A conceptual guide to measuring species diversity

Extra terrestrials: drought creates niche space for rare invertebrates in a large-scale and long-term field experiment

Freshwater habitats are drying more frequently and for longer under the combined pressures of climate change and overabstraction. Unsurprisingly, many aquatic species decline or become locally extinct as their benthic habitat is lost during stream droughts, but less is known about the potential 'winners': those terrestrial species that may exploit emerging niches in drying riverbeds. In particular, we do not know how these transient ecotones will respond as droughts become more extreme in the future. To find out we used a large-scale, long-term mesocosm experiment spanning a wide gradient of drought intensity, from permanent flows to full streambed dewatering, and analysed terrestrial invertebrate community assembly after 1 year. Droughts that caused stream fragmentation gave rise to the most diverse terrestrial invertebrate assemblages, including 10 species with UK conservation designations, and high species turnover between experimental channels. Droughts that caused streambed dewatering produced lower terrestrial invertebrate richness, suggesting that the persistence of instream pools may benefit these taxa as well as aquatic biota. Particularly intense droughts may therefore yield relatively few 'winners' among either aquatic or terrestrial species, indicating that the threat to riverine biodiversity from future drought intensification could be more pervasive than widely acknowledged.

Tuning Expectations to Reality: Don't Expect Increased Gut Microbiota Diversity with Dietary Fiber

Dietary approaches, particularly those including fiber supplementation, can be used to promote health benefits by shaping gut microbial communities. Whereas community diversity measures, such as richness and evenness, are often used in microbial ecology to make sense of these complex and vast microbial ecosystems, it is less clear how these concepts apply when dietary fiber supplementation is given. In this perspective, we summarize and demonstrate how factors including experimental approach, number of bacteria sharing a dietary fiber, and initial relative abundances of bacteria that use a fiber can significantly affect diversity outcomes in fiber fermentation studies. We also show that a reduction in alpha diversity is possible, and perhaps expected, for most approaches that use fermentable fibers to beneficially shape the gut microbial community while still achieving health-related improvements.

Frugivore-mediated seed dispersal in fragmented landscapes: Compositional and functional turnover from forest to matrix

Seed dispersal by frugivores is a fundamental function for plant community dynamics in fragmented landscapes, where forest remnants are typically embedded in a matrix of anthropogenic habitats. Frugivores can mediate both connectivity among forest remnants and plant colonization of the matrix. However, it remains poorly understood how frugivore communities change from forest to matrix due to the loss or replacement of species with traits that are less advantageous in open habitats and whether such changes ultimately influence the composition and traits of dispersed plants via species interactions. Here, we close this gap by using a unique dataset of seed-dispersal networks that were sampled in forest patches and adjacent matrix habitats of seven fragmented landscapes across Europe. We found a similar diversity of frugivores, plants, and interactions contributing to seed dispersal in forest and matrix, but a high turnover (replacement) in all these components. The turnover of dispersed seeds was smaller than that of frugivore communities because different frugivore species provided complementary seed dispersal in forest and matrix. Importantly, the turnover involved functional changes toward larger and more mobile frugivores in the matrix, which dispersed taller, larger-seeded plants with later fruiting periods. Our study provides a trait-based understanding of frugivore-mediated seed dispersal through fragmented landscapes, uncovering nonrandom shifts that can have cascading consequences for the composition of regenerating plant communities. Our findings also highlight the importance of forest remnants and frugivore faunas for ecosystem resilience, demonstrating a high potential for passive forest restoration of unmanaged lands in the matrix.

Paludiculture can support biodiversity conservation in rewetted fen peatlands

Paludiculture, the productive use of wet or rewetted peatlands, offers an option for continued land use by farmers after rewetting formerly drained peatlands, while reducing the greenhouse gas emissions from peat soils. Biodiversity conservation may benefit, but research on how biodiversity responds to paludiculture is scarce. We conducted a multi-taxon study investigating vegetation, breeding bird and arthropod diversity at six rewetted fen sites dominated by Carex or Typha species. Sites were either unharvested, low- or high-intensity managed, and were located in Mecklenburg-Vorpommern in northeastern Germany. Biodiversity was estimated across the range of Hill numbers using the iNEXT package, and species were checked for Red List status. Here we show that paludiculture sites can provide biodiversity value even while not reflecting historic fen conditions; managed sites had high plant diversity, as well as Red Listed arthropods and breeding birds. Our study demonstrates that paludiculture has the potential to provide valuable habitat for species even while productive management of the land continues.

Bird diversity along an urban to rural gradient in large tropical cities peaks in mid-level urbanization

The gradient from natural to urban areas strongly associates with the structure of avian communities over that gradient. Most research on urban birds is from temperate areas and knowledge from tropical Southeast Asia is lacking. We examined bird species diversity, relative abundance, and species composition along an urban to rural gradient in three Myanmar cities, and assessed potential environmental factors responsible for the changes. We counted birds within 40 point-count sites with 50-m fixed-radius in three large cities of Myanmar, namely Mandalay, Mawlamyine, and Myeik. We distinguished four urban habitat types (Downtown-urban, University Campus-suburban, Paddy Field-agriculture, Hill-forest). We classified all species into migrant or resident and into major feeding groups and related with several environmental parameters such as 'impervious surface'. We counted 5,423 individuals of 103 species with roughly equal species diversity between the three cities. Rock Pigeon (Columba livia) was the most frequent species. The species composition differed significantly between the four major habitat types. Omnivores were more abundant in the city center than all other functional groups. Interestingly, insectivores were also predominant in the city center. In addition, more generalist' species occurred towards the city center compared to the periphery, indicating that the periphery has increased relevance for specialized birds. We found some marked differences in species composition between the three cities of Mandalay, Mawlamyine, and Myeik. Additionally to species composition, species diversity and relative abundance differed significantly between each of the four major habitat types in all three cities.

Early-melting snowpatch plant communities are transitioning into novel states

Snowpatch plant community distribution and composition are strongly tied to the duration of long-lasting snow cover in alpine areas; they are vulnerable to global climatic changes that result in warmer temperatures and longer growing seasons. We used a revisitation study to quantify early-melting snowpatch floristic and functional diversity change in southern Australia, and document shrub size-class distributions over time to detect evidence for their encroachment into snowpatches, a key prediction with climatic change. Early-melting snowpatch vegetation has declined in areal extent, changed in species composition, and shrub and tussock grass cover has increased, but changes in functional trait diversity were less clear. Species gains, particularly by non-clonal species, accounted for most of the floristic change observed. Shrub recruitment was ongoing by most shrub species. Biotic differentiation is occurring; many early-melting snowpatches are transitioning to a novel state with changed composition and taller vegetation structure, but there is little evidence for species loss having occurred. Given enough time, however, the long-term loss of species is likely (i.e. biotic homogenisation) if taller shrubs outcompete short-statured snowpatch species. Our results provide evidence that this alpine ecosystem is forming a novel community with an uncertain future.

Effects of ultra-strong static magnetic field on the gut microbiota of humans and mice

To explore the effect of ultra-strong static magnetic field on gut microbiota, 16 T static magnetic field was used to study the changes in the structure and composition of human and mouse gut microbiota in this environment. In the mouse gut microbiota, at the genus level, the magnetic field significantly decreased the relative abundances of Escherichia-Shigella, Lactobacillus, Enterococcus, Burkholderia-Caballeronia-Paraburkholderia, Parasutterella, and Ralstonia and significantly increased those of Parabacteroides, Alloprevotella, Alistipes, Odoribacter, Bacteroides, Mucispirillum, Sutterella, and Prevotellaceae_UCG-001. Similarly, at the genus level, the relative abundances of Bacteroides, Parabacteroides, Romboutsia, and Streptococcus significantly decreased in the human gut microbiota. Contrary to the changing trend of the abundance in the mouse gut, the abundances of Bacteroides and Parabacteroides in the human gut were significantly reduced under magnetic field. The BugBase phenotypic prediction analysis showed that the relative abundances of five phenotypes, including anaerobism, mobile elements, potential pathogenicity, stress-tolerant, and biofilm formation, changed significantly in the mouse gut microbiota, while the relative abundances of two phenotypes, including Gram-positive and Gram-negative phenotypes, changed significantly in the human gut microbiota. The 16 T magnetic field could differently affect the composition, structure, and phenotypes of gut microbiota in human and mice, suggesting the importance of model selection in studying the biological effects of magnetic field.

Giants of the Amazon: How does environmental variation drive the diversity patterns of large trees?

For more than three decades, major efforts in sampling and analyzing tree diversity in South America have focused almost exclusively on trees with stems of at least 10 and 2.5 cm diameter, showing highest species diversity in the wetter western and northern Amazon forests. By contrast, little attention has been paid to patterns and drivers of diversity in the largest canopy and emergent trees, which is surprising given these have dominant ecological functions. Here, we use a machine learning approach to quantify the importance of environmental factors and apply it to generate spatial predictions of the species diversity of all trees (dbh ≥ 10 cm) and for very large trees (dbh ≥ 70 cm) using data from 243 forest plots (108,450 trees and 2832 species) distributed across different forest types and biogeographic regions of the Brazilian Amazon. The diversity of large trees and of all trees was significantly associated with three environmental factors, but in contrasting ways across regions and forest types. Environmental variables associated with disturbances, for example, the lightning flash rate and wind speed, as well as the fraction of photosynthetically active radiation, tend to govern the diversity of large trees. Upland rainforests in the Guiana Shield and Roraima regions had a high diversity of large trees. By contrast, variables associated with resources tend to govern tree diversity in general. Places such as the province of Imeri and the northern portion of the province of Madeira stand out for their high diversity of species in general. Climatic and topographic stability and functional adaptation mechanisms promote ideal conditions for species diversity. Finally, we mapped general patterns of tree species diversity in the Brazilian Amazon, which differ substantially depending on size class.

Metabarcoding Used for the First Time to Identify Prey of Wild Totoaba macdonaldi

Totoaba macdonaldi is an endangered endemic fish of the Gulf of California. Overexploitation resulted in the Mexican government banning the fishing of this species in 1975, and it being listed as endangered. However, the species is still subject to illegal fishing. Despite its conservation status, little is known about totoaba biology. The present study aimed to implement, for the first time, a metabarcoding protocol to describe the totoaba diet. Four wild totoaba individuals, seized by Mexican law enforcement agents, were dissected, and their stomach contents were collected. Three representative amplicon libraries were generated for cephalopods, chordates, and eukaryotes. After sequencing, 18 different taxa were identified, of which 11 species were recognized as prey. The totoaba were found to have consumed Pacific anchovy (Cetengraulis mysticetus), flathead grey mullet (Mugil cephalus), bigeye croaker (Micropogonias megalops), northern anchovy (Engraulis mordax), ocean whitefish (Caulolatilus princeps), milkfish (Chanos chanos), and Pacific sardine (Sardinops sagax). Members of the Euphausiidae family (krill) were also identified. This study identified up to four times more species in much fewer samples than previous studies based on morphological recognition, thus confirming metabarcoding as an effective method for studying the feeding habits of this species and one providing the tools required for further analysis of the totoaba diet.

Whistle repertoire and structure reflect ecotype distinction of pantropical spotted dolphins in the Eastern Tropical Pacific

The pantropical spotted dolphin in the Eastern Tropical Pacific (ETP) is found in two genetically and phenotypically diverged ecotypes, coastal and offshore. These habitats have distinct acoustic characteristics, which can lead to the evolution of distinct acoustic communication. Whistles are sounds widely used by dolphins to mediate species and individual recognition and social interactions. Here, we study the whistle acoustic structure and repertoire diversity of offshore and coastal pantropical spotted dolphins. Our results show that there is significantly more within- and across-group variation in whistle fundamental frequency between ecotypes than between offshore groups and between coastal groups. A Random Forest classification analysis performed with an accuracy of 83.99% and identified duration, peak and minimum frequency as the most informative variables for distinguishing between ecotypes. Overall, coastal spotted dolphins produced significantly shorter whistles that were significantly lower in frequency (peak, minimum and maximum, and start and end) than offshore dolphins. Ecotypes produced whistle repertoires that were similar in diversity, but different in contour composition, with the coastal ecotype producing more upsweep whistles than offshore dolphins. The results of this study suggest that acoustic adaptations to coastal and offshore environments could be important contributors to intraspecific variation of dolphin whistle repertoires.

Anthropogenic Influence on Moth Populations: A Comparative Study in Southern Sweden

As moths are vital components of ecosystems and serve as important bioindicators, understanding the dynamics of their communities and the factors influencing these dynamics, such as anthropogenic impacts, is crucial to understand the ecological processes. Our study focuses on two provinces in southern Sweden, Västergötland and Småland, where we used province records from 1974 to 2019 in combination with light traps (in 2020) to record the presence and abundance of moth species, subsequently assessing species traits to determine potential associations with their presence in anthropogenically modified landscapes. This study design provides a unique opportunity to assess temporal changes in moth communities and their responses to shifts in environmental conditions, including anthropogenic impacts. Across the Västergötland and Småland provinces in Sweden, we recorded 776 moth taxa belonging to fourteen different taxonomic families of mainly Macroheterocera. We captured 44% and 28% of the total moth species known from these provinces in our traps in Borås (Västergötland) and Kalmar (Småland), respectively. In 2020, the species richness and abundance were higher in Borås than in Kalmar, while the Shannon and Simpson diversity indices revealed a higher species diversity in Kalmar. Between 1974 and 2019, the colonisation rates of the provinces increased faster in Småland. Ninety-three species were found to have colonised these provinces since 1974, showing that species richness increased over the study period. We reveal significant associations between the probability of a species being present in the traps and distinct traits compared to a provincial species pool. Traits over-represented in the traps included species with a high variation in colour patterns, generalist habitat preferences, extended flight periods, lower host plant specificity, and overwintering primarily as eggs. Our findings underscore the ongoing ecological filtering that favours certain species-specific traits. This study sheds light on the roles of climate change and anthropogenic impacts in shaping moth biodiversity, offers key insights into the ecological processes involved, and can guide future conservation efforts.

Potential long consequences from internal and external ecology: loss of gut microbiota antifragility in children from an industrialized population compared with an indigenous rural lifestyle

Human health is strongly mediated by the gut microbiota ecosystem, which, in turn, depends not only on its state but also on its dynamics and how it responds to perturbations. Healthy microbiota ecosystems tend to be in criticality and antifragile dynamics corresponding to a maximum complexity configuration, which may be assessed with information and network theory analysis. Under this complex system perspective, we used a new analysis of published data to show that a children's population with an industrialized urban lifestyle from Mexico City exhibits informational and network characteristics similar to parasitized children from a rural indigenous population in the remote mountainous region of Guerrero, México. We propose then, that in this critical age for gut microbiota maturation, the industrialized urban lifestyle could be thought of as an external perturbation to the gut microbiota ecosystem, and we show that it produces a similar loss in criticality/antifragility as the one observed by internal perturbation due to parasitosis by the helminth A. lumbricoides. Finally, several general complexity-based guidelines to prevent or restore gut ecosystem antifragility are discussed.

The joint effects of forest habitat area and fragmentation on dung beetles

Habitat loss and habitat fragmentation usually occur together, at the same time and place. However, while there is a consensus that habitat loss is the preeminent threat to biodiversity, the effects of fragmentation are contentious. Some argue that habitat fragmentation is not bad for biodiversity, and even that it is good. Generally, the studies that find no harm or positive outcomes of fragmentation invariably assume that it is independent of habitat loss. However, dissociating the effects of habitat fragmentation from habitat loss is questionable because the two are essentially coupled. Accordingly, we evaluated how forest area and fragmentation (via edge effects) influenced dung beetles per se, and through their effects on the abundance of mammals, using structural equation modeling (SEM). Dung beetles are very sensitive to forest habitat loss and fragmentation and to changes in the abundance of mammals on which they depend for dung. Our study area was in the Tana River, Kenya, where forest fragments are depauperated of mammals except for two endemic species of monkeys. We mapped 12 forests, counted the resident monkeys, and sampled 113,955 beetles from 288 plots. Most of the 87 species of beetles found were small tunnellers. After implementing a fully latent Structural Regression SEM, the optimal model explained a significant 26% of the variance in abundance, and 89% of diversity. The main drivers of beetle abundance were positive, direct, effects of forest area and number of monkeys, and negative edge effects. The main drivers of diversity were the direct effects of the beetle abundance, indirect effects of forest area and abundance of mammals, and indirect negative edge effects. Thus, forest area, fragmentation (via edge effects), and the number of monkeys jointly influenced the abundance and diversity of the beetles directly and indirectly.

Challenges and directions in analytical paleobiology

Over the last 50 years, access to new data and analytical tools has expanded the study of analytical paleobiology, contributing to innovative analyses of biodiversity dynamics over Earth's history. Despite-or even spurred by-this growing availability of resources, analytical paleobiology faces deep-rooted obstacles that stem from the need for more equitable access to data and best practices to guide analyses of the fossil record. Recent progress has been accelerated by a collective push toward more collaborative, interdisciplinary, and open science, especially by early-career researchers. Here, we survey four challenges facing analytical paleobiology from an early-career perspective: (1) accounting for biases when interpreting the fossil record; (2) integrating fossil and modern biodiversity data; (3) building data science skills; and (4) increasing data accessibility and equity. We discuss recent efforts to address each challenge, highlight persisting barriers, and identify tools that have advanced analytical work. Given the inherent linkages between these challenges, we encourage discourse across disciplines to find common solutions. We also affirm the need for systemic changes that reevaluate how we conduct and share paleobiological research.

Probiotic supplementation during antibiotic treatment is unjustified in maintaining the gut microbiome diversity: a systematic review and meta-analysis

BACKGROUND

Probiotics are often used to prevent antibiotic-induced low-diversity dysbiosis, however their effect is not yet sufficiently summarized in this regard. We aimed to investigate the effects of concurrent probiotic supplementation on gut microbiome composition during antibiotic therapy.

METHODS

We performed a systematic review and meta-analysis of randomized controlled trials reporting the differences in gut microbiome diversity between patients on antibiotic therapy with and without concomitant probiotic supplementation. The systematic search was performed in three databases (MEDLINE (via PubMed), Embase, and Cochrane Central Register of Controlled Trials (CENTRAL)) without filters on 15 October 2021. A random-effects model was used to estimate pooled mean differences (MD) with 95% confidence intervals (CI). This review was registered on PROSPERO (CRD42021282983).

RESULTS

Of 11,769 identified articles, 15 were eligible in the systematic review and 5 in the meta-analyses. Quantitative data synthesis for Shannon (MD = 0.23, 95% CI: [(-)0.06-0.51]), Chao1 (MD = 11.59 [(-)18.42-41.60]) and observed OTUs (operational taxonomic unit) (MD = 17.15 [(-)9.43-43.73]) diversity indices revealed no significant difference between probiotic supplemented and control groups. Lacking data prevented meta-analyzing other diversity indices; however, most of the included studies reported no difference in the other reported α- and ß-diversity indices between the groups. Changes in the taxonomic composition varied across the eligible studies but tended to be similar in both groups. However, they showed a potential tendency to restore baseline levels in both groups after 3-8 weeks. This is the first meta-analysis and the most comprehensive review of the topic to date using high quality methods. The limited number of studies and low sample sizes are the main limitations of our study. Moreover, there was high variability across the studies regarding the indication of antibiotic therapy and the type, dose, and duration of antimicrobials and probiotics.

CONCLUSIONS

Our results showed that probiotic supplementation during antibiotic therapy was not found to be influential on gut microbiome diversity indices. Defining appropriate microbiome diversity indices, their standard ranges, and their clinical relevance would be crucial.

A framework for the detection and attribution of biodiversity change

The causes of biodiversity change are of great scientific interest and central to policy efforts aimed at meeting biodiversity targets. Changes in species diversity and high rates of compositional turnover have been reported worldwide. In many cases, trends in biodiversity are detected, but these trends are rarely causally attributed to possible drivers. A formal framework and guidelines for the detection and attribution of biodiversity change is needed. We propose an inferential framework to guide detection and attribution analyses, which identifies five steps-causal modelling, observation, estimation, detection and attribution-for robust attribution. This workflow provides evidence of biodiversity change in relation to hypothesized impacts of multiple potential drivers and can eliminate putative drivers from contention. The framework encourages a formal and reproducible statement of confidence about the role of drivers after robust methods for trend detection and attribution have been deployed. Confidence in trend attribution requires that data and analyses used in all steps of the framework follow best practices reducing uncertainty at each step. We illustrate these steps with examples. This framework could strengthen the bridge between biodiversity science and policy and support effective actions to halt biodiversity loss and the impacts this has on ecosystems. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

Theory and application of an improved species richness estimator

Species richness is an essential biodiversity variable indicative of ecosystem states and rates of invasion, speciation and extinction both contemporarily and in fossil records. However, limited sampling effort and spatial aggregation of organisms mean that biodiversity surveys rarely observe every species in the survey area. Here we present a non-parametric, asymptotic and bias-minimized richness estimator, Ω by modelling how spatial abundance characteristics affect observation of species richness. Improved asymptotic estimators are critical when both absolute richness and difference detection are important. We conduct simulation tests and applied Ω to a tree census and a seaweed survey. Ω consistently outperforms other estimators in balancing bias, precision and difference detection accuracy. However, small difference detection is poor with any asymptotic estimator. An R-package, Richness, performs the proposed richness estimations along with other asymptotic estimators and bootstrapped precisions. Our results explain how natural and observer-induced variations affect species observation, how these factors can be used to correct observed richness using the estimator Ω on a variety of data, and why further improvements are critical for biodiversity assessments. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

Biodiversity-ecosystem function relationships change in sign and magnitude across the Hill diversity spectrum

Motivated by accelerating anthropogenic extinctions, decades of biodiversity-ecosystem function (BEF) experiments show that ecosystem function declines with species loss from local communities. Yet, at the local scale, changes in species' total and relative abundances are more common than species loss. The consensus best biodiversity measures are Hill numbers, which use a scaling parameter, ℓ, to emphasize rarer versus more common species. Shifting that emphasis captures distinct, function-relevant biodiversity gradients beyond species richness. Here, we hypothesized that Hill numbers that emphasize rare species more than richness does may distinguish large, complex and presumably higher-functioning assemblages from smaller and simpler ones. In this study, we tested which values of ℓ produce the strongest BEF relationships in community datasets of ecosystem functions provided by wild, free-living organisms. We found that ℓ values that emphasized rare species more than richness does most often correlated most strongly with ecosystem functions. As emphasis shifted to more common species, BEF correlations were often weak and/or negative. We argue that unconventional Hill diversities that shift emphasis towards rarer species may be useful for describing biodiversity change, and that employing a wide spectrum of Hill numbers can clarify mechanisms underlying BEF relationships. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

Effects of forest management on native bee biodiversity under the tallest trees in the world

It is not clear if mature secondary growth coniferous forests can support similar pollinator communities as old growth coniferous forests, or how active management (e.g., retention forestry) in mature secondary growth forests may affect pollinator communities. We compare the native bee community and plant-bee interaction networks of old growth, naturally regenerating and actively managed (retention forestry) mature secondary growth forests of similar stand age. Old growth forests had a higher bee species richness and Shannon's diversity index, but not Simpson's diversity index, than both actively managed and naturally regenerating mature secondary forests. Forest type (old-growth, naturally regenerating mature secondary growth, and actively managed mature secondary growth) had a significant effect on bee community composition. Redwood forest bee-plant interaction networks were small in size and had lower complexity than expected and few connector species. While studies suggest that small-scale timber harvest may increase bee biodiversity in the short-term in other coniferous forest habitats, our study suggests that there may be long-term negative effects of clear-cutting that lower bee biodiversity in mature secondary growth forests as compared to mature old-growth forests.

Tree islands enhance biodiversity and functioning in oil palm landscapes

In the United Nations Decade on Ecosystem Restoration1, large knowledge gaps persist on how to increase biodiversity and ecosystem functioning in cash crop-dominated tropical landscapes2. Here, we present findings from a large-scale, 5-year ecosystem restoration experiment in an oil palm landscape enriched with 52 tree islands, encompassing assessments of ten indicators of biodiversity and 19 indicators of ecosystem functioning. Overall, indicators of biodiversity and ecosystem functioning, as well as multidiversity and ecosystem multifunctionality, were higher in tree islands compared to conventionally managed oil palm. Larger tree islands led to larger gains in multidiversity through changes in vegetation structure. Furthermore, tree enrichment did not decrease landscape-scale oil palm yield. Our results demonstrate that enriching oil palm-dominated landscapes with tree islands is a promising ecological restoration strategy, yet should not replace the protection of remaining forests.

Evolutionary repeatability of emergent properties of ecological communities

Most species belong to ecological communities where their interactions give rise to emergent community-level properties, such as diversity and productivity. Understanding and predicting how these properties change over time has been a major goal in ecology, with important practical implications for sustainability and human health. Less attention has been paid to the fact that community-level properties can also change because member species evolve. Yet, our ability to predict long-term eco-evolutionary dynamics hinges on how repeatably community-level properties change as a result of species evolution. Here, we review studies of evolution of both natural and experimental communities and make the case that community-level properties at least sometimes evolve repeatably. We discuss challenges faced in investigations of evolutionary repeatability. In particular, only a handful of studies enable us to quantify repeatability. We argue that quantifying repeatability at the community level is critical for approaching what we see as three major open questions in the field: (i) Is the observed degree of repeatability surprising? (ii) How is evolutionary repeatability at the community level related to repeatability at the level of traits of member species? (iii) What factors affect repeatability? We outline some theoretical and empirical approaches to addressing these questions. Advances in these directions will not only enrich our basic understanding of evolution and ecology but will also help us predict eco-evolutionary dynamics. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.

Response of soil bacterial populations to application of biosolids under short-term flooding

Biosolids are applied to agricultural land as a soil conditioner and source of crop nutrients. However, there is concern that bacteria from biosolids may become established in soils, particularly if that soil becomes water-logged. This study examined the microbial community of arable soils cultivated with barley under different applications of biosolids (0, 24t/ha, 48t/ha) in laboratory mesocosms which simulated a 10-day flood. Nutrients (P and N) and organic matter in the soil increased with application rate, but plant growth was not affected by biosolid application. The biosolids contained 10× more genetic material than the soil, with much lower bacterial diversity, yet application did not significantly change the taxonomy of the soil microbiome, with minor changes related to increased nutrients and SOM. Anaerobic conditions developed rapidly during flooding, causing shifts in the native soil microbiome. Some bacterial taxa that were highly abundant in biosolids had slightly increased relative abundance in amended soils during the flood. After flooding, soil bacterial populations returned to their pre-flood profiles, implying that the native microbial community is resilient to transient changes. The short-term changes in the microbiome of biosolid-amended soils during flooding do not appear to increase the environmental risk posed by biosolid application.

Multi-marker DNA metabarcoding reveals spatial and sexual variation in the diet of a scarce woodland bird

Avian diet can be affected by site-specific variables, such as habitat, as well as intrinsic factors such as sex. This can lead to dietary niche separation, which reduces competition between individuals, as well as impacting how well avian species can adapt to environmental variation. Estimating dietary niche separation is challenging, due largely to difficulties in accurately identifying food taxa consumed. Consequently, there is limited knowledge of the diets of woodland bird species, many of which are undergoing serious population declines. Here, we show the effectiveness of multi-marker fecal metabarcoding to provide in-depth dietary analysis of a declining passerine in the UK, the Hawfinch (Coccothraustes coccothraustes). We collected fecal samples from (n = 262) UK Hawfinches prior to, and during, the breeding seasons in 2016-2019. We detected 49 and 90 plant and invertebrate taxa, respectively. We found Hawfinch diet varied spatially, as well as between sexes, indicating broad dietary plasticity and the ability of Hawfinches to utilize multiple resources within their foraging environments.

Heatwave restructures marine intertidal communities across a stress gradient

Significant questions remain about how ecosystems that are structured by abiotic stress will be affected by climate change. Warmer temperatures are hypothesized to shift species along abiotic gradients such that distributions track changing environments where physical conditions allow. However, community-scale impacts of extreme warming in heterogeneous landscapes are likely to be more complex. We investigated the impacts of a multiyear marine heatwave on intertidal community dynamics and zonation on a wave-swept rocky coastline along the Central Coast of British Columbia, Canada. Leveraging an 8-year time series with high seaweed taxonomic resolution (116 taxa) that was established 3 years prior to the heatwave, we document major shifts in zonation and abundance of populations that led to substantial reorganization at the community level. The heatwave was associated with shifts in primary production away from upper elevations through declines in seaweed cover and partial replacement by invertebrates. At low elevations, seaweed cover remained stable or recovered rapidly following decline, being balanced by increases in some species and decreases in others. These results illustrate that, rather than shifting community zonation uniformly along abiotic stress gradients, intense and lasting warming events may restructure patterns of ecological dominance and reduce total habitability of ecosystems, especially at extreme ends of pre-existing abiotic gradients.

Experimental disturbance and productivity gradients drive community diversity in aquatic mesocosms

Combined effects of disturbance and productivity on ecological diversity have been considered for decades as the dynamic equilibrium model (DEM) but are rarely tested together. Instead, most studies focus on either the intermediate disturbance hypothesis or sometimes the intermediate productivity hypothesis. In addition, most analyses of disturbance and productivity effects have relied on nonexperimental patterns, limited sample sizes, inaccurate proxies for productivity, and/or simple measures of diversity. The DEM operates at regional and local scales; here, we conducted a year-long experiment at local scales using submersed aquatic vegetation in outdoor mesocosms with a factorial combination of physical disturbance and productivity treatments. We evaluated diversity in several ways, directly measured productivity, and compared alternative hypotheses using model selection. The DEM was supported for effective diversity; both productivity and disturbance effects were clear, though productivity effects were stronger. Other diversity measures for the simple communities in the mesocosms did not clearly reflect treatments. The DEM is a valuable general framework for understanding disturbance and productivity effects on ecological systems and is made more general by minor conceptual adjustments here.

The microbiome of a brownfield highly polluted with mercury and arsenic

Abandoned brownfields represent a challenge for their recovery. To apply sustainable remediation technologies, such as bioremediation or phytoremediation, indigenous microorganisms are essential agents since they are adapted to the ecology of the soil. Better understanding of microbial communities inhabiting those soils, identification of microorganisms that drive detoxification process and recognising their needs and interactions will significantly improve the outcome of the remediation. With this in mind we have carried out a detailed metagenomic analysis to explore the taxonomic and functional diversity of the prokaryotic and eukaryotic microbial communities in soils, several mineralogically distinct types of pyrometallurgic waste, and groundwater sediments of a former mercury mining and metallurgy site which harbour very high levels of arsenic and mercury pollution. Prokaryotic and eukaryotic communities were identified, which turned out to be more diverse in the surrounding contaminated soils compared to the pyrometallurgic waste. The highest diversity loss was observed in two environments most contaminated with mercury and arsenic (stupp, a solid mercury condenser residue and arsenic-rich soot from arsenic condensers). Interestingly, microbial communities in the stupp were dominated by an overwhelming majority of archaea of the phylum Crenarchaeota, while Ascomycota and Basidiomycota fungi comprised the fungal communities of both stump and soot, results that show the impressive ability of these previously unreported microorganisms to colonize these extreme brownfield environments. Functional predictions for mercury and arsenic resistance/detoxification genes show their increase in environments with higher levels of pollution. Our work establishes the bases to design sustainable remediation methods and, equally important, to study in depth the genetic and functional mechanisms that enable the subsistence of microbial populations in these extremely selective environments.

Statistical signals of copying are robust to time- and space-averaging

Cattle brands (ownership marks left on animals) are subject to forces influencing other graphic codes: the copying of constituent parts, pressure for distinctiveness and pressure for complexity. The historical record of cattle brands in some US states is complete owing to legal registration, providing a unique opportunity to assess how sampling processes leading to time- and space-averaging influence our ability to make inferences from limited datasets in fields like archaeology. In this preregistered study, we used a dataset of ~81,000 Kansas cattle brands (1990-2016) to explore two aspects: (1) the relative influence of copying, pressure for distinctiveness and pressure for complexity on the creation and diffusion of brand components; and (2) the effects of time- and space-averaging on statistical signals. By conducting generative inference with an agent-based model, we found that the patterns in our data are consistent with copying and pressure for intermediate complexity. In addition, by comparing mixed and structured datasets, we found that these statistical signals of copying are robust to, and possibly boosted by, time- and space-averaging.

Tipping points and interactive effects of chronic human disturbance and acute heat stress on coral diversity

Multiple anthropogenic stressors co-occur ubiquitously in natural ecosystems. However, multiple stressor studies often produce conflicting results, potentially because the nature and direction of stressor interactions depends upon the strength of the underlying stressors. Here, we first examine how coral α- and β-diversities vary across sites spanning a gradient of chronic local anthropogenic stress before and after a prolonged marine heatwave. Developing a multiple stressor framework that encompasses non-discrete stressors, we then examine interactions between the continuous and discrete stressors. We provide evidence of additive effects, antagonistic interactions (with heatwave-driven turnover in coral community composition diminishing as the continuous stressor increased), and tipping points (at which the response of coral Hill-richness to stressors changed from additive to near synergistic). We show that community-level responses to multiple stressors can vary, and even change qualitatively, with stressor intensity, underscoring the importance of examining complex, but realistic continuous stressors to understand stressor interactions and their ecological impacts.

How does spatial extent and environmental limits affect the accuracy of species richness estimates from ecological niche models? A case study with North American Pinaceae and Cactaceae

Measuring species richness at varying spatial extents can be challenging, especially at large extents where exhaustive species surveys are difficult or impossible. Our work aimed at determining the reliability of species richness estimates from stacked ecological niche models at different spatial extents for taxonomic groups with vastly different environmental dependencies and interactions. To accomplish this, we generated ecological niche models for the species of Cactaceae and Pinaceae that occur within 180 published floras from North America north of Mexico. We overlaid or stacked the resulting species' potential distribution estimates over the bounding boxes representing each of the 180 floras to generate predictions of species richness. In general, our stacked models of Cactaceae and Pinaceae were poor predictors of species richness. The relationships between observed and predicted values improved noticeably with the size of spatial extents. However, the stacked models tended to overpredict the richness of Cactaceae and over- and underpredict the richness of Pinaceae. Cactaceae stacked models showed higher sensitivity and lower specificity than those for Pinaceae. We conclude that stacked ecological niche models may be somewhat poor predictors of species richness at smaller spatial extents and should be used with caution for this purpose. Perhaps more importantly, abilities to compensate for their limitations or apply corrections to their reliability may vary with taxonomic groups.

Evaluating the sampling effort for the metabarcoding‐based detection of fish environmental DNA in the open ocean

Clarifying the effect of the sampling protocol on the detection of environmental DNA (eDNA) is essential for appropriately designing biodiversity research. However, technical issues influencing eDNA detection in the open ocean, which consists of water masses with varying environmental conditions, have not been thoroughly investigated. This study evaluated the sampling effort for the metabarcoding‐based detection of fish eDNA using replicate sampling with filters of different pore sizes (0.22 and 0.45 μm) in the subtropical and subarctic northwestern Pacific Ocean and Arctic Chukchi Sea. The asymptotic analysis predicted that the accumulation curves for detected taxa did not saturate in most cases, indicating that our sampling effort (7 or 8 replicates, corresponding to 10.5–40 L of filtration in total) was insufficient to fully assess the species diversity in the open ocean and that tens of replicates or a substantial filtration volume were required. The Jaccard dissimilarities between filtration replicates were comparable with those between the filter types at any site. In subtropical and subarctic sites, turnover dominated the dissimilarity, suggesting that the filter pore size had a negligible effect. In contrast, nestedness dominated the dissimilarity in the Chukchi Sea, implying that the 0.22 μm filter could collect a broader range of eDNA than the 0.45 μm filter. Therefore, the effect of filter selection on the collection of fish eDNA likely varies depending on the region. These findings highlight the highly stochastic nature of fish eDNA collection in the open ocean and the difficulty of standardizing the sampling protocol across various water masses.

Mediterranean university campuses enhance butterfly (Lepidoptera) and beetle (Coleoptera) diversity

Human population growth is causing an expansion of urban areas, a phenomenon known to deeply impact on the Earth’s biodiversity. Therefore, it is key to understand how to conceal urban development with biodiversity conservation. In this context, university campuses can play an important role as they usually present a large array of different environments and green areas, crucial aspects for promoting urban biodiversity as well as human-nature interactions. Several studies have analyzed the biodiversity of university campuses, however, there are still important taxonomic (e.g., insects) and geographical biases (e.g., Mediterranean hotspot) in our current understanding of these urban areas. Insects are fundamental in many ecosystems as pollinators, prey, pest controllers or decomposers among others. This further increases the need to study this group in the urban context. In this study, we have investigated diurnal Lepidoptera and ground-dwelling Coleoptera in three university campuses and three non-campus areas of the city of Granada (Spain). We used spatial and temporal replicates for each area in order to explore whether university campuses hold higher levels of insect biodiversity (e.g., species richness or common species) than other nearby urban areas. In addition, we investigated the potential influence of several additional predictors on insect diversity such as type of land cover, vegetation origin, management intensity, and distance to the outskirts. Our results suggest that Lepidoptera species and Coleoptera families are more diverse in university campuses than in other urban areas, showing also a positive association with the proportion of bare soil and herbaceous cover. Furthermore, they also seem to be benefited from low vegetation management intensity whereas Coleoptera are favored by native vegetation providing clear management recommendations in order to promote such animal groups in cities. Our study indicates that university campuses are important urban areas to preserve insect biodiversity but also highlights the heterogeneity of response among insect groups.

Diminishing influence of negative relationship between species richness and evenness on the modeling of grassland α-diversity metrics

Species richness and evenness have been widely used to investigate the spatiotemporal variation of α-diversity. However, some studies have indicated that a negative relationship exists between species richness and evenness. The question is how the differing sensitivity of α-diversity metrics and interactive behavior between richness and evenness affect the modeling of α-diversity variation. Here, we explored the response of species diversity, represented by three Hill numbers (i.e., species richness, exponential of Shannon index – expShannon, and inverse of Simpson index – invSimpson) focusing on the abundance of rare and common species, and Pielou index underlining the evenness of a community, to α-diversity variation through structural equation modeling (SEM). The model scheme integrated three categories of variables, spectral variation hypothesis (SVH), community pattern, and vertical structure, along the precipitation gradient spanning three steppes, including meadow steppe, typical steppe, and desert steppe. Our results showed that there were large differences in species richness across the three steppes, with v-shaped patterns emerging along the gradient (low-point in the typical steppe). Differences between steppes were diminished in the expShannon or invSimpson indices, though the v-shaped patterns persisted. The Pielou index showed the opposite pattern, with the peak in the typical steppe. Accordingly, a negative relationship between species richness and Pielou index was found across the three steppes. The concurrent increases in annual species number and dominant species abundance in response to precipitation variations led to the negative relationship. As a result, the SEM fitness on expShannon and invSimpson indices over the region was substantially diminished by the negative relationship. Overall, community pattern better explained the variation in species richness, invSimpson and Pielou indices. The performance of SVH differed among α-diversity metrics due to the collinearity with the variables of community pattern and vertical structure. This study emphasizes the variability of α-diversity metrics in response to environmental change. Particularly, distinguishing the asynchronous behaviors between species richness and evenness is paramount to account for α-diversity variation over heterogeneous ecosystems.

Forest edges increase pollinator network robustness to extinction with declining area

Edge effects often exacerbate the negative effects of habitat loss on biodiversity. In forested ecosystems, however, many pollinators actually prefer open sunny conditions created by edge disturbances. We tested the hypothesis that forest edges have a positive buffering effect on plant-pollinator interaction networks in the face of declining forest area. In a fragmented land-bridge island system, we recorded ~20,000 plant-pollinator interactions on 41 islands over 3 yr. We show that plant richness and floral resources decline with decreasing forest area at both interior and edge sites, but edges maintain 10-fold higher pollinator abundance and richness regardless of area loss. Edge networks contain highly specialized species, with higher nestedness and lower modularity than interior networks, maintaining high robustness to extinction following area loss while forest interior networks collapse. Anthropogenic forest edges benefit community diversity and network robustness to extinction in the absence of natural gap-phase dynamics in small degraded forest remnants.

Discrepancies between the drivers of alpha and beta plant diversity in arable field margins

Field margins are major habitats for biodiversity conservation and ecosystem functioning in agricultural landscapes, but biotic homogenization of plant communities threatens their ecological and agronomic functions. Our objective is to determine the drivers of plant diversity in field margins for conservation and restoration purposes. To do so, we assessed the effects of field margin structure and long-term management over 20 years (1995-2015) on the taxonomic and functional α- and β-diversity, and the functional composition of herbaceous plant communities. In 2015, we surveyed 302 field margins in bocage landscapes of Brittany, northwestern France. Results were very similar between taxonomic and functional diversity but revealed important discrepancies between the drivers of α- and β-diversity. Deep ditches, mowing and grazing increased α-diversity but did not affect β-diversity. Denser hedgerows had lower α-diversity than other field margins but strongly contributed to β-diversity by harbouring more unique sets of species or life strategies. Long-term herbicide spraying in field margins and cropping intensity in adjacent habitats did not affect α-diversity, but had more complex effects on β-diversity and selected for common weeds. All in all, preservation of dense hedgerows, abandonment of herbicide spraying, and protection against agrochemical drifts are key measures to prevent the establishment of common weeds and biotic homogenization of herbaceous plant communities in field margins. Above all, our study shows how important it is to go beyond α-diversity to make robust conservation and restoration decisions.

Impacts of Semiochemical Traps Designed for Bruchus rufimanus Boheman 1833 (Coleoptera: Chrysomelidae) on Nontarget Beneficial Entomofauna in Field Bean Crops

Broad bean weevils (BBWs-Coleoptera: Chrysomelidae) are serious pests of field bean seeds that hamper the promotion of this crop in the diversification of European cropping systems. Recent research has identified different semiochemical lures and trap devices for the development of semiochemical-based control strategies of BBWs. In this study, two field trials were carried out in order to provide necessary information supporting the implementation of sustainable field use of semiochemical traps against BBWs. More particularly, three principal objectives were followed including (i) the identification of the most efficient traps for BBWs capture and the influence of trapping modality on BBWs sex-ratio, (ii) the assessment of eventual collateral effects on crop benefits including aphidophagous and pollinator insects such as Apidae, Syrphidae and Coccinellidae, (iii) the assessment of the crop developmental stage influence on the capture by semiochemical traps. Three different semiochemical lures were tested in combination with two trapping devices across two field trials in early and late flowering field bean crops. The crop phenology and climate parameters were integrated into the analyses to interpret the spatiotemporal evolution of the captured insect populations. A total of 1380 BBWs and 1424 beneficials were captured. White pan traps combined with floral kairomones were the most efficient traps for the capture of BBWs. We demonstrated that the crop phenology (c.f., the flowering stage) exerted strong competition on the attractiveness of semiochemical traps. Community analysis revealed that only one species of BBWs was captured in field bean crops (i.e., Bruchus rufimanus), and no trend was highlighted concerning the sex ratios according to the trapping devices. The beneficial insect community included 67 different species belonging to bees, hoverflies and ladybeetles. Semiochemical traps manifested a strong impact on beneficial insect communities that included some species under extinction threats and need to be further adapted to minimize such collateral effects. Based on these results, recommendations are provided for the implementation of the most sustainable BBWs control method that minimizes the impact on the recruitment of beneficial insects, which is an important ecosystem service for faba bean crops.

Microbiome Alterations in Alcohol Use Disorder and Alcoholic Liver Disease

Microbiome alterations are emerging as one of the most important factors that influence the course of alcohol use disorder (AUD). Recent advances in bioinformatics enable more robust and accurate characterization of changes in the composition of the microbiome. In this study, our objective was to provide the most comprehensive and up-to-date evaluation of microbiome alterations associated with AUD and alcoholic liver disease (ALD). To achieve it, we have applied consistent, state of art bioinformatic workflow to raw reads from multiple 16S rRNA sequencing datasets. The study population consisted of 122 patients with AUD, 75 with ALD, 54 with non-alcoholic liver diseases, and 260 healthy controls. We have found several microbiome alterations that were consistent across multiple datasets. The most consistent changes included a significantly lower abundance of multiple butyrate-producing families, including Ruminococcaceae, Lachnospiraceae, and Oscillospiraceae in AUD compared to HC and further reduction of these families in ALD compared with AUD. Other important results include an increase in endotoxin-producing Proteobacteria in AUD, with the ALD group having the largest increase. All of these alterations can potentially contribute to increased intestinal permeability and inflammation associated with AUD and ALD.

Affix polyfunctionality in French deverbal nominalizations

This article investigates the semantic polyfunctionality of affixes, i.e. their ability to serve a variety of distinct semantic functions. Based on the analysis of a sample of 3,091 deverbal nouns ending with 46 different suffixes in French, the study examines the diversity of semantic functions realized by deverbal suffixes, the distribution of these functions across suffixes and the relationships that may exist between different functions. It appears that polyfunctionality is widespread among French deverbal suffixes and involves a large number of semantic functions, with highly variable realization frequency. Several fundamental aspects of affix polyfunctionality are further highlighted. A probabilistic analysis shows that polyfunctionality can be driven by non-arbitrary semantic associations between functions. A hierarchy of functions can also be postulated depending on whether they can be instantiated by monosemous or only polysemous derivatives. In addition, polyfunctionality appears to be inseparable from rivalry relationships and to determine the degree of rivalry between affixes. Overall, the study illustrates that affix polyfunctionality is governed by systematic organizing principles whose ramifications touch on lexical ambiguity and morphological competition.

A longitudinal study to examine the influence of farming practices and environmental factors on pathogen prevalence using structural equation modeling

The contamination of fresh produce with foodborne pathogens has been an on-going concern with outbreaks linked to these commodities. Evaluation of farm practices, such as use of manure, irrigation water source, and other factors that could influence pathogen prevalence in the farming environment could lead to improved mitigation strategies to reduce the potential for contamination events. Soil, water, manure, and compost were sampled from farms in Ohio and Georgia to identify the prevalence of Salmonella, Listeria monocytogenes (Lm), Campylobacter, and Shiga-toxin-producing Escherichia coli (STEC), as well as Arcobacter, an emerging human pathogen. This study investigated agricultural practices to determine which influenced pathogen prevalence, i.e., the percent positive samples. These efforts identified a low prevalence of Salmonella, STEC, and Campylobacter in soil and water (< 10%), preventing statistical modeling of these pathogens. However, Lm and Arcobacter were found in soil (13 and 7%, respectively), manure (49 and 32%, respectively), and water samples (18 and 39%, respectively) at a comparatively higher prevalence, suggesting different dynamics are involved in their survival in the farm environment. Lm and Arcobacter prevalence data, soil chemical characteristics, as well as farm practices and weather, were analyzed using structural equation modeling to identify which factors play a role, directly or indirectly, on the prevalence of these pathogens. These analyses identified an association between pathogen prevalence and weather, as well as biological soil amendments of animal origin. Increasing air temperature increased Arcobacter and decreased Lm. Lm prevalence was found to be inversely correlated with the use of surface water for irrigation, despite a high Lm prevalence in surface water suggesting other factors may play a role. Furthermore, Lm prevalence increased when the microbiome's Simpson's Diversity Index decreased, which occurred as soil fertility increased, leading to an indirect positive effect for soil fertility on Lm prevalence. These results suggest that pathogen, environment, and farm management practices, in addition to produce commodities, all need to be considered when developing mitigation strategies. The prevalence of Arcobacter and Lm versus the other pathogens suggests that multiple mitigation strategies may need to be employed to control these pathogens.

Bat diversity is driven by elevation and distance to the nearest watercourse in a terra firme forest in the northeastern Brazilian Amazon

Variations in environmental conditions along gradients play an important role in species distribution through environmental filtering of morphological and physiological traits; however, their effects on bat diversity remain poorly understood. Here, we investigate the effect of the distance to the nearest watercourse, terrain elevation, vegetation clutter, basal area and canopy height on taxonomic, functional and phylogenetic diversity and on the predominance of some functional traits (body mass, wing morphology and trophic level) of bat assemblages (phyllostomid and mormoopid bats) in a terra firme forest, in the northeastern Brazilian Amazon. We captured bats using mist nets in 15 permanent plots over a 25 km2 area of continuous forest. We captured 279 individuals belonging to 28 species with a total of 77.760 m2.h of sampling effort. Our results showed that bat richness increases as a function of distance to the nearest watercourse and that the assemblage also changes, with more diverse taxonomic and functional groups in areas further from the watercourse. Furthermore, elevation positively affects species richness, and the basal area of the forest positively influences the average body mass of bats. Taken together, our results demonstrate that subtle variations in the environmental conditions along a local scale gradient impact on the main dimensions of bat diversity in primary forests.

Effect of nitrogen and glyphosate on the plant community composition in a simulated field margin ecosystem: Model-based ordination of pin-point cover data

The effect of nitrogen and glyphosate on the plant community composition was investigated in a simulated field margin ecosystem. The plant community composition was inferred from pin-point cover data using a model-based ordination method that is suited for modelling pin-point cover data. The mean structure of the ordination model is analogous to a standard linear model, which enabled us to estimate the mean effects of nitrogen and glyphosate and their interaction in the two-dimensional ordination space. There were significant effects of both nitrogen and glyphosate on the plant community composition and overall species diversity. The effects of nitrogen and glyphosate on the plant community composition differed significantly. Furthermore, the estimated combined effects of nitrogen and glyphosate indicated that nitrogen and glyphosate enforced the effect of each other on the plant community composition by synergistic interactions. Addition of nitrogen and glyphosate was found to favor a plant community that was dominated by perennial grasses, and there was a tendency for glyphosate to select for plant communities in which annual plants were more frequent. The results suggest that using the notion of plant functional types and specific knowledge of the degree of glyphosate tolerance may be effective for predicting the effect of glyphosate on the community composition.

CA, Garitano-Zavala Á, Campos J, Benedetti Y, Ortega-Álvarez R, Contreras Rodríguez AI, Souza López D, Suertegaray Fontana C, da Silva TW, Zalewski Vargas SS, Barbosa Toledo MC, Sarquis JA, Giraudo A, Echevarria AL, Fanjul ME, Martínez MV, Haedo J, Cano Sanz LG, Peña Y, Fernandez V, Marinero V, Abilhoa V, Amorin R, Escobar Ibáñez JF, Juri MD, Camín S, Marone L, Piratelli AJ, Franchin AG, Crispim L, Morelli F. Bird diversity-environment relationships in urban parks and cemeteries of the Neotropics during breeding and non-breeding seasons

Background

Urbanization will increase in the next decades, causing the loss of green areas and bird diversity within cities. There is a lack of studies at a continental scale analyzing the relationship between urban green areas, such as parks and cemeteries, and bird species richness in the Neotropical region. Bird diversity-environment relationships in urban parks and cemeteries may be influenced by latitudinal gradients or species-area relationships. However, the seasonal variation of species diversity- environment has not been analyzed at a continental scale in the Neotropics.

Methods

Bird surveys were conducted in 36 cemeteries and 37 parks within 18 Neotropical cities during non-breeding and breeding seasons. Bird diversity was assessed through Hill numbers, focusing on species richness, the effective number of species derived from Shannon index and the Simpson index. Environmental variables included latitude, altitude, and local scale variables such as area size, habitat diversity and pedestrian traffic.

Results

Species richness and Shannon diversity were higher during the breeding season, whereas Simpson diversity did not vary between seasons. During both seasons, species richness increased with area size, was negatively related to altitude, and was the highest at 20° latitude. Species richness was also positively related to habitat diversity, pedestrian traffic, and was highest in suburban areas during the non-breeding season. Shannon and Simpson diversity showed significant relationships with habitat diversity and area size during the breeding season. Bird diversity was similar between parks and cemeteries.

Discussion

Our results showed that urban parks and cemeteries have similar roles in conserving urban bird diversity in Neotropical cities. However, species diversity-environment relations at the continental scale varied between seasons, highlighting the importance of conducting annual studies.

The community ecology perspective of omics data

The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datasets. Analyses of these datasets have successfully been borrowed from community ecology to characterize the molecular diversity of samples (ɑ-diversity) and to assess how these profiles change in response to experimental treatments or across gradients (β-diversity). However, sample preparation and data collection methods generate biases and noise which confound molecular diversity estimates and require special attention. Here, we examine how technical biases and noise that are introduced into multivariate molecular data affect the estimation of the components of diversity (i.e., total number of different molecular species, or entities; total number of molecules; and the abundance distribution of molecular entities). We then explore under which conditions these biases affect the measurement of ɑ- and β-diversity and highlight how novel methods commonly used in community ecology can be adopted to improve the interpretation and integration of multivariate molecular data. Video Abstract.

Wetland characteristics affect abundance and diversity of wintering birds: A case study in South-Western Iran

Water availability is an important driver of bird population change, and its effects are likely to increase in coming decades under climate change. Here we assess effects of temperature, precipitation, and water area on wintering bird populations in Miyangaran Wetland in southwestern Iran. Modeling methods including, generalized linear model (GLM) and hierarchical partitioning were used to examine the relative importance of variables. The number of wintering species, inhabiting the wetland, varied among years, ranging from 10 to 48 species. The total number of wintering birds showed a significant decreasing trend. A significant increasing trend was obtained for shorebirds, while waterfowl species were significantly decreased. The GLM showed that species abundance, richness, and diversity were significantly correlated with the standardized precipitation index (SPI), annual precipitation, and normalized difference water index (NDWI). Hierarchical partitioning analysis also identified NDWI, SPI, and annual precipitation as the most important variables with average independent effects of 35, 36 (p < .01) and 17% (p < .05), respectively. Our results revealed that the water area plays a major role in determining the structure of bird diversity and abundance, affecting both waterfowl and shorebirds.

Agricultural policies against invasive species generate contrasting outcomes for climate change mitigation and biodiversity conservation

Direct consequences of biological invasions on biodiversity and the environment have been largely documented. Yet collateral indirect effects mediated by changes in agri-environmental policies aimed at combating invasions remain little explored. Here we assessed the effects of recent changes in water management in rice farming, which are aimed at buffering the impact of the invasive apple snail (Pomacea maculata, Lamarck) on greenhouse gas emissions and diversity of waterbird communities. We used observational data from a 2-year field monitoring (2015-2016) performed at the Ebro Delta regional scale. We found that drying rice fields reduced methane emission rates by 82% (2015) and 51% (2016), thereby reflecting the contribution of rice farming to climate change. However, there was a marked reduction (75% in 2015 and 57% in 2016) in waterbird diversity in dry fields compared with flooded fields, thus suggesting that post-invasion policies might hinder biodiversity conservation. Our results highlight the need for accounting for potential collateral effects during the policy decision-making process to design efficient agricultural management plans that lessen undesirable agri-environmental outcomes.

Can botanic gardens serve as refuges for taxonomic and functional diversity of Odonata? The case of the botanic garden of Castilla-La Mancha (Spain)

In a scenario with declining biodiversity and habitat loss, botanic gardens could serve as refuges for invertebrates, but the opportunities they offer for animal conservation are still poorly understood. Odonata is a good model group for conservation studies, because it includes threatened species and responses to habitat disturbance are well documented. In this study, we assessed the role of the botanic garden of Castilla-La Mancha in Spain as a refuge for members of Odonata by analysing their taxonomic and functional diversity. We explored if the small size of the botanic garden might constrain the taxonomic diversity of Odonata and if low habitat diversity might limit their functional diversity. We sampled adult Odonata from five water bodies along a gradient of human impact and characterized the Odonata communities based on 12 functional traits in Odonata. We used a species-area relationship to control for differences in the size of water bodies. Compared with natural lakes, the Odonata communities contained less species and their functional diversity was lower in the botanic garden ponds, where generalist species were basically hosted. Despite these limitations, the botanic garden ponds hosted the number of species expected for natural water bodies with the moderate surface area and functional diversity, thereby demonstrating that they are a valuable habitat for Odonata in an urban environment. Appropriate management involving the removal of exotic fish and habitat diversification, including creating lotic environments, would increase the taxonomic and functional diversity of Odonata in this urban system.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10201-022-00704-3.

Diet drives the gut microbiome composition and assembly processes in winter migratory birds in the Poyang Lake wetland, China

The complex gut bacterial communities may facilitate the function, distribution, and diversity of birds. For migratory birds, long-distance traveling poses selection pressures on their gut microbiota, ultimately affecting the birds’ health, fitness, ecology, and evolution. However, our understanding of mechanisms that underlie the assembly of the gut microbiome of migratory birds is limited. In this study, the gut microbiota of winter migratory birds in the Poyang Lake wetland was characterized using MiSeq sequencing of 16S rRNA genes. The sampled bird included herbivorous, carnivorous, and omnivorous birds from a total of 17 species of 8 families. Our results showed that the gut microbiota of migratory birds was dominated by four major bacterial phyla: Firmicutes (47.8%), Proteobacteria (18.2%), Fusobacteria (12.6%), and Bacteroidetes (9.1%). Dietary specialization outweighed the phylogeny of birds as an important factor governing the gut microbiome, mainly through regulating the deterministic processes of homogeneous selection and stochastic processes of homogeneous dispersal balance. Moreover, the omnivorous had more bacterial diversity than the herbivorous and carnivorous. Microbial networks for the gut microbiome of the herbivorous and carnivorous were less integrated, i.e., had lower average node degree and greater decreased network stability upon node attack removal than those of the omnivorous birds. Our findings advance the understanding of host-microbiota interactions and the evolution of migratory bird dietary flexibility and diversification.

Genetic and microenvironmental intra-tumor heterogeneity impacts colorectal cancer evolution and metastatic development

Colorectal cancer (CRC) is a highly diverse disease, where different genomic instability pathways shape genetic clonal diversity and tumor microenvironment. Although intra-tumor heterogeneity has been characterized in primary tumors, its origin and consequences in CRC outcome is not fully understood. Therefore, we assessed intra- and inter-tumor heterogeneity of a prospective cohort of 136 CRC samples. We demonstrate that CRC diversity is forged by asynchronous forms of molecular alterations, where mutational and chromosomal instability collectively boost CRC genetic and microenvironment intra-tumor heterogeneity. We were able to depict predictor signatures of cancer-related genes that can foresee heterogeneity levels across the different tumor consensus molecular subtypes (CMS) and primary tumor location. Finally, we show that high genetic and microenvironment heterogeneity are associated with lower metastatic potential, whereas late-emerging copy number variations favor metastasis development and polyclonal seeding. This study provides an exhaustive portrait of the interplay between genetic and microenvironment intra-tumor heterogeneity across CMS subtypes, depicting molecular events with predictive value of CRC progression and metastasis development.

How does variation in total and relative abundance contribute to gradients of species diversity?

Patterns of biodiversity provide insights into the processes that shape biological communities around the world. Variation in species diversity along biogeographical or ecological gradients, such as latitude or precipitation, can be attributed to variation in different components of biodiversity: changes in the total abundance (i.e., more-individual effects) and changes in the regional species abundance distribution (SAD). Rarefaction curves can provide a tool to partition these sources of variation on diversity, but first must be converted to a common unit of measurement. Here, we partition species diversity gradients into components of the SAD and abundance using the effective number of species (ENS) transformation of the individual-based rarefaction curve. Because the ENS curve is unconstrained by sample size, it can act as a standardized unit of measurement when comparing effect sizes among different components of biodiversity change. We illustrate the utility of the approach using two data sets spanning latitudinal diversity gradients in trees and marine reef fish and find contrasting results. Whereas the diversity gradient of fish was mostly associated with variation in abundance (86%), the tree diversity gradient was mostly associated with variation in the SAD (59%). These results suggest that local fish diversity may be limited by energy through the more-individuals effect, while species pool effects are the larger determinant of tree diversity. We suggest that the framework of the ENS-curve has the potential to quantify the underlying factors influencing most aspects of diversity change.