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Estimating biodiversity change across the planet in the context of widespread human modification is a critical challenge. Here, we review how biodiversity has changed in recent decades across scales and taxonomic groups, focusing on four diversity metrics: species richness, temporal turnover, spatial beta-diversity and abundance. At local scales, change across all metrics includes many examples of both increases and declines and tends to be centred around zero, but with higher prevalence of declining trends in beta-diversity (increasing similarity in composition across space or biotic homogenization) and abundance. The exception to this pattern is temporal turnover, with changes in species composition through time observed in most local assemblages. Less is known about change at regional scales, although several studies suggest that increases in richness are more prevalent than declines. Change at the global scale is the hardest to estimate accurately, but most studies suggest extinction rates are probably outpacing speciation rates, although both are elevated. Recognizing this variability is essential to accurately portray how biodiversity change is unfolding, and highlights how much remains unknown about the magnitude and direction of multiple biodiversity metrics at different scales. Reducing these blind spots is essential to allow appropriate management actions to be deployed. This article is part of the theme issue ‘Detecting and attributing the causes of biodiversity change: needs, gaps and solutions’.

Funding: A.E.M. thanks the Leverhulme Trust (RPG-2019–402) for support. Recent research has uncovered rapid compositional and structural reorganization of ecological assemblages, with these changes particularly evident in marine ecosystems. However, the extent to which these ongoing changes in taxonomic diversity are a proxy for change in functional diversity is not well understood. Here we focus on trends in rarity to ask how taxonomic rarity and functional rarity covary over time. Our analysis, drawing on 30 years of scientific trawl data, reveals that the direction of temporal shifts in taxonomic rarity in two Scottish marine ecosystems is consistent with a null model of change in assemblage size (i.e. change in numbers of species and/or individuals). In both cases, however, functional rarity increases, as assemblages become larger, rather than showing the expected decrease. These results underline the importance of measuring both taxonomic and functional dimensions of diversity when assessing and interpreting biodiversity change. Publisher PDF

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.

Funding: Jane and Aatos Erkko Foundation (LHA); Japan Society for the Promotion of Science (JP19K21569) (HS); Leverhulme Trust (RPG-2019-402) (AEM, MD, FM, AP); Leverhulme Trust Research Centre - the Leverhulme Centre for Anthropocene Biodiversity (MD); USA National Science Foundation grant 2019470 (BJM, NJG); USA National Science Foundation/ UKRI Natural Environment Research Council grant NE/V009338/1 (MD). The species composition of plant and animal assemblages across the globe has changed substantially over the past century. How do the dynamics of individual species cause this change? We classified species into seven unique categories of temporal dynamics based on the ordered sequence of presences and absences that each species contributes to an assemblage time series. We applied this framework to 14,434 species trajectories comprising 280 assemblages of temperate marine fishes surveyed annually for 20 or more years. Although 90% of the assemblages diverged in species composition from the baseline year, this compositional change was largely driven by only 8% of the species` trajectories. Quantifying the reorganization of assemblages based on species shared temporal dynamics should facilitate the task of monitoring and restoring biodiversity. We suggest ways in which our framework could provide informative measures of compositional change, as well as leverage future research on pattern and process in ecological systems. Publisher PDF

Spatial structure of species change Biodiversity is undergoing rapid change driven by climate change and other human influences. Blowes et al. analyze the global patterns in temporal change in biodiversity using a large quantity of time-series data from different regions (see the Perspective by Eriksson and Hillebrand). Their findings reveal clear spatial patterns in richness and composition change, where marine taxa exhibit the highest rates of change. The marine tropics, in particular, emerge as hotspots of species richness losses. Given that human activities are affecting biodiversity in magnitudes and directions that differ across the planet, these findings will provide a much needed biogeographic understanding of biodiversity change that can help inform conservation prioritization. Science , this issue p. 339 ; see also p. 308

Funding: I.T.S. thanks CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior -Coordination for the Improvement of Higher Education Personnel), process number: #88881.129579/2016–01 (Finance Code 001) for a PhD scholarship. A.E.M. thanks the Leverhulme Trust (RPG-2019–402) for support. Rare species, which represent a large fraction of the taxa in ecological assemblages, account for much of the biological diversity on Earth. These species make substantial contributions to ecosystem functioning, and are targets of conservation policy. Here we adopt an integrated approach, combining information on the rarity of species trait combinations, and their spatial restrictedness, to quantify the biogeography of rare fish (a taxon with almost 13,000 species) in the world’s oceans. We find concentrations of rarity, in excess of what is predicted by a null expectation, near the coasts and at higher latitudes. We also observe mismatches between these rarity hotspots and marine protected areas. This pattern is repeated for both major groupings of fish, the Actinopterygii (bony fish) and Elasmobranchii (sharks, skates and rays). These results uncover global patterns of rarity that were not apparent from earlier work, and highlight the importance of using metrics that incorporate information on functional traits in the conservation and management of global marine fishes. Publisher PDF

Funding: CAPES (Coordination for the Improvement of Higher Education Personnel), process number: #88881.129579/2016–01 (Finance Code 001). A.E.M. and F.M.thank the ERC (ERC AdG BioTIME 250189 and ERC PoC BioCHANGE 727440) and the Leverhulme Trust (RPG-2019–402) for support. Overexploitation is recognized as one of the main threats to global biodiversity. Here, we report a widespread change in the functional diversity of fisheries catches from the large marine ecosystems (LMEs) of the world over the past 65 years (1950 to 2014). The spatial and temporal trends of functional diversity exploited from the LMEs were calculated using global reconstructed marine fisheries catch data provided by the Sea Around Us initiative (including subsistence, artisanal, recreational, industrial fisheries, and discards) and functional trait data available in FishBase. Our analyses uncovered a substantial increase in the functional richness of both ray-finned fishes (80% of LMEs) and cartilaginous species (sharks and rays) (75% of LMESs), in line with an increase in the taxonomic richness, extracted from these ecosystems. The functional evenness and functional divergence of these catches have also altered substantially over the time span of this study, with considerable geographic variation in the patterns detected. These trends show that global fisheries are increasingly targeting species that play diverse roles within the marine ecosystem and underline the importance of incorporating functional diversity in ecosystem management. Postprint

Funding: FM and AEM are grateful to the European Research Council (ERCAdG BioTIME 250189 and ERCPoC BioCHANGE 727440). Marine fish are an irreplaceable resource but are currently under threat due to overfishing and climate change. To date, most of the emphasis has been on single stocks or populations of economic importance. However, commercially valuable species are embedded in assemblages of many species and there is only limited understanding of the extent to which the structure of whole communities has altered in recent years. Most assemblages are dominated by one or a few species, with these highly abundant species underpinning ecosystem services and harvesting decisions. This paper shows that there have been marked temporal changes in the dominance structure of Scottish marine assemblages over the last three decades, where dominance is measured as the proportional numerical abundance of the most dominant species. We report contrasting patterns in both the identity of the dominant species, and shifts in the relative abundance of the dominant in assemblages to the east and west of Scotland. This result highlights the importance of multi-species analyses of harvested stocks and has implications not only for fisheries management but also for consumer choices. Postprint

ITS was supported by stipends provided by CAPES (Coordination for the Improvement of Higher Education Personnel, #88881.129579/2016-01) and CNPq (National Council for Scientific and Technological Development). SFG has been supported by CNPq (#303180/2016-1 and #402469/2016-0), CAPES/FAPITEC (#88881.157961/2017-01; #88881.157451/2017-01) and Instituto Serrapilheira (G-1709-18372). AEM and FM acknowledge funding from ERC (ERCAdG BioTIME 250189 and ERCPoC BioCHANGE 727440). ITS, PAM and SFG are members of the National Science and Technology Institute of Ecology, Evolution, and Conservation of Biodiversity – INCT EECBio (CNPq/FAPEG). Environmental catastrophes may precipitate local species extinctions, hence altering community composition (i.e., β-diversity) at the regional scale. Assessments of the impacts of such disturbance may be hindered by the availability of sufficiently high-quality before/after data. However, simulations can provide key insights into the nature of the biodiversity change involved, even when data are limited. Using a simulation approach, we asked how disturbances might have affected regional patterns of β-diversity, following the ‘Mariana disaster’ at the Bento Rodrigues dam in the Doce River Basin. To do this we evaluated the possible consequences of different levels of local species extinctions on the regional taxonomic and functional β-diversity. Our analysis drew on information from all six neighbouring river basins and contrasted the β-diversity prior to the disaster with four hypothetical scenarios of species removal from the Doce Basin of 25, 50, 75, and 100%. We found that local species extinction increases regional taxonomic β-diversity as a result of a higher contribution of nestedness (from 13% to 19%). Functional β-diversity also increases, but with an even greater contribution of nestedness (67–81%). Our results suggest that, if the disaster prompted any extinction, this was likely to lead to altered patterns of regional β-diversity by making assemblages taxonomically more distinct but functionally more similar. These changes result from the loss of unique species and, in particular, their functional traits. Our work highlights the utility of simulation approaches in environmental impact assessment and conservation management in data-poor circumstances. Publisher PDF

This project was funded by the European Research Council (AdG BioTIME 250189 and PoC BioCHANGE 727440). A.E.M. also acknowledges support from the Royal Society and M.D. from the Scottish Funding Council (Marine Alliance for Science and Technology for Scotland Grant HR09011). The Earth’s ecosystems are under unprecedented pressure, yet the nature of contemporary biodiversity change is not well understood. Growing evidence that community size is regulated highlights the need for improved understanding of community dynamics. As stability in community size could be underpinned by marked temporal turnover, a key question is the extent to which changes in both biodiversity dimensions (temporal α- and temporal β-diversity) covary within and among the assemblages that comprise natural communities. Here, we draw on a multiassemblage dataset (encompassing vertebrates, invertebrates, and unicellular plants) from a tropical freshwater ecosystem and employ a cyclic shift randomization to assess whether any directional change in temporal α-diversity and temporal β-diversity exceeds baseline levels. In the majority of cases, α-diversity remains stable over the 5-y time frame of our analysis, with little evidence for systematic change at the community level. In contrast, temporal β-diversity changes are more prevalent, and the two diversity dimensions are decoupled at both the within- and among-assemblage level. Consequently, a pressing research challenge is to establish how turnover supports regulation and when elevated temporal β-diversity jeopardizes community integrity. Postprint Postprint

Authors acknowledge the following funding: European Research Council (ERC) Advanced Grant (AdG) BioTIME (250198) and ERC Proof of Concept (PoC) BioCHANGE (727440) to AEM. Issue Biodiversity change, that is how the taxonomic identities and abundances of species in ecological systems are changing over time, has two facets: temporal α diversity and temporal β diversity. To date, temporal α diversity has received most attention even though compositional shifts in assemblages exceed expectations based on ecological theory. Growing concern about the state of the world’s biodiversity highlights the need for better understanding of the extent, and consequences, of compositional reorganization in ecological systems. Challenges Most methods of measuring β diversity have been developed in a spatial context. We discuss the additional challenges involved in the assessment of temporal change, summarize existing methodological approaches, highlight the importance of establishing relevant baselines, and identify the need for appropriate null models of temporal β diversity. Given considerable potential for research on the macroecology of temporal β diversity we suggest future directions and challenges. Conclusions Although data availability remains the main impediment to improved quantification of temporal β diversity at macroecological scales, there are substantial opportunities for improved methodology and theory. Taxonomic β diversity has received most attention, but other dimensions of diversity, including functional and phylogenetic, should be part of integrated assessments of biodiversity change. Future approaches need to be ecologically meaningful and interpretable as well as statistically robust. Postprint

The authors are grateful to the European Research Council (AdG BioTIME 250189 and PoC BioCHANGE 72744) for funding. MD is funded by a Leverhulme Fellowship from the Leverhulme Trust and by the John Templeton Foundation grant #60501 ‘Putting the Extended Evolutionary Synthesis to the Test’. BJM was funded by a USDA Hatch grant to MAFES #1011538 and NSF ABI grant #1660000. Scientists disagree about the nature of biodiversity change. While there is evidence for widespread declines from population surveys, assemblage surveys reveal a mix of declines and increases. These conflicting conclusions may be caused by the use of different metrics: assemblage metrics may average out drastic changes in individual populations. Alternatively, differences may arise from data sources: populations monitored individually, versus whole-assemblage monitoring. To test these hypotheses, we estimated population change metrics using assemblage data. For a set of 23 241 populations, 16 009 species, in 158 assemblages, we detected significantly accelerating extinction and colonisation rates, with both rates being approximately balanced. Most populations (85%) did not show significant trends in abundance, and those that did were balanced between winners (8%) and losers (7%). Thus, population metrics estimated with assemblage data are commensurate with assemblage metrics and reveal sustained and increasing species turnover. Postprint Postprint

SummaryHuman activities have fundamentally altered biodiversity. Extinction rates are elevated and model projections suggest drastic biodiversity declines. Yet, observed temporal trends in recent decades are highly variable, despite consistent change in species composition. Here, we uncover clear spatial patterns within this variation. We estimated trends in the richness and composition of assemblages in over 50,000 time-series, to provide the most comprehensive assessment of temporal change in biodiversity across the planet to date. The strongest, most consistent pattern shows compositional change dominated by species turnover, with marine taxa experiencing up to fourfold the variation in rates of change of terrestrial taxa. Richness change ranged from no change to richness gains or losses of ~10% per year, with tropical marine biomes experiencing the most extreme changes. Earth is undergoing a process of spatial reorganisation of species and, while few areas are unaffected, biodiversity change is consistently strongest in the oceans.

Motivation The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. Main types of variables included The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record. Spatial location and grain BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2). Time period and grain BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year. Major taxa and level of measurement BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates. Software format .csv and .SQL., Global Ecology and Biogeography, 27 (7), ISSN:1466-822X, ISSN:1466-8238

Temporal fluctuations in species richness are frequently regulated, exhibiting a tendency to return toward a central level., Many theoretical models of community dynamics predict that species richness (S) and total abundance (N) are regulated in their temporal fluctuations. We present novel evidence for widespread regulation of biodiversity. For 59 plant and animal assemblages from around the globe monitored annually for a decade or more, the majority exhibited regulated fluctuations compared to the null hypothesis of an unconstrained random walk. However, there was little evidence for statistical artifacts, regulation driven by correlations with average annual temperature, or local-scale compensatory fluctuations in S or N. In the absence of major environmental perturbations, such as urbanization or cropland transformation, species richness and abundance may be buffered and exhibit some resilience in their temporal trajectories. These results suggest that regulatory processes are occurring despite unprecedented environmental change, highlighting the need for community-level assessment of biodiversity trends, as well as extensions of existing theory to address open source pools and shifting environmental conditions.

Changing Assemblages Although the rate of species extinction has increased markedly as a result of human activity across the biosphere, conservation has focused on endangered species rather than on shifts in assemblages. Dornelas et al. (p. 296 ; see the Perspective by Pandolfi and Lovelock ), using an extensive set of biodiversity time series of species occurrences in both marine and terrestrial habitats from the past 150 years, find species turnover above expected but do not find evidence of systematic biodiversity loss. This result could be caused by homogenization of species assemblages by invasive species, shifting distributions induced by climate change, and asynchronous change across the planet. All of which indicates that it is time to review conservation priorities.

Two recent meta-analyses of local-scale biodiversity change over time, by the authors of the present paper, have been subject to a harsh critique. Here we use new data and analyses to respond to the main points of this critique. First, a central argument of the critique was that short-term time series lead to biased estimates of long-term biodiversity change. However, we show here that this conclusion was based entirely on two fundamental mistakes in the simulations used to support it. Second, we show that the critic's conclusion that there are negative relationships between temporal biodiversity change and study duration is entirely dependent on: (i) the unrealistic assumption that biodiversity change can be positive when study duration = 0; (ii) the use of only a subset of the available data; (iii) inclusion of a single outlier data point in a single study (out of 100 in this case); and/or (iv) a choice to use log ratios rather than slopes (when available) as the metric of temporal biodiversity change. In short, the evidence does not support the conclusion that studies of longer duration tend to find local diversity decline. Finally, the critique highlighted the obviously true fact that studies in the ecological literature represent a geographically biased sample of locations on Earth; this issue was noted in both original papers, and is relevant for all ecological data syntheses. This fact was used by the critics to cast doubt on our conclusion that, outside of areas converted to croplands or asphalt, the distribution of temporal biodiversity trends is centered on zero. As a scientific rule, future studies based on more or different data may cause us to modify our conclusion, but at present, alternative conclusions based on the geographic-bias argument rely entirely on speculation. In sum, the critique raises points of uncertainty typical of all ecological studies, but it falls far short of providing an evidence-based alternative interpretation for our results, which are now supported by syntheses of hundreds of individual data sets of temporal biodiversity change.

The role human activities play in reshaping biodiversity is increasingly apparent in terrestrial ecosystems. However, the responses of entire marine assemblages are not well-understood, in part, because few monitoring programs incorporate both spatial and temporal replication. Here, we analyse an exceptionally comprehensive 29-year time series of North Atlantic groundfish assemblages monitored over 5° latitude to the west of Scotland. These fish assemblages show no systematic change in species richness through time, but steady change in species composition, leading to an increase in spatial homogenization: the species identity of colder northern localities increasingly resembles that of warmer southern localities. This biotic homogenization mirrors the spatial pattern of unevenly rising ocean temperatures over the same time period suggesting that climate change is primarily responsible for the spatial homogenization we observe. In this and other ecosystems, apparent constancy in species richness may mask major changes in species composition driven by anthropogenic change., The response of marine fish assemblages to global change is not fully understood. Analysing a 29-year time-series, Magurran et al. show that despite little change in species richness, high species turnover is leading to North Atlantic groundfish assemblages becoming spatially homogenized, likely as a result of climatic change.