Rarity is a more reliable indicator of land-use impacts on soil invertebrate communities than other diversity metrics

Micro-CT data of complete metamorphosis process in Harmonia axyridis

Insect metamorphosis involves significant changes in insect internal structure and is thus a critical focus of entomological research. Investigating the morphological transformation of internal structures is vital to understanding the origins of adult insect organs. Beetles are among the most species-rich groups in insects, but the development and transformation of their internal organs have yet to be systematically documented. In this study, we have acquired a comprehensive dataset that includes 27 detailed whole-body tomographic image sets of Harmonia axyridis, spanning from the prepupal to the pupal stages. Utilizing this data, we have created intricate 3D models of key internal organs, encompassing the brain, ventral nerve cord, digestive and excretion systems, as well as the body wall muscles. These data documented the transformation process of these critical organs and correlations between the origin of adult and larval organs and can be used to enhance the understanding of holometabolous adult organ genesis and offers a valuable reference model for investigating complete metamorphosis in insects.

Tree mortality and recruitment in secondary Andean tropical mountain forests along a 3000 m elevation gradient

This study addresses the understudied dynamics of mortality and recruitment in Tropical Mountain forests, critical determinants of forest structural processes and biomass turnover. We examine how these demographic processes change with elevation and varying degrees of forest recovery by utilizing two forest censuses (2015 and 2019) from 16 plots (0.36 ha) across a 600-3500 m asl elevation gradient in the Ecuadorian Andes. Employing multivariate PCA analyses, we characterize successional forest dynamics and explore relationships between demographic rates, elevation, and indicators of forest recovery using standard linear regression and generalized additive models (GAMs). Contrary to our hypothesis, mortality exhibits a unimodal response, peaking at mid-elevations, with no significant relationship to above-ground biomass productivity (AGBp). In our successional forests, dominance by fast-growing species alters expected patterns, leading to increased mortality rates and AGBp, particularly at low-mid elevations. Forest recovery emerges as a significant driver of mortality and the sole predictor of recruitment, especially across different recovery statuses. Although forest recovery doesn't impact mortality rates, it elucidates the identity of declining species in forests with varying recovery degrees. Our findings underscore that while forest recovery does not alter mortality rates, it provides critical insights into understanding which species are affected under varying recovery conditions. Recruitment, primarily driven by successional dynamics, exhibits higher rates in sites with less recovery. Furthermore, we demonstrate the utility of forest structure indicators, such as above-ground biomass, in inferring successional dynamics when the time since the last disturbance is unknown. The study emphasizes the importance of considering disturbances in comprehending the intricate interplay between the environment and forest dynamics in secondary forests.

Biotic homogenisation and differentiation as directional change in beta diversity: synthesising driver-response relationships to develop conceptual models across ecosystems

Biotic homogenisation is defined as decreasing dissimilarity among ecological assemblages sampled within a given spatial area over time. Biotic differentiation, in turn, is defined as increasing dissimilarity over time. Overall, changes in the spatial dissimilarities among assemblages (termed 'beta diversity') is an increasingly recognised feature of broader biodiversity change in the Anthropocene. Empirical evidence of biotic homogenisation and biotic differentiation remains scattered across different ecosystems. Most meta-analyses quantify the prevalence and direction of change in beta diversity, rather than attempting to identify underlying ecological drivers of such changes. By conceptualising the mechanisms that contribute to decreasing or increasing dissimilarity in the composition of ecological assemblages across space, environmental managers and conservation practitioners can make informed decisions about what interventions may be required to sustain biodiversity and can predict potential biodiversity outcomes of future disturbances. We systematically reviewed and synthesised published empirical evidence for ecological drivers of biotic homogenisation and differentiation across terrestrial, marine, and freshwater realms to derive conceptual models that explain changes in spatial beta diversity. We pursued five key themes in our review: (i) temporal environmental change; (ii) disturbance regime; (iii) connectivity alteration and species redistribution; (iv) habitat change; and (v) biotic and trophic interactions. Our first conceptual model highlights how biotic homogenisation and differentiation can occur as a function of changes in local (alpha) diversity or regional (gamma) diversity, independently of species invasions and losses due to changes in species occurrence among assemblages. Second, the direction and magnitude of change in beta diversity depends on the interaction between spatial variation (patchiness) and temporal variation (synchronicity) of disturbance events. Third, in the context of connectivity and species redistribution, divergent beta diversity outcomes occur as different species have different dispersal characteristics, and the magnitude of beta diversity change associated with species invasions also depends strongly on alpha and gamma diversity prior to species invasion. Fourth, beta diversity is positively linked with spatial environmental variability, such that biotic homogenisation and differentiation occur when environmental heterogeneity decreases or increases, respectively. Fifth, species interactions can influence beta diversity via habitat modification, disease, consumption (trophic dynamics), competition, and by altering ecosystem productivity. Our synthesis highlights the multitude of mechanisms that cause assemblages to be more or less spatially similar in composition (taxonomically, functionally, phylogenetically) through time. We consider that future studies should aim to enhance our collective understanding of ecological systems by clarifying the underlying mechanisms driving homogenisation or differentiation, rather than focusing only on reporting the prevalence and direction of change in beta diversity, per se.

Monitoring insect biodiversity and comparison of sampling strategies using metabarcoding: A case study in the Yanshan Mountains, China

Insects are the richest and most diverse group of animals and yet there remains a lack, not only of systematic research into their distribution across some key regions of the planet, but of standardized sampling strategies for their study. The Yanshan Mountains, being the boundary range between the Inner Mongolian Plateau and the North China Plain, present an indispensable piece of the insect biodiversity puzzle: both requiring systematic study and offering opportunities for the development of standardized methodologies. This is the first use of DNA metabarcoding to survey the insect biodiversity of the Yanshan Mountains. The study focuses on differences of community composition among samples collected via different methods and from different habitat types. In total, 74 bulk samples were collected from five habitat types (scrubland, woodland, wetland, farmland and grassland) using three collection methods (sweep netting, Malaise traps and light traps). After DNA extraction, PCR amplification, sequencing and diversity analysis were performed, a total of 7427 Operational Taxonomic Units (OTUs) at ≥97% sequence similarity level were delimited, of which 7083 OTUs were identified as belonging to Insecta. Orthoptera, Diptera, Coleoptera and Hemiptera were found to be the dominant orders according to community composition analysis. Nonmetric multidimensional scaling (NMDS) analysis based on Bray-Curtis distances revealed highly divergent estimates of insect community composition among samples differentiated by the collection method (R = .524802, p = .001), but nonsignificant difference among samples differentiated according to habitat (R = .051102, p = .078). The study therefore appears to indicate that the concurrent use of varied collection methods is essential to the accurate monitoring of insect biodiversity.

Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects

Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world's food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security.

Habitat loss predicts the functional extinction of fish from Amazonian streams during the Anthropocene

The evaluation of extinction risk has typically focused on individual species, although a shift to a focus on ecosystem functioning would appear to be an urgent priority for conservation planning, especially considering that a sixth mass extinction event has already begun. In the present study, we investigated how fish extinction driven by habitat loss may modify the functioning of freshwater Amazonian ecosystems. We sampled the fish and environmental conditions of 63 streams in the eastern Amazon and simulated extinction based on the vulnerability of the species to habitat loss, which is the principal threat to tropical biodiversity. The simulated extinction of vulnerable species led to a decrease in both the mean body size of the community and functional rarity and culminated in abrupt losses of ecosystem functions after 5% and 10% of extinction at local and regional scales. Our functional approach demonstrated the progressive loss of ecological functions in Amazon streams, which may collapse altogether following the extinction of functions related to protection against biological invasions, and associated alterations in nutrient cycling and water quality. We provide robust predictions on the modification of the ecosystem following the extinction of fish species, which is a major step toward the development of effective conservation measures that ensure the avoidance of the predicted processes, and help to prevent the loss of biodiversity and the potentially irreversible modifications to ecosystem functioning.

Multiple species delimitation approaches with COI barcodes poorly fit each other and morphospecies – An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae)

DNA taxonomy including barcoding and metabarcoding is widely used to explore the diversity in biodiversity hotspots. In most of these hotspot areas, chafers are represented by a multitude of species, which are well defined by the complex shape of male genitalia. Here, we explore how well COI barcode data reflect morphological species entities and thus their usability for accelerated species inventorization. We conducted dedicated field surveys in Sri Lanka to collect the species‐rich and highly endemic Sericini chafers (Coleoptera: Scarabaeidae). Congruence among results of a series of protocols for de novo species delimitation and with morphology‐based species identifications was investigated. Different delimitation methods, such as the Poisson tree processes (PTP) model, Statistical Parsimony Analysis (TCS), Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning (ASAP), and Barcode Index Number (BIN) assignments, resulted in different numbers of molecular operational taxonomic units (MOTUs). All methods showed both over‐splitting and lumping of morphologically identified species. Only 18 of the observed 45 morphospecies perfectly matched MOTUs from all methods. The congruence of delimitation between MOTUs and morphospecies expressed by the match ratio was low, ranging from 0.57 to 0.67. TCS and multirate PTP (mPTP) showed the highest match ratio, while (BIN) assignment resulted in the lowest match ratio and most splitting events. mPTP lumped more species than any other method. Principal coordinate analysis (PCoA) on a match ratio‐based distance matrix revealed incongruent outcomes of multiple DNA delimitation methods, although applied to the same data. Our results confirm that COI barcode data alone are unlikely to correctly delimit all species, in particular, when using only a single delimitation approach. We encourage the integration of various approaches and data, particularly morphology, to validate species boundaries.

Analysis of complex trophic networks reveals the signature of land-use intensification on soil communities in agroecosystems

Increasing evidence suggests that agricultural intensification is a threat to many groups of soil biota, but how the impacts of land-use intensity on soil organisms translate into changes in comprehensive soil interaction networks remains unclear. Here for the first time, we use environmental DNA to examine total soil multi-trophic diversity and food web structure for temperate agroecosystems along a gradient of land-use intensity. We tested for response patterns in key properties of the soil food webs in sixteen fields ranging from arable crops to grazed permanent grasslands as part of a long-term management experiment. We found that agricultural intensification drives reductions in trophic group diversity, although taxa richness remained unchanged. Intensification generally reduced the complexity and connectance of soil interaction networks and induced consistent changes in energy pathways, but the magnitude of management-induced changes depended on the variable considered. Average path length (an indicator of food web redundancy and resilience) did not respond to our management intensity gradient. Moreover, turnover of network structure showed little response to increasing management intensity. Our data demonstrates the importance of considering different facets of trophic networks for a clearer understanding of agriculture-biodiversity relationships, with implications for nature-based solutions and sustainable agriculture.

Land use, but not distance, drives fungal beta diversity

Fungi are one of the most diverse taxonomic groups on the planet, but much of their diversity and community organization remains unknown, especially at local scales. Indeed, a consensus on how fungal communities change across spatial or temporal gradients-beta diversity-remains nascent. Here, we use a data set of plant-associated fungal communities (leaf, root, and soil) across multiple land uses from a New Zealand-wide study to look at fungal community turnover at small spatial scales (<1 km). Using hierarchical Bayesian beta regressions and Hill-number-based diversity profiles, we show that fungal communities are often markedly dissimilar at even small distances, regardless of land use. Moreover, diversity profile plots indicate that leaf, root, and soil-associated communities show different patterns in the dominance or rarity of dissimilar species. Leaf-associated communities differed from site to site in their low-abundance species, whereas root-associated communities differed between sites in the dominant species; soil-associated communities were intermediate. Land-use differences were largely driven by the lower turnover between high-productivity grassland sites. Further, we discuss the implications and benefits of using diversity profile plots of turnover to draw inferences into the mechanisms of how communities are structured across spatial gradients.

Changes in diversity and community assembly of jumping spiders (Araneae: Salticidae) after rainforest conversion to rubber and oil palm plantations

Rainforest conversion into monoculture plantations results in species loss and community shifts across animal taxa. The effect of such conversion on the role of ecophysiological properties influencing communities, and conversion effects on phylogenetic diversity and community assembly mechanisms, however, are rarely studied in the same context. Here, we compare salticid spider (Araneae: Salticidae) communities between canopies of lowland rainforest, rubber agroforest (“jungle rubber”) and monoculture plantations of rubber or oil palm, sampled in a replicated plot design in Jambi Province, Sumatra, Indonesia. Overall, we collected 912 salticid spider individuals and sorted them to 70 morphospecies from 21 genera. Salticid richness was highest in jungle rubber, followed by rainforest, oil palm and rubber, but abundance of salticids did not differ between land-use systems. Community composition was similar in jungle rubber and rainforest but different from oil palm and rubber, which in turn were different from each other. The four investigated land-use systems differed in aboveground plant biomass, canopy openness and land use intensity, which explained 12% of the observed variation in canopy salticid communities. Phylogenetic diversity based on ~850 bp 28S rDNA fragments showed similar patterns as richness, that is, highest in jungle rubber, intermediate in rainforest, and lowest in the two monoculture plantations. Additionally, we found evidence for phylogenetic clustering of salticids in oil palm, suggesting that habitat filtering is an important factor shaping salticid spider communities in monoculture plantations. Overall, our study offers a comprehensive insight into the mechanisms shaping communities of arthropod top predators in canopies of tropical forest ecosystems and plantations, combining community ecology, environmental variables and phylogenetics across a land-use gradient in tropical Asia.

Relationship of taxonomic error to frequency of observation

Biological nomenclature is the entry point to a wealth of information related to or associated with living entities. When applied accurately and consistently, communication between and among researchers and investigators is enhanced, leading to advancements in understanding and progress in research programs. Based on freshwater benthic macroinvertebrate taxonomic identifications, inter-laboratory comparisons of >900 samples taken from rivers, streams, and lakes across the U.S., including the Great Lakes, provided data on taxon-specific error rates. Using the error rates in combination with frequency of observation (FREQ; as a surrogate for rarity), six uncertainty/frequency classes (UFC) are proposed for approximately 1,000 taxa. The UFC, error rates, FREQ each are potentially useful for additional analyses related to interpreting biological assessment results and/or stressor response relationships, as weighting factors for various aspects of ecological condition or biodiversity analyses and helping set direction for taxonomic research and refining identification tools.