Local Diversity Research Articles

Winter agri-environment schemes and local landscape composition influence the distribution of wintering farmland birds

Since 1992, the European Union puts in place agri-environment schemes (AES), such as unharvested set-aside fields with winter bird crops (WBC), to counteract farmland biodiversity declines that are associated with agricultural intensification since the second half of the 20th century. These measures aim at, among other things, improving habitat quality and food availability for farmland birds throughout the year. In this study in Dry Hesbaye, an agricultural region in eastern Flanders (Belgium), we use spatial generalized linear mixed models to investigate how species richness and the observation probability of ten bird species with different food diets are associated during winter (November - March) with WBC implementation in arable crop fields and the presence of landscape elements within 50 m of these fields. Our results show that species richness and the observation probabilities of nine out of ten wintering farmland bird species under study are increased at crop fields with WBC implementation. Species richness and observation probabilities are also associated with the presence of nearby landscape elements such as hedgerows, woodland, unpaved roads, or grass margins. We conclude that unharvested set-aside fields promote local diversity and observation probabilities of most of the species under study. In addition, AES measures should be implemented after considering the aforementioned natural or semi-natural nearby landscape elements, which also influence local diversity and species’ observation probability.

Archaeogenetics: Local genetic diversity and ethnic fluidity in post-Roman Pannonia

During the fifth century, the Roman Empire underwent dramatic changes. New, ethnically identified polities emerged in the Mediterranean region. Historical research has highlighted the social complexities of this process. Archaeogenetics now shows the remarkably high genetic diversity of post-Roman local societies.

Gene mining and functional analysis related to maize (Zea mays L.) seed size

Maize has widely been studied as a model of plant-growth promoting rhizobacteria (PGPR). Here, the genome sequences of 9P. The strains, together with 26 other sequenced Maize were comparatively studied. Phylogenetic analysis of the concatenated 244 single-copy core genes suggests that the 9P. The strains and 5 other Paenibacillus spp., isolated from diverse geographic regions and ecological niches, formed a closely related clade (here it is called Poly-clade). Analysis of single nucleotide polymorphisms (SNPs) reveals local diversification of the 14 Poly-clade genomes. SNPs were not evenly distributed throughout the 14 genomes and the regions with high SNP density contain the genes related to secondary metabolism, including genes coding for polyketide. Recombination played an important role in the genetic diversity of this clade, although the rate of recombination was clearly lower than mutation. The distinction among people and different creatures can be gotten by relative examinations. This study reveals that both maize and its closely related species have plant growth promoting traits and they have great potential uses in agriculture and horticulture as PGPR.

Beetle mania: Understanding pond aquatic beetles diversity patterns through a multiple-facet approach

Ecological studies searching for drivers of biodiversity variation have frequently focused on taxonomic richness. However, more aspects of biodiversity, namely diversity facets can be considered to properly assess biotic-environment relationships. Here, we explore the environmental factors that could control the four biodiversity facets of aquatic Coleoptera from 93 regionally sampled Patagonian ponds. We also explore which are the ponds with high diversity values of all facets to prioritize them with a high conservation value. We fitted generalized additive models (GAM) to test relationships among environment (i.e., local and climatic variables) and aquatic beetles diversity facets (i.e., richness (SD), functional diversity (FD), phylogenetic diversity (PD), and local contribution to local beta diversity (LCBD). Climatic drivers were the most important predictors of beetle diversity facets, which exhibited linear and nonlinear responses. Thus, ponds from warmer Patagonia exhibited the highest values of SD and PD, whereas LCBD also peaked on colder sites suggesting that ponds under extreme temperatures sustain unique beetle assemblages. Moreover, ponds located in areas with higher precipitation variability exhibit the highest values of LCBD (i.e., unique assemblages). This result in addition to arid conditions in Patagonia prevailing since 16 m.y.a made us think that Patagonian beetle pond-dwellers are basally adapted to aridity. We calculated an index that summarizes the four facets patterns, to assign high conservation value to those ponds with higher index values. The relative importance of each facet varies from pond to pond. Hence, this multifaceteded approach not only allows us to identify priority areas for biodiversity conservation but also focuses on the importance of including multiple facets to understand biodiversity spatial patterns.

Perceived efficiency and local consensus as factors shaping medicinal plant knowledge

Environmental perception goes through physiological, psychological, and cultural filters and can influ- ence the selection and usage of species. Additionally, sharing cultural information is a crucial social strategy for our species’ survival. From this standpoint, knowledge that aligns with the local context is typically the most widely "expressed" and/or "replicated" by individuals. Building upon this premise, our objective was to investigate whether knowledge about local medicinal plants is influenced by certain adaptive factors, such as perceived efficacy, perceived availability, and perceived frequency of diseases. The study was conducted with 73 individuals from five rural communities in Vale do Catimbau Na- tional Park, Buíque, Pernambuco, Brazil. A free list of medicinal plants and their therapeutic uses was employed. Using these free lists, we employed a salience index to determine consensus within the local diversity. We employed a generalized linear model with a binomial distribution to ascertain whether perceived efficacy, perceived availability, and perceived disease frequency account for the local consen- sus. Of the three variables analyzed, only perceived efficiency explained the local consensus on the use of medicinal plants (p < 0.002). This result indicates that perceived efficiency is the key factor deter- mining the most popular medicinal plant when requested for memory recall, regardless of the perceived availability of the plant or the perceived frequency of diseases it treats. However, looking through the evolutionary perspective, the main question is to understand whether this factor is the only determi- nant in explaining the nature of the generation of medicinal plants’ salience, or if other ’cofactors’ of the social-ecological systems act together in an important way to guide this process as well.

Ecological and evolutionary consequences of temporal variation in dispersal

The importance of dispersal rates and distances has long been appreciated by ecologists and evolutionary biologists. An emerging field of research is revealing how temporal variation in dispersal can substantially influence ecological and evolutionary outcomes. We review how dispersal rates can temporally vary substantially in many ecosystems, a pattern that is particularly well‐documented for aquatic organisms but is likely pervasive in terrestrial ecosystems as well. We then synthesize the effects of temporal variation in dispersal on five key ecological and evolutionary processes: 1) metapopulation dynamics, 2) local adaptation, 3) range limits and range expansions, 4) species coexistence and 5) metacommunity dynamics. Our review demonstrates that temporal variation in dispersal is more than just statistical ‘noise' but can in fact lead to different outcomes than expected were dispersal temporally constant. For example, increasing the magnitude of temporal variation in dispersal can lead to lower metapopulation growth rates, permit greater local adaptation, facilitate and accelerate range expansion, increase regional coexistence, and alter local and regional species diversity. These effects of temporal variation in dispersal can inform conservation and natural resource management decisions such as prioritization in spatial planning, management of spillover from domesticated or captive populations into native populations, and the design of effective control strategies for invasive species.

Natural mega disturbances drive spatial and temporal changes in diversity and genetic structure on the toadfish Aphos porosus

Natural disturbances can modify extinction-colonization dynamics, driving changes in the genetic diversity and structure of marine populations. Along Chilean coast (36°S, 73°W), a strong hypoxic-upwelling event in 2008, and a mega earthquake-tsunami in 2010 caused mass mortality within the Aphos porosus population, which is a vulnerable species with low dispersal potential. We evaluated the effects of these two major disturbances on the diversity and spatial-temporal genetic structure of Aphos porosus in two neighboring areas that were impacted on different levels (High level: Coliumo Bay; Low level: Itata Shelf). Thirteen microsatellites (from 2008 to 2015) amplified in individuals collected from both locations were used to evaluate the effects of the two disturbances. Results showed that after the strong hypoxic-upwelling event and the mega earthquake-tsunami, Aphos porosus populations exhibited lower genetic diversity and less effective population sizes (Ne < 20), as well as asymmetries in migration and spatial-temporal genetic structure. These findings suggest a rise in extinction-recolonization dynamics in local Aphos porosus populations after the disturbances, which led to a loss of local genetic diversity (mainly in Coliumo Bay area impacted the most), and to greater spatial-temporal genetic structure caused by drift and gene flow. Our results suggest that continuous genetic monitoring is needed in order to assess potential risks for Aphos porosus in light of new natural and anthropogenic disturbances.

Conversion of steppe to cropland increases spatial heterogeneity of soil functional genes.

The microbiome function responses to land use change are important for the long-term prediction and management of soil ecological functions under human influence. However, it has remains uncertain how the biogeographic patterns of soil functional composition change when transitioning from natural steppe soils (NS) to agricultural soils (AS). We collected soil samples from adjacent pairs of AS and NS across 900 km of Mollisol areas in northeast China, and the soil functional composition was characterized using shotgun sequencing. AS had higher functional alpha-diversity indices with respect to KO trait richness and a higher Shannon index than NS. The distance-decay slopes of functional gene composition were steeper in AS than in NS along both spatial and environmental gradients. Land-use conversion from steppe to farmland diversified functional gene profiles both locally and spatially; it increased the abundances of functional genes related to labile carbon, but decreased those related to recalcitrant substrate mobilization (e.g., lignin), P cycling, and S cycling. The composition of gene functional traits was strongly driven by stochastic processes, while the degree of stochasticity was higher in NS than in AS, as revealed by the neutral community model and normalized stochasticity ratio analysis. Alpha-diversity of core functional genes was strongly related to multi-nutrient cycling in AS, suggesting a key relationship to soil fertility. The results of this study challenge the paradigm that the conversion of natural to agricultural habitat will homogenize soil properties and biology while reducing local and regional gene functional diversity.

Genetic diversity patterns of lionfish in the Southwestern Atlantic Ocean reveal a rapidly expanding stepping-stone bioinvasion process

In 2020, multiple lionfish (Pterois spp.) records along the equatorial Southwestern (SW) Atlantic revealed a new expansion of these potentially damaging invasive populations, which could impact over 3500 km of Brazilian coastline over the next few years, as well as unique ecosystems and marine protected areas in its path. To assess the taxonomic status, invasion route, and correlation with other centres of distribution, we investigated the genetic diversity patterns of lionfish caught in 2022 at the Amazonia, Northeastern Brazil, and Fernando de Noronha and Rocas Atoll ecoregions, using two molecular markers, the mitochondrial COI and the nuclear S7 RP1. The data indicate that all studied lionfish belong to what is generally accepted as P. volitans, and share the same genetic signature as lionfish present in the Caribbean Sea. The shared haplotypes and alleles indicate that the SW Atlantic invasion derives from an active movement of adult individuals from the Caribbean Sea into the Brazilian coast. The Amazon mesophotic reefs likely served as a stepping-stone to overcome the biogeographical barrier represented by the Amazon-Orinoco River plume. New alleles found for S7 RP1 suggest the onset of local genetic diversification, heightening the environmental risks as this bioinvasion heads towards other South Atlantic ecoregions.

Local Evidence and Diversity in Minipublics

Local Evidence and Diversity in Minipublics

Land surface diversity: A geomorphodiversity index of Italy

AbstractGeomorphodiversity refers to the variety of landforms and morphological processes characterizing the landscape. The definition of an index to quantify geomorphodiversity is a relevant step for multiple fields of Earth sciences, since it is widely accepted that the variability of the geosphere deeply influences the diversity of the biosphere. Such an index should describe the number and type of landforms and geomorphological processes. We propose a quantitative land surface diversity index valid for Italy, considering multiple input quantities to describe geological constraints and geomorphological processes. Critical issues were the selection of moving window size for focal statistics operations, to calculate local diversity of slope, lithology, drainage density and terrain forms in individual raster maps. We compared the index with traditional geomorphological maps, in selected locations, in which information was available. Results show that a minimal set of heterogeneous data is a satisfactory approach to investigate the landscape diversity. Relating processing parameters and terrain spatial characteristics to the dataset resolution is a good choice to assess a reproducible land surface diversity index. Inclusion of drainage density allows the improvement of results in flat areas, in which other factors show trivial results. We argue that the index is relevant for land use management, assessment of ecodiversity, and it may help describing the interaction between abiotic and biotic compartments.

Ecological health analysis of wetlands in the middle reaches of Yangtze River under changing environment

ABSTRACT Changes in wetland ecosystems have a critical impact on the local ecology and species diversity. Different development scenarios and policies are key factors influencing their changes. Therefore, we studied changes of wetlands in the middle Yangtze River basin (MYRB) in 2001–2020, and a patch-generated land use simulation (PLUS) model and random forest (RF) method were applied to predict and analyze the changes under different scenarios in the MYRB in the future (i.e.2035–2095). The results indicated that: (1) The regions with high wetland proportions were concentrated in the central and eastern MYRB in 2001–2020, with a 1.5% decrease in overall wetland area; (2) The RF could simulate the future ecological quality with training and testing accuracies of 0.98 and 0.92, respectively; (3) Remote Sensing Ecological Index (RSEI) less than 0.5 in the central and eastern regions and 13.3% reduction in the northwest in the SSP245 scenario. In general, the study provides a basis for future regional studies of ecosystem quality and provides data to support wetland conservation and management.

Association of vaccination, international travel, public health and social measures with lineage dynamics of SARS-CoV-2

Continually emerging SARS-CoV-2 variants of concern that can evade immune defenses are driving recurrent epidemic waves of COVID-19 globally. However, the impact of measures to contain the virus and their effect on lineage diversity dynamics are poorly understood. Here, we jointly analyzed international travel, public health and social measures (PHSM), COVID-19 vaccine rollout, SARS-CoV-2 lineage diversity, and the case growth rate (GR) from March 2020 to September 2022 across 63 countries. We showed that despite worldwide vaccine rollout, PHSM are effective in mitigating epidemic waves and lineage diversity. An increase of 10,000 monthly travelers in a single country-to-country route between endemic countries corresponds to a 5.5% (95% CI: 2.9 to 8.2%) rise in local lineage diversity. After accounting for PHSM, natural immunity from previous infections, and waning immunity, we discovered a negative association between the GR of cases and adjusted vaccine coverage (AVC). We also observed a complex relationship between lineage diversity and vaccine rollout. Specifically, we found a significant negative association between lineage diversity and AVC at both low and high levels but not significant at the medium level. Our study deepens the understanding of population immunity and lineage dynamics for future pandemic preparedness and responsiveness.

The Evolutionary Ecology of Plant Chemical Defenses: From Molecules to Communities

Classic theory relates herbivore pressure to the ecology and evolution of plant defenses. Here, we summarize current trends in the study of plant–herbivore interactions and how they shape the evolution of plant chemical defenses, host choice, and community composition and diversity. Inter- and intraspecific variation in defense investment is driven by resource availability. The evolution of defenses at deeper nodes of plant phylogeny is conserved, yet defenses are highly labile at the tips. On an ecological timescale, while greater specialization of tropical herbivores enhances local diversity by reducing the performance of plants with similar defenses, in temperate ecosystems with more generalist herbivores, rare defense profiles are at a disadvantage. On an evolutionary timescale, host choice by herbivores is largely determined by plant defenses rather than host phylogeny, leading to evolutionary tracking by herbivores rather than cocladogenesis. The interplay between plants and herbivores shapes both the origin and maintenance of diversity.

Data-driven large-scale genomic analysis reveals an intricate phylogenetic and functional landscape in J-domain proteins

The 70-kD heat shock protein (Hsp70) chaperone system is a central hub of the proteostasis network that helps maintain protein homeostasis in all organisms. The recruitment of Hsp70 to perform different and specific cellular functions is regulated by the J-domain protein (JDP) co-chaperone family carrying the small namesake J-domain, required to interact and drive the ATPase cycle of Hsp70s. Besides the J-domain, prokaryotic and eukaryotic JDPs display a staggering diversity in domain architecture, function, and cellular localization. Very little is known about the overall JDP family, despite their essential role in cellular proteostasis, development, and its link to a broad range of human diseases. In this work, we leverage the exponentially increasing number of JDP gene sequences identified across all kingdoms owing to the advancements in sequencing technology and provide a broad overview of the JDP repertoire. Using an automated classification scheme based on artificial neural networks (ANNs), we demonstrate that the sequences of J-domains carry sufficient discriminatory information to reliably recover the phylogeny, localization, and domain composition of the corresponding full-length JDP. By harnessing the interpretability of the ANNs, we find that many of the discriminatory sequence positions match residues that form the interaction interface between the J-domain and Hsp70. This reveals that key residues within the J-domains have coevolved with their obligatory Hsp70 partners to build chaperone circuits for specific functions in cells.

Non-native ants drive dramatic declines in animal community diversity: A meta-analysis.

Non-native ants can cause ecosystem-wide ecological change, and these changes are generally assumed to be negative. Despite this, the evidence base has never been holistically synthesised to quantify whether and to what degree non-native ants impact native species diversity.In this study, we performed a meta-analysis of the effects of ant invasion on animal communities. We extracted data from 46 published articles investigating abundance (156 effect sizes) and richness (53 effect sizes) responses of animal taxa to ant invasion in locations relatively unimpacted by other stressors (e.g. human disturbance, other non-native species) to help isolate the effects of invasion.Overall, local animal diversity declined severely, with species abundance and richness lower by 42.79% and 53.56%, respectively, in areas with non-native ants compared with intact uninvaded sites. We then combined responses of individual animal taxa extracted from an article into a singleresponse to represent the 'community' abundance (40 effect sizes) or richness (28 effect sizes) response to non-native ants represented in each article. Local communities decreased substantially in total abundance (52.67%) and species richness (53.47%) in invaded sites.These results highlight non-native ants as the drivers, rather than passengers, of large net-negative reductions to animal community diversity in relatively undisturbed systems around the world, approximately halving local species abundance and richness in invaded areas. Improved international prevention processes, early detection systems harnessing emerging technologies, and well-designed control measures deployable by conservation practitioners are urgently needed if these effects are to be mitigated, prevented or reversed.

Geographic patterns of taxonomic and phylogenetic β-diversity of angiosperm genera in regional floras across the world

Beta diversity (β-diversity) is the scalar between local (α) and regional (γ) diversity. Understanding geographic patterns of β-diversity is central to ecology, biogeography, and conservation biology. A full understanding of the origin and maintenance of geographic patterns of β-diversity requires exploring both taxonomic and phylogenetic β-diversity, as well as their respective turnover and nestedness components, and exploring phylogenetic β-diversity at different evolutionary depths. In this study, we explore and map geographic patterns of β-diversity for angiosperm genera in regional floras across the world. We examine both taxonomic and phylogenetic β-diversity and their constituent components, and both tip-weighted and basal-weighted phylogenetic β-diversity, and relate them to latitude. On the one hand, our study found that the global distribution of β-diversity is highly heterogeneous. This is the case for both taxonomic and phylogenetic β-diversity, and for both tip-weighted and basal-weighted phylogenetic β-diversity. On the other hand, our study found that there are highly consistent geographic patterns among different metrics of β-diversity. In most cases, metrics of β-diversity are negatively associated with latitude, particularly in the Northern Hemisphere. Different metrics of taxonomic β-diversity are strongly and positively correlated with their counterparts of phylogenetic β-diversity.

Restoration of a fish-attracting flow field downstream of a dam based on the swimming ability of endemic fishes: A case study in the upper Yangtze River basin

The construction of fish passage facilities can mitigate the negative effects of dams and other water engineering construction on river connectivity and have a significant positive effect on the conservation of local fish diversity. To attract target fishes into fish passage facilities effectively, the optimal flow velocity range to attract fish must be determined. Three local endemic species of the Mishi Reservoir were considered as the protection targets. However, their swimming abilities remain unclear. Therefore, the induced swimming speed (Uind), critical swimming speed (Ucrit) and burst swimming speed (Uburst) of three fish species were tested. Based on these results, we identified the optimal flow velocity to attract fish, which falls within the range of 0.15–0.51 m/s. A validated three-dimensional hydrodynamic model was used to simulate different schemes. By comparing the flow field simulation results of different schemes, we obtained the optimal measure to restore the flow field, namely, a multiple engineering measure combining increased the fish attraction flow in the fish collection pond and the construction of a spur dike. This study offers a solution for the specific case and enhances the database of swimming characteristics of endemic fish in the upstream reaches of the Yangtze River. It also provides a valuable reference for designing fish-attracting flows and potential measures for restoring flow fields in similar future projects.

Fusarium phytopathogens as insect mutualists.

As vectors of numerous plant pathogens, herbivorous insects play a key role in the epidemiology of plant disease. But how phytopathogens impact the metabolism, physiology, and fitness of their insect vectors is often unexplored within these tripartite interactions. Here, we examine the diverse symbioses forged between insects and members of the ascomycete fungal genus Fusarium. While Fusarium features numerous plant pathogens that are causal to diseases such as wilts and rots, many of these microbes also engage in stable mutualisms across several insect clades. Matching a diversity in symbiont localization and transmission routes, we highlight the various roles fusaria fulfill towards their insect hosts, from upgrading their nutritional physiology to providing defense against natural enemies. But as the insect partner is consistently herbivorous, we emphasize the convergent benefit Fusarium derives in exchange: propagation to a novel host plant. Collectively, we point to the synergy arising between a phytopathogen and its insect vector, and the consequences inflicted on their shared plant.

Uncovering the hidden: Leveraging sub-pixel spectral diversity to estimate plant diversity from space

Remotely sensed spectral diversity has emerged as a promising proxy for plant diversity. However, spectral diversity approaches relate image spectra to plant community diversity by only incorporating variation among adjacent pixels, considering each pixel as a homogeneous entity composed of one class, and disregarding the within-pixel variability. Although such approaches might work for remotely-sensed data with fine spatial resolution, they might not be viable solutions to estimate plant diversity using coarse-resolution data from forthcoming spaceborne imagers. To address the limitations associated with spectral diversity approaches, we proposed a novel approach, known as endmember diversity, for remote estimation of plant diversity through quantifying spectral diversity at the sub-pixel level and taking into account the within-pixel variability. The approach consisted of deriving the number and abundance of distinct spectral entities within each pixel via spectral unmixing. In doing so, we considered the spectral signature of each pixel as a mixture of distinct spectral entities, commonly known as endmembers. We then used the per-pixel endmembers and their abundance to calculate different spectral diversity metrics for every pixel. We assessed the performance of the endmember diversity approach at estimating plant taxonomic and phylogenetic diversity based on two experiments using a simulated spectral dataset and a real-world spaceborne DESIS (DLR Earth Sensing Imaging Spectrometer) dataset. In both experiments, we found significant associations between endmember diversity and in situ plant diversity. Additionally, our method applied to DESIS data outperformed a conventional spectral diversity metric based on the coefficient of variation when applied to 1-m airborne imaging spectroscopy data. Collectively, our results demonstrate the capability of forthcoming spaceborne imagers to monitor local plant diversity.