation programs and suggest that mowing later in the season and periodic soil disturbance can increase floral diversity. The analytical framework that we introduced in this research can also be used to explore weed community assembly in other systems.

Agricultural production systems that reduce the use of in-crop herbicides could greatly reduce risks of environmental damage and the development of herbicide-resistant weeds. Few studies have investigated the long-term effects of in-crop herbicide omissions on weed seedbank community size and structure. A crop-rotation study was sampled 10 yr after a strictly annual rotation and an annual/perennial rotation were exposed to different in-crop herbicide omission treatments. In-crop herbicides were applied either in all annual crops (control), omitted from oats only, or omitted from both flax and oats. Seedbank densities were greatest when in-crop herbicides were omitted from flax and oats, and this treatment also reduced crop yield. Shannon-Wiener diversity differed among crops in the annual crop rotation and among herbicide omission treatments in the perennial rotation. Herbicide omissions changed the weed-community structure in flax and in wheat and canola crops in the annual rotation enough to warrant alternate control methods in some treatments. The magnitude of the effects on the seedbank parameters depended largely on the competitive ability of the crop in which herbicides were omitted. No yield response to omitting herbicides in oats indicated that standard weed management practices have reduced weed populations below yield-loss thresholds.

Invasive plants are a common problem in the management and restoration of degraded lands in the semiarid western United States, but are often not the primary focus of restoration ecologists. Likewise, restoring native vegetation has not been a major concern of weed scientists. But trends in the literature demonstrate increasing overlap of these fields, and greater collaboration between them can lead to improved efficacy of restoration efforts. Succession and ecosystem development are the products of complex interactions of abiotic and biotic factors. Our greatest restoration and invasive plant management successes should result when we take advantage of these natural processes. Recent shifts in management objectives have generated approaches to directing plant community development that utilize species that are strong competitors with invasive species as a bridge to the establishment of native perennial vegetation. Soil water and nutrient characteristics and their interactions can affect desired and undesired plant species differentially and may be manipulated to favor establishment and persistence of desired perennial plant communities. Selection of appropriate plant materials is also essential. Species assemblages that suppress or exclude invaders and competitive plant materials that are well adapted to restoration site conditions are important keys to success. We provide guidelines for restoration based on the fundamental ecological principles underlying succession. Knowledge of the complex interactions among the biotic and abiotic factors that affect successional processes and ecosystem development, and increased collaboration between weed scientists and restoration ecologists hold promise for improving restoration success and invasive species management.

Community assembly theory provides a useful framework to assess the response of weed communities to agricultural management systems and to improve the predictive power of weed science. Under this framework, weed community assembly is constrained by abiotic and biotic “filters” that act on species traits to determine community composition. We used an assembly approach to investigate the response of weed seed banks to 25 yr of management-related filtering in three different row-crop management systems in southeastern Pennsylvania: organic manure-based, organic legume-based, and conventional. Weed seed banks were sampled in April of 2005 and 2006 and quantified by direct germination in a greenhouse. We also assessed the filtering effects of weed management practices and relationships between assembled seed bank and emergent weed communities by allowing or excluding weed control practices within each management system and measuring emergent weed community response. Germinable weed seed bank densities and species richness in the final year of the study were over 40% and 15% higher, respectively, in the organic systems relative to the conventional system. Seed bank community structure in the organic systems was different from the conventional system, and the relationships between assembled seed banks and the emergent flora varied. Primary tillage, weed control, timing of planting, and fertility management appeared to be the main filters that differentiated weed seed banks in the three systems. Weed life history, emergence periodicity, seed size, and responsiveness to soil fertility and hydrology appeared to be the most important functional traits determining how weed species responded to management-related filters. Our results suggest that management systems can exert strong filtering effects that can persist over relatively long (greater than one growing season) time scales. Legacy effects of community-level filtering might be more important than previously assumed, and should be incorporated into predictive models of weed community assembly.

The intensification of crop management in the U.K. over the past 60 years has resulted in the decline of the populations of a number of annual plant species adapted to arable habitats. In contrast, other species continue to be common as arable weeds. A community assembly approach was taken to explain these recent changes in the weed flora using databases of plant functional traits, a pot experiment, and weed surveys of the Broadbalk long-term experiment. The hypothesis was tested that species that have been selected against by increased fertilizer inputs and herbicide use share an adverse combination of traits. An analysis comparing the combination of maximum height, seed weight, and time of first flowering of 29 common and 32 rare or threatened U.K. autumn weeds established that rare or threatened species occupied an area of trait space that was distinct from the common species. A rare weed trait syndrome of short stature, large seed, and late flowering was identified. The theory that species with a trait syndrome that is currently unfavorable are better adapted for less fertile environments was supported by the pot experiment. Species with a combination of short stature and large seed had a relatively greater competitive ability in low compared to high fertility treatments. Analysis of survey data from the Broadbalk long-term experiment confirmed that, as N inputs increased, the abundance of the two functional groups that contained only common species remained stable or increased; whereas, the groups dominated by rare or threatened species declined as fertility increased. An understanding of the response traits of arable plants to management filters, including fertilizer inputs and herbicide, is valuable for designing conservation strategies for rare species or predicting future shifts in the functional diversity of weed communities including the potential for invasive species to establish.

The dynamics of soil seed banks in crop rotations of corn, soybean, and winter wheat were investigated to determine whether weed seed inputs associated with the winter wheat phases of the rotation were present in the readily germinable fraction of the seed bank in subsequent phases. Two studies were conducted, each in chisel-plowed systems. In one study, we compared seed banks in plots after 8 yr of corn grown continuously and with rotation that included winter wheat and soybean. A second study followed seed bank composition and abundance for 3 yr in plots that were planted to corn and soybean in successive years after planting to winter wheat. Seed banks were measured by direct germination in a heated greenhouse. In the first study, seed banks in plots planted to continuous corn (never planted to winter wheat) and the corn phase of the rotation (winter wheat planted 3 yr earlier) did not differ in species composition or abundance despite significant differences in seed banks in plots that had been planted to winter wheat the previous season. In the second study, seed bank abundance and composition in plots planted to winter wheat in 2001 rapidly changed after planting of corn and soybean in 2002 and 2003, respectively. Data from the two experiments suggest that seed banks in annual row crops experience rapid change in composition and abundance and can be strongly influenced by the most recent crop. This could limit our ability to infer longer term trends associated with changes in management practices from studies of soil seed banks.

Environmental filtering and competitive interactions are important ecological processes in community assembly. The contribution of the two processes to community assembly can be evaluated by shifts in functional diversity patterns. We examined the correlations between functional diversity of six traits (leaf chlorophyll concentration, dry matter content, size, specific leaf area, thickness and wood density) and environmental gradients (topography and soil) for 92 species in the 20-ha Dinghushan forest plot in China. A partial Mantel test showed that most of the community-weighted mean trait values changed with terrain convexity and soil fertility, which implied that environmental filtering was occurring. Functional diversity of many traits significantly increased with increasing terrain convexity and soil fertility, which was associated with increased light and below-ground resources respectively. These results suggest that co-occurring species are functionally convergent in regions of strong abiotic stress under the environmental filtering, but functionally divergent in more benign environments due to resource partitioning and competitive interactions. Single-trait diversity and multivariate functional diversity had different relationships with environmental factors, indicating that traits were related to different niche axes, and associated with different ecological processes, which demonstrated the importance of focusing niche axes in traits selection. Between 9% and 41% of variation in functional diversity of different traits was explained by environmental factors in stepwise multiple regression models. Terrain convexity and soil fertility were the best predictors of functional diversity, which contributed 30.5% and 29.0% of total R2 to the model. These provided essential evidence that different environmental factors had distinguishing impacts on regulating diversity of traits.

We investigated the effects of host tree on epiphyte diversity, controlling for microclimate. We measured the light profiles of the lower trunks of 20 individuals, each from three host groups (tree ferns, dicots, palms) occupying the understorey in a tropical montane forest in Panama. The per cent cover and species richness of vascular and non-vascular epiphytes were surveyed on the lower trunks of each understorey host. Light varied considerably between trees (5–21% total transmitted light) but mean light level did not vary between types of host. Light was not significant as a covariate with host in any model. Tree ferns had higher covers than dicots and palms of filmy ferns (15%, 0.02% and 0.2%), other ferns (7%, 0% and 0.5%) and other vascular epiphytes (16%, 3% and 3.4%), and greater species richness of vascular epiphytes (filmy ferns: 3, 0.4 and 0.5; other ferns: 2, 0.2 and 0; other vascular: 7, 2 and 2). Dicots had a higher cover of liverworts (53%) than palms (18%) and tree ferns (27%). Palms and tree ferns were the compositional extremes. We conclude that the differences in species composition and cover between the three host groups relate better to physical differences between hosts than differences in light climate.

The pattern of coarse-root distribution was analysed in the woody plant community along a 200-m edaphic gradient on a Kalahari sand woodland catena in Zimbabwe. The root systems of 45 trees and shrubs were excavated, mapped, and digitized to analyse rooting depth and architecture. Patterns of change in the above-ground community were also identified along this transect. Rooting depth increased, and the centre of mass of the root profile shifted towards the maximum rooting depth as a function of distance up the catena. The data also suggest that interspecific variation in rooting depth may increase up the catena. The below-ground pattern was accompanied by above-ground changes: species richness and basal area also increased up the catena. It is hypothesized that increasing soil depth allows greater coexistence of alternative water-use strategies, resulting in the observed increase in species richness up the catena.