Functional Beta Diversity Research Articles

Beta-diversity of ectoparasites at two spatial scales: nested hierarchy, geography and habitat type.

Beta-diversity of biological communities can be decomposed into (a) dissimilarity of communities among units of finer scale within units of broader scale and (b) dissimilarity of communities among units of broader scale. We investigated compositional, phylogenetic/taxonomic and functional beta-diversity of compound communities of fleas and gamasid mites parasitic on small Palearctic mammals in a nested hierarchy at two spatial scales: (a) continental scale (across the Palearctic) and (b) regional scale (across sites within Slovakia). At each scale, we analyzed beta-diversity among smaller units within larger units and among larger units with partitioning based on either geography or ecology. We asked (a) whether compositional, phylogenetic/taxonomic and functional dissimilarities of flea and mite assemblages are scale dependent; (b) how geographical (partitioning of sites according to geographic position) or ecological (partitioning of sites according to habitat type) characteristics affect phylogenetic/taxonomic and functional components of dissimilarity of ectoparasite assemblages and (c) whether assemblages of fleas and gamasid mites differ in their degree of dissimilarity, all else being equal. We found that compositional, phylogenetic/taxonomic, or functional beta-diversity was greater on a continental rather than a regional scale. Compositional and phylogenetic/taxonomic components of beta-diversity were greater among larger units than among smaller units within larger units, whereas functional beta-diversity did not exhibit any consistent trend regarding site partitioning. Geographic partitioning resulted in higher values of beta-diversity of ectoparasites than ecological partitioning. Compositional and phylogenetic components of beta-diversity were higher in fleas than mites but the opposite was true for functional beta-diversity in some, but not all, traits.

Fire exclusion and climate change interact to affect long‐term changes in the functional composition of plant communities

AbstractAimPlant functional traits allow us to mechanistically link changes in species composition to changes in ecosystem functions. Understanding how and why changes occur in functional composition of plant communities can thus help us better conserve and restore biodiversity. We aim to examine long‐term effects of fire exclusion and climate change on the functional composition of fire‐maintained pine barrens in central Wisconsin.LocationCentral Wisconsin, USA.MethodsUsing a database that included vegetation data of surveys (1958) and resurveys (2012) of 30 sites, we quantified functional composition (α and β functional diversity, community‐weighted means) of each site at both time periods. We then applied linear regression and linear mixed models to study effects of fire exclusion and climate change on changes in functional composition.ResultsWe observed shifts towards larger specific leaf area, greater seed mass and other traits related to shade tolerance. These communities thus appear to be undergoing ecological succession, favouring plant adaptions to better harvest light and carbon in darker, warmer and wetter habitats. Functional alpha diversity increased, while functional beta diversity decreased even after controlling for changes in taxonomic diversity. Fire exclusion and climate change both contributed to these increases in local functional diversity but neither is related to the functional homogenization observed. Fire exclusion and climate change also interacted negatively to affect local functional diversity, suggesting that future climate change and succession may soon reduce alpha functional diversity.Main conclusionsOur study provides a rare record of long‐term functional dynamics and demonstrates that fire exclusion and climate change can interact to affect the functional composition of plant communities. Thus, we should consider changes in local ecological conditions as we seek to predict how climate change will affect the functional composition of plant communities.

Performance of partitioning functional beta‐diversity indices: Influence of functional representation and partitioning methods

AbstractAimTwo frameworks (BASVIL and PODCAR), based on two different functional representations (ordination and dendrogram), have been proposed for partitioning overall functional beta diversity into two analogous components: turnover and nestedness‐resultant dissimilarity, or replacement and difference of functional richness, respectively. We compared the two frameworks by testing the influence of functional representations and partitioning methods on the measurement of overall functional beta diversity and its components.InnovationWe computed beta‐diversity indices from the two frameworks on a set of communities simulated according to five scenarios of assembly: random, richness gradient, pure nestedness, pure turnover and mixed turnover/loss scenarios. To disentangle the effects of the partitioning approach and those of the functional representation on measurement of functional beta diversity, we also computed PODCAR indices in multidimensional space.Main conclusionsBASVIL and PODCAR frameworks led to different results for overall functional beta diversity and their analogous partitioning components. Most of the difference between the two frameworks was due to the functional representation used. The goodness‐of‐fit measure (mean squared deviation, mSD) to assess the quality of functional spaces showed that the one computed on the basis of the dendrogram used in PODCAR remained lower than that of the functional ordination considered in BASVIL. In addition, only functional turnover derived from the BASVIL framework is independent of difference in functional richness. Finally, BASVIL measured functional variations derived from nested phenomena while PODCAR did not allow separation of this variation derived from richness difference. However, the sensitivity of BASVIL to functionally extreme species may make it difficult to know whether variations of the nestedness‐resultant dissimilarity components are due to a turnover with few extreme species or a loss in functional richness. Particular attention with regard to the properties of the two frameworks is required before drawing conclusions regarding processes that structure communities.

Fish trait diversity in littorals of two floodplain lakes of the highly biodiverse Caura River, Venezuela

AbstractWe studied the trait diversity and structure in the fish communities of two floodplain lakes of the Caura River: Aricagua and Paramuto, during one hydrological cycle. We calculated taxonomic and a functional alpha and beta diversities and made comparisons among hydrological seasons and among habitats within each lake based on rarefactions. The trait structure was explored with an RLQ (analysis of a table R of environmental conditions, a table L of abundances of species and a table Q of species traits) analysis, and pairwise relationships between environmental variables and traits were explored with fourth‐corner analyses. Despite its smaller extension, Paramuto showed higher alpha taxonomic and trait diversities. The substrates of open sand and those covered by leaf litter were the most diverse habitats in terms of both species and traits. The trait structure of the fish communities was influenced by the hydrological seasons, the lakes as well as water pH and temperature, and in a lesser degree dissolved oxygen, habitat type and total dissolved solids in the water. These factors constitute the habitat templet for the fish community's composition and trait structure.

Stochastic assembly in a subtropical forest chronosequence: evidence from contrasting changes of species, phylogenetic and functional dissimilarity over succession.

Deterministic and stochastic processes jointly determine the community dynamics of forest succession. However, it has been widely held in previous studies that deterministic processes dominate forest succession. Furthermore, inference of mechanisms for community assembly may be misleading if based on a single axis of diversity alone. In this study, we evaluated the relative roles of deterministic and stochastic processes along a disturbance gradient by integrating species, functional, and phylogenetic beta diversity in a subtropical forest chronosequence in Southeastern China. We found a general pattern of increasing species turnover, but little-to-no change in phylogenetic and functional turnover over succession at two spatial scales. Meanwhile, the phylogenetic and functional beta diversity were not significantly different from random expectation. This result suggested a dominance of stochastic assembly, contrary to the general expectation that deterministic processes dominate forest succession. On the other hand, we found significant interactions of environment and disturbance and limited evidence for significant deviations of phylogenetic or functional turnover from random expectations for different size classes. This result provided weak evidence of deterministic processes over succession. Stochastic assembly of forest succession suggests that post-disturbance restoration may be largely unpredictable and difficult to control in subtropical forests.

Multi‐component β‐diversity approach reveals conservation dilemma between species and functions of coral reef fishes

AbstractAimWe applied a multicomponent approach based on the decomposition of taxonomic (both presence–absence and abundance) and functional beta diversity to determine the influence of ecological factors in shaping spatial distribution diversity of coral reef fishes, and the implications for conservation decisions.LocationLagoons of ten atolls characterized by low human pressure but with contrasted geomorphology in the Tuamotu Archipelago, French Polynesia.MethodsWe computed beta diversities and their partitioning components, both at local (inter‐transect, from 200 m to 10 km) and large (among atolls, from 22 to 350 km) spatial scales. Null models were applied to test whether the observed beta diversity differed from random expectation. Multiple generalized dissimilarity models were run to test which environmental factors were the best predictors of observed beta diversities.ResultsBeta diversity was indistinguishable from randomness at both spatial scales. Species remained generally interchangeable among transects within an atoll and to some extent among atolls. However, strong deviance explained by models showed that the number of species, the number of individuals and functional traits present in transects and atolls were determined by deterministic factors (i.e. environmental factors). Modelling each beta diversity component separately also revealed partial mismatch among atolls and among species and functional dissimilarities. The influence of environmental variables strongly varied among atolls, species and functional dissimilarities.Main conclusionsBy revealing the spatial scaling of ecological factors and partial congruence among species and functional diversity, assessment of beta diversity provides insight into conservation planning. Our results support the idea that conservation planning applied to protect taxonomic diversity cannot be fully extended to functional diversity. We have addressed the dilemma of which diversity component should be favoured in conservation strategies.

Reorganization of taxonomic, functional, and phylogenetic ant biodiversity after conversion to rubber plantation

AbstractAgricultural activity associated with habitat conversion is a major driver of biodiversity loss across the tropics. The decline of species richness is a common outcome of conversion to agricultural land use, but the associated changes in functional and phylogenetic diversities, and spatial patterns of beta diversity, are not well understood. These patterns may shed light on underlying ecological processes that are of both basic and applied interest; for example the relative roles of stochastic assembly, ecological filtering, and competition in structuring ecological communities as well as broader consequences for ecological functioning in agroecosystems. Here we investigate the effects of conversion to rubber plantation (Hevea brasiliensis), a rapidly spreading agroecosystem in Southeast Asia, on leaf‐litter ant taxonomic, functional, and phylogenetic diversities at local and among‐sites scales in Xishuangbanna, Southeast China. We found a sharp decline of ant species richness in rubber plantations compared with nearby forest habitat, with low beta diversity indicating spatial homogeneity of communities in rubber plantations. In addition, patterns of both functional alpha and beta diversities suggested the emergence of a functionally distinct ant community in the agroecosystem compared to the forest habitats. These results support a role of ecological filtering in structuring the taxonomic and functional composition of both rubber and forest habitats. In contrast, changes in phylogenetic diversity were modest and not significantly different from random expectations despite strong phylogenetic signal of functional traits. This study highlights the need for a pluralistic approach to characterizing the loss of biodiversity in agroecosystems, as well as understanding the underlying mechanisms of community assembly driving this biodiversity loss.

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.

Local-scale Partitioning of Functional and Phylogenetic Beta Diversity in a Tropical Tree Assemblage.

The relative degree to which stochastic and deterministic processes underpin community assembly is a central problem in ecology. Quantifying local-scale phylogenetic and functional beta diversity may shed new light on this problem. We used species distribution, soil, trait and phylogenetic data to quantify whether environmental distance, geographic distance or their combination are the strongest predictors of phylogenetic and functional beta diversity on local scales in a 20-ha tropical seasonal rainforest dynamics plot in southwest China. The patterns of phylogenetic and functional beta diversity were generally consistent. The phylogenetic and functional dissimilarity between subplots (10 × 10 m, 20 × 20 m, 50 × 50 m and 100 × 100 m) was often higher than that expected by chance. The turnover of lineages and species function within habitats was generally slower than that across habitats. Partitioning the variation in phylogenetic and functional beta diversity showed that environmental distance was generally a better predictor of beta diversity than geographic distance thereby lending relatively more support for deterministic environmental filtering over stochastic processes. Overall, our results highlight that deterministic processes play a stronger role than stochastic processes in structuring community composition in this diverse assemblage of tropical trees.

Space and seasonality effects on the aquatic macrophyte community of temporary Neotropical upland lakes

Temporal and spatial scales are key factors that affect species distribution. Temporary lakes may be intensely affected by both scales, and the aquatic macrophyte community can rapidly respond to such environmental changes. Here, we investigate 26 Neotropical temporary upland lakes and describe the species richness and composition as well as the species richness within functional groups and the functional composition of aquatic macrophytes to better understand the effect of spatial and temporal scales on these attributes. Additionally, we highlight the scenarios where we found rare and endemic species during sampling. Our findings mainly suggest that spatial and temporal scales do not affect the total species richness or species richness within the functional groups. However, the temporal scale affects the species composition and functional-group composition. The species composition changes between dry and rainy seasons (beta-diversity), and such change was less dramatic six years after the first sampling. The identical pattern was found for the functional-group composition (functional beta-diversity). We also found small or few endemic species populations that co-occurred with potentially invasive species, which could threaten endemic species and lead to global extinctions. Finally, we suggest that the temporal dynamics of temporary lakes are fundamental in maintaining regional biodiversity. However, this dynamic may change over time by moving towards a future with a more homogeneous aquatic macrophyte assemblage, what may create a scenario with more functionally redundant species. Subsequently, applied ecological studies in such environments to better understand the temporal dynamics of the aquatic macrophyte community may help to improve future proposals of biodiversity management and protection.

Contrasting species and functional beta diversity in montane ant assemblages.

AimBeta diversity describes the variation in species composition between sites and can be used to infer why different species occupy different parts of the globe. It can be viewed in a number of ways. First, it can be partitioned into two distinct patterns: turnover and nestedness. Second, it can be investigated from either a species identity or a functional‐trait point of view. We aim to document for the first time how these two aspects of beta diversity vary in response to a large environmental gradient.LocationMaloti‐Drakensberg Mountains, southern Africa.MethodsWe sampled ant assemblages along an extensive elevational gradient (900–3000 m a.s.l.) twice yearly for 7 years, and collected functional‐trait information related to the species’ dietary and habitat‐structure preferences. We used recently developed methods to partition species and functional beta diversity into their turnover and nestedness components. A series of null models were used to test whether the observed beta diversity patterns differed from random expectations.ResultsSpecies beta diversity was driven by turnover, but functional beta diversity was composed of both turnover and nestedness patterns at different parts of the gradient. Null models revealed that deterministic processes were likely to be responsible for the species patterns but that the functional changes were indistinguishable from stochasticity.Main conclusionsDifferent ant species are found with increasing elevation, but they tend to represent an increasingly nested subset of the available functional strategies. This finding is unique and narrows down the list of possible factors that control ant existence across elevation. We conclude that diet and habitat preferences have little role in structuring ant assemblages in montane environments and that some other factor must be driving the non‐random patterns of species turnover. This finding also highlights the importance of distinguishing between different kinds of beta diversity.

Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa.

The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD), functional (FBD) and phylogenetic (PBD) facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools) and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants) from two contrasting biomes (subtropical forest and grassland) and land uses (tree plantations and cropfields) in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland), and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation.

Mechanisms underlying local functional and phylogenetic beta diversity in two temperate forests.

Although trait information has been widely used to explore underlying mechanisms of forest community structure, most studies have focused on local patterns of phylogenetic or functional alpha diversity. Investigations of functional beta diversity, on the other hand, have not been conducted at local scales in a spatially explicit way. In this study, we provide a powerful methodology based on recent advances in spatial point pattern analysis using fully mapped data of large and small trees in two large temperate forest plots. This approach allowed us to assess the relative importance of different ecological processes and mechanisms for explaining patterns of local phylogenetic and functional beta diversity. For both forests and size classes, we found a clear hierarchy of scales: habitat filtering accounted for patterns of phylogenetic and functional beta diversity at larger distances (150-250 m), dispersal limitation accounted for the observed decline in beta diversity at distances below 150 m, and species interactions explained small departures from functional and phylogenetic beta diversity at the immediate plant-neighborhood scale (below 20 m). Thus, both habitat filtering and dispersal limitation influenced the observed patterns in phylogenetic and functional beta diversity at local scales. This result contrasts with a previous study from the same forests, where dispersal limitation alone approximated the observed species beta diversity for distances up to 250 m. In addition, species interactions were relatively unimportant for predicting phylogenetic and functional beta diversity. Our analysis suggests that phylogenetic and functional beta diversity can provide insights into the mechanisms of local community assembly that are missed by studies focusing exclusively on species beta diversity.

Investigating the evolutionary assembly of a Mediterranean biodiversity hotspot: deep phylogenetic signal in the distribution of eudicots across elevational belts

AbstractAimTo reconstruct the historical assembly of the eudicot flora of Mediterranean sierras by examining compositional (CBD), phylogenetic (PBD) and functional (FBD) beta diversity between elevational belts among disjunct mountain ranges (sierras), and relating these measures of turnover to environmental and geographical distances.LocationBaetic ranges, Andalusia, southern Spain.MethodsWe compiled eudicot species and subspecies (‘entities’) checklists for three elevational belts within each of eight sierras of Andalusia (‘sites’) and tested for non‐random patterns of PBD and FBD of all entities and of endemic entities separately among sites between and within sierras. Multiple regression on distance matrices was used to determine the respective contribution of climate, lithology and geographical distance to CBD, PBD and FBD. Finally, we decomposed PBD into the turnover and nestedness components of beta diversity, and quantified the phylogenetic diversity (PD) within sites.ResultsThe observed PBD and FBD among elevational belts within sierras for all entities were generally higher than expected based on their respective null distributions, whereas CBD among elevational belts within sierras was similar or even lower than between sierras. In contrast, the observed PBD and FBD for endemics were non‐significant in most of the comparisons. Temperature‐related variables best explained patterns of CBD, PBD and FBD for all entities, whereas lithology and geographical distance were the main drivers of endemic CBD. The observed PBD among elevational belts within sierras was mainly attributable to differences in PD rather than ‘true’ turnover.Main conclusionsThere is strong structuring of plant lineages along elevational gradients in the Baetic range, probably due to habitat filtering acting on life forms and character syndromes that show strong phylogenetic signal. The differentiation of the endemic flora that contributed to the emergence of this western Mediterranean biodiversity hotspot was probably driven by geographical isolation and/or by repeated specialization to contrasting lithologies.

Species contribute differently to the taxonomic, functional, and phylogenetic alpha and beta diversity of freshwater fish communities

AbstractAimWe examined the current biogeographical patterns of native fish communities throughout France, using a multifaceted taxonomic, functional and phylogenetic diversity approach. We then identified the contribution of individual species to each facet of watershed's native fish diversity.LocationContinental France.MethodsThe taxonomic, functional and phylogenetic diversity of the fish communities were quantified at the watershed‐scale (i.e. alpha diversity approach), and congruencies between diversity facets were assessed. Variation between watersheds was then quantified (i.e. beta diversity approach) using Jaccard's dissimilarity index for all three facets of diversity, and congruencies were assessed. We subsequently determined the relationship between alpha and beta diversity for each diversity facet. Lastly, the mean relative contribution of each species to watershed's alpha taxonomic, functional and phylogenetic diversity was quantified. The conservation status of each species was considered to determine if threatened and endangered species contributed more significantly to watershed alpha diversity than common species.ResultsAcross all watersheds, taxonomic, functional and phylogenetic diversity facets were found to be highly congruent using both the alpha and beta diversity approaches. In contrast, the relationship between the watersheds' alpha and beta diversity was primarily negative; watersheds with decreased beta diversity tended to have increased alpha diversity for all three facets. Individual species also rarely contributed prominently to more than one diversity facet, with conservation status insignificantly influencing species relative contributions.Main conclusionsWe found that native fish diversity ‘hotspots’ exist in France; exhibited in our results by areas of high, overlapping taxonomic, functional and phylogenetic diversity. Consequently, conservation planning approaches supported by species‐based metrics may concurrently target areas of increased ecological and evolutionary importance at the watershed‐scale. Interestingly, a diverse mosaic of species accounted for the different facets of diversity, suggesting that future reductions in species richness could have differential effects on each watershed's diversity facets.

Using functional diversity patterns to explore metacommunity dynamics: a framework for understanding local and regional influences on community structure

The metacommunity concept, describing how local and regional scale processes interact to structure communities, has been successfully applied to patterns of taxonomic diversity. Functional diversity has proved useful for understanding local scale processes, but has less often been applied to understanding regional scale processes. Here, we explore functional diversity patterns within a metacommunity context to help elucidate how local and regional scale processes influence community assembly. We detail how each of the four metacommunity perspectives (species sorting, mass effects, patch dynamics, neutral) predict different patterns of functional beta‐ and alpha‐diversity and spatial structure along two key gradients: dispersal limitation and environmental conditions. We then apply this conceptual model to a case study from alpine tundra plant communities. We sampled species composition in 17 ‘sky islands’ of alpine tundra in the Colorado Rocky Mountains, USA that differed in geographic isolation and area (key factors related to dispersal limitation) and temperature and elevation (key environmental factors). We quantified functional diversity in each site based on specific leaf area, leaf area, stomatal conductance, plant height and chlorophyll content. We found that colder high elevation sites were functionally more similar to each other (decreased functional beta‐diversity) and had lower functional alpha‐diversity. Geographic isolation and area did not influence functional beta‐ or alpha‐diversity. These results suggest a strong role for environmental conditions structuring alpine plant communities, patterns consistent with the species sorting metacommunity perspective. Incorporating functional diversity into metacommunity theory can help elucidate how local and regional factors structure communities and provide a framework for observationally examining the role of metacommunity dynamics in systems where experimental approaches are less tractable.

Is taxonomic homogenization linked to functional homogenization in temperate forests?

AbstractAimBiotic homogenization – the tendency for communities to converge in species composition – has occurred in many ecosystems, creating management challenges. The extent to which this convergence in species composition is related to convergence in trait composition (‘functional homogenization’), however, remains unresolved.LocationNorth America, Wisconsin.MethodsUsing extensive plant community survey data from the 1950s and 2000s, and values for 11 traits measured on 169 species, we examined changes in functional beta diversity across 151 upland forest stands distributed across southern and northern Wisconsin. To estimate functional beta diversity, we used two recently developed pairwise functional dissimilarity metrics, plus an additive partitioning of functional diversity approach.ResultsUsing pairwise functional dissimilarity metrics, we found no significant changes in functional beta diversity through time in either southern or northern upland forests. Under additive partitioning, species alpha diversity was lower than species beta diversity; whereas functional alpha diversity was much higher than functional beta diversity in both time periods and across all forest types. This suggests a high turnover of species but a low turnover of traits among communities.Main conclusionsAlthough upland forests in Wisconsin have experienced taxonomic homogenization, they have not undergone functional homogenization, which may reflect a high functional redundancy among Wisconsin forest plants. As species decline further or disappear in response to habitat fragmentation and other global changes, functional redundancy may decline in a way that could diminish the functional diversity of Wisconsin's forests at both local and regional scales.

Partitioning taxon, phylogenetic and functional beta diversity into replacement and richness difference components

AbstractAimTo propose a unified framework for quantifying taxon (Tβ), phylogenetic (Pβ) and functional (Fβ) beta diversity via pairwise comparisons of communities, which allows these types of beta diversity to be partitioned into ecologically meaningful additive components.LocationGlobal, with case studies in Europe and the Azores archipelago.MethodsUsing trees as a common representation for taxon, phylogenetic and functional diversity, we partition total beta diversity (βtotal) into its replacement (turnover, βrepl) and richness difference (βrich) components according to which part of a global tree was shared by or unique to communities that were being compared. We demonstrate the application of this framework using artificial and empirical examples (mammals in Europe and epigean arthropods in the Azores).ResultsOur empirical examples show that comparing Pβ and Fβ with the most commonly used Tβ revealed previously hidden patterns of beta diversity. More importantly, we demonstrate that partitioning Pβtotal and Fβtotal into their respective βrepl and βrich components facilitates the detection of more complex patterns than using the overall coefficients alone, further elucidating the different forces operating in community assembly.Main conclusionsThe methods presented here allow the integration and full comparison of Tβ, Pβ and Fβ. They provide a tool for effectively disentangling the replacement (turnover) and richness difference components of the different biodiversity facets within the same methodological framework.

Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics

Little is known about the diversity and structuring of freshwater microbial communities beyond the patterns revealed by tracing their distribution in the landscape with common taxonomic markers such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial lineages was also reflected in phylogenies of functional genes, and there were also significant differences in functional beta-diversity. The pathways and functions that accounted for these differences are involved in osmoregulation, active transport, carbohydrate and amino acid metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes. This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic- compared with freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities.

Contrasting changes in taxonomic, phylogenetic and functional diversity during a long‐term succession: insights into assembly processes

Summary Theory predicts that the processes generating biodiversity after disturbance will change during succession. Comparisons of phylogenetic and functional (alpha and beta) diversity with taxonomic diversity can provide insights into the extent to which community assembly is driven by deterministic or stochastic processes, but comparative approaches have yet to be applied to successional systems. We characterized taxonomic, phylogenetic and functional plant (alpha and beta) diversity within and between four successional stages in a > 270‐year‐long arable‐to‐grassland chronosequence. Null models were used to test whether functional and phylogenetic turnover differed from random expectations, given the levels of species diversity. The three facets of diversity showed different patterns of change during succession. Between early and early‐mid succession, species richness increased but there was no increase in functional or phylogenetic diversity. Higher than predicted levels of functional similarity between species within the early and early‐mid successional stages, indicate that abiotic filters have selected for sets of functionally similar species within sites. Between late‐mid and late succession, there was no further increase in species richness, but a significant increase in functional alpha diversity, suggesting that functionally redundant species were replaced by functionally more dissimilar species. Functional turnover between stages was higher than predicted, and higher than within‐stage turnover, indicating that different assembly processes act at different successional stages. Synthesis. Analysis of spatial and temporal turnover in different facets of diversity suggests that deterministic processes generate biodiversity during post‐disturbance ecosystem development and that the relative importance of assembly processes has changed over time. Trait‐mediated abiotic filtering appears to play an important role in community assembly during the early and early‐mid stages of arable‐to‐grassland succession, whereas the relative importance of competitive exclusion appears to have increased towards the later successional stages. Phylogenetic diversity provided a poor reflection of functional diversity and did not contribute to inferences about underlying assembly processes. Functionally deterministic assembly suggests that it may be possible to predict future post‐disturbance changes in biodiversity, and associated ecosystem attributes, on the basis of species’ functional traits but not phylogeny.