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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.

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.

The impact of species loss on ecosystems functioning depends on the amount of trait similarity between species, i.e. functional redundancy, but it is also influenced by the order in which species are lost. Here we investigated redundancy and sensitivity patterns across fish assemblages in lakes, rivers and estuaries. Several scenarios of species extinction were simulated to determine whether the loss of vulnerable species (with high propensity of extinction when facing threats) causes a greater functional alteration than random extinction. Our results indicate that the functional redundancy tended to increase with species richness in lakes and rivers, but not in estuaries. We demonstrated that i) in the three systems, some combinations of functional traits are supported by non-redundant species, ii) rare species in rivers and estuaries support singular functions not shared by dominant species, iii) the loss of vulnerable species can induce greater functional alteration in rivers than in lakes and estuaries. Overall, the functional structure of fish assemblages in rivers is weakly buffered against species extinction because vulnerable species support singular functions. More specifically, a hotspot of functional sensitivity was highlighted in the Iberian Peninsula, which emphasizes the usefulness of quantitative criteria to determine conservation priorities info:eu-repo/semantics/publishedVersion

[Departement_IRSTEA]Eaux [TR1_IRSTEA]QUASARE; International audience; The impact of species loss on ecosystems functioning depends on the amount of trait similarity between species, i.e. functional redundancy, but it is also influenced by the order in which species are lost. Here we investigated redundancy and sensitivity patterns across fish assemblages in lakes, rivers and estuaries. Several scenarios of species extinction were simulated to determine whether the loss ofvulnerable species (with high propensity of extinction when facing threats) causes a greater functional alteration than random extinction. Our results indicate that the functional redundancy tended toincrease with species richness in lakes and rivers, but not in estuaries. We demonstrated that i) in the three systems, some combinations of functional traits are supported by non-redundant species, ii) rarespecies in rivers and estuaries support singular functions not shared by dominant species, iii) the loss of vulnerable species can induce greater functional alteration in rivers than in lakes and estuaries. Overall, the functional structure of fish assemblages in rivers is weakly buffered against species extinction because vulnerable species support singular functions. More specifically, a hotspot of functionalsensitivity was highlighted in the Iberian Peninsula, which emphasizes the usefulness of quantitative criteria to determine conservation priorities.

International audience; Multiple anthropogenic pressures including the widespread introductions of non‐native species threaten biodiversity and ecosystem functioning notably by modifying the trophic structure of communities. Here, we provided a global evaluation of the impacts of non‐native species on the isotopic structure (δ13C and δ15N) of freshwater fish communities. We gathered the stable isotope values (n = 4030) of fish species in 496 fish communities in lentic (lakes, backwaters, reservoirs) and lotic (running waters such as streams, rivers) ecosystems throughout the world and quantified the isotopic structure of communities. Overall, we found that communities containing non‐native species had a different isotopic structure than communities without non‐native species. However, these differences varied between ecosystem types and the trophic positions of non‐native species. In lotic ecosystems, communities containing non‐native species had a larger total isotopic niche than communities without non‐native species. This was primarily driven by the addition of non‐native predators at the top of the food chain that increased δ15N range without modifying the isotopic niche size of native species. In lentic ecosystems, non‐native primary consumers increased δ15N range and this was likely driven by an increase of resource availability for species at higher trophic levels, increasing food chain length. The introduction of non‐native secondary consumers at the centre of the isotopic niche of recipient communities decreased the core isotopic niche size, the δ13C range of recipient communities and the total isotopic niche of coexisting native species. These results suggested a modified contribution of the basal resources consumed (e.g. multi‐chain omnivory) and an increase level of competition with native species. Our results notably imply that, by affecting the isotopic structure of freshwater fish communities at a global scale, non‐native species represent an important source of perturbations that should be accounted for when investigating macro‐ecological patterns of community structure and biotic interactions.