Quantifying sample completeness and comparing diversities among assemblages

Variations in the Odonata Assemblages: How Do the Dry Season and Water Bodies Influence Them?

Diverse abiotic and biotic factors drive the ecological variation of communities across spatial and temporal dimensions. Within the Amazonian landscape, various freshwater environments exhibit distinct physicochemical characteristics. Thus, our study delved into the fluctuations of Odonata assemblages amidst distinct water bodies within Amazonia, encompassing two distinct climatic seasons. Comparative analysis was conducted on Odonata species diversity and assemblage composition across a blackwater pond, a lake, and a stream, spanning the initiation and culmination of the dry season in the southwestern Amazon region in Peru. Our methodology involved capturing adult Odonata using entomological nets on three separate occasions between 11:00 and 14:00 h for each water body in May (beginning of the dry season) and October (end of the dry season) of 2018. We also evaluated the influence of temperature, precipitation, and percent cloud cover on the abundance and richness of adult Odonata. Species richness and composition differed among the three water bodies in both periods of the dry season. No effect of the dry season periods on species richness and abundance was observed. However, except in the oxbow lake, the more abundant species were substituted to the end of the dry season. Our study highlights the influence of water body types on Odonata species diversity and composition. The effects of the sampling period during the dry season may not be immediately apparent in conventional diversity metrics, such as species richness and abundance. Instead, its effects manifest predominantly in the relative abundance of the species that compose these assemblages.

Changes in floristic and vegetation structure in a chronosequence of abandoned gold-mining lands in a tropical Amazon forest

This study analyzes floristic and vegetation structure changes during forest succession after disturbances caused by small-scale gold mining in Madre de Dios (Peru). We compared the floristic and vegetation structure of a reference forest against three sites with different periods of abandonment after mining (5, 11 and 23-years). Three 20 × 60 m plots were defined on each site, and all tree species with a DBH >1 cm within the plots were inventoried. To evaluate species diversity and similarity, the Importance Value, effective numbers of species (0D, 1D, and 2D), and Chao-Jaccard similarity index were calculated. We used the Nonmetric multidimensional scaling for similarity ordination and the PERMANOVA test to evaluate differences in floristic composition. We recorded 129 tree species in the study areas and statistically significant differences between initial and intermediate stages were observed regarding floristic composition, basal area, height, and DBH. The transition from the initial successional stage to the reference forest produces an increase in basal area, species diversity, and floristic similarity. The 23-year-old stand had more species in common with the 11-year-old stand than the reference forest. Our results showed a high proportion of pioneer species and anemochory dispersal syndrome in the initial successional stages, but they decreased in later stages of the chronosequence. The floristic and structural attributes of forests throughout the chronosequence showed a fast recovery during secondary succession. After 23 years, the recovery of tree species density was 77 % of reference forest, while the relative recovery of species composition was much slower, on average 23 %. These results provide essential information to guide the selection of suitable species in ecological restoration projects after abandonment. Implementing forest restoration strategies based on reliable information to accelerate the process of vegetation succession is critical for recuperating areas degraded by gold mining at the Peruvian Amazon.

Upper mesophotic reef fish assemblages at Bahía de Banderas, Mexico

There is no information on the species associated with the mesophotic reefs of Banderas Bay, located in the central Mexican Pacific. This study analysed the reef fish assemblage from three depths (50, 60 and 70 m) in three sampling sites of the southern submarine canyon of the Bay: Los Arcos, Bajo de Emirio and Majahuitas. Several analyses were performed to test the hypothesis that there are important differences in fish abundance and species composition between sites and depths. Twenty-two species of bony fishes grouped in 14 families were recorded. PERMANOVA results showed that there were no significant differences in fish diversity parameters between sites, indicating a certain uniformity in their distribution. However, nine species were exclusive to one site and depth (five singleton species with only one individual recorded and four unique species recorded only once). On the other hand, there were significant differences between depths, mainly between 50 and 70 m. Diversity decreases with depth and species composition changes. SIMPER, Shade Plot and NMDS analysis show the most representative species at each depth, with at least half of the species (11) recorded only at 50 m and four species at the deeper levels (60 - 70 m). The observed assemblage includes several of the most caught species in the shallow water artisanal fishery, which is the most traditional and common type of fishery in the Bay. In addition, the Pomacanthuszonipectus (Cortés angelfish) is of particular interest, as it has a special protection status in the official Mexican standard (NOM-059-SEMARNAT, 2010) due to its use as an ornamental species in aquaria. We hypothesised that the mesophotic zone may serve as a refuge for these fishes, so we propose that the information obtained is an important basis for new research aimed at the sustainable management of fisheries in the area.

The role of habitat heterogeneity and timescales on the recovery of reef epifaunal communities affected by a massive oil spill in the tropics

From August 2019 to January 2020 the Brazilian Coast was impacted by the largest oil spill in the Tropical oceans ever since. Paiva Beach, one of the most preserved sandy beaches in the northeast tropical Brazilian coast, was among the most affected regions by the oil spill in October 2019. This area has important reef systems that harbor abundant macroalgal assemblages with very diverse epifaunal communities. The present study aims to evaluate the impacts of the 2019 oil spill on epifauna associated with the seaweed species Jania capillacea and Penicillus capitatus collected in Paiva Beach from July 2019 to October 2022, and use the interaction macroalgae/epifauna/timescale as a proxy to quantify the effects of oil spills on communities structure and recovery. The epifauna of both algae did not suffer severe changes in abundance immediately after the spill, however, the abundance of taxa like echinoderms, sea spiders (Pycnogonida) and peracarid crustaceans dropped during or soon after the event, whereas others, like sabellid worms, had strong increase in abundance, possibly related to the spill. Both phytal assemblages also had distinct temporal patterns in species diversity and abundance, the last being strongly correlated to amphipod abundance for some taxa. The epifauna of J. capillacea had a short-term tendency of decrease in taxonomic diversity, whereas the epifaunal communities of P. capitatus gained a few taxa in the months immediately after the disaster. The diversity profiles of both communities returned to pre-spill conditions a few months later, with a slower abundance recovery in J. capillacea. Local environmental characteristics like landscape heterogeneity, connectivity with other environments, and critical-species (mainly amphipods) were possibly the main buffering factors for the phytal communities after the oil spill.

Mapping wild vascular plant species diversity in urban areas in California using crowdsourcing data by regression kriging: Examining socioeconomic disparities

Biodiversity is crucial for human health, but previous methods of measuring biodiversity require intensive resources and have other limitations. Crowdsourced datasets from citizen scientists offer a cost-effective solution for characterizing biodiversity on a large spatial scale. This study has two aims: 1) to generate fine-resolution plant species diversity maps in California urban areas using crowdsourced data and extrapolation methods; and 2) to examine their associations with sociodemographic factors and identify subpopulations with low biodiversity exposure. We used iNaturalist observations from 2019 to 2022 to calculate species diversity metrics by exploring the sampling completeness in a 5 × 5-km2 grid and then computing species diversity metrics for grid cells with at least 80 % sample completeness (841 out of 4755 grid cells). A generalized additive model with ordinary kriging (GAM OK) provided moderately reliable estimates, with correlations of 0.64-0.66 between observed and extrapolated metrics, relative mean absolute errors of 21 %-23 %, and relative root mean squared errors of 27 %-30 % for grid cells with ≥80 % sample completeness from 10-fold cross-validation. GAM OK was further applied to extrapolate species diversity metrics from saturated grid cells (N = 841) to the remaining grid cells with <80 % sample completeness (N = 3914) and generate diversity maps that cover the grid. Further, generalized linear mixed models were used to examine the associations between species diversity and sociodemographic indicators at census tract level. The wild vascular plant species diversity metrics were inversely associated with neighborhood socioeconomic status (i.e., unemployment, linguistic isolation, educational attainment, and poverty rate). Minority populations (i.e., African American, Asian American, and Hispanic) and children had significantly lower diversity exposure in their neighborhoods. Crowdsourcing data offers a cost-effective solution for characterizing large-scale biodiversity in urban areas.

Diversity and biological traits of bees visiting flowers of Cucurbita maxima var. zapallito differ between biodiversity-based and conventional management practices

Low diversity of pollinators and the modified composition of functional groups of bees have been proposed as the causes of pollination deficiency in cultivated Cucurbitaceae species. Functional groups of bees are determined by traits, such as body size, nesting site, and social behavior. The presence of bees with specific traits can be differentially affected by agricultural management practices. This work aimed to assess how management types (agroecological and conventional) in Cucurbita maxima var. zapallito crops affect the abundance of bees with different biological traits. The study was conducted on four farms located in horticultural areas of central-eastern Santa Fe province, Argentina. A total of 108 10-min censuses were conducted to record bee species abundance in flowers. The species were assigned to categories for each of the three biological traits. A total of 552 individuals, belonging to 16 bee species, were recorded. Honey bees were more abundant under conventional management, whereas the native bees Eucera fervens and other species were more abundant under agroecological management. Species of the categories analyzed (body size: small, medium, and large; nesting site: above-ground cavities or ground-nesting; and social behavior: solitary or social) were present on farms under both management types. We found that management type affected bees, and their effects differed among bees with specific biological traits. Medium-sized and small bees, ground-nesting bees, and solitary bees were found in greater abundance on agroecological farms than on conventional farms. Our data allowed us to explain the diversity and abundance of bees relative to the management type and biological traits of the species. Implications for insect conservation: This study suggests that incorporating biodiversity-based management strategies might increase abundance and richness of native bees with different biological traits, ensuring the free pollination service they provide and a taxonomically and functionally diverse assemblage.

Changes in diversity and species composition in the assemblage of live and dead bats at wind farms in a highly diverse region

Besides direct mortality, wind farms also affect aerial fauna by modifying their communities, reducing species diversity and richness through disturbance. During three consecutive years, we used mist nets and acoustic recorders, and conducted carcass searches, to characterize the assemblage of bat species and to estimate bat mortality at two nearby wind farms sited <5 km apart in a highly biodiverse region. We asked whether the diversity, richness and evenness of the assemblages varied yearly, predicting it would decrease through time. Richness and evenness did not change, but the diversity of species recorded acoustically, 96% being aerial insectivores, was significantly lower the third year. We estimate 4 - 15.7 fatalities/MW/year by wind farm, with 63% of species found as carcasses being aerial insectivores. We found >40% of dissimilarity in the species composition of bat assemblages between wind farms despite the short distance between them, with species turnover accounting for more than half of the dissimilarity every year. Similarly, species turnover accounted for >15% of the dissimilarity in the composition of the assemblage of live bats (captured and recorded acoustically) and the assemblage obtained through carcass searches. Our findings suggest that nearby wind farms impact bat communities differentially and aerial insectivores disproportionally. Long term, multi-method surveys are needed to characterize bat communities in highly diverse regions and to evaluate the post-construction effects that wind farms have on them.

Elevational homogenization of mountain parasitoids across six decades

Elevational gradients are characterized by strong environmental changes within small geographical distances, providing important insights on the response of biological communities to climate change. Mountain biodiversity is particularly sensitive to climate change, given the limited capacity to colonize new areas and the competition from upshifting lowland species. Knowledge on the impact of climate change on mountain insect communities is patchy, but elevation is known to influence parasitic interactions which control insect communities and functions within ecosystems. We analyzed a European dataset of bristle flies, a parasitoid group which regulates insect herbivory in both managed and natural ecosystems. Our dataset spans six decades and multiple elevational bands, and we found marked elevational homogenization in the host specialization of bristle fly species through time. The proportion of specialized parasitoids has increased by ca. 70% at low elevations, from 17 to 29%, and has decreased by ca. 20% at high elevations, from 48 to 37%. As a result, the strong elevational gradient in bristle fly specialization observed in the 1960s has become much flatter over time. As climate warming is predicted to accelerate, the disappearance of specialized parasitoids from high elevations might become even faster. This parasitoid homogenization can reshape the ecological function of mountain insect communities, increasing the risk of herbivory outbreak at high elevations. Our results add to the mounting evidence that symbiotic species might be especially at risk from climate change: Monitoring the effects of these changes is urgently needed to define effective conservation strategies for mountain biodiversity.

Soil Micro-eukaryotic Diversity Patterns Along Elevation Gradient Are Best Estimated by Increasing the Number of Elevation Steps Rather than Within Elevation Band Replication

The development of high-throughput sequencing (HTS) of environmental DNA (eDNA) has stimulated the study of soil microbial diversity patterns and drivers at all scales. However, given the heterogeneity of soils, a challenge is to define effective and efficient sampling protocols that allow sound comparison with other records, especially vegetation. In studies of elevational diversity pattern, a trade-off is choosing between replication within elevation bands vs. sampling more elevation bands. We addressed this question for soil protists along an elevation gradient on Mt. Asahi, Hokkaido, Japan. We compared two sampling approaches: (1) the replicate strategy (five replicates at six elevational bands, total = 30) and (2) the transect strategy (one sample in each of 16 different elevational bands). Despite a nearly twofold lower sampling effort, the transect strategy yielded congruent results compared to the replicate strategy for the estimation of elevational alpha diversity pattern: the regression coefficients between diversity indices and elevation did not differ between the two options. Furthermore, for a given total number of samples, gamma diversity estimated across the entire transect was higher when sampling more elevational bands as compared to replication from fewer elevational bands. Beta diversity (community composition turnover) was lower within a given elevational band than between adjacent bands and increased with elevation distance. In redundancy analyses, soil organic matter-related variable (the first principal component of soil organic matter, water content, total organic carbon, and nitrogen by whom were highly correlated) and elevation best explained elevational beta diversity pattern for both sampling approaches. Taken together, our results suggest that sampling a single plot per elevation band will be sufficient to obtain a good estimate of soil micro-eukaryotic diversity patterns along elevation gradients. This study demonstrated the effectiveness of the transect strategy in estimating diversity patterns along elevation gradients which is instructive for future environmental or even experimental studies. While not advocating for completely replacing replication-based sampling practices, it is important to note that both replicate and transect strategies have their merits and can be employed based on specific research goals and resource limitations.

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.

The diversity of macromycetes in peatlands: nine years of plot-based monitoring and barcoding in the raised bog "Mukhrino", West Siberia

Background

Peatland ecosystems are defined by soils with sufficient under-decomposed organic layer, called peat, formed under anoxic conditions. Peatlands are widespread around the world, with several highly paludified regions, one of which is the Western Siberian Plain. Peatlands store large amounts of carbon and are important in their intact state to counteract climate change, as well as for a variety of other ecosystem functions. From the practical aspect, these ecosystems are used as a source of peat for fuel, peat-based fertilisers and growing media, berries and Sphagnum plantations. Fungi are the key part of the decomposer community of peatlands, playing a critical role in the aerobic decomposition in the upper peat layer. The community of peatland fungi is adapted to decomposition of peat and dead parts of Sphagnum in wet acidic conditions; they form specific mycorrhizal associations with a variety of plants. Thus, the research of fungal diversity of peatlands is important for several reasons: 1) adding knowledge of peatland fungal diversity to local or global biodiversity databases; 2) studying carbon cycling in peatlands; 3) using peat and peatlands for different applications, such as cultivation of Sphagnum with regards to some parasitic species of fungi and 4) peatland restoration and conservation, to mention a few.

New information

The community of macromycetes of the raised bog "Mukhrino" in Western Siberia was studied using plot-based monitoring throughout a 9-year observation period. The revealed species diversity is represented by approximately 500 specimens in the Fungarium of Yugra State University collection. Selected specimens were used for barcoding of the ITS region to reveal a total of 95 species from 33 genera and three classes. The barcoding effort confirmed morphological identifications for most specimens and identified a number of cryptic species and several potentially new taxa. Based on regular all-season observations, we describe the phenology of the community sporophore production. The quantitative community structure, based on sporophores, revealed a difference in abundance between species by four orders of magnitude, with rare species representing nearly half of the species list. The inter-annual fruiting abundance varied several times by the total number of sporophores per year. To make the comparisons with global studies, we created an open access database of literature-based observations of fungi in peatlands, based on about 120 published papers (comprising about 1300 species) and compared our species list with this database.As a result, the study created an accurate representation of taxonomic and quantitative structure of the community of macromycetes in raised bogs in the region. The raw data of plot-based counts was published as a sampling-event dataset and the sequenced specimens with the sequence information as an DNA-derived extension dataset in GBIF.

Occurrence-based diversity estimation reveals macroecological and conservation knowledge gaps for global woody plants

Incomplete sampling of species' geographic distributions has challenged biogeographers for many years to precisely quantify global-scale biodiversity patterns. After correcting for the spatial inequality of sample completeness, we generated a global species diversity map for woody angiosperms (82,974 species, 13,959,780 occurrence records). The standardized diversity estimated more pronounced latitudinal and longitudinal diversity gradients than the raw data and improved the spatial prediction of diversity based on environmental factors. We identified areas with potentially high species richness and rarity that are poorly explored, unprotected, and threatened by increasing human pressure: They are distributed mostly at low latitudes across central South America, Central Africa, subtropical China, and Indomalayan islands. These priority areas for botanical exploration can help to efficiently fill spatial knowledge gaps for better describing the status of biodiversity and improve the effectiveness of the protected area network for global woody plant conservation.

Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data

Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.

Mathematical Characterization of Private and Public Immune Receptor Sequences

Diverse T and B cell repertoires play an important role in mounting effective immune responses against a wide range of pathogens and malignant cells. The number of unique T and B cell clones is characterized by T and B cell receptors (TCRs and BCRs), respectively. Although receptor sequences are generated probabilistically by recombination processes, clinical studies found a high degree of sharing of TCRs and BCRs among different individuals. In this work, we use a general probabilistic model for T/B cell receptor clone abundances to define "publicness" or "privateness" and information-theoretic measures for comparing the frequency of sampled sequences observed across different individuals. We derive mathematical formulae to quantify the mean and the variances of clone richness and overlap. Our results can be used to evaluate the effect of different sampling protocols on abundances of clones within an individual as well as the commonality of clones across individuals. Using synthetic and empirical TCR amino acid sequence data, we perform simulations to study expected clonal commonalities across multiple individuals. Based on our formulae, we compare these simulated results with the analytically predicted mean and variances of the repertoire overlap. Complementing the results on simulated repertoires, we derive explicit expressions for the richness and its uncertainty for specific, single-parameter truncated power-law probability distributions. Finally, the information loss associated with grouping together certain receptor sequences, as is done in spectratyping, is also evaluated. Our approach can be, in principle, applied under more general and mechanistically realistic clone generation models.

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.

Quantifying and estimating ecological network diversity based on incomplete sampling data

An ecological network refers to the ecological interactions among sets of species. Quantification of ecological network diversity and related sampling/estimation challenges have explicit analogues in species diversity research. A unified framework based on Hill numbers and their generalizations was developed to quantify taxonomic, phylogenetic and functional diversity. Drawing on this unified framework, we propose three dimensions of network diversity that incorporate the frequency (or strength) of interactions, species phylogenies and traits. As with surveys in species inventories, nearly all network studies are based on sampling data and thus also suffer from under-sampling effects. Adapting the sampling/estimation theory and the iNEXT (interpolation/extrapolation) standardization developed for species diversity research, we propose the iNEXT.link method to analyse network sampling data. The proposed method integrates the following four inference procedures: (i) assessment of sample completeness of networks; (ii) asymptotic analysis via estimating the true network diversity; (iii) non-asymptotic analysis based on standardizing sample completeness via rarefaction and extrapolation with network diversity; and (iv) estimation of the degree of unevenness or specialization in networks based on standardized diversity. Interaction data between European trees and saproxylic beetles are used to illustrate the proposed procedures. The software iNEXT.link has been developed to facilitate all computations and graphics. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

Ocean temperature drove changes in the mesopelagic fish community at the edge of the Pacific Warm Pool over the past 460,000 years

Field observations and theoretical modeling suggest that ongoing anthropogenic ocean warming will lead to marine ecosystem degradation. Mesopelagic fish are a fundamental component of the pelagic ecosystem, and their role in linking the surface- and deep-ocean ecosystems is essential for the biological carbon pump. However, their response to a warmer ocean is unconstrained because of data scarcity. Using extraordinarily well-preserved fish otoliths, we reconstruct a continuous mesopelagic fish community record in the Pacific Warm Pool region over 460,000 years. Fish production and diversity followed hump-shaped temperature gradients, with lower tipping point temperatures for the diversity than the production by ~1.5° to 2.0°C. During warmer-than-present interglacial periods, both production and diversity declined drastically. Our findings imply that the temperature-sensitive mesopelagic fish community at the southwestern margin of the Pacific Warm Pool, and possibly other hydrographically similar regions, may be especially affected if ocean warming continues unabated in the future.

Abundance does not predict extinction risk in the fossil record of marine plankton

A major premise of ecological neutral theory is that population size is inversely related to extinction risk. This idea is central to modern biodiversity conservation efforts, which often rely on abundance metrics to partially determine species extinction risk. However, limited empirical studies have tested whether extinction is indeed more probable for species with low abundances. Here we use the fossil record of Neogene radiolaria to test the relationship between relative abundance and longevity (time from first to last occurrence). Our dataset includes abundance histories for 189 polycystine radiolarian species from the Southern Ocean, and 101 species from the tropical Pacific. Using linear regression analyses, we show that neither maximum nor average relative abundance are significant predictors of longevity in either oceanographic region. This suggests that neutral theory fails to explain the plankton ecological-evolutionary dynamics we observe. Extrinsic factors are likely more important than neutral dynamics in controlling radiolarian extinction.

It's a small world for parasites: evidence supporting the North American invasion of European Echinococcus multilocularis

Echinococcus multilocularis (Em), the causative agent of human alveolar echinococcosis (AE), is present in the Holarctic region, and several genetic variants deem to have differential infectivity and pathogenicity. An unprecedented outbreak of human AE cases in Western Canada infected with a European-like strain circulating in wild hosts warranted assessment of whether this strain was derived from a recent invasion or was endemic but undetected. Using nuclear and mitochondrial markers, we investigated the genetic diversity of Em in wild coyotes and red foxes from Western Canada, compared the genetic variants identified to global isolates and assessed their spatial distribution to infer possible invasion dynamics. Genetic variants from Western Canada were closely related to the original European clade, with lesser genetic diversity than that expected for a long-established strain and spatial genetic discontinuities within the study area, supporting the hypothesis of a relatively recent invasion with various founder events.

Species Composition and Structure of Beetle Associations in Caves of the Częstochowa Upland, Poland

This paper presents the study’s results on beetles (Insecta: Coleoptera) inhabiting caves in the Częstochowa Upland, southern Poland. During two years of research, 2084 specimens, representing 105 species from 19 beetle families, were collected. The obtained results indicate that many beetle species choose to inhabit caves despite lacking specific adaptations for living in such environments. The cave entrance zone is the most attractive place for surface species to inhabit because its climatic conditions are more stable than outside the cave, some sunlight is present, and the availability of organic matter is high. In the deeper parts of the studied caves, the number of occurring species rapidly decreased. Three species were recognised as troglobionts, four as troglophiles and 32 as subtroglophiles. Speonomus normandi hydrophilus, Choleva lederiana gracilenta and Quedius mesomelinus mesomelinus were identified as the most frequent in the studied caves. Speonomus normandi hydrophilus is endemic to the Arize massif in the Central Pyrenees (France) and was experimentally introduced into the Dzwonnica cave (Poland) in 1982, while Ch. lederiana gracilenta is one of two troglobitic beetles native to Polish caves and Q. imesomelinus mesomelinus is a widespread, very common troglophile.

Food webs reveal coexistence mechanisms and community organization in carnivores

Globally, massive carnivore guild extirpations have led to trophic downgrading and compromised ecosystem services. However, the complexity of multi-carnivore food webs complicates accurate identification of species interactions and community organization. Here, we used fecal DNA metabarcoding to investigate three communities that together encompass eight large- and meso-carnivore species and their 44 prey taxa of the Qinghai-Tibet Plateau (QTP), one of the last places on Earth that still harbors intact carnivore assemblages. Quantitative food-web analyses revealed pronounced interspecific variations in the carnivores' prey compositions and dietary partitioning both between and within guilds. Additionally, body masses of the carnivores and their prey exhibited consistent hump-shaped correlations across communities. Overall, differences in prey diversity, size category, and proportional utilization among the carnivore species result in trophic niche segregation that likely promotes carnivore coexistence in the harsh QTP environment. Network structure analyses detected significant modularity in all food webs but nestedness in only one. Furthermore, network characterization identified pikas (Ochotona spp.), bharal (Pseudois nayaur), and domestic yak (Bos grunniens) as potential keystone prey across the areas. Our results paint a holistic and detailed picture of the QTP carnivore assemblages' trophic networks and demonstrate that the combined use of the molecular dietary approach and network analysis can generate structural insights into carnivore coexistence and can identify functionally important species in complex communities. Such knowledge can help safeguard carnivore guild integrity and enhance community resilience to environmental perturbations in the sensitive QTP ecosystems.

Does Ungulate Herbivory Translate into Diversity of Woody Plants? A Long-Term Study in a Montane Forest Ecosystem in Austria

Different species-specific traits of woody plant species, feeding preferences of herbivores together with resulting effects on plant competition are expected to translate into different plant community structures and expressions of biodiversity. We studied the diversity of woody plant species (trees and shrubs) and structural diversity of forest trees, using a 30-year and an 18-year dataset of ungulate exclosure-control plot pairs in a mixed alpine forest community in Austria. We surveyed the tallest individuals per tree species and plot and analyzed the collective of top-height individuals per plot pair. Incidence data for exclosure and control plots were aggregated. Comparing species diversity and diversity of height classes on the plots throughout time, we calculated diversity profiles based on Hill numbers. Diversity of top height individuals and structural diversity, expressed by height classes, were two diversity aspects that differed between exclosures and control plots. Other diversity estimates of woody plant species showed huge variation without significant differences between plots. Height growth was significantly suppressed by ungulate herbivory. Effects of ungulate herbivores in forest ecosystems are highly complex and context-dependent and thus not reducible to simple top-down forces. Long-term surveys provide data that reflect “ultimate” effects of herbivory interacting with other drivers of community dynamics.

Monitoring recovery of tree diversity during tropical forest restoration: lessons from long-term trajectories of natural regeneration

Given the importance of species diversity as a tool for assessing recovery during forest regeneration and active restoration, robust approaches for assessing changes in tree species diversity over time are urgently needed. We assessed changes in tree species diversity during natural regeneration over 12-20 years in eight 1-ha monitoring plots in NE Costa Rica, six second-growth forests and two old-growth reference forests. We used diversity profiles to show successional trajectories in measures of observed, asymptotic and standardized tree diversity and evenness as well as sample completeness. We randomly subsampled 1-ha plot data to evaluate how well smaller spatial subsamples would have captured temporal trajectories. Annual surveys in eight 1-ha plots were missing substantial numbers of rare or infrequent species. Older second-growth sites showed consistent declines in tree diversity, whereas younger sites showed fluctuating patterns or increases. Subsample areas of 0.5 ha or greater were sufficient to infer the diversity of abundant species, but smaller subsamples failed to capture temporal trajectories of species richness and yielded positively biased estimates of evenness. In tropical forest regions with high levels of diversity, species diversity from small sample plots should be assessed using methods that incorporate abundance information and that standardize for sample coverage. This article is part of the theme issue 'Understanding forest landscape restoration: reinforcing scientific foundations for the UN Decade on Ecosystem Restoration'.

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.

Decreasing Species Richness with Increase in Elevation and Positive Rapoport Effects of Crambidae (Lepidoptera) on Mount Taibai

Rapoport's rule proposes that a species' range size increases with the increase in a gradient (such as latitude, altitude or water depth). However, altitudinal distributions and Rapoport's rule have rarely been tested for Asian Lepidoptera. Pyraustinae and Spilomelinae (Lepidoptera: Crambidae) are extremely diverse in temperate Asia, including on Mount Taibai, which is considered a hotspot area for studying the vertical distribution patterns of insect species. Based on the investigation of altitudinal distribution data with identification by using both DNA barcoding and the morphological classification of Pyraustinae and Spilomelinae, this paper determines the altitudinal gradient pattern for these two subfamilies on the north slope of Mount Taibai, and provides a test of the universality of Rapoport's rule in Lepidoptera by using four methods, including Stevens' method, Pagel's method, Rohde's method, and the cross-species method. Our results show that the alpha diversity of Pyraustinae and Spilomelinae both decrease with rising altitude. By contrast, the species' ranges increase with rising altitude. Three of the four methods used to test Rapoport's rule yielded positive results, while Rohde's results show a unimodal distribution model and do not support Rapoport's rule. Our findings fill the research gap on the elevational diversity of Lepidoptera in temperate Asia.

Environmental Effects on Taxonomic Turnover in Soil Fauna across Multiple Forest Ecosystems in East Asia

The large-scale spatial variation in and causes of biotic turnover of soil fauna remain poorly understood. Analyses were conducted based on published data from 14 independent sampling sites across five forest ecosystems in East Asia. Jaccard and Sørensen's indices were used to measure turnover rates in soil fauna orders. A redundancy analysis was used to investigate multiple environmental controls of the composition of soil fauna communities. The results showed that both Jaccard's and Sørensen's index increased significantly with increasing latitude difference. The environment explained 54.1%, 50.6%, 57.3% and 50.9% of the total variance, and spatial factors explained 13.8%, 15.9%, 21.0% and 12.6% of the total variance in the orders' composition regarding overall, phytophagous, predatory and saprophagous fauna, respectively. In addition, climate factors in environmental processes were observed to have a stronger effect than soil factors on the orders' turnover rates. Our results support the hypothesis that the effect of environment factors on soil animal taxa turnover is more important than the effect of spatial factors. Climatic factors explained more variation in the turnover of phytophagic fauna, but soil and environment factors equally explained the variation in the turnover of predatory fauna. This study provides evidence to support both environmental filtering and dispersal limitation hypotheses at the regional and population scales.

Influence of grazing and solar panel installation on tenebrionid beetles (Coleoptera Tenebrionidae) of a central Asian steppe

Grazing may represent a major threat to biodiversity in arid grasslands. The increasing use of grasslands for solar parks may represent a new important threat. No study has investigated the effects of solar parks on soil insects. Tenebrionids are a major component of the arthropod fauna of grasslands of central Asia. These ecosystems are threatened by grazing and increasing land use for solar parks. Aim of this work was to investigate the effects of grazing and solar panels on tenebrionids in arid grasslands (desert steppe) in China by comparing their community structure in ungrazed, heavily grazed, and solar park sites. Beetles were sampled by pitfall traps, and sites were compared for abundance and diversity (Hill numbers). All sites were characterized by simple, strongly dominated tenebrionid communities. Species proportions varied among sites. Grazing negatively influenced overall abundance, but did not alter species proportions; by contrast, solar panels had no effect on the average abundance, but reduced the proportion of the most abundant species. Compared with the other two sites, the solar park was characterized by a higher plant biomass and lower temperatures. A major availability of resources and less harsh conditions in the solar park might have a role in reducing the dominance of the most abundant species, allowing other species to attain higher abundances. This led to a more balanced community structure, with higher values of diversity. Although neither grazing nor solar panel installation modified radically tenebrionid species-abundance distribution or diversity, grazing and solar panel installation had different effects in species abundances and their impact might amplify the effect of other disturbance factors such as the ongoing climate change.

Plasmodium falciparum Genetic Diversity in Coincident Human and Mosquito Hosts

Population genetic diversity of Plasmodium falciparum antigenic loci is high despite large bottlenecks in population size during the parasite life cycle. The prevalence of genetically distinct haplotypes at these loci, while well characterized in humans, has not been thoroughly compared between human and mosquito hosts. We assessed parasite haplotype prevalence, diversity, and evenness using human and mosquito P. falciparum infections collected from the same households during a 14-month longitudinal cohort study using amplicon deep sequencing of two antigenic gene fragments (ama1 and csp). To a prior set of infected humans (n = 1,175/2,813; 86.2% sequencing success) and mosquito abdomens (n = 199/1,448; 95.5% sequencing success), we added sequences from infected mosquito heads (n = 134/1,448; 98.5% sequencing success). The overall and sample-level parasite populations were more diverse in mosquitoes than in humans. Additionally, haplotype prevalences were more even in the P. falciparum human population than in the mosquito population, consistent with balancing selection occurring at these loci in humans. In contrast, we observed that infections in humans were more likely to harbor a dominant haplotype than infections in mosquitoes, potentially due to removal of unfit strains by the human immune system. Finally, within a given mosquito, there was little overlap in genetic composition of abdomen and head infections, suggesting that infections may be cleared from the abdomen during a mosquito’s lifespan. Taken together, our observations provide evidence for the mosquito vector acting as a reservoir of sequence diversity in malaria parasite populations.

Does urbanization impact terrestrial vertebrate ectotherms across a biodiversity hotspot?

Urbanization is increasing at an alarming rate altering biodiversity. As urban areas sprawl, it is vital to understand the effects of urbanization on biodiversity. Florida is ideal for this research; it has many reptile species and has experienced multiple anthropogenic impacts. Herein, we aim to evaluate human impacts on registered reptile richness across an urbanization gradient in Florida. The expectation is that highly urbanized areas would harbor a lower number of species. To represent urbanization, we used Venter et al. (2016) human footprint index. We downloaded georeferenced occurrence records from the Global Biodiversity Information Facility to collate species richness. We ran generalized linear regressions controlling for spatial autocorrelation structure to test the association between urbanization and reptile records across Florida. We found a positive association between urbanization and registered reptiles across Florida for total and non-native species richness; however, a lack of association occurred for native species. We performed rarefaction curves due to an inherent bias of citizen science data. The positive association was supported for non-native reptile species richness with greater species richness located at urban centers. Interestingly, total and native species richness were largest at low as well as moderate levels of urbanization. Thus, moderately urbanized areas may have the potential to harbor a similar number of reptile species compared to areas with low urbanization. Nevertheless, a difference exists in sample completeness between the urbanization categories. Thus, a more systematic monitoring of reptile species across an urbanization gradient, not only focusing on urban and wild areas but also including moderate levels of urbanization, is needed to provide informed conservation strategies for urban development planning. Advances in environmental sensors, environmental DNA, and citizen science outreach are necessary to implement if we are to effectively monitor biodiversity at the accelerated rate of urbanization.

Elevational biodiversity gradients in the Neotropics: Perspectives from freshwater caddisflies (Insecta: Trichoptera)

Aquatic insects in the order Trichoptera are extremely diverse in number of species and their trophic roles. However, their distribution and diversity patterns are poorly known in the Neotropics, including the species restricted to tropical mountain ecosystems. Recent studies in tropical mountains have shown high levels of endemism of aquatic insects and changes in the composition of communities over short distances. Still, the incidence of environmental filters that explain such patterns has not been addressed quantitatively. Given the relevance of understanding Trichoptera spatial diversity patterns to prioritize conservation areas for freshwaters, as well as to obtain baseline information to predict changes in aquatic communities facing global environmental changes, we assessed the species distribution and assemblages of caddisflies along an elevational gradient from 600 to 3,600 m a.s.l. on the equatorial Andes. In this area, we had long-term continuous climate data with hourly resolution. We collected adult caddisflies in seven localities along this gradient using light traps. We sampled each locality for two hours after sunset for three consecutive days. All specimens collected were identified to species or morphospecies. Our results showed an increase in species and genera numbers with decreasing altitude, albeit no significant. Minimum air temperature is the main environmental variable explaining Trichoptera community assemblages. β‐diversity (taxon turnover among sites), as opposed to species richness, increased with altitude and showed a bimodal distribution along the elevation gradient for both genera and species assemblages, which resulted in a significant shift in community composition of species and genera at 2,000 m a.s.l. Our null-models confirm the observed patterns of B-diversity are non-random and suggest a strong environmental filtering of tropical caddisflies community assemblies and turnover. Geographic distance coupled with changes in environmental conditions along the elevation gradient explained a high percentage of community variance, as documented for other taxa (e.g., vascular plants), suggesting the importance of securing habitat connectivity along the altitudinal gradient to protect aquatic insect diversity effectively.

Interspecific competition limits bird species' ranges in tropical mountains

Species' geographic ranges are limited by climate and species interactions. Climate is the prevailing explanation for why species live only within narrow elevational ranges in megadiverse biodiverse tropical mountains, but competition can also restrict species' elevational ranges. We test contrasting predictions of these hypotheses by conducting a global comparative test of birds' elevational range sizes within 31 montane regions, using more than 4.4 million citizen science records from eBird to define species' elevational ranges in each region. We find strong support that competition, not climate, is the leading driver of narrow elevational ranges. These results highlight the importance of species interactions in shaping species' ranges in tropical mountains, Earth's hottest biodiversity hotspots.

Periodical Changes of Feces Microbiota and Its Relationship with Nutrient Digestibility in Early Lambs

Early mammal gut microorganism colonization affects host health, the feed conversion rate, and production performance. Herein, we explored how fecal microbiota develops and the interactions between microorganisms and nutrients. The lambs were separated from ewes at 7 days old, artificial feeding with milk replacer completely replaced lactation, and the starter diet was added. At 21 days old, the lambs were fed with complete starter and milk replacer was stopped. At day 7, 21, 35, and 49 after birth, fecal samples were collected. Then 16S rRNA gene sequencing in the fecal samples revealed that the alpha diversity increased significantly with age. Principal coordinates analysis showed clear clustering by age (p < 0.05). At the genus level, the relative abundance of 8 genera declined, 12 genera increased (p < 0.1), and 4 genera changed dramatically with age (p < 0.05). The apparent digestibility of dry matter, protein, fat, neutral detergent fiber, and acid detergent fiber significantly decreased by 21.77%, 23.15%, 23.62%, 19.38%, and 45.24%, respectively, from 7 to 35 days of age (p < 0.05), but not thereafter (p > 0.05). Fecal nutrient contents affected the abundance of bacterial genera (p < 0.05). Enterobacteriaceae_unclassified, Clostridium XlVb, Bifidobacterium, and other genera had no relationship with the fecal nutrient content; however, they were closely related to nutrient intake and digestibility, possibly promoting nutrient digestion. Our results suggested that nutrient digestion of young lambs changed rapidly, which was closely related to intestinal microbial colonization.

The effect of natural disturbances on forest biodiversity: an ecological synthesis

Disturbances alter biodiversity via their specific characteristics, including severity and extent in the landscape, which act at different temporal and spatial scales. Biodiversity response to disturbance also depends on the community characteristics and habitat requirements of species. Untangling the mechanistic interplay of these factors has guided disturbance ecology for decades, generating mixed scientific evidence of biodiversity responses to disturbance. Understanding the impact of natural disturbances on biodiversity is increasingly important due to human-induced changes in natural disturbance regimes. In many areas, major natural forest disturbances, such as wildfires, windstorms, and insect outbreaks, are becoming more frequent, intense, severe, and widespread due to climate change and land-use change. Conversely, the suppression of natural disturbances threatens disturbance-dependent biota. Using a meta-analytic approach, we analysed a global data set (with most sampling concentrated in temperate and boreal secondary forests) of species assemblages of 26 taxonomic groups, including plants, animals, and fungi collected from forests affected by wildfires, windstorms, and insect outbreaks. The overall effect of natural disturbances on α-diversity did not differ significantly from zero, but some taxonomic groups responded positively to disturbance, while others tended to respond negatively. Disturbance was beneficial for taxonomic groups preferring conditions associated with open canopies (e.g. hymenopterans and hoverflies), whereas ground-dwelling groups and/or groups typically associated with shady conditions (e.g. epigeic lichens and mycorrhizal fungi) were more likely to be negatively impacted by disturbance. Across all taxonomic groups, the highest α-diversity in disturbed forest patches occurred under moderate disturbance severity, i.e. with approximately 55% of trees killed by disturbance. We further extended our meta-analysis by applying a unified diversity concept based on Hill numbers to estimate α-diversity changes in different taxonomic groups across a gradient of disturbance severity measured at the stand scale and incorporating other disturbance features. We found that disturbance severity negatively affected diversity for Hill number q = 0 but not for q = 1 and q = 2, indicating that diversity-disturbance relationships are shaped by species relative abundances. Our synthesis of α-diversity was extended by a synthesis of disturbance-induced change in species assemblages, and revealed that disturbance changes the β-diversity of multiple taxonomic groups, including some groups that were not affected at the α-diversity level (birds and woody plants). Finally, we used mixed rarefaction/extrapolation to estimate biodiversity change as a function of the proportion of forests that were disturbed, i.e. the disturbance extent measured at the landscape scale. The comparison of intact and naturally disturbed forests revealed that both types of forests provide habitat for unique species assemblages, whereas species diversity in the mixture of disturbed and undisturbed forests peaked at intermediate values of disturbance extent in the simulated landscape. Hence, the relationship between α-diversity and disturbance severity in disturbed forest stands was strikingly similar to the relationship between species richness and disturbance extent in a landscape consisting of both disturbed and undisturbed forest habitats. This result suggests that both moderate disturbance severity and moderate disturbance extent support the highest levels of biodiversity in contemporary forest landscapes.

Community structure of benthic macroinvertebrates in native and introduced mangroves of northern Beibu Gulf, China: Implication for restoring mangrove ecosystems

Introduced mangroves are widely used to restore mangrove ecosystems in South China. Results of potential impacts on indicative benthic macroinvertebrates are divergent. We explored the community structure of benthic macroinvertebrates in the mangrove ecosystem of northern Beibu Gulf, China across four habitats: native Avicennia marina mangrove, introduced Laguncularia racemosa mangrove, native-introduced mixed mangrove, and unvegetated intertidal flat. Based on the Hill number, community structure was estimated from the dimensions of estimated species richness, diversity, evenness, and species composition similarity. Benthic macroinvertebrates in the unvegetated flat significantly differed from the other three assemblages in mangroves; introduced L. racemosa mangrove had relatively distinct benthic macroinvertebrate assemblage from the native A. marina and the mixed mangroves, with lower species richness and similarity but higher diversity and evenness. Considering the lack of unanimous conclusion of potential impact on benthic macroinvertebrates under complex species interactions, native mangroves should be of top priority in ecosystem restoration.

Fleshy red algae mats act as temporary reservoirs for sessile invertebrate biodiversity

Many coastal ecosystems, such as coral reefs and seagrass meadows, currently experience overgrowth by fleshy algae due to the interplay of local and global stressors. This is usually accompanied by strong decreases in habitat complexity and biodiversity. Recently, persistent, mat-forming fleshy red algae, previously described for the Black Sea and several Atlantic locations, have also been observed in the Mediterranean. These several centimetre high mats may displace seagrass meadows and invertebrate communities, potentially causing a substantial loss of associated biodiversity. We show that the sessile invertebrate biodiversity in these red algae mats is high and exceeds that of neighbouring seagrass meadows. Comparative biodiversity indices were similar to or higher than those recently described for calcifying green algae habitats and biodiversity hotspots like coral reefs or mangrove forests. Our findings suggest that fleshy red algae mats can act as alternative habitats and temporary sessile invertebrate biodiversity reservoirs in times of environmental change.

Comparative analyses of fleshy red algae mats and seagrass meadows highlight their value in fostering sessile invertebrate biodiversity.

Diversity begets diversity: Low resource heterogeneity reduces the diversity of nut-nesting ants in rubber plantations

One of the most general patterns in ecology is the positive relationship between environmental heterogeneity and local diversity. On the one hand, increased resource heterogeneity provides more resources for diverse consumers in the community. On the other hand, increased structural heterogeneity creates variation in the environment's physical structure, thus allowing the coexistence of diverse species with different environmental requirements. Here, we examined the relative importance of resource and structural heterogeneity in determining the taxonomic, functional, and phylogenetic diversity of nut-nesting ants in natural rainforest and rubber plantation. The species richness of nut-nesting ants was 70% higher in rainforest than in rubber plantation. The clustered functional and phylogenetic structure in rubber plantation suggested a strong effect of environmental filtering in shaping ant functional and phylogenetic structure. Nesting heterogeneity (nut diversity) was the major factor explaining variation in taxonomic, functional, and phylogenetic diversity, suggesting that resource heterogeneity plays a major role in shaping the biodiversity patterns of nut-nesting ants. Overall, these results indicate that decreased resource diversity following the conversion of rainforest to rubber plantation can drive biodiversity loss in nut-nesting ants, through its effect on reducing both ant species, functional, and phylogenetic diversity. The decline in species richness and functional and phylogenetic diversity in the local ant community might have major effects on ecosystem functioning.

Temperature preferences drive additive biotic homogenization of Orthoptera assemblages

The degradation of natural habitats is causing ongoing homogenization of biological communities and declines in terrestrial insect biodiversity, particularly in agricultural landscapes. Orthoptera are focal species of nature conservation and experienced significant diversity losses over the past decades. However, the causes underlying these changes are not yet fully understood. We analysed changes in Orthoptera assemblages surveyed in 1988, 2004 and 2019 on 198 plots distributed across four major grassland types in Central Europe. We demonstrated compositional differences in Orthoptera assemblages found in wet, dry and mesic grasslands, as well as ruderal habitats decreased, indicating biotic homogenization. However, mean α-diversity of Orthoptera assemblages increased over the study period. We detected increasing numbers of species with preferences for higher temperatures in mesic and wet grasslands. By analysing the temperature, moisture and vegetation preferences of Orthoptera, we found that additive homogenization was driven by a loss of species adapted to extremely dry and nitrogen-poor habitats and a parallel spread of species preferring warmer macroclimates.

Forgotten books: The application of unseen species models to the survival of culture

The study of ancient cultures is hindered by the incomplete survival of material artifacts, so we commonly underestimate the diversity of cultural production in historic societies. To correct this survivorship bias, we applied unseen species models from ecology to gauge the loss of narratives from medieval Europe, such as the romances about King Arthur. The estimates obtained are compatible with the scant historic evidence. In addition to events such as library fires, we identified the original evenness of cultural populations as an overlooked factor in these assemblages' stability in the face of immaterial loss. We link the elevated evenness in island literatures to analogous accounts of ecological and cultural diversity in insular communities. These analyses call for a wider application of these methods across the heritage sciences.

Pristine and sulfidized ZnO nanoparticles alter microbial community structure and nitrogen cycling in freshwater lakes

Zinc oxide nanoparticles (ZnO NPs) and its sulfidized form (ZnS NPs) are increasingly entering into freshwater systems through multiple pathways. However, their impacts on the composition and function of sedimentary microbial communities are still largely unknown. Here, two kinds of lake-derived microcosms were constructed and incubated with ZnO NPs, or ZnS NPs to investigate the short-term (7 days) and long-term (50 days) impacts on sedimentary microbial communities and nitrogen cycling. After 7 days, both ZnO NPs and ZnS NPs dosed microbial communities experienced distinct alterations as compared to the undosed controls. By day 50, the structural shifts of microbial communities caused by ZnO NPs were significantly enlarged, while the microbial shifts induced by ZnS NPs were largely resolved. Additionally, ZnO NPs and ZnS NPs could significantly alter nitrogen species and nitrogen cycling genes in sediments, revealing their non-negligible impacts on nitrogen cycling processes. Furthermore, our data clearly indicated that the impacts of ZnO NPs and ZnS NPs on nitrogen cycling differed distinctly in different lake-derived microcosms, and the impacts were significantly correlated with microbial community structure. Overall, this research suggests that the entrance of pristine or sulfidized ZnO NPs into freshwater systems may significantly impact the sedimentary microbial community structure and nitrogen cycling.

The number of tree species on Earth

One of the most fundamental questions in ecology is how many species inhabit the Earth. However, due to massive logistical and financial challenges and taxonomic difficulties connected to the species concept definition, the global numbers of species, including those of important and well-studied life forms such as trees, still remain largely unknown. Here, based on global ground-sourced data, we estimate the total tree species richness at global, continental, and biome levels. Our results indicate that there are ∼73,000 tree species globally, among which ∼9,000 tree species are yet to be discovered. Roughly 40% of undiscovered tree species are in South America. Moreover, almost one-third of all tree species to be discovered may be rare, with very low populations and limited spatial distribution (likely in remote tropical lowlands and mountains). These findings highlight the vulnerability of global forest biodiversity to anthropogenic changes in land use and climate, which disproportionately threaten rare species and thus, global tree richness.

Patch, matrix and disturbance variables negatively influence bird community structure in small-sized managed green spaces located in urban core areas

Patch, matrix and human-induced disturbance variables are important in determining the structure of urban bird communities. Although green spaces in urban core areas are usually small and disturbed, they can be important for local bird diversity. Because such areas are often overlooked, their study is critical for successfully incorporating biodiversity conservation in urban planning. Furthermore, comparing bird communities from different biogeographical areas would help identify generalizable patterns and propose common management actions. We compared the structure of breeding season bird assemblages of managed small public green spaces in the urban core areas of two similar-sized European cities, Kavala (Greece) and Rovaniemi (Finland), and studied the influence of environmental variables on community structure. Species composition differed between the cities. Abundance and evenness were higher in Kavala, while richness and diversity did not differ between the cities. Abundance did not respond in a general way to the same variables in the two cities. It increased with decreasing shrub cover and distance from the city center and with increasing midday noise and ground cover in Kavala, but increased with increasing distance from the city center and decreased with increasing car traffic and midday noise in Rovaniemi. This might be explained by the lower abundance of bird dwellers in Rovaniemi. Primarily gray cover, but also other variables, at both the patch and matrix levels (e.g., noise, car traffic, distance from the city center), negatively affected richness, evenness and diversity in both cities. Green space size was positively correlated with richness and diversity in Kavala, but not in Rovaniemi, possibly due to the smaller size variation in Rovaniemi. Results emphasized that increasing gray cover is harmful for birds in small-sized green spaces in urban core areas. However, urban managers should note that not all bird community metrics responded in similar ways to same environmental variables.

Global biogeography of living brachiopods: Bioregionalization patterns and possible controls

The global distribution patterns of 14918 geo-referenced occurrences from 394 living brachiopod species were mapped in 5° grid cells, which enabled the visualization and delineation of distinct bioregions and biodiversity hotspots. Further investigation using cluster and network analyses allowed us to propose the first systematically and quantitatively recognized global bioregionalization framework for living brachiopods, consisting of five bioregions and thirteen bioprovinces. No single environmental or ecological variable is accountable for the newly proposed global bioregionalization patterns of living brachiopods. Instead, the combined effects of large-scale ocean gyres, climatic zonation as well as some geohistorical factors (e.g., formation of land bridges and geological recent closure of ancient seaways) are considered as the main drivers at the global scale. At the regional scale, however, the faunal composition, diversity and biogeographical differentiation appear to be mainly controlled by seawater temperature variation, regional ocean currents and coastal upwelling systems.

Climate and land-use interactively shape butterfly diversity in tropical rainforest and savanna ecosystems of southwestern China

Human-induced habitat conversion and degradation, along with accelerating climatic change, have resulted in considerable global biodiversity loss. Nevertheless, how local ecological assemblages respond to the interplay between climate and land-use change remains poorly understood. Here, we examined the effects of climate and land-use interactions on butterfly diversity in different ecosystems of southwestern China. Specifically, we investigated variation in the alpha and beta diversities of butterflies in different landscapes along human-modified and climate gradients. We found that increasing land-use intensity not only caused a dramatic decrease in butterfly alpha diversity but also significantly simplified butterfly species composition in tropical rainforest and savanna ecosystems. These findings suggest that habitat modification by agricultural activities increases the importance of deterministic processes and leads to biotic homogenization. The land-use intensity model best explained species richness variation in the tropical rainforest, whereas the climate and land-use intensity interaction model best explained species richness variation in the savanna. These results indicate that climate modulates the effects of land-use intensity on butterfly alpha diversity in the savanna ecosystem. We also found that the response of species composition to climate varied between sites: specifically, species composition was strongly correlated with climatic distance in the tropical rainforest but not in the savanna. Taken together, our long-term butterfly monitoring data reveal that interactions between human-modified habitat change and climate change have shaped butterfly diversity in tropical rainforest and savanna. These findings also have important implications for biodiversity conservation under the current era of rapid human-induced habitat loss and climate change.

Decomposing Spatial β-Diversity in the temperate forests of Northeastern China

β-Diversity, which describes the extent of change in species composition in a given region, has become a core issue in ecology in recent years. However, it is hard to understand the underlying mechanisms of β-diversity by using indices that yield identical values under species replacement and nestedness pattern. Partitioning β-diversity into turnover (caused by species replacement among plots) and nestedness components (caused by species loss or gain among plots) may provide improved understanding of the variation in species composition. Here, we collected presence-absence data of 456 one-tenth ha circular plots in the temperate forests of Northeastern China spanning a latitudinal range of 12° (41-53°N). We decomposed β-diversity to assess the relative contribution of the turnover and nestedness components across latitudinal gradients. We used regression analysis to assess the relationship between spatial distance and β-diversity. We applied variation partitioning to evaluate the importance of the measured environmental and spatial variables in explaining β-diversity. We used the Tukey honest significant difference test to test the differences of β-diversity along latitudinal gradients. Pearson correlations (r) and significance (p-value) were computed using the Mantel tests to verify the relationship between distance and β-diversity. The ANOVA test was used to verify whether the variation of β-diversity explained by the environment and distance was significant. Our results showed that (1) β-diversity and the turnover component were higher at low latitudes (zones A and B) than at high latitudes (zones C and D), while there was no relationship between the nestedness component and latitude. (2) The turnover component was dominant. (3) The spatial distance explained more variation of β-diversity than the measured environmental factors. Therefore, we conclude that β-diversity is mainly a product of species turnover in our temperate forests, suggesting that different localities harbor different species. We find that decomposing β-diversity into the turnover and nestedness components is a useful approach to explore the variation of community composition and their causes.