Past and future decline of tropical pelagic biodiversity.

A major research question concerning global pelagic biodiversity remains unanswered: when did the apparent tropical biodiversity depression (i.e., bimodality of latitudinal diversity gradient [LDG]) begin? The bimodal LDG may be a consequence of recent ocean warming or of deep-time evolutionary speciation and extinction processes. Using rich fossil datasets of planktonic foraminifers, we show here that a unimodal (or only weakly bimodal) diversity gradient, with a plateau in the tropics, occurred during the last ice age and has since then developed into a bimodal gradient through species distribution shifts driven by postglacial ocean warming. The bimodal LDG likely emerged before the Anthropocene and industrialization, and perhaps ∼15,000 y ago, indicating a strong environmental control of tropical diversity even before the start of anthropogenic warming. However, our model projections suggest that future anthropogenic warming further diminishes tropical pelagic diversity to a level not seen in millions of years.

Assessing the equilibrium between assemblage composition and climate: A directional distance-decay approach.

The variation of assemblage composition in space is characterised by the decrease in assemblage similarity with spatial distance. Climatic constraint and dispersal limitation are major drivers of distance-decay of similarity. Distance-decay of similarity is usually conceptualised and modelled as an isotropic pattern, that is, assuming that similarity decays with the same rate in all directions. Because climatic gradients are markedly anisotropic, that is, they have different strength in different directions, if species distributions were in equilibrium with climate, the decay of assemblage similarity should be anisotropic in the same direction as the climatic gradient, that is, faster turnover in the direction that maximises the climatic gradient. Thus, deviations from equilibrium between assemblage composition and climatic conditions would result in differences in anisotropy between distance-decay of similarity and climatic gradients. We assessed anisotropy in distance-decay patterns in marine plankton assemblages, terrestrial vertebrates and European beetles, using two procedures: (a) measuring the correlation between the residuals of a distance-decay model and the angle in which pairs of sites are separated and (b) computing two separate distance-decay models for each dataset, one using only pairwise cases that are separated on North-South direction and another one using pairwise cases separated on East-West direction. We also analysed whether the degree of anisotropy in distance-decay is related to dispersal ability (proportion of wingless species and body size) and ecological niche characteristics (main habitat and trophic position) by assessing these relationships among beetle taxonomic groups (n = 21). Anisotropy varied markedly across realms and biological groups. Despite climatic gradients being steeper in North-South direction than in East-West direction in all datasets, North-South distance-decays tended to be steeper than East-West distance-decays in plankton and most vertebrate assemblages, but flatter in European amphibians and most beetle groups. Anisotropy also markedly varied across beetle groups depending on their dispersal ability, as the proportion of wingless species explained 60% of the variance in the difference between North-South and East-West distance-decay slopes. Our results suggest that the degree of equilibrium decreases from marine to terrestrial realms, and is markedly different between vertebrates and beetles. This has profound implications on the expected ability of different groups to track their suitable climates, and thus on the impact of climate change on biodiversity.

Functional and phylogenetic structure of island bird communities.

Biodiversity change in anthropogenically transformed habitats is often nonrandom, yet the nature and importance of the different mechanisms shaping community structure are unclear. Here, we extend the classic Theory of Island Biogeography (TIB) to account for nonrandom processes by incorporating species traits and phylogenetic relationships into a study of faunal relaxation following habitat loss and fragmentation. Two possible mechanisms can create nonrandom community patterns on fragment islands. First, small and isolated islands might consist of similar or closely related species because they are environmentally homogeneous or select for certain shared traits, such as dispersal ability. Alternatively, communities on small islands might contain more dissimilar or distantly related species than on large islands because limited space and resource availability result in greater competitive exclusion among species with high niche overlap. Breeding birds were surveyed on 36 islands and two mainland sites annually from 2010 to 2014 in the Thousand Island Lake region, China. We assessed community structure of breeding birds on these subtropical land-bridge islands by integrating species' trait and evolutionary distances. We additionally analysed habitat heterogeneity and variance in size ratios to distinguish biotic and abiotic processes of community assembly. Results showed that functional-phylogenetic diversity increased with island area, and decreased with isolation. Bird communities on the mainland were more diverse and generally less clustered than island bird communities and not different than randomly assembled communities. Bird communities on islands tend to be functionally similar and phylogenetically clustered, especially on small and isolated islands. The nonrandom decline in species diversity and change in bird community structure with island area and isolation, along with the relatively homogeneous habitats on small islands, support the environmental filtering hypothesis. Our study demonstrates the importance of integrating multiple forms of diversity for understanding the effects of habitat loss and fragmentation, and further reveals that TIB could be extended to community measures by moving beyond assumptions of species equivalency in colonisation rates and extinction susceptibilities.

Selective extinction drives taxonomic and functional alpha and beta diversities in island bird assemblages.

Taxonomic diversity considers all species being equally different from each other and thus disregards species' different ecological functions. Exploring taxonomic and functional aspects of biodiversity simultaneously can better understand the processes of community assembly. We analysed taxonomic and functional alpha and beta diversities of breeding bird assemblages on land-bridge islands in the Thousand Island Lake, China. Given the high dispersal ability of most birds at this spatial scale (several kilometres), we predicted (i) selective extinction driving alpha and beta diversities after the creation of land-bridge islands of varying area and (ii) low taxonomic and functional beta diversities that were not correlated to spatial distance. Breeding birds were surveyed on 37 islands annually from 2007 to 2014. We decomposed beta diversity of breeding birds into spatial turnover and nestedness-resultant components, and related taxonomic and functional diversities to island area and isolation using power regression models (for alpha diversity) and multiple regression models on distance matrices (for beta diversity). We then ran simulations to assess the strength of the correlations between taxonomic and functional diversities. Results revealed that both taxonomic and functional alpha diversities increased with island area. The taxonomic nestedness-resultant and turnover components increased and decreased with difference in area, respectively, but functional counterparts did not. Isolation played a minor role in explaining alpha- and beta-diversity patterns. By partitioning beta diversity, we found low levels of overall taxonomic and functional beta diversities. The functional nestedness-resultant component dominated overall functional beta diversity, whereas taxonomic turnover was the dominant component for taxonomic beta diversity. The simulation showed that functional alpha and beta diversities were significantly correlated with taxonomic diversities, and the observed values of correlations were significantly different from null expectations of random extinction. Our assessment of island bird assemblages validated the predictions of no distance effects and low beta diversity due to pervasive dispersal events among islands and also suggested that selective extinction drives taxonomic and functional alpha and beta diversities. The contrasting turnover and nestedness-resultant components of taxonomic and functional beta diversities demonstrate the importance of considering the multifaceted nature of biodiversity when examining community assembly.

Ice age climate, evolutionary constraints and diversity patterns of European dung beetles.

Current climate and Pleistocene climatic changes are both known to be associated with geographical patterns of diversity. We assess their associations with the European Scarabaeinae dung beetles, a group with high dispersal ability and well-known adaptations to warm environments. By assessing spatial stationarity in climate variability since the last glacial maximum (LGM), we find that current scarab richness is related to the location of their limits of thermal tolerance during the LGM. These limits mark a strong change in their current species richness-environment relationships. Furthermore, northern scarab assemblages are nested and composed of a phylogenetically clustered subset of large-range sized generalist species, whereas southern ones are diverse and variable in composition. Our results show that species responses to current climate are limited by the evolution of assemblages that occupied relatively climatically stable areas during the Pleistocene, and by post-glacial dispersal in those that were strongly affected by glaciations.

Phylogenetic patterns in zopherine beetles are related to ecological niche width and dispersal limitation.

Niche conservatism has been proposed as the mechanism driving speciation in temperate montane clades through range fragmentation during climatic oscillations. Thus, a negative relationship between speciation rates and niche width is expected. Here, we test this prediction using American zopherine beetles. Our phylogenetic analyses recovered two clades in addition to that of the genus Zopherus: the genera Verodes and Phloeodes, which originated most likely in the Eocene, and diversified during the Miocene and the Pliocene. The assessment of clade niche width in relation to clade diversity supported the proposition of narrow niches leading to a higher probability of range fragmentation during climatic oscillations, thus increasing speciation. Additionally, almost all current populations of Phloeodes and Verodes are located within regions that retained favourable climatic conditions across warm and cold Pleistocene periods, suggesting that dispersal limitation is a strong factor controlling clade distribution. In sum, our results suggest that (i) niche width is a major determinant of the probability of speciation in temperate montane clades, by controlling the probability of potential range fragmentation and (ii) dispersal limitation is also a major determinant of the speciation process, by increasing the fragmentation of realized ranges even when potential distributions are cyclically fused during climatic oscillations. When dispersal limitation is extreme, as in zopherine beetles, populations persist just in those areas that have retained suitable conditions during extremes of past climatic oscillations. Paradoxically, this relict condition confers zopherine beetles great resilience for facing future climate change.

Climate, history and neutrality as drivers of mammal beta diversity in Europe: insights from multiscale deconstruction.

1. Environmental sorting, historical factors and neutral dynamics may all drive beta diversity (change in species composition across space), but their relative importance remains unresolved. In the case of European mammals, key potential drivers of large-scale beta diversity include current climate, neutral dynamics and two historical factors: Pleistocene glaciations and peninsular dynamics (immigration from extra-regional eastern faunal source areas and inter-linked relictual survival and evolutionary differentiation in isolated areas). 2. We assessed the relative importance of these drivers using a novel analytical framework to deconstruct beta diversity of non-volant mammals in Europe (138 species) into its turnover (change in species composition because of species replacements) and nestedness components (change in species composition because of species richness differences) at continental and regional (250,000 km(2) ) scales. 3. We found continental-scale mammal beta diversity to be mainly caused by spatial turnover (99·9%), with only a small contribution (0·1%) from nestedness. 4. Current climate emerged as an important driver of beta diversity, given the strong continental-scale turnover, particularly in north-south direction, i.e., in line with the latitudinal climate gradient, and, more directly, the strong correlation of climate with spatial turnover at both continental and regional scales. 5. However, there was also evidence for the importance of non-climatic drivers. Notably, the compositional variation purely accounted for by space was greater than that purely accounted for by environment for both the turnover and the nestedness component of beta diversity. Furthermore, the strong longitudinal turnover within Southern Europe is in accordance with the region's long-term climatic stability having allowed multiple refugia and local evolutionary diversification. As expected from peninsular dynamics, there was increasing dissimilarity with geographic distance in an east-west direction because of nestedness, but only in Central and Northern Europe. 6. In conclusion, European mammal beta diversity mainly reflects spatial turnover and only to a limited extent nestedness and is driven by current climate in combination with historical - and perhaps, neutral - dynamics. These findings suggest that a key challenge for climate-change predictive studies will be taking the influence of non-climatic factors into account.

Diversity patterns in Iberian Calathus (Coleoptera, Carabidae: Harpalinae): species turnover shows a story overlooked by species richness.

We assessed the relationships between diversity patterns of Iberian Calathus and current environmental gradients or broad-scale spatial constraints, using 50-km grid cells as sampling units. We assessed the completeness of the inventories using nonparametric estimators to avoid spurious results based on sampling biases. We modeled species richness and beta diversity, using spatial position, and 23 topographical, climatic, and geological variables as predictors in regression and constrained analysis of principal coordinates modeling. Geographical situation does not seem to affect Calathus species richness, because no spatial pattern was detected. The environmental variables only explained 23% of the variation in richness. Spatial and environmental predictors explained a large part of the variation in species composition (58%). The fraction shared by both groups of variables was relatively large, but the pure effect of each model was still important. Our results show that it is necessary to assess the completeness of inventories to avoid drawing false conclusions. Also, Iberian Calathus represent a clear example of the need for combined analyses of species richness and beta diversity patterns, because the lack of patterns in the former does not imply the invariance of biotic communities.

Climatic niche divergence drives patterns of diversification and richness among mammal families.

A major goal of evolutionary biology is to understand why clades differ dramatically in species richness. A key to this challenge is to uncover the correlates of variation in diversification rate (speciation - extinction) among clades. Here, we explore the relationship between diversification rates and the climatic niches of species and clades among 92 families of terrestrial mammals. We use a time-calibrated molecular phylogeny of mammals and climatic data from 3335 species. We show that considerable variation in net diversification rates among mammal families is explained by niche divergence (59%) and rates of niche change (51%). Diversification rates in turn explain most variation in species richness among families (79%). Contrary to expectations, patterns of diversification are not explained by differences in geographic range areas of clades, nor by their climatic niche position (i.e. whether they are primarily tropical or temperate). Overall, these results suggest that speciation through climatic niche divergence may help drive large-scale patterns of diversification and richness. Our results help explain diversification patterns in a major clade of vertebrates, and suggest that similar underlying principles may explain the diversification of many terrestrial clades.

Fine-scale determinants of conservation value of river reaches in a hotspot of native and non-native species diversity.

Global freshwater biodiversity is declining at unprecedented rates while non-native species are expanding. Examining diversity patterns across variable river conditions can help develop better management strategies. However, many indicators can be used to determine the conservartion value of aquatic communities, and little is known of how well they correlate to each other in making diagnostics, including when testing for the efficacy of protected areas. Using an extensive data set (99,700km2, n=530 sites) across protected and unprotected river reaches in 15 catchments of NE Spain, we examine correlations among 20 indicators of conservation value of fish communities, including the benefits they provide to birds and threatened mammals and mussels. Our results showed that total native fish abundance or richness correlated reasonably well with many native indicators. However, the lack of a strong congruence led modelling techniques to identify different river attributes for each indicator of conservation value. Overall, tributaries were identified as native fish refugees, and nutrient pollution, salinization, low water velocity and poor habitat structure as major threats to the native biota. We also found that protected areas offered limited coverage to major components of biodiversity, including rarity, threat and host-parasite relationships, even though values of non-native indicators were notably reduced. In conclusion, restoring natural hydrological regimes and water chemical status is a priority to stem freshwater biodiversity loss in this region. A complementary action can be the protection of tributaries, but more studies examining multiple components of diversity are necessary to fully test their potential as fluvial reserves in Mediterranean climate areas.

Spatial and environmental correlates of species richness and turnover patterns in European cryptocephaline and chrysomeline beetles.

Despite some general concordant patterns (i.e. the latitudinal richness gradient), species richness and composition of different European beetle taxa varies in different ways according to their dispersal and ecological traits. Here, the patterns of variation in species richness, composition and spatial turnover are analysed in European cryptocephaline and chrysomeline leaf beetles, assessing their environmental and spatial correlates. The underlying rationale to use environmental and spatial variables of diversity patterns is to assess the relative support for niche- and dispersal-driven hypotheses. Our results show that despite a broad congruence in the factors correlated with cryptocephaline and chrysomeline richness, environmental variables (particularly temperature) were more relevant in cryptocephalines, whereas spatial variables were more relevant in chrysomelines (that showed a significant longitudinal gradient besides the latitudinal one), in line with the higher proportion of flightless species within chrysomelines. The variation in species composition was also related to environmental and spatial factors, but this pattern was better predicted by spatial variables in both groups, suggesting that species composition is more linked to dispersal and historical contingencies than species richness, which would be more controlled by environmental limitations. Among historical factors, Pleistocene glaciations appear as the most plausible explanation for the steeper decay in assemblage similarity with spatial distance, both in cryptocephalines and chrysomelines.

The mossy north: an inverse latitudinal diversity gradient in European bryophytes.

It remains hotly debated whether latitudinal diversity gradients are common across taxonomic groups and whether a single mechanism can explain such gradients. Investigating species richness (SR) patterns of European land plants, we determine whether SR increases with decreasing latitude, as predicted by theory, and whether the assembly mechanisms differ among taxonomic groups. SR increases towards the south in spermatophytes, but towards the north in ferns and bryophytes. SR patterns in spermatophytes are consistent with their patterns of beta diversity, with high levels of nestedness and turnover in the north and in the south, respectively, indicating species exclusion towards the north and increased opportunities for speciation in the south. Liverworts exhibit the highest levels of nestedness, suggesting that they represent the most sensitive group to the impact of past climate change. Nevertheless, although the extent of liverwort species turnover in the south is substantially and significantly lower than in spermatophytes, liverworts share with the latter a higher nestedness in the north and a higher turn-over in the south, in contrast to mosses and ferns. The extent to which the similarity in the patterns displayed by spermatophytes and liverworts reflects a similar assembly mechanism remains, however, to be demonstrated.

Temporal Beta Diversity of Bird Assemblages in Agricultural Landscapes: Land Cover Change vs. Stochastic Processes.

Temporal variation in the composition of species assemblages could be the result of deterministic processes driven by environmental change and/or stochastic processes of colonization and local extinction. Here, we analyzed the relative roles of deterministic and stochastic processes on bird assemblages in an agricultural landscape of southwestern France. We first assessed the impact of land cover change that occurred between 1982 and 2007 on (i) the species composition (presence/absence) of bird assemblages and (ii) the spatial pattern of taxonomic beta diversity. We also compared the observed temporal change of bird assemblages with a null model accounting for the effect of stochastic dynamics on temporal beta diversity. Temporal assemblage dissimilarity was partitioned into two separate components, accounting for the replacement of species (i.e. turnover) and for the nested species losses (or gains) from one time to the other (i.e. nestedness-resultant dissimilarity), respectively. Neither the turnover nor the nestedness-resultant components of temporal variation were accurately explained by any of the measured variables accounting for land cover change (r(2)<0.06 in all cases). Additionally, the amount of spatial assemblage heterogeneity in the region did not significantly change between 1982 and 2007, and site-specific observed temporal dissimilarities were larger than null expectations in only 1% of sites for temporal turnover and 13% of sites for nestedness-resultant dissimilarity. Taken together, our results suggest that land cover change in this agricultural landscape had little impact on temporal beta diversity of bird assemblages. Although other unmeasured deterministic process could be driving the observed patterns, it is also possible that the observed changes in presence/absence species composition of local bird assemblages might be the consequence of stochastic processes in which species populations appeared and disappeared from specific localities in a random-like way. Our results might be case-specific, but if stochastic dynamics are generally dominant, the ability of correlative and mechanistic models to predict land cover change effects on species composition would be compromised.

Revealing Beta-diversity patterns of breeding bird and lizard communities on inundated land-bridge islands by separating the turnover and nestedness components.

Beta diversity describes changes in species composition among sites in a region and has particular relevance for explaining ecological patterns in fragmented habitats. However, it is difficult to reveal the mechanisms if broad sense beta-diversity indices (i.e. yielding identical values under nestedness and species replacement) are used. Partitioning beta diversity into turnover (caused by species replacement from site to site) and nestedness-resultant components (caused by nested species losses) could provide a unique way to understand the variation of species composition in fragmented habitats. Here, we collected occupancy data of breeding birds and lizards on land-bridge islands in an inundated lake in eastern China. We decomposed beta diversity of breeding bird and lizard communities into spatial turnover and nestedness-resultant components to assess their relative contributions and respective relationships to differences in island area, isolation, and habitat richness. Our results showed that spatial turnover contributed more to beta diversity than the nestedness-resultant component. The degree of isolation had no significant effect on overall beta diversity or its components, neither for breeding birds nor for lizards. In turn, in both groups the nestedness-resultant component increased with larger differences in island area and habitat richness, respectively, while turnover component decreased with them. The major difference among birds and lizards was a higher relevance of nestedness-resultant dissimilarity in lizards, suggesting that they are more prone to local extinctions derived from habitat fragmentation. The dominance of the spatial turnover component of beta diversity suggests that all islands have potential conservation value for breeding bird and lizard communities.

Assessing community-level and single-species models predictions of species distributions and assemblage composition after 25 years of land cover change.

To predict the impact of environmental change on species distributions, it has been hypothesized that community-level models could give some benefits compared to species-level models. In this study we have assessed the performance of these two approaches. We surveyed 256 bird communities in an agricultural landscape in southwest France at the same locations in 1982 and 2007. We compared the ability of CQO (canonical quadratic ordination; a method of community-level GLM) and GLMs (generalized linear models) to i) explain species distributions in 1982 and ii) predict species distributions, community composition and species richness in 2007, after land cover change. Our results show that models accounting for shared patterns between species (CQO) slightly better explain the distribution of rare species than models that ignore them (GLMs). Conversely, the predictive performances were better for GLMs than for CQO. At the assemblage level, both CQO and GLMs overestimated species richness, compared with that actually observed in 2007, and projected community composition was only moderately similar to that observed in 2007. Species richness projections tended to be more accurate in sites where land cover change was more marked. In contrast, the composition projections tended to be less accurate in those sites. Both modelling approaches showed a similar but limited ability to predict species distribution and assemblage composition under conditions of land cover change. Our study supports the idea that our community-level model can improve understanding of rare species patterns but that species-level models can provide slightly more accurate predictions of species distributions. At the community level, the similar performance of both approaches for predicting patterns of assemblage variation suggests that species tend to respond individualistically or, alternatively, that our community model was unable to effectively account for the emergent community patterns.

Rare failures of DNA barcodes [corrected] to separate morphologically distinct species in a biodiversity survey of Iberian leaf beetles.

During a survey of genetic and species diversity patterns of leaf beetle (Coleoptera: Chrysomelidae) assemblages across the Iberian Peninsula we found a broad congruence between morphologically delimited species and variation in the cytochrome oxidase (cox1) gene. However, one species pair each in the genera Longitarsus Berthold and Pachybrachis Chevrolat was inseparable using molecular methods, whereas diagnostic morphological characters (including male or female genitalia) unequivocally separated the named species. Parsimony haplotype networks and maximum likelihood trees built from cox1 showed high genetic structure within each species pair, but no correlation with the morphological types and neither with geographic distributions. This contrasted with all analysed congeneric species, which were recovered as monophyletic. A limited number of specimens were sequenced for the nuclear 18S rRNA gene, which showed no or very limited variation within the species pair and no separation of morphological types. These results suggest that processes of lineage sorting for either group are lagging behind the clear morphological and presumably reproductive separation. In the Iberian chrysomelids, incongruence between DNA-based and morphological delimitations is a rare exception, but the discovery of these species pairs may be useful as an evolutionary model for studying the process of speciation in this ecological and geographical setting. In addition, the study of biodiversity patterns based on DNA requires an evolutionary understanding of these incongruences and their potential causes.

Whole-community DNA barcoding reveals a spatio-temporal continuum of biodiversity at species and genetic levels.

A correlation of species and genetic diversity has been proposed but not uniformly supported. Large-scale DNA barcoding provides qualitatively novel data to test for correlations across hierarchical levels (genes, genealogies and species), and may help to unveil the underlying processes. Here we analyse sequence variation in communities of aquatic beetles across Europe (>5,000 individuals) to test for self-similarity of beta diversity patterns at multiple hierarchical levels. We show that community similarity at all levels decreases exponentially with geographic distance, and initial similarity is correlated with the lineage age, consistent with a molecular clock. Log-log correlations between lineage age, number of lineages, and range sizes, reveal a fractal geometry in time and space, indicating a spatio-temporal continuum of biodiversity across scales. Simulations show that these findings mirror dispersal-constrained models of haplotype distributions. These novel macroecological patterns may be explained by neutral evolutionary processes, acting continuously over time to produce multi-scale regularities of biodiversity.