Temporal Patterns Of Biodiversity Research Articles

When good turns to bad and alien predators appear: The dynamics of biodiversity change in boreal waterbird communities

Temporal patterns of biodiversity are often difficult to interpret because of our limited understanding of how communities vary through time and how processes drive this variation. A further challenge with dynamic systems is choosing an appropriate baseline against which biodiversity change is judged. We used abundance time series of breeding waterbirds in eutrophic lakes in Finland for 1946–2022 to study the dynamics of biodiversity change in local communities and the relative role of two presumed main drivers, i.e. eutrophication and alien predators, in contributing to historical and recent trends in local abundances and biodiversity. We set the cut-off for the historical and recent study periods in the mid-1980 s, because the systematic monitoring of breeding waterbirds in Finland started in 1986 and recent analyses of biodiversity change and population trends in European boreal waterbird communities are mainly based on time series and data gathered since 1986. Both species richness and the total abundance of waterbirds in local communities showed contrasting trends between historical (gathered before the mid-1980 s) and current (gathered after the mid-1980 s) community time series, with the current time series indicating a decline and the historical time series indicating an increase. The abundances of habitat specialists (species preferring eutrophic lakes) and habitat generalists (species using both eutrophic and oligotrophic lakes) showed a corresponding difference between the current and historical time series. The local extinction rates were higher among habitat specialists than among habitat generalists. The trend indices for wetland-nesting species (highly vulnerable to predation by two alien species (the raccoon dog, Nyctereutes procyonoides, and American mink, Neovison vison) in terms of nest site) abundances were more negative than the trend indices of species nesting further away from waterbodies (less vulnerable to predation by two alien species). In addition, bottom-feeding species (presumably more sensitive to negative impacts of eutrophication) did not show more negative population trends than surface-feeding species (presumably less sensitive to negative impacts of eutrophication). Regardless of equal sensitivity to negative impacts of eutrophication, two species highly vulnerable to two alien predators showed more negative population trends than a less vulnerable species. The results suggest that increased predation has been an important driver of the population and biodiversity declines in the studied waterbird communities. The mid-1980 s may not provide an ecologically appropriate baseline against which changes in the populations and biodiversity of boreal waterbird communities are judged.

Community Assembly of Forest Vegetation along Compound Habitat Gradients across Different Climatic Regions in China

Community assembly research has mostly focused on areas with single vegetation types; however, the abiotic and biotic factors affecting community assembly act across regions. Integrating biotic and abiotic factors into “compound” habitats has gained attention as an emerging strategy to analyze spatial and temporal patterns of biodiversity. We used a compound habitat approach to explore the relative roles of habitat filtering, biotic competition, and stochastic processes in the forest community assembly of four climatic zones (tropical, subtropical, temperate, and cold temperate forests). Specifically, we combined biotic and abiotic factors in four compound ecological gradients by principal component analysis (PCA), which we used to assess the geographic and phylogenetic distribution of multiple woody plant functional traits. We found that forest functional and phylogenetic diversity shifted from clustered to overdispersed along the first compound habitat gradient (PC1) across climate zones. This finding indicates that competitive exclusion strongly affected the community assembly in tropical and subtropical forests, while habitat filtering played a key role in cold temperate forests; these mechanisms may both exist and interact in temperate forests. We also found that both habitat filtering and biotic competition affected forest community assembly across climatic regions in China. Our results elucidate the underlying mechanisms driving geographical differentiation of forest vegetation across climatic zones, and bolster empirical evidence for the conservation of forest biodiversity in China. Further research is also needed to explore whether the patterns found in this paper are prevalent in different locations in different climatic zones in China.

Distinct coral reef habitat communities characterized by environmental DNA metabarcoding

Coral reefs are biodiversity hotspots, places of high endemicity and provide essential services to billions of people globally. With increasing threats to these reefs worldwide, there is a need to implement faster, more efficient ways to monitor spatial and temporal patterns of biodiversity. Environmental DNA (eDNA) metabarcoding offers a promising tool to address this issue, as it has revolutionized our ability to monitor biodiversity from complex environmental samples such as seawater. However, the capacity for eDNA to resolve fine scale shifts in community composition across habitats in seascapes is yet to be fully explored. Here, we applied eDNA metabarcoding using the rRNA 18S Universal eukaryote assay to explore differences in community profiles between samples collected from the lagoon and reef slope habitats across more than 170 km of the Ningaloo Coast World Heritage Area in Western Australia. We recovered 2061 amplicon sequence variants that comprised of 401 taxa spanning 14 different metazoan phyla such as cnidarians, poriferans, molluscs, algae, worms, and echinoderms. Our results revealed strong clustering of samples by habitat type across the length of the reef. Community dissimilarity (beta diversity) between samples collected from the reef slope and lagoon habitats was high and was driven largely by a strong rate of spatial turnover, indicating a distinct set of taxa representing each reef zone community. We also detected a strong pattern of isolation by distance within our slope samples, suggesting that communities are spatially stratified across the length of the reef. Despite high connectivity due to regular flushing of the lagoon environment, our results demonstrate that metabarcoding of seawater eDNA from different habitats can resolve fine scale community structure. By generating multi-trophic biodiversity data, our study also provided baseline data for Ningaloo from which future changes can be assessed.

Mismatches between birds' spatial and temporal dynamics reflect their delayed response to global changes

Global changes alter the dynamics of biodiversity, and are forecasted to continue or worsen in the decades to come. Modelling approaches used to anticipate these impacts are mainly based on the equivalence between spatial and temporal response to environmental forcings, generally called space‐for‐time substitution. However, several processes are known to generate deviations between spatial and temporal responses, potentially undermining the prediction based on space‐for‐time substitution. We here used high‐resolution data from the french breeding bird survey to quantify and map the deviation between spatial and temporal patterns of bird abundances resulting from the dynamics of 124 species monitored in 2133 sites between 2001 and 2012. Using independent empirical data, we then tested specific predictions linked to the determinants (anthropogenic activities) and processes (lagged responses to environmental changes) potentially generating these deviations. We found that deviations between spatial and temporal patterns of abundances were particularly structured in space for bird communities. Following our predictions, these space–time deviations were positively correlated with the human influence on ecosystems, and linked with colonization–extinction ratios and community completeness, two markers of ongoing delayed responses to environmental changes. Our results suggest that the deviations between spatial and temporal patterns are related to recent anthropogenic environmental changes and disequilibrium responses to these changes. Investigating deviations between spatial and temporal patterns of biodiversity might open promising perspectives for a formal quantification of disequilibrium state of biodiversity at large spatial scale.

DNA Metabarcoding of Deep-Sea Sediment Communities Using COI: Community Assessment, Spatio-Temporal Patterns and Comparison with 18S rDNA

Among the complex ecosystems and habitats that form the deep sea, submarine canyons and open slope systems are regarded as potential hotspots of biodiversity. We assessed the spatial and temporal patterns of biodiversity in sediment communities of a NW Mediterranean Canyon and its adjacent open slope (Blanes Canyon) with DNA metabarcoding. We sampled three layers of sediment and four different depths (900–1750 m) at two seasons, and used a fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) as a metabarcoding marker. The final dataset contained a total of 15,318 molecular operational taxonomic units (MOTUs). Metazoa, Stramenopiles and Archaeplastida were the dominant taxa and, within metazoans, Arthropoda, Nematoda and Cnidaria were the most diverse. There was a trend towards decreasing MOTU richness and diversity in the first few cm (1 to 5) of the sediment, with only 26.3% of the MOTUs shared across sediment layers. Our results show the presence of heterogeneous communities in the studied area, which was significantly different between zones, depths and seasons. We compared our results with the ones presented in a previous study, obtained using the v7 region of the 18S rRNA gene in the same samples. There were remarkable differences in the total number of MOTUs and in the most diverse taxa. COI recovered a higher number of MOTUs, but more remained unassigned taxonomically. However, the broad spatio-temporal patterns elucidated from both datasets coincided, with both markers retrieving the same ecological information. Our results showed that COI can be used to accurately characterize the studied communities and constitute a high-resolution method to detect ecological shifts. We also highlight that COI reference databases for deep-sea organisms have important gaps, and their completeness is essential in order to successfully apply metabarcoding techniques.

BioTIME: A database of biodiversity time series for the Anthropocene.

MotivationThe 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 includedThe 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 grainBioTIME 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 grainBioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.Major taxa and level of measurementBioTIME 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.

Explaining high-diversity death assemblages: Undersampling of the living community, out-of-habitat transport, time-averaging of rare taxa, and local extinction

Molluscan benthic assemblages provide unique opportunities for understanding both spatial and temporal patterns of biodiversity. Species richness in the shell remains found at a site (i.e. the death assemblage) is typically several times higher than in the counterpart living assemblage, reflecting a complex history of settlement, dissemination and decomposition post-mortem. We used high-density temporal and spatial sampling (>37000 individuals representing 196 taxa) of a shallow (5–8m) nearshore sandy habitat off the coast of south-east Sardinia (Italy, Mediterranean Sea) to study the factors responsible for differences in the relative diversity of living and death assemblages. We found that death assemblages at all sites were considerably more diverse than living communities (1.5–3.5x more dead than living taxa after sample-size standardization), with 78% of all taxa solely recovered as empty shells, resulting in low live-dead agreement. By carefully filtering the raw data and combining them with habitat information extracted from the literature, we disentangled the major causes of this discordance and quantified their individual effects. Increased dead diversities could not be attributed to undersampling of the living community, but instead resulted from three phenomena of decreasing importance: the post-mortem, out-of-habitat transport of non-indigenous taxa (57% of dead-only taxa were allochthonous), the time-averaged presence of rare indigenous taxa (40% of dead-only taxa), and the likely local extirpation of a small number of species (3% of dead-only taxa). Our approach demonstrates how ecological inferences based on death assemblages can be improved by restricting analyses to demonstrably indigenous taxa, and highlights how mollusc shell remains can be used to provide information over both ecological and evolutionary timescales.

Integrating land cover structure and functioning to predict biodiversity patterns: a hierarchical modelling framework designed for ecosystem management

Context Land-use/land-cover (LU/LC) dynamics is one of the main drivers of global environmental change. In the last years, aerial and satellite imagery have been increasingly used to monitor the spatial extent of changes in LU/LC, deriving relevant biophysical parameters (i.e. primary productivity, climate and habitat structure) that have clear implications in determining spatial and temporal patterns of biodiversity, landscape composition and ecosystem services.

Impacts of dispersal limitation on temporal biodiversity patterns in a neutral model

In this brief report, potential impacts of different dispersal assumptions on the temporal biodiversity patterns in a neutral model were evaluated using a simple spatially explicit lattice model. The results show that, immigration from metacommunity is much more important than local dispersal from neighboring sites to determine the temporal species richness of local neutral community. Such an observation was consistent over different initial configurations and various immigration rates. Moreover, the calculation of Jaccard's similarity index suggests that, when regional immigration is spatially limited (i.e., individuals of species can only disperse to the edge areas of the local community from the metacommunity), temporal species compositional similarity would be usually larger than those scenarios where regional immigration is not limited. That is, species replacement in spatially limited scenarios is much slower than those scenarios where dispersal of species is unlimited. In conclusion, regional dispersal limitation plays deterministic roles on structuring species diversity patterns in local neutral communities.

Testing the spectral diversity hypothesis using spectroscopy data in a simulated wetland community

The spectral diversity hypothesis proposes that as the number of plant species increases for a given area, the diversity of spectra observed from that area should also increase. This approach could be very useful as an assessment and monitoring tool to help ecologists understand the spatial and temporal patterns of biodiversity without relying on consistently detecting individual species. While the spectral diversity hypothesis has been examined for a wide range of ecosystems using a variety of remote sensing data, it has not been tested using spectroscopy (i.e. hyperspectral) data for wetlands. Previous studies have not explicitly considered the impact that flowers may have on spectral diversity and how this may impact the spectral diversity hypothesis. To test the spectral diversity hypothesis and the potential impact on flowers, we used a simulation approach to combine leaf and flower spectra collected from a diverse prairie fen wetland ecosystem into datasets of virtual plots with varying levels of species diversity and different combination of species. To address the high dimensionality of the data, we compared spectral diversity and floristic diversity using partial least squares regression. Our results found that defining floristic diversity using the Shannon's diversity index, which accounts for plant abundance in each plot, produced the best predictive models where the predicted values had a RMSE less than 40% of the mean observed value. We also found that the inclusion of flower spectra with leaf spectra did increase the RMSE of the best model, but across all models, correlation increased. Our results indicate that spectral diversity could be used as an initial biodiversity assessment tool for wetlands, especially with on-going advancements in unmanned aerial vehicle technology that can provide a low altitude platform for imaging spectroscopy.

Insights into the origin and distribution of biodiversity in the Brazilian Atlantic forest hot spot: a statistical phylogeographic study using a low-dispersal organism.

The relative importance of the processes that generate and maintain biodiversity is a major and controversial topic in evolutionary biology with large implications for conservation management. The Atlantic Forest of Brazil, one of the world's richest biodiversity hot spots, is severely damaged by human activities. To formulate an efficient conservation policy, a good understanding of spatial and temporal biodiversity patterns and their underlying evolutionary mechanisms is required. With this aim, we performed a comprehensive phylogeographic study using a low-dispersal organism, the land planarian species Cephaloflexa bergi (Platyhelminthes, Tricladida). Analysing multi-locus DNA sequence variation under the Approximate Bayesian Computation framework, we evaluated two scenarios proposed to explain the diversity of Southern Atlantic Forest (SAF) region. We found that most sampled localities harbour high levels of genetic diversity, with lineages sharing common ancestors that predate the Pleistocene. Remarkably, we detected the molecular hallmark of the isolation-by-distance effect and little evidence of a recent colonization of SAF localities; nevertheless, some populations might result from very recent secondary contacts. We conclude that extant SAF biodiversity originated and has been shaped by complex interactions between ancient geological events and more recent evolutionary processes, whereas Pleistocene climate changes had a minor influence in generating present-day diversity. We also demonstrate that land planarians are an advantageous biological model for making phylogeographic and, particularly, fine-scale evolutionary inferences, and propose appropriate conservation policies.

Benthic meiofauna as indicator of ecological changes in estuarine ecosystems: The use of nematodes in ecological quality assessment

Estuarine meiofauna communities have been only recently considered to be good indicators of ecological quality, exhibiting several advantages over macrofauna, such as their small size, high abundance, rapid generation times and absence of a planktonic phase. In estuaries we must account not only for a great natural variability along the estuarine gradient (e.g. sediment type and dynamics, oxygen availability, temperature and flow speed) but also for the existence of anthropogenic pressures (e.g. high local population density, presence of harbors and dredging activities).Spatial and temporal biodiversity patterns of meiofauna and free-living marine nematodes were studied in the Mondego estuary (Portugal). Both taxonomic and functional approaches were applied to nematode communities in order to describe the community structure and to relate it with the environmental parameters along the estuary. At all sampling events, nematode assemblages reflected the estuarine gradient, and salinity and grain size composition were confirmed to be the main abiotic factors controlling the distribution of the assemblages.Moreover, the low temporal variability may indicate that natural variability is superimposed by the anthropogenic pressures present in some areas of the estuary. The characterization of both meiofauna and nematode assemblages highlighted the usefulness of the integration of both taxonomic and functional attributes, which must be taken into consideration when assessing the ecological status of estuaries.

Patterns of temporal community turnover are spatially synchronous across boreal lakes

Summary1. Ecosystems are often exposed to broad‐scale environmental change, which can potentially synchronise community dynamics and biodiversity trends. Detection of temporal coherence may, however, depend on the metrics used and their sensitivity to detect change, requiring several lines of evidence to elucidate the full range of temporal responses to environmental change.2. Here, we tested whether the patterns of synchrony among littoral invertebrate communities of Swedish lakes over 20 years (1988–2007) differed when analysed using univariate (taxon richness, evenness, Shannon diversity and total abundance) or multivariate (temporal turnover in community composition) metrics. We included both culturally acidified and circumneutral lakes to examine whether anthropogenic stress influenced the patterns of synchrony.3. Average total abundance, taxon richness and temporal turnover in community composition changed monotonically with time, while evenness and Shannon diversity fluctuated around a long‐term mean. However, among‐lake variability was high, resulting in a weak temporal coherence. Only trends of temporal turnover changed synchronously across lakes, irrespective of their acidification history.4. Spatially synchronous trends in turnover across lakes were correlated with increasing water colour and decreasing sulphate concentrations, showing the importance of regional drivers of spatiotemporal coherence.5. Our results underpin an increasing body of evidence that the detection of diversity patterns varies among metrics that ignore (taxon richness, evenness, Shannon diversity) or consider (turnover) species identities. More generally, our results suggest that community‐level studies of synchrony are suitable for elucidating the role of intrinsic versus extrinsic factors in mediating complex community assembly processes in the long term. This, in turn, contributes to our understanding of temporal patterns of biodiversity.

Biodiversity patterns of free-living marine nematodes in a tropical bay: Cienfuegos, Caribbean Sea

Spatial and temporal biodiversity patterns of free-living marine nematodes were studied in Cienfuegos Bay, a tropical semi-enclosed basin in the Caribbean Sea. Taxonomic (to species level) and functional (biological trait) approaches were applied for describing the assemblage structure and relating it to abiotic environment based on a sampling scheme in six subtidal stations and three months. Biological trait approach added relevant information to species pattern regarding relationships between diversity patterns and the abiotic environment. The most common morphotypes were deposit feeding nematodes, with colonising abilities of 2–3 (in a scale from 1 to 5), tail conical cylindrical or filiforme and body slender; and their abundance were correlated with depth, organic matter and silt/clay fraction. In spite of a high turnover of species, functional diversity of assemblages did not change notably in space and time. A result probably due to sampling of the habitat pool of species and to low heterogeneity of the studied muddy bottoms. Chemical pollution (organic enrichment and heavy metals) and hydrodynamic regime possibly drove the biodiversity patterns. Spatial distribution of assemblages support the existence of two well differentiated basins inside the bay, the northern basin more polluted than the southern one. The low hydrodynamic regime would determine a poor dispersion of nematodes resulting in high spatial variance in the assemblage structure; and also the associated hypoxic conditions and pollutants in sediments can explain the dominance of tolerant nematode species such as Daptonema oxycerca, Sabatieria pulchra, Terschellingia gourbaultae, and Terschellingia longicaudata. A comparison of spatial–temporal patterns of biodiversity between Cienfuegos Bay and other semi-enclosed bays in temperate regions suggests several similarities: nematode assemblages are strongly influenced by anthropogenic disturbance, temporal trends are weak or overridden by spatial ones, and few cosmopolitan genera/species tolerant to pollution and hypoxic conditions are dominant.

Prospects for tropical forest biodiversity in a human‐modified world

The future of tropical forest biodiversity depends more than ever on the effective management of human-modified landscapes, presenting a daunting challenge to conservation practitioners and land use managers. We provide a critical synthesis of the scientific insights that guide our understanding of patterns and processes underpinning forest biodiversity in the human-modified tropics, and present a conceptual framework that integrates a broad range of social and ecological factors that define and contextualize the possible future of tropical forest species. A growing body of research demonstrates that spatial and temporal patterns of biodiversity are the dynamic product of interacting historical and contemporary human and ecological processes. These processes vary radically in their relative importance within and among regions, and have effects that may take years to become fully manifest. Interpreting biodiversity research findings is frequently made difficult by constrained study designs, low congruence in species responses to disturbance, shifting baselines and an over-dependence on comparative inferences from a small number of well studied localities. Spatial and temporal heterogeneity in the potential prospects for biodiversity conservation can be explained by regional differences in biotic vulnerability and anthropogenic legacies, an ever-tighter coupling of human-ecological systems and the influence of global environmental change. These differences provide both challenges and opportunities for biodiversity conservation. Building upon our synthesis we outline a simple adaptive-landscape planning framework that can help guide a new research agenda to enhance biodiversity conservation prospects in the human-modified tropics.

Vertical and Temporal Patterns of Biodiversity of Fruit-Feeding Butterflies in a Tropical Forest in Uganda

Vertical and Temporal Patterns of Biodiversity of Fruit-Feeding Butterflies in a Tropical Forest in Uganda