Remembrance of things past: modelling the relationship between species' abundances in living communities and death assemblages

Accumulations of dead skeletal material are a valuable archive of past ecological conditions. However, such assemblages are not equivalent to living communities because they mix the remains of multiple generations and are altered by post-mortem processes. The abundance of a species in a death assemblage can be quantitatively modelled by successively integrating the product of an influx time series and a post-mortem loss function (a decay function with a constant half-life). In such a model, temporal mixing increases expected absolute dead abundance relative to average influx as a linear function of half-life and increases variation in absolute dead abundance values as a square-root function of half-life. Because typical abundance distributions of ecological communities are logarithmically distributed, species' differences in preservational half-life would have to be very large to substantially alter species' abundance ranks (i.e. make rare species common or vice-versa). In addition, expected dead abundances increase at a faster rate than their range of variation with increased time averaging, predicting greater consistency in the relative abundance structure of death assemblages than their parent living community.     

Ecological fidelity of open marine molluscan death assemblages: effects of post-mortem transportation, shelf health, and taphonomic inertia

Based on 38 molluscan datasets from modern open shelf settings, disturbance from human activities – especially anthropogenic eutrophication (AE) – has the strongest negative effect on the fidelity of death assemblages to local living communities, suggesting that the composition of the death assemblage has lagged behind changes in the living community (taphonomic inertia). Fidelity is poorest where shelves are both AE and narrow (≤ 50 km from shore to the 200-m isobath), suggesting that cross-shelf post-mortem transportation might contribute bias, but this does not dominate and shelf width does not emerge as significant among non-AE shelves. Clear signatures of post-mortem transportation are present only in four shoreface datasets, all from wide shelves, that receive abundant allochthonous specimens from adjacent estuaries or rocky intertidal zones.
Shelves experiencing minimal human impact yield fidelity estimates that are most relevant for evaluating (paleo)ecological trends. There, death assemblages are on average 25% richer than a single census of the living molluscan community and show high similarity in taxonomic composition and species relative abundance that, based on a very limited number of studies, is comparable to or better than the agreement found among successive live censuses. Molluscan death assemblages on open shelves are thus generally good samplers of living community diversity and composition under natural conditions, and where the community is undergoing anthropogenic modification, retain a strong record of the precursor community. Taphonomic inertia will be strongest where the change in the community has been especially strong (outside the normal range of natural variability) and/or where the 'new' community has lower net rates of shell input than its precursor, so that input only slowly dilutes the time-averaged skeletal remains of the 'old' community.     

Fishes of Indiana streams: current and historic assemblage structure

We examined Indiana fish assemblages using taxonomy and ecological categories to assess temporal shifts in community structure and recent environmental relationships. Historic (1945) and recent (1996–2007) presence/absence data were compiled by subbasin and analyzed with Nonmetric Multidimensional Scaling (NMS) ordination and by species richness. Canonical Correspondence Analysis (CCA) was used to test taxonomic identity and ecological category abundance data for explanation with recent (1996–2007) environmental variables. We found a decrease in assemblage heterogeneity for recent assemblages and an increase in the number of tolerant species per subbasin. Recent Indiana streams are dominated by tolerant fishes with generalist life history strategies and low functional variation. The use of ecological categories resulted in weaker relationships with environmental variables than analyses with taxonomic identities. Analyses using taxonomy resulted in strong assemblage explanation from stream size and flow variation, while analyses using ecological categories resulted in strong assemblage explanation from habitat variation in silt substrates and flow. Analyses of recent assemblage structure using ecological categories resulted in decreased assemblage variation among subbasins than in analyses using taxonomic identities. We found that fish assemblages of Indiana streams are structured primarily by habitat complexity and have been altered during the past 50 years through multiple disturbances including fragmentation, siltation, and species introductions.     

Nonparametric tests for homogeneity of species assemblages: a data depth approach

Testing homogeneity of species assemblages has important applications in ecology. Due to the unique structure of abundance data often collected in ecological studies, most classical statistical tests cannot be applied directly. In this article, we propose two novel nonparametric tests for comparing species assemblages based on the concept of data depth. They can be considered as a natural generalization of the Kolmogorov-Smirnov and the Cramér-von Mises tests (KS and CM) in this species assemblage comparison context. Our simulation studies show that the proposed test is more powerful than other existing methods under various settings. A real example is used to demonstrate how the proposed method is applied to compare species assemblages using plant community data from a highly diverse tropical forest at Barro Colorado Island, Panama.     

Phylogenetic and morphological relationships between nonvolant small mammals reveal assembly processes at different spatial scales

The relative roles of historical processes, environmental filtering, and ecological interactions in the organization of species assemblages vary depending on the spatial scale. We evaluated the phylogenetic and morphological relationships between species and individuals (i.e., inter‐ and intraspecific variability) of Neotropical nonvolant small mammals coexisting in grassland‐forest ecotones, in landscapes and in regions, that is, three different scales. We used a phylogenetic tree to infer evolutionary relationships, and morphological traits as indicators of performance and niche similarities between species and individuals. Subsequently, we applied phylogenetic and morphologic indexes of diversity and distance between species to evaluate small mammal assemblage structures on the three scales. The results indicated a repulsion pattern near forest edges, showing that phylogenetically similar species coexisted less often than expected by chance. The strategies for niche differentiation might explain the phylogenetic repulsion observed at the edge. Phylogenetic and morphological clustering in the grassland and at the forest interior indicated the coexistence of closely related and ecologically similar species and individuals. Coexistence patterns were similar whether species‐trait values or individual values were used. At the landscape and regional scales, assemblages showed a predominant pattern of phylogenetic and morphological clustering. Environmental filters influenced the coexistence patterns at three scales, showing the importance of phylogenetically conserved ecological tolerances in enabling taxa co‐occurrence. Evidence of phylogenetic repulsion in one region indicated that other processes beyond environmental filtering are important for community assembly at broad scales. Finally, ecological interactions and environmental filtering seemed important at the local scale, while environmental filtering and historical colonization seemed important for community assembly at broader scales.     

Latitudinal gradient of nestedness and its potential drivers in stream detritivores

Understanding what mechanisms shape the diversity and composition of biological assemblages across broad‐scale gradients is central to ecology. Litter‐consuming detritivorous invertebrates in streams show an unusual diversity gradient, with α‐diversity increasing towards high latitudes but no trend in γ‐diversity. We hypothesized this pattern to be related to shifts in nestedness and several ecological processes shaping their assemblages (dispersal, environmental filtering and competition). We tested this hypothesis, using a global dataset, by examining latitudinal trends in nestedness and several indicators of the above processes along the latitudinal gradient. Our results suggest that strong environmental filtering and low dispersal in the tropics lead to often species‐poor local detritivore assemblages, nested in richer regional assemblages. At higher latitudes, dispersal becomes stronger, disrupting the nested assemblage structure and resulting in local assemblages that are generally more species‐rich and non‐nested subsets of the regional species pools. Our results provide evidence that mechanisms underlying assemblage composition and diversity of stream litter‐consuming detritivores shift across latitudes, and provide an explanation for their unusual pattern of increasing α‐diversity with latitude. When we repeated these analyses for whole invertebrate assemblages of leaf litter and for abundant taxa showing reverse or no diversity gradients we found no latitudinal patterns, suggesting that function‐based rather than taxon‐based analyses of assemblages may help elucidate the mechanisms behind diversity gradients.     

The Effects of Sub-Regional Climate Velocity on the Distribution and Spatial Extent of Marine Species Assemblages

Many studies illustrate variable patterns in individual species distribution shifts in response to changing temperature. However, an assemblage, a group of species that shares a common environmental niche, will likely exhibit similar responses to climate changes, and these community-level responses may have significant implications for ecosystem function. Therefore, we examine the relationship between observed shifts of species in assemblages and regional climate velocity (i.e., the rate and direction of change of temperature isotherms). The assemblages are defined in two sub-regions of the U.S. Northeast Shelf that have heterogeneous oceanography and bathymetry using four decades of bottom trawl survey data and we explore temporal changes in distribution, spatial range extent, thermal habitat area, and biomass, within assemblages. These sub-regional analyses allow the dissection of the relative roles of regional climate velocity and local physiography in shaping observed distribution shifts. We find that assemblages of species associated with shallower, warmer waters tend to shift west-southwest and to shallower waters over time, possibly towards cooler temperatures in the semi-enclosed Gulf of Maine, while species assemblages associated with relatively cooler and deeper waters shift deeper, but with little latitudinal change. Conversely, species assemblages associated with warmer and shallower water on the broad, shallow continental shelf from the Mid-Atlantic Bight to Georges Bank shift strongly northeast along latitudinal gradients with little change in depth. Shifts in depth among the southern species associated with deeper and cooler waters are more variable, although predominantly shifts are toward deeper waters. In addition, spatial expansion and contraction of species assemblages in each region corresponds to the area of suitable thermal habitat, but is inversely related to assemblage biomass. This suggests that assemblage distribution shifts in conjunction with expansion or contraction of thermal habitat acts to compress or stretch marine species assemblages, which may respectively amplify or dilute species interactions to an extent that is rarely considered. Overall, regional differences in climate change effects on the movement and extent of species assemblages hold important implications for management, mitigation, and adaptation on the U.S. Northeast Shelf.     

Geographic variation in seed removal of a myrmecochorous herb: influence of variation in functional guild and species composition of the disperser assemblage through spatial and temporal scales

The ecological influence of changes in the functional guild and species composition of ant assemblages on ant‐dispersal mutualisms is still poorly known. Using a multi‐scale approach over an 800 km range within the Iberian Peninsula, we tested the hypothesis that variation in seed removal rate was related to functional guild rather than to species composition variations of disperser assemblages in the myrmecochore herb Helleborus foetidus. At least two premises must be confirmed to validate this hypothesis: 1) ant assemblages that are dissimilar in species composition but with similar functional guild composition will not differ significantly in seed removal, and 2) assemblages with different functional guild composition will render different seed removal services. We conducted 3328 ant‐visitor censuses on 462 individual plants to identify both the species composition and functional guild variation of the ant‐disperser assemblage, and the plant seed removal rate. Functional guild composition of the ant assemblage was determined by the proportion of visits of ants acting as legitimate dispersers, facultative dispersers or elaiosome predators. Results showed that ant‐seed dispersal success seemed to be more sensitive to species composition changes of the ant assemblage than to functional guild shifts. However, this sensitivity was scale‐dependent. Thus, at the fine, inter‐individual scale, seed removal covaried with the species and functional guild composition of the ant assemblages; at the inter‐populational scale, differences in seed removal tended to be related to the dissimilarity of the assemblage species composition rather than the assemblage functional guild; finally, inter‐regional differences in seed removal were unrelated to dissimilarities of the ant assemblage composition or functional guild. Though differences in seed removal and the relative frequency of the legitimate dispersers tended to be positively correlated, none of the above premises were fully confirmed in this study. Therefore, our results did not support in full the hypothesis that the variation in seed removal was explained by shifts in functional guild composition, rather than shifts in species composition.     

SESAM – a new framework integrating macroecological and species distribution models for predicting spatio‐temporal patterns of species assemblages

Two different approaches currently prevail for predicting spatial patterns of species assemblages. The first approach (macroecological modelling, MEM) focuses directly on realized properties of species assemblages, whereas the second approach (stacked species distribution modelling, S‐SDM) starts with constituent species to approximate the properties of assemblages. Here, we propose to unify the two approaches in a single ‘spatially explicit species assemblage modelling’ (SESAM) framework. This framework uses relevant designations of initial species source pools for modelling, macroecological variables, and ecological assembly rules to constrain predictions of the richness and composition of species assemblages obtained by stacking predictions of individual species distributions. We believe that such a framework could prove useful in many theoretical and applied disciplines of ecology and evolution, both for improving our basic understanding of species assembly across spatio‐temporal scales and for anticipating expected consequences of local, regional or global environmental changes. In this paper, we propose such a framework and call for further developments and testing across a broad range of community types in a variety of environments.     

A balance of winners and losers in the Anthropocene

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.     

Convergence of temperate and tropical stream fish assemblages

The hypothesis of convergence takes the deterministic view that community (or assemblage) structure can be predicted from the environment, and that the environment is expected to drive evolution in a predictable direction. Here we present results of a comparative study of freshwater fish assemblages from headwater streams in four continents (Europe, North America, Africa and South America), with the general objective of testing whether these assemblages display convergent structures under comparable environmental conditions (i.e. assemblage position in the stream longitudinal continuum). We tested this hypothesis by comparing species richness and trophic guilds of those stream fish assemblages represented in available data from multiple sites on each continent. Independent of phylogenetic and historical constraints, fish assemblage richness and trophic structure in the four continents converged along the stream continua to a substantial degree. For the four continents, assemblage richness increased, the proportion of invertivorous species decreased, and the proportion of omnivorous species increased from upstream to downstream, supporting theoretical predictions of the river continuum concept. However, the herbivore/detritivore and piscivore guilds were virtually absent from our small European and North American stream sites, unlike our African and South American stream sites. This divergence can be linked to differences in energy availability between temperate and tropical systems.     

The spatial scale of homogenisation and differentiation in Chihuahuan Desert fish assemblages

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Effects of Global Warming on Predatory Bugs Supported by Data Across Geographic and Seasonal Climatic Gradients

Global warming may affect species abundance and distribution, as well as temperature-dependent morphometric traits. In this study, we first used historical data to document changes in Orius (Heteroptera: Anthocoridae) species assemblage and individual morphometric traits over the past seven decades in Israel. We then tested whether these changes could have been temperature driven by searching for similar patterns across seasonal and geographic climatic gradients in a present survey. The historical records indicated a shift in the relative abundance of dominant Orius species; the relative abundance of O. albidipennis, a desert-adapted species, increased while that of O. laevigatus decreased in recent decades by 6 and 10–15 folds, respectively. These shifts coincided with an overall increase of up to 2.1°C in mean daily temperatures over the last 25 years in Israel. Similar trends were found in contemporary data across two other climatic gradients, seasonal and geographic; O. albidipennis dominated Orius assemblages under warm conditions. Finally, specimens collected in the present survey were significantly smaller than those from the 1980’s, corresponding to significantly smaller individuals collected now during warmer than colder seasons. Taken together, results provide strong support to the hypothesis that temperature is the most likely driver of the observed shifts in species composition and body sizes because (1) historical changes in both species assemblage and body size were associated with rising temperatures in the study region over the last few decades; and (2) similar changes were observed as a result of contemporary drivers that are associated with temperature.     

Relationship between assemblages of mycorrhizal fungi and bacteria on grass roots

Soils support an enormous microbial diversity, but the ecological drivers of this diversity are poorly understood. Interactions between the roots of individual grass species and the arbuscular mycorrhizal (AM) fungi and bacteria in their rhizoplane were studied in a grazed, unimproved upland pasture. Individual root fragments were isolated from soil cores, DNA extracted and used to identify plant species and assess rhizoplane bacterial and AM fungal assemblages, by amplifying part of the small-subunit ribosomal RNA gene, followed by terminal restriction fragment length polymorphism analysis. For the first time we showed that AM fungal and bacterial assemblages are related in situ and that this relationship occurred at the community level. Principal coordinate analyses of the data show that the AM fungi were a major factor determining the bacterial assemblage on grass roots. We also report a strong influence of the composition of the plant community on AM fungal assemblage. The bacterial assemblage was also influenced by soil pH and was spatially structured, whereas AM fungi were influenced neither by the bacteria nor by soil pH. Our study shows that linkages between plant roots and their microbial communities exist in a complex web of interactions that act at individual and at community levels, with AM fungi influencing the bacterial assemblage, but not the other way round.     

Explaining ecological shifts: the roles of temperature and primary production in the long‐term dynamics of benthic faunal composition

Predicting the ecological consequences of environmental change requires that we can identify the drivers of long‐term ecological variation. Biological assemblages can exhibit abrupt deviations from temporal trends, potentially resulting in irreversible shifts in species composition over short periods of time. Such dynamics are hypothesised to occur as gradual forcing eventually causes biological thresholds to be crossed, but could also be explained by biota simply tracking abrupt changes to their environment. Here, we modelled temporal variation in a North Sea benthic faunal assemblage over a 40‐year period (1972–2012) to test for changes to temporal trends of biota and determine whether they could be explained by underlying patterns in sea temperature and primary production. These extrinsic factors were postulated to influence community dynamics through their roles in determining and sustaining the metabolic demands of organisms, respectively. A subset of mainly large and long‐lived taxa (those loaded on the first principal component of taxa densities) exhibited two significant changes to their temporal trends, which culminated in a shift in assemblage composition. These changes were explained by an increase in pelagic primary production, and hence detrital food input to the seabed, but were unrelated to variation in sea temperature. A second subset of mainly small and short‐lived taxa (those loaded on the second principal component) did not experience any significant changes to their temporal trends, as enhanced pelagic primary production appeared to mitigate the impact of warming on these organisms. Our results suggest that abrupt ecological shifts can occur as biota track underlying variation in extrinsic factors, in this case primary production. Changes to the structure of ecosystems may therefore be predictable based on environmental change projections.     

Quantifying regional biodiversity in the tropics: A case study of freshwater fish in Trinidad and Tobago

Extinction rates are predicted to accelerate during the Anthropocene. Quantifying and mitigating these extinctions demands robust data on distributions of species and the diversity of taxa in regional biotas. However, many assemblages, particularly those in the tropics, are poorly characterized. Targeted surveys and historical museum collections are increasingly being used to meet the urgent need for accurate information, but the extent to which these contrasting data sources support meaningful inferences about biodiversity change in regional assemblages remains unclear. Here, we seek to elucidate uncertainty surrounding regional biodiversity estimates by evaluating the performance of these alternative methods in estimating the species richness and assemblage composition of the freshwater fish of Trinidad & Tobago. We compared estimates of regional species richness derived from two freshwater fish datasets: a targeted two year survey of Trinidad & Tobago rivers and historical museum collection records submitted to The University of the West Indies Zoology Museum. Richness was estimated using rarefaction and extrapolation, and assemblage composition was benchmarked against a recent literature review. Both datasets provided similar estimates of regional freshwater fish species richness (50 and 46 species, respectively), with a large overlap (85%) in species identities. Regional species richness estimates based on survey and museum data are thus comparable, and consistent in the species they include. Our results suggest that museum collection data are a viable option for setting reliable baselines in many tropical systems, thereby widening options for meaningful monitoring and evaluation of temporal trends. Abstract in Spanish is available with online material.     

Rapid biodiversity assessment and monitoring method for highly diverse benthic communities: a case study of mediterranean coralligenous outcrops

Increasing anthropogenic pressures urge enhanced knowledge and understanding of the current state of marine biodiversity. This baseline information is pivotal to explore present trends, detect future modifications and propose adequate management actions for marine ecosystems. Coralligenous outcrops are a highly diverse and structurally complex deep-water habitat faced with major threats in the Mediterranean Sea. Despite its ecological, aesthetic and economic value, coralligenous biodiversity patterns are still poorly understood. There is currently no single sampling method that has been demonstrated to be sufficiently representative to ensure adequate community assessment and monitoring in this habitat. Therefore, we propose a rapid non-destructive protocol for biodiversity assessment and monitoring of coralligenous outcrops providing good estimates of its structure and species composition, based on photographic sampling and the determination of presence/absence of macrobenthic species. We used an extensive photographic survey, covering several spatial scales (100s of m to 100s of km) within the NW Mediterranean and including 2 different coralligenous assemblages: Paramuricea clavata (PCA) and Corallium rubrum assemblage (CRA). This approach allowed us to determine the minimal sampling area for each assemblage (5000 cm(2) for PCA and 2500 cm(2) for CRA). In addition, we conclude that 3 replicates provide an optimal sampling effort in order to maximize the species number and to assess the main biodiversity patterns of studied assemblages in variability studies requiring replicates. We contend that the proposed sampling approach provides a valuable tool for management and conservation planning, monitoring and research programs focused on coralligenous outcrops, potentially also applicable in other benthic ecosystems.     

Looking for long-term changes in hydroid assemblages (Cnidaria,Hydrozoa) in Alboran Sea (South-Western Mediterranean): a proposal of a monitoring point for the global warming

In the last 20–30 years, the temperature of the Mediterranean Sea has increased and global warming is allowing the establishment of tropical-affinity species into more temperate zones. Sessile communities are particularly useful as a baseline for ecological monitoring; however, a lack of historical data series exists for sessile marine organisms without commercial interest. Hydroids are ubiquitous components of the benthic sessile fauna on rocky shores and have been used as bio-indicators of environmental conditions. In this study on the benthic hydroid assemblages of the Chafarinas Islands (Alboran Sea, South-Western Mediterranean), we characterized the hydroid assemblages, identified the bathymetric gradients, and compared them with a previous study carried out in 1991. Hydroid assemblages showed a significant difference both between year and among depths. Furthermore, eight species not present in 1991 were found, including two possible new species and the tropical and subtropical species Sertularia marginata. Due to its strategic position at the entrance of the Mediterranean and the existence of previous data on hydroid assemblages, the Chafarinas Islands are proposed as a possible monitoring point for entrance of Atlantic tropical species into the Mediterranean Sea.     

Upstream effects of a reservoir on fish assemblages 45 years following impoundment

Fish assemblage structure, rarefied species richness, species diversity and evenness of assemblages upstream of a reservoir in Oklahoma, U.S.A., were compared pre and post‐impoundment as well as in contemporary collections from streams above and below the reservoir. There were significant shifts in assemblage structure between historical and contemporary collections above the reservoir but not between contemporary assemblages above and below the impoundment. Indicator species analysis revealed that the sand shiner Notropis stramineus and fathead minnow Pimephales promelas have declined, whereas largemouth bass Micropterus salmoides and western mosquitofish Gambusia affinis have increased in relative abundance in assemblages upstream of the impoundment. Species richness was lower in contemporary assemblages compared with historical assemblages. Furthermore, contemporary assemblages below the dam had lower species richness, diversity and evenness compared with contemporary collections above the dam. These results highlight the spatial and temporal extent of reservoirs altering fish assemblages upstream of impoundments.     

Fidelity of molluscan life and death assemblages on sublittoral hard substrata around granitic islands of the Seychelles

This study quantified the degree of coincidence between living and dead molluscan faunas in a shallow-water coral reef environment in the Indian Ocean. The results were compared with those from a similar life:death study in the northern Red Sea, and with those published for reef corals and soft substrata molluscs. The proportions of quantitatively important taxa are robust to sampling intensity, but fidelity indices and rank-order correlations are strongly influenced by quantitatively unimportant taxa. Distinct differences between life and death assemblages were recognized, which are due to distinct biases in the death assemblage. Bivalves that lived in close contact with living corals are preferentially overgrown after death and should provide considerable temporal and ecological information in a potential fossil record, as they will be preserved within a rapidly growing reef framework. Some gastropod taxa are preferentially transported into surrounding soft substrata postmortem. Here they will be affected by time-averaging and taphonomic disintegration typically occurring in sediments resulting in the associated loss of much temporal information. Most gastropod shells, however, are inhabited by hermit crabs postmortem, which may strongly alter the fossil gastropod community structure. The results are similar to a comparable study in the northern Red Sea, with a major exception being the strong dominance of hermit crab-inhabited gastropod shells in the death assemblage of the Seychelles. Comparison of life:death assemblages between hard and soft substrata, in keeping with the northern Red Sea study, showed the strong dominance of dead shells in the soft substrata with the converse on the hard substrata. This results from different accumulation conditions for dead shells in soft substrata. Fidelity indices are well suited to demonstrate that sedimentary death assemblages are typically remarkably robust reflections of local community composition but they do not record the strong biases in death assemblages of coral reef associated hard substrata molluscs and are therefore unsuitable for comparisons of life and death assemblages in reef environments.