A conceptual guide to measuring species diversity

The community ecology perspective of omics data

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

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

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

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

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

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

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

SUPPLEMENTARY INFORMATION

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

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

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

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

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

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

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

The Heavy Mineral Map of Australia: Vision and Pilot Project

We describe a vision for a national-scale heavy mineral (HM) map generated through automated mineralogical identification and quantification of HMs contained in floodplain sediments from large catchments covering most of Australia. The composition of the sediments reflects the dominant rock types in each catchment, with the generally resistant HMs largely preserving the mineralogical fingerprint of their host protoliths through the weathering-transport-deposition cycle. Heavy mineral presence/absence, absolute and relative abundance, and co-occurrence are metrics useful to map, discover and interpret catchment lithotype(s), geodynamic setting, magmatism, metamorphic grade, alteration and/or mineralization. Underpinning this vision is a pilot project, focusing on a subset from the national sediment sample archive, which is used to demonstrate the feasibility of the larger, national-scale project. We preview a bespoke, cloud-based mineral network analysis (MNA) tool to visualize, explore and discover relationships between HMs as well as between them and geological settings or mineral deposits. We envisage that the Heavy Mineral Map of Australia and MNA tool will contribute significantly to mineral prospectivity analysis and modeling, particularly for technology critical elements and their host minerals, which are central to the global economy transitioning to a more sustainable, lower carbon energy model.

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.

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.

On the restoration of hedgerow ground vegetation: Local and landscape drivers of plant diversity and weed colonization

Hedgerows are among the most stable refugia for biodiversity in agricultural landscapes, providing food and shelter to many living organisms. However, the destruction and alteration of hedgerow ground vegetation compromise their potential for biodiversity conservation. The purpose of this study was to find local and landscape-scale drivers that promote plant diversity in hedgerows and prevent their colonization by troublesome weeds. Using a functional approach, we assessed the effects of hedgerow features, adjacent farming systems (conventional vs organic) and landscape context (bocage, semi-natural habitat cover, organic farming cover) on the diversity and composition of plant communities in 40 hedgerows, in Brittany (France). Hedgerow features had no effect on species diversity, but influenced functional diversity measured as a standardized effect size (SES), i.e. independent of species diversity. Organic farming at local scale was the main driver increasing both species and functional diversity (SES), doubling the cover of insect-pollinated forbs. High organic farming cover in the landscape increased species diversity, but not functional diversity (SES), of hedgerows adjoining conventional farming systems. Besides, high cover of semi-natural habitats and organic farming in the landscape prevented colonization of hedgerows by troublesome weeds. Promoting extensive management at both local and landscape scale is thus necessary for successful restoration of hedgerow ground vegetation, which should favour biodiversity conservation and ecosystem service provision.

Phenotypic Diversity in Wild and Cultivated Date Palm (Phoenix, Arecaceae): Quantitative Analysis Using Information Theory

The quantitative study of genetic diversity requires tools to describe quantitatively and in parallel the whole phenotypic diversity in order to produce meaningful comparisons. The genus Phoenix offers examples of species with very different levels of diversity or heterogeneity. Within Phoenix, date palm (Phoenix dactylifera L.) is a major food crop of global relevance. The concept of information entropy was introduced by Claude Shannon; although initially intended to evaluate data communication systems, it has been used to measure biodiversity in terms of richness, evenness and dominance. In the present work, we will use it to describe heterogeneity within the different taxonomic units in the genus Phoenix. The description of the Phoenix morphological diversity in the present work is based on 596 accessions or populations belonging to 43 mutually exclusive taxonomic units (species, subspecies, varieties, landrace groups and hybrids). As Phoenix is a dioecious palm genus, female and male individuals are described separately. Each accession or sample is described using 116 characters totaling 449 states. The Shannon information entropy index allows the quantitative representation of the different levels of heterogeneity in the various taxonomic units of the genus Phoenix. Morphology, consistency and coloration of fruit and seed, followed by the inflorescences and female flowers, comprise the taxonomic characters that contribute the most to heterogeneity. Vegetative characters contribute less than the characters of the reproductive organs as a whole. Phoenix dactylifera and related Mediterranean and Macaronesian taxa present the maximum heterogeneity. Immediately afterwards we find P. loureiroi and, behind, the group of P. pusilla. At the lower limit of heterogeneity, we find species restricted in their distribution area: P. rupicola, P. theophrasti, P. roebelenii and P. acaulis. Phoenix dactylifera conforms to a complex of landraces and cultivars that coexist as phenotypically well-defined geographical groups with numerous intermediate forms and the long-distance translocation of otherwise local cultivars. This results in high heterogeneity. For the western and eastern groups of Phoenix dactylifera, it is extremely difficult to find a set of well-defined differential characters. However, some of the variables analyzed here allow us to propose a set of their respective syndromes. The high phenotypic heterogeneity in various Phoenix species is related to the genetic diversity, age and ancestry of different taxa, hybridization events and introgressions prior to domestication, and selective pressures after domestication and, again, interspecific crosses after domestication.

Hurricane María drives increased indoor proliferation of filamentous fungi in San Juan, Puerto Rico: a two-year culture-based approach

Extensive flooding caused by Hurricane María in Puerto Rico (PR) created favorable conditions for indoor growth of filamentous fungi. These conditions represent a public health concern as contamination by environmental fungi is associated with a higher prevalence of inflammatory respiratory conditions. This work compares culturable fungal spore communities present in homes that sustained water damage after Hurricane María to those present in dry, non-flooded homes. We collected air samples from 50 houses in a neighborhood in San Juan, PR, 12 and 22 months after Hurricane María. Self-reported data was used to classify the homes as flooded, water-damage or dry non-flooded. Fungi abundances, composition and diversity were analyzed by culturing on two media. Our results showed no significant differences in indoor fungal concentrations (CFU/m3) one year after the Hurricane in both culture media studied (MEA and G25N). During the second sampling period fungal levels were 2.7 times higher in previously flooded homes (Median = 758) when compared to dry homes (Median = 283), (p-value < 0.005). Fungal profiles showed enrichment of Aspergillus species inside flooded homes compared to outdoor samples during the first sampling period (FDR-adjusted p-value = 0.05). In contrast, 22 months after the storm, indoor fungal composition consisted primarily of non-sporulated fungi, most likely basidiospores, which are characteristic of the outdoor air in PR. Together, this data highlights that homes that suffered water damage not only have higher indoor proliferation of filamentous fungi, but their indoor fungal populations change over time following the Hurricane. Ultimately, after nearly two years, indoor and outdoor fungal communities converged in this sample of naturally ventilated homes.

Contributions of mean temperature and temperature variation to population stability and community diversity

Future climate changes are predicted to not only increase global temperatures but also alter temporal variation in temperature. As thermal tolerances form an important component of a species' niche, changes to the temperature regime have the capacity to negatively impact species, and therefore, the diversity of the communities they inhabit. In this study, we used protist microcosms to assess how mean temperature, as well as temporal variation in temperature, affected diversity. Communities consisted of seven species in a multitrophic food web. Each ecosystem was inoculated with the same abundances of each species at the start of the experiment, and species densities, Hill's numbers (based on Shannon diversity), the number of extinctions, and the probability the microcosm contained predators were all calculated at the end of the experiment. To assess how mean temperature and temperature fluctuations affect stability, we also measured population densities through time. We found that increased temporal variation in temperature increased final densities, increased Hill's numbers (at low mean temperatures), decreased rates of extinctions, and increased the probability that predators survived till the end of the experiment. Mean temperatures did not significantly affect either the number of extinctions or the probability of predators, but did reduce the positive effect of increased temporal variation in temperature on overall diversity. Our results indicate that climatic changes have the potential to impact the composition of ecological communities by altering multiple components of temperature regimes. However, given that some climate forecasts are predicting increased mean temperatures and reduced variability, our finding that increased mean temperature and reduced temporal variation are both generally associated with negative consequences is somewhat concerning.

Influence of Tourism Safety Perception on Destination Image: A Case Study of Xinjiang, China

Tourism safety perception is one of the factors influencing destination image, but there is a lack of systematic research on the multidimensional influence of tourism safety perception on destination image. In this paper, based on the survey data collected from 623 tourists traveling in Xinjiang, China, we classified the respondents into three types of high, medium, and low levels of tourism safety perception by cluster analysis, and studied the influence of tourism safety perception on destination image in multiple dimensions by means of content analysis, diversity index, one-way ANOVA, and factor analysis. We found that tourism safety perception significantly affects the cognitive image, affective image, and conative image of the destination. Tourists with a high safety perception evaluate and affectively experience destination attributes more positively with higher satisfaction and stronger willingness to revisit and recommend. Tourism safety perception affects the stereotype image of the destination to a certain extent. Tourists in general produce a broadly homogeneous stereotype image, but there are differences in diversity and emotions. Tourists with a high safety perception have a richer and more positive stereotype image. This study enriches and deepens the theory regarding the influence of tourism safety perception on destination image, and also provides a richer theoretical basis for destination image construction and precision marketing.

DNA metabarcoding reveals introduced species predominate in the diet of a threatened endemic omnivore, Telfair's skink (Leiolopisma telfairii)

Introduced species can exert disproportionately negative effects on island ecosystems, but their potential role as food for native consumers is poorly studied. Telfair's skinks are endemic omnivores living on Round Island, Mauritius, a globally significant site of biodiversity conservation. We aimed to determine the dietary diversity and key trophic interactions of Telfair's skinks, whether introduced species are frequently consumed, and if diet composition changes seasonally between male and female skinks. We used DNA metabarcoding of skink fecal samples to identify animals (COI) and plants (ITS2) consumed by skinks. There were 389 dietary presence counts belonging to 77 dietary taxa found across the 73 Telfair's skink fecal samples. Introduced taxa were cumulatively consumed more frequently than other categories, accounting for 49.4% of all detections, compared to cryptogenic (20.6%), native (20.6%), and endemic taxa (9.5%). The most frequently consumed introduced species was the ant, Pheidole megacephala, present in 40% of samples. Blue latan palm, Latania loddigesii, was the most frequently consumed endemic species, present in 33% of samples but was only detected in the dry season, when fruits are produced. We found a strong seasonal difference in diet composition explained by the presence of certain plant species solely or primarily in one season and a marked increase in the consumption of animal prey in the dry season. Male and female skinks consumed several taxa at different frequencies. These results present a valuable perspective on the role of introduced species in the trophic network of their invaded ecosystem. Both native and introduced species provide nutritional resources for skinks, and this may have management implications in the context of species conservation and island restoration.

Decrease in Carabid Beetles in Grasslands of Northwestern China: Further Evidence of Insect Biodiversity Loss

Ground-dwelling beetles are important functional components in nutrient-poor grasslands of middle temperate steppe ecosystems in China. Here, we assessed the changes in ground beetle (Coleoptera: Carabidae) communities in the grasslands of northwestern China over 12 years to improve the management and conservation of beetles all over the world. The Generalized Additive Model (GAM) was applied to estimate the changes in carabid beetle communities in two regions: a desert steppe (Yanchi region), and a typical steppe and meadow steppe (Guyuan region). During the 12-year investigation, a total of 34 species were captured. We found that species abundance and richness per survey declined by 0.2 and 11.2%, respectively. Precipitation was the main factor affecting the distribution of carabid beetles. A distinct decline in carabid beetle species in the Yanchi region indicated that they may be threatened by less precipitation and loss of habitat, which could be due to climate change. Overall, species richness was stable in the Guyuan region. It is necessary to estimate and monitor the changes in carabid beetle communities in a temperate steppe of northern China and to protect them. Extensive desertification seriously threatens the distribution of carabid beetles. Future research should develop methods to protect carabid beetle communities in temperate steppes in China.

Composition, richness and nestedness of gallery forest bird assemblages in an Amazonian savanna landscape: lessons for conservation

Gallery forests are important to the maintenance of a substantial portion of the biodiversity in neotropical savanna regions, but management guidelines specific to this forest type are limited. Here, we use birds as study group to assess if: (1) functional traits can predict the abundance and occupancy of forest species within a savanna landscape, (2) habitat structures influence the taxonomic, functional, and phylogenetic diversity of forest assemblages, and (3) less diverse gallery forest assemblages are a nested subset of more diverse assemblages living near continuous forests. Then, we propose strategies on how gallery forests can be managed to maintain their species assemblages amidst the fast expansion of human activities across tropical savanna landscapes. We studied 26 sites of gallery forests in an Amazonian savanna landscape and found that: (1) habitat specificity is the only functional trait that predicts species abundance and occupancy across a landscape; (2) phylogenetic diversity is negatively correlated with understory foliage density; (3) the percentage of forests and savannas around sites is positively correlated with both phylogenetic and functional diversity; (4) increasing human activities around gallery forest negatively influences taxonomic and functional diversity; and (5) forest bird assemblages are not distributed at random across the landscape but show a nested pattern caused by selective colonization mediated by habitat filtering. Our combined findings have three implications for the design of conservation strategies for gallery forest bird assemblages. First, maintaining the connectivity between gallery forests and adjacent continuous forests is essential because gallery forest bird assemblages are derived from continuous forest species assemblages. Second, because most species use the savanna matrix to move across the landscape, effectively managing the savanna matrices where gallery forests are embedded is as important to maintaining viable populations of forest bird species as managing the gallery forest themselves. Third, in savanna landscapes planned to be used for agriculture production, protecting gallery forests alone is not enough. Instead, gallery forests should be protected with surrounding savanna buffers to avoid the detrimental effects (edge effects and isolation) of human activities on their biodiversity.

Multidimensional tropical forest recovery

[Figure: see text].

Biodiversity and ecosystem functions depend on environmental conditions and resources rather than the geodiversity of a tropical biodiversity hotspot

Biodiversity and ecosystem functions are highly threatened by global change. It has been proposed that geodiversity can be used as an easy-to-measure surrogate of biodiversity to guide conservation management. However, so far, there is mixed evidence to what extent geodiversity can predict biodiversity and ecosystem functions at the regional scale relevant for conservation planning. Here, we analyse how geodiversity computed as a compound index is suited to predict the diversity of four taxa and associated ecosystem functions in a tropical mountain hotspot of biodiversity and compare the results with the predictive power of environmental conditions and resources (climate, habitat, soil). We show that combinations of these environmental variables better explain species diversity and ecosystem functions than a geodiversity index and identified climate variables as more important predictors than habitat and soil variables, although the best predictors differ between taxa and functions. We conclude that a compound geodiversity index cannot be used as a single surrogate predictor for species diversity and ecosystem functions in tropical mountain rain forest ecosystems and is thus little suited to facilitate conservation management at the regional scale. Instead, both the selection and the combination of environmental variables are essential to guide conservation efforts to safeguard biodiversity and ecosystem functions.

What does measuring species diversity in estuarine seagrass systems actually assess?

Relationships between species diversity and other species-density and species-richness metrics were investigated in the seagrass macrobenthos of Knysna estuarine bay, South Africa. Although a wide range of species density occurred across sites, neither Hill-Shannon nor Hill-Simpson diversity showed any significant relationship with it, although they did with species richness. Instead species diversity was very closely related to relative evenness, and (negatively) to overall assemblage abundance. No significant relationship was found between species density and evenness. Whilst there was a clear and marked decrease in species density upstream along the main estuarine channel, only one of the species-diversity indices (the Hill-Shannon) showed a significant equivalent decrease. Relationships depended on how 'species richness' was assessed, and were very strongly influenced by the superabundant local occurrence of a few individual faunal components (three gastropod and one tanaid species). Species-diversity analysis contributes nothing new in such estuarine seagrass meadows and seems best avoided.

Plant Sedimentary Ancient DNA From Far East Russia Covering the Last 28,000 Years Reveals Different Assembly Rules in Cold and Warm Climates

Woody plants are expanding into the Arctic in response to the warming climate. The impact on arctic plant communities is not well understood due to the limited knowledge about plant assembly rules. Records of past plant diversity over long time series are rare. Here, we applied sedimentary ancient DNA metabarcoding targeting the P6 loop of the chloroplast trnL gene to a sediment record from Lake Ilirney (central Chukotka, Far Eastern Russia) covering the last 28 thousand years. Our results show that forb-rich steppe-tundra and dwarf-shrub tundra dominated during the cold climate before 14 ka, while deciduous erect-shrub tundra was abundant during the warm period since 14 ka. Larix invasion during the late Holocene substantially lagged behind the likely warmest period between 10 and 6 ka, where the vegetation biomass could be highest. We reveal highest richness during 28–23 ka and a second richness peak during 13–9 ka, with both periods being accompanied by low relative abundance of shrubs. During the cold period before 14 ka, rich plant assemblages were phylogenetically clustered, suggesting low genetic divergence in the assemblages despite the great number of species. This probably originates from environmental filtering along with niche differentiation due to limited resources under harsh environmental conditions. In contrast, during the warmer period after 14 ka, rich plant assemblages were phylogenetically overdispersed. This results from a high number of species which were found to harbor high genetic divergence, likely originating from an erratic recruitment process in the course of warming. Some of our evidence may be of relevance for inferring future arctic plant assembly rules and diversity changes. By analogy to the past, we expect a lagged response of tree invasion. Plant richness might overshoot in the short term; in the long-term, however, the ongoing expansion of deciduous shrubs will eventually result in a phylogenetically more diverse community.

Effects of different types of low-intensity management on plant-pollinator interactions in Estonian grasslands

In the face of global pollinator decline, extensively managed grasslands play an important role in supporting stable pollinator communities. However, different types of extensive management may promote particular plant species and thus particular functional traits. As the functional traits of flowering plant species (e.g., flower size and shape) in a habitat help determine the identity and frequency of pollinator visitors, they can also influence the structures of plant-pollinator interaction networks (i.e., pollination networks). The aim of this study was to examine how the type of low-intensity traditional management influences plant and pollinator composition, the structure of plant-pollinator interactions, and their mediation by floral and insect functional traits. Specifically, we compared mown wooded meadows to grazed alvar pastures in western Estonia. We found that both management types fostered equal diversity of plants and pollinators, and overlapping, though still distinct, plant and pollinator compositions. Wooded meadow pollination networks had significantly higher connectance and specialization, while alvar pasture networks achieved higher interaction diversity at a standardized sampling of interactions. Pollinators with small body sizes and short proboscis lengths were more specialized in their preference for particular plant species and the specialization of individual pollinators was higher in alvar pastures than in wooded meadows. All in all, the two management types promoted diverse plant and pollinator communities, which enabled the development of equally even and nested pollination networks. The same generalist plant and pollinator species were important for the pollination networks of both wooded meadows and alvar pastures; however, they were complemented by management-specific species, which accounted for differences in network structure. Therefore, the implementation of both management types in the same landscape helps to maintain high species and interaction diversity.

Does diet breadth affect the complexity of the phytophagous insect microbiota? The case study of Chrysomelidae

Chrysomelidae is a family of phytophagous insects with a highly variable degree of trophic specialization. The aim of this study is to test whether species feeding on different plants (generalists) harbour more complex microbiotas than those feeding on a few or a single plant species (specialists). The microbiota of representative leaf beetle species was characterized with a metabarcoding approach targeting V1–V2 and V4 regions of the bacterial 16S rRNA. Almost all the analysed species harbour at least one reproductive manipulator bacteria (e.g., Wolbachia, Rickettsia). Two putative primary symbionts, previously isolated only from a single species (Bromius obscurus), have been detected in two species of the same subfamily, suggesting a widespread symbiosis in Eumolpinae. Surprisingly, the well‐known aphid symbiont Buchnera is well represented in the microbiota of Orsodacne humeralis. Moreover, in this study, using Hill numbers to dissect the components of the microbiota diversity (abundant and rare bacteria), it has been demonstrated that generalist insect species harbour a more diversified microbiota than specialists. The higher microbiota diversity associated with a wider host‐plant spectrum could be seen as an adaptive trait, conferring new metabolic potential useful to expand the diet breath, or as a result of environmental stochastic acquisition conveyed by diet.

Effects of a natural precipitation gradient on fish and macroinvertebrate assemblages in coastal streams

Anthropogenic climate change is expected to increase the aridity of many regions of the world. Surface water ecosystems are particularly vulnerable to changes in the water-cycle and may suffer adverse impacts in affected regions. To enhance our understanding of how freshwater communities will respond to predicted shifts in water-cycle dynamics, we employed a space for time approach along a natural precipitation gradient on the Texas Coastal Prairie. In the spring of 2017, we conducted surveys of 10 USGS-gauged, wadeable streams spanning a semi-arid to sub-humid rainfall gradient; we measured nutrients, water chemistry, habitat characteristics, benthic macroinvertebrates, and fish communities. Fish diversity correlated positively with precipitation and was negatively correlated with conductivity. Macroinvertebrate diversity peaked within the middle of the gradient. Semi-arid fish and invertebrate communities were dominated by euryhaline and live-bearing taxa. Sub-humid communities contained environmentally sensitive trichopterans and ephemeropterans as well as a variety of predatory fish which may impose top-down controls on primary consumers. These results warn that aridification coincides with the loss of competitive and environmentally sensitive taxa which could yield less desirable community states.

Rarity facets of biodiversity: Integrating Zeta diversity and Dark diversity to understand the nature of commonness and rarity

Measuring commonness and rarity is pivotal to ecology and conservation. Zeta diversity, the average number of species shared by multiple sets of assemblages, and Dark diversity, the number of species that could occur in an assemblage but are missing, have been recently proposed to capture two aspects of the commonness-rarity spectrum. Despite a shared focus on commonness and rarity, thus far, Zeta and Dark diversities have been assessed separately. Here, we review these two frameworks and suggest their integration into a unified paradigm of the "rarity facets of biodiversity." This can be achieved by partitioning Alpha and Beta diversities into five components (the Zeta, Eta, Theta, Iota, and Kappa rarity facets) defined based on the commonness and rarity of species. Each facet is assessed in traditional and multiassemblage fashions to bridge conceptual differences between Dark diversity and Zeta diversity. We discuss applications of the rarity facets including comparing the taxonomic, functional, and phylogenetic diversity of rare and common species, or measuring species' prevalence in different facets as a metric of species rarity. The rarity facets integrate two emergent paradigms in biodiversity science to better understand the ecology of commonness and rarity, an important endeavor in a time of widespread changes in biodiversity across the Earth.

A keystone mutualism promotes resistance to invasion

It is not uncommon for one or a few species, and their interactions, to have disproportionate effects on other species in ecological communities. Such keystone interactions might affect how communities respond to the invasion of non-native species by preventing or inhibiting the establishment, spread or impact of non-native species. We explore whether a keystone mutualism among a hummingbird-mistletoe-marsupial promotes ecological resistance to an invasive pollinator, the bumblebee Bombus terrestris, by comparing data collected at sites prior to bumblebee invasion to data collected 11 years after the invasion in sites with and without the keystone mutualism. We built pollination networks and focused on network motifs, regarded as building blocks of networks, to identify the central pollinators and estimate the change in their interactions after invasion of B. terrestris. We also estimated the interaction rewiring across the season in post-invasion networks and tested it as a possible mechanism explaining how the keystone mutualism increased ecological resistance to invasion. We found two times more species in post-invasion sites with the keystone mutualism than in post-invasion sites without the keystone mutualism. Moreover, we found that invasive bumblebee reduced the strength and interaction niche of the five central pollinator species while increasing its own strength and interaction niche, suggesting a replacement of interactions. Also, we found that the keystone mutualism promoted resistance to B. terrestris invasion by reducing its negative impacts on central species. In the presence of the keystone mutualism, central species had three times more direct interactions than in sites without this keystone mutualism. The higher interaction rewiring, after invasion of B. terrestris, in sites with the keystone mutualism indicates greater chances of central pollinators to form new interactions and reduces their competence for resources with the non-native bumblebee. Our results demonstrate that a keystone mutualism can enhance community resistance against the impacts of a non-native invasive pollinator by increasing species diversity and promoting interaction rewiring in the community. This study suggests that the conservation of mutualisms, especially those considered keystone, could be essential for long-term preservation of natural communities under current and future impacts of global change.

Biogeography, diversity and environmental relationships of shelf and deep-sea benthic Amphipoda around Iceland

The waters around Iceland, bounding the Northern North Atlantic and the Nordic seas, are a region characterized by complex hydrography and seabed topography. This and the presence of the Greenland-Iceland-Faroe-Scotland ridge (GIFR) are likely to have a major impact on the diversity and distribution of the benthic fauna there. Biodiversity in this region is also under increasing threat from climate-induced changes, ocean warming and acidification in particular, affecting the marine realm. The aim of the present study was to investigate the biodiversity and distributional patterns of amphipod crustaceans in Icelandic waters and how it relates to environmental variables and depth. A comprehensive data set from the literature and recent expeditions was compiled constituting distributional records for 355 amphipod species across a major depth gradient (18–3,700 m). Using a 1° hexagonal grid to map amphipod distributions and a set of environmental factors (depth, pH, phytobiomass, velocity, dissolved oxygen, dissolved iron, salinity and temperature) we could identify four distinct amphipod assemblages: A Deep-North, Deep-South, and a Coastal cluster as well as one restricted to the GIFR. In addition to depth, salinity and temperature were the main parameters that determined the distribution of amphipods. Diversity differed greatly between the depth clusters and was significantly higher in coastal and GIFR assemblages compared to the deep-sea clusters north and south of the GIFR. A variety of factors and processes are likely to be responsible for the perceived biodiversity patterns, which, however, appear to vary according to region and depth. Low diversity of amphipod communities in the Nordic basins can be interpreted as a reflection of the prevailing harsh environmental conditions in combination with a barrier effect of the GIFR. By contrast, low diversity of the deep North Atlantic assemblages might be linked to the variable nature of the oceanographic environment in the region over multiple spatio-temporal scales. Overall, our study highlights the importance of amphipods as a constituent part of Icelandic benthos. The strong responses of amphipod communities to certain water mass variables raise the question of whether and how their distribution will change due to climate alteration, which should be a focus of future studies.

Patterns and drivers determining phyllostomid bat diversity in land-bridge islands off the south-east coast of Brazil

Few studies that apply the theory of island biogeography have considered the functional and phylogenetic dimensions of diversity. However, the joint use of the three diversity dimensions, i.e. taxonomic, functional and phylogenetic, can help us to gain a better understanding of the mechanisms underlying ecological and evolutionary processes. Here, we compare phyllostomid bat assemblages between five land-bridge islands off the south-east coast of Brazil and compare these islands with three sites on the mainland. For this, we have estimated the three dimensions of α- and β-diversity, nestedness and community indexes based on mean trait values for the islands and the mainland. The mainland showed higher species richness and taxonomic, functional and phylogenetic diversity. In addition, only species richness and phylogenetic diversity were positively related to island area. Taxonomically and functionally, the poorest assemblages (minor islands) were subgroups of the richer assemblages (mainland and larger islands). Taken together, our results show that bat assemblages of smaller islands tend to be more sensitive to changes in species richness than those of larger islands, with the larger islands working as a ‘source’ of species for small islands. These results demonstrate the high conservation value of the larger islands, which has direct consequences for local population dynamics of phyllostomid bats.

The use of diversity indices for local assessment of marine sediment quality

Diversity indices are commonly used to measure changes in marine benthic communities. However, the reliability (and therefore suitability) of these indices for detecting environmental change is often unclear because of small sample size and the inappropriate choice of communities for analysis. This study explored uncertainties in taxonomic density and two indices of community structure in our target region, Japan, and in two local areas within this region, and explored potential solutions. Our analysis of the Japanese regional dataset showed a decrease in family density and a dominance of a few species as sediment conditions become degraded. Local case studies showed that species density is affected by sediment degradation at sites where multiple communities coexist. However, two indices of community structure could become insensitive because of masking by community variability, and small sample size sometimes caused misleading or inaccurate estimates of these indices. We conclude that species density is a sensitive indicator of change in marine benthic communities, and emphasise that indices of community structure should only be used when the community structure of the target community is distinguishable from other coexisting communities and there is sufficient sample size.