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Biotic responses to global change include directional shifts in organismal traits. Body size, an integrative trait that determines demographic rates and ecosystem functions, is often thought to be shrinking in the Anthropocene. Here, we assess the prevalence of body size change in six taxon groups across 5,032 assemblage time-series spanning 1960-2020. Using the Price equation to partition this change into within-species body size versus compositional changes, we detect prevailing decreases in body size through time. Change in assemblage composition contributes more to body size changes than within-species trends, but both components show substantial variation in magnitude and direction. The biomass of assemblages remains remarkably stable as decreases in body size trade-off with increases in abundance.One-Sentence SummaryVariable within-species and compositional trends combine into shrinking body size, abundance increases and stable biomass.

Earth’s biodiversity continues to change rapidly through the Anthropocene1, including widespread reordering of species in space2,3 and time4,5. A common expectation of this reordering is that the species composition of sites is becoming increasingly similar across space, known as biotic homogenization, due to anthropogenic pressures and invasive species6,7. While many have argued that homogenisationis a common phenomenon (e.g., 6–10), it is equally plausible that communities can become more different through time, known as differentiation, including through human impacts11,12. Here, we used a novel adaptation of Whittaker’s (1960)13 spatial-scale explicit diversity partition to assess the prevalence of biotic homogenisation and differentiation, and associated changes in species richness at smaller and larger spatial scales. We applied this approach to a compilation of species assemblages from 205 metacommunities that were surveyed for 10-64 years, and 54 ‘checklists’ that spanned 50-500+ years. Scale-dependent changes of species richness were highly heterogeneous, with approximately equal evidence for homogenisation(i.e., lower β-diversity) and differentiation (i.e., higher β-diversity) through time across all regions, taxa and data types. Homogenisation was most often due to increased numbers of widespread species, which tended to increase both local and regional richness through time. These results emphasise that an explicit consideration of spatial scale is needed to fully understand biodiversity change in the Anthropocene.

SAB, TE, AS, and JMC were supported by the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, funded by the German Research Foundation (FZT 118). Biodiversity metrics often integrate data on the presence and abundance of multiple species. Yet our understanding of covariation between changes to the numbers of individuals, the evenness of species relative abundances, and the total number of species remains limited. Using individual-based rarefaction curves, we introduce a conceptual framework to understand how expected positive relationships among changes in abundance, evenness and richness arise, and how they can break down. We then examined interdependencies between changes in abundance, evenness and richness in more than 1100 assemblages sampled either through time or across space. As predicted, richness changes were greatest when abundance and evenness changed in the same direction, and countervailing changes in abundance and evenness acted to constrain the magnitude of changes in species richness. Site-to-site differences in abundance, evenness, and richness were often decoupled, and pairwise relationships between these components across assemblages were weak. In contrast, changes in species richness and relative abundance were strongly correlated for assemblages varying through time. Temporal changes in local biodiversity showed greater inertia and stronger relationships between the component changes when compared to site-to-site variation. Overall, local variation in assemblage diversity was rarely due to repeated passive samples from an approximately static species abundance distribution. Instead, changing species relative abundances often dominated local variation in diversity. Moreover, how changing relative abundances combined with changes to total abundance frequently determined the magnitude of richness changes. Embracing the interdependencies between changing abundance, evenness and richness can provide new information for better understanding biodiversity change in the Anthropocene. Publisher PDF

1. The process of standardizing taxon names, taxonomic name harmonization, is necessary to properly merge data indexed by taxon names. The large variety of taxonomic databases and related tools are often not well described. It is often unclear which databases are actively maintained or what is the original source of taxonomic information. In addition, software to access these databases is developed following non-compatible standards, which creates additional challenges for users. As a result, taxonomic harmonization has become a major obstacle in ecological studies that seek to combine multiple datasets. 2. Here, we review and categorize a set of major taxonomic databases publicly available as well as a large collection of R packages to access them and to harmonize lists of taxon names. We categorized available taxonomic databases according to their taxonomic breadth (e.g. taxon-specific vs multi-taxa) and spatial scope (e.g. regional vs global), highlighting strengths and caveats of each type of database. We divided R packages according to their function, (e.g. syntax standardization tools, access to online databases, etc.) and highlighted overlaps among them. We present our findings (e.g. network of linkages, data and tool characteristics) in a ready-to-use Shiny web application (available at: https://mgrenie.shinyapps.io/taxharmonizexplorer/). 3. We also provide general guidelines and best practice principles for taxonomic name harmonization. As an illustrative example, we harmonized taxon names of one of the largest databases of community time series currently available. We showed how different workflows can be used for different goals, highlighting their strengths and weaknesses and providing practical solutions to avoid common pitfalls. 4. To our knowledge, our opinionated review represents the most exhaustive evaluation of links among and of taxonomic databases and related R tools. Finally, based on our new insights in the field, we make recommendations for users, database managers, and package developers alike.

The quantity and quality of ecological data have rapidly increased in the last decades, bringing ecology into the realm of big data. Frequently, multiple databases with different origins and data characteristics are combined to address new research questions. Taxonomic name harmonization, i.e., the process of standardizing taxon names according to common sources such as taxonomic databases (TD), is necessary to properly combine multiple databases using species names. In order to be able to develop proper data matching workflows, TDs and tools using them need to be clearly and comprehensively described. But this is rarely the case. Common problems users have to deal with are: poorly described taxonomic concepts behind biological databases, lack of information when TDs are actively updated, and details regarding where the primary source of taxonomic information comes from (e.g., secondary TDs taking information from primary TDs). In addition, software to access these TDs is not always advertised, partly redundant, or developed with incompatible standards, creating additional challenges for users. As a result, taxonomic name harmonization has become a major difficulty in ecological studies. Researchers face a jungle of primary and secondary TDs with a diversity of tools to access them and no clear workflow on how to practically proceed. As a consequence, it is hard for users to know which TD, tool and workflow will fit the task at hand and lead to the most robust results when combining different biological datasets. Here, we present an overview of major TDs as well as an extensive review of R packages to access TDs, and to harmonize taxa names. We developed an R Shiny web application summarizing meta-data and linkages among TDs and R packages (Figs 1, 2), which users can explore to learn about general features of TDs and tools and how they are linked among one another. This is particularly helpful to assist users when deciding on the TDs and tools that best fit the tasks and data at hand and to develop more informed workflows for taxonomic name harmonization. Finally, from our review and using the Shiny app, we were able to provide general best practice principles to harmonize taxonomic names and avoid common pitfalls. To our knowledge, this study represents the most exhaustive review of TDs and R tools for taxonomic name harmonization. Our intuitive Shiny app can help make practical decisions when harmonizing taxonomic names across multiple datasets. Finally, our proposed workflows, based on conservative guideline principles (e.g., making sure incompatible taxonomic hypotheses are not combined together), provide a hands-on approach for taxonomic harmonization, which focuses on the quality of the end results while maximizing the number of species correctly matched.

Biodiversity metrics often integrate data on the presence and abundance of multiple species. Yet our understanding of how changes to the numbers of individuals, the evenness of species’ relative abundances, and the total number of species covary remains limited, both theoretically and empirically. Using individual-based rarefaction curves, we first show how expected positive relationships among changes in abundance, evenness and richness arise, and how they can break down. We then examined the interdependency between changes in abundance, evenness and richness more than 1100 assemblages sampled either through time or across space. As expected, richness changes were greatest when abundance and evenness changed in the same direction, whereas countervailing changes in abundance and evenness acted to constrain the magnitude of changes in species richness. Site-to-site variation in diversity was greater than rates of change through time. Moreover, changes in abundance, evenness, and richness were often spatially decoupled, and pairwise relationships between changes in these components were weak between sites. In contrast, changes in species richness and relative abundance were strongly correlated for assemblages sampled through time, meaning temporal changes in local biodiversity showed greater inertia and stronger relationships between the components changes when compared to site-to-site variation. Both temporal and spatial variation in local assemblage diversity were rarely attributable solely to changes in assemblage size sampling more or less of a static species abundance distribution. Instead, changing species’ relative abundances often dominate local variation in diversity. Moreover, how these altered patterns of relative abundance combine with changes to total abundance strongly determine the magnitude of richness changes. Interdependencies found here suggest looking beyond changes in abundance, evenness and richness as separate responses offering unique insights into diversity change can increase our understanding of biodiversity change.

Aim: The island species���area relationship (ISAR) quantifies how the number of species increases as the area of an island or island-like habitat gets larger and is one of the most general patterns in ecology. However, studies that measure the ISAR often confound variation in sampling methodology and analyses, precluding appropriate syntheses of its underlying mechanisms. Most ISAR studies use only presence���absence data at the whole-island scale, whereas we planned to use a framework that applies individual-based rarefaction to synthesize whether and how the ISAR differs from the null expectation of the passive sampling hypothesis. Location: Five hundred and five islands from 34 different archipelagos across the world, including oceanic islands, lake islands and forest islands. Major taxa studied: Local assemblages of plants, invertebrates, herpetofauna, birds and mammals. Methods: We collated local-scale species abundance data from multiple archipelagos (median of 12 islands per study) and used a rarefaction-based approach to synthesize the relationship between island size and (1) sample effort-controlled rarefied species richness, or (2) an effective number of species derived from the probability of interspecific encounter (an index of community evenness). Results: When we applied rarefaction to control for sampling effort, the numbers of species and their relative abundances across all studies differed from the passive sampling hypothesis. Our measure of evenness also increased with island size, suggesting that the disproportionate effects we observed influenced both rarer and more common species. We found few associations between the slope of this effect and island type or taxon, but we did find that island archipelagos with greater elevational heterogeneity also deviated more from the null expectation than those with less heterogeneity. Main conclusions: Using a synthetic approach across island archipelagos, we reject the null expectation that passive sampling causes the ISAR and instead suggest that ecological mechanisms leading to disproportionate (non-random) effects on larger relative to smaller islands are predominant.

Background and aims Since its emergence in the mid‐20th century, invasion biology has matured into a productive research field addressing questions of fundamental and applied importance. Not only has the number of empirical studies increased through time, but also has the number of competing, overlapping and, in some cases, contradictory hypotheses about biological invasions. To make these contradictions and redundancies explicit, and to gain insight into the field’s current theoretical structure, we developed and applied a Delphi approach to create a consensus network of 39 existing invasion hypotheses. Results The resulting network was analysed with a link‐clustering algorithm that revealed five concept clusters (resource availability, biotic interaction, propagule, trait and Darwin’s clusters) representing complementary areas in the theory of invasion biology. The network also displays hypotheses that link two or more clusters, called connecting hypotheses , which are important in determining network structure. The network indicates hypotheses that are logically linked either positively (77 connections of support) or negatively (that is, they contradict each other; 6 connections). Significance The network visually synthesizes how invasion biology’s predominant hypotheses are conceptually related to each other, and thus, reveals an emergent structure – a conceptual map – that can serve as a navigation tool for scholars, practitioners and students, both inside and outside of the field of invasion biology, and guide the development of a more coherent foundation of theory. Additionally, the outlined approach can be more widely applied to create a conceptual map for the larger fields of ecology and biogeography., Global Ecology and Biogeography, 29 (6), ISSN:1466-822X, ISSN:1466-8238

Associated data is available at: https://doi.org/10.5061/dryad.595718c; International audience; Habitat destruction is the single greatest anthropogenic threat to biodiversity. Decades of research on this issue have led to the accumulation of hundreds of data sets comparing species assemblages in larger, intact, habitats to smaller, more fragmented, habitats. Despite this, little synthesis or consensus has been achieved, primarily because of non-standardized sampling methodology and analyses of notoriously scale-dependent response variables (i.e., species richness). To be able to compare and contrast the results of habitat fragmentation on species’ assemblages, it is necessary to have the underlying data on species abundances and sampling intensity, so that standardization can be achieved. To accomplish this, we systematically searched the literature for studies where abundances of species in assemblages (of any taxa) were sampled from many habitat patches that varied in size. From these, we extracted data from several studies, and contacted authors of studies where appropriate data were collected but not published, giving us 117 studies that compared species assemblages among habitat fragments that varied in area. Less than one-half (41) of studies came from tropical forests of Central and South America, but there were many studies from temperate forests and grasslands from all continents except Antarctica. Fifty-four of the studies were on invertebrates (mostly insects), but there were several studies on plants (15), birds (16), mammals (19), and reptiles and amphibians (13). We also collected qualitative information on the length of time since fragmentation. With data on total and relative abundances (and identities) of species, sampling effort, and affiliated meta-data about the study sites, these data can be used to more definitively test hypotheses about the role of habitat fragmentation in altering patterns of biodiversity. There are no copyright restrictions. Please cite this data paper and the associated Dryad data set if the data are used in publications.

Biological indicators are frequently used to assess the effects of anthropogenic stressors on freshwater ecosystems. The structure of fish communities and their response to stressors have been commonly described by taxonomic richness, diversity and evenness. More recently, functional structure of communities has also been suggested to be a reliable indicator of disturbance. This article aimed at testing whether taxonomic and functional diversity metrics can provide comparable or complementary information on the response of fish communities to eutrophication and abundance of non-native species in reservoirs. Comparison of the responses of taxonomic and functional diversities to biogeography, habitat and stressors was made in 112 French reservoirs. Widely observed effects of biogeographic and habitat variables on taxonomic and functional diversities were identified. Taxonomic and functional richness metrics notably increased with lake area and temperature respectively. Taxonomic diversity metrics did not respond to any stressor, while all functional diversity metrics were found to be impacted by non-native species. Eutrophication was further found to decrease the impact of non-native species on two functional diversity metrics: evenness and divergence. Our study therefore reveals that functional metrics are more sensitive than taxonomic metrics to anthropogenic stressors in the studied reservoirs. Still, the multiple linear regressions tested had overall low explanatory power. Further refinements will thus be needed to use this type of metrics in an impact assessment scheme.

In naturally disturbed systems, harsh environmental conditions act as filters on the regional species pool, restricting the number of taxa able to form a local community to those with traits promoting resistance or resilience. Thus, communities in highly disturbed ecosystems may be less sensitive to a given disturbance than those in less disturbed ecosystems. We explored this idea by examining the response of aquatic invertebrate communities to flow intermittence in gravel-bed, braided rivers (BRs). Flow intermittence is considered a major driver of communities in rivers, but its influence on communities in BRs, which are recognized as naturally highly disturbed environments, is relatively unexplored. We used a multisite Before-After–Control-Impact (BACI) design to quantify the effects of drying events of different durations (moderate: 2–3 wk, severe: 1–3 mo) on invertebrate communities in 8 BRs in southeastern France. As predicted, no effects of flow intermittence were detected 1 to 4 mo after fl...

In this study we developed a novel methodology based on fish communities to assess the ecological potential of central European reservoirs. Using the hindcasting approach, our index predicts values that could be observed in the absence of pressures for each reservoir depending on their environmental characteristics. Fish data were collected from 144 French and Czech reservoirs between 2005 and 2013 by standardized benthic gillnet sampling and transformed to functional and taxonomical metrics. After all validation by multiple testing of models redundancy and pressure-response, the final index was composed of three metrics: total biomass of fish, abundance of invertivores/piscivores, and abundance of planktivorous fish. The index accurately identifies reservoirs that are lightly, moderately and heavily affected by eutrophication. In addition to French and Czech reservoirs, this index could be a useful tool for countries with few reservoirs and the basis for further collaborative studies.