Computing additive beta-diversity from presence and absence scores: a critique and alternative parameters

Whittaker first proposed to measure the variation in species composition among plots or beta-diversity as the ratio between regional diversity (gamma-diversity) and average local diversity (alpha-diversity). More recently, an alternative way of partitioning diversity for which beta-diversity is obtained as the difference between gamma-diversity and average alpha-diversity has become very popular for linking the structure of species assemblages to ecosystem functioning in a spatially explicit manner. Unfortunately, additive beta-diversity computed from species presences and absences suffers from the major drawback of being dependent on regional species richness. For instance, if the separation between beta-diversity and gamma-diversity is incomplete, so that variation in species composition is affected by species richness, then differences in beta-diversity values among different sets of plots could reflect differences in the species count rather than any fundamental difference in species composition among the plots. Based on the above observation, in this paper I will first propose a basic requirement for beta-diversity measures that adequately captures our intuitive notion of independence of species richness. Next, I will show that additive beta-diversity computed from species presence and absence scores can be interpreted within the framework of fuzzy set theory. Finally, based on this unusual "fuzzy" interpretation of additive beta-diversity, I will introduce two families of parametric beta-diversity measures whose members have varying sensitivities to the presence of rare and frequent species.     

Aggregation and species coexistence in fleas parasitic on small mammals

The aggregation model of coexistence states that species coexistence is facilitated if interspecific aggregation is reduced relative to intraspecific aggregation. We investigated the relationship between intraspecific and interspecific aggregation in 17 component communities (the flea assemblage of a host population) of fleas parasitic on small mammals and hypothesized that interspecific interactions should be reduced relative to intraspecific interactions, facilitating species coexistence. We predicted that the reduction of the level of interspecific aggregation in relation to the level of intraspecific aggregation would be positively correlated with total flea abundance and species richness of flea assemblages. We also expected that the higher degree of facilitation of flea coexistence would be affected by host parameters such as body mass, basal metabolic rate (BMR) and depth and complexity of burrows. Results of this study supported the aggregation model of coexistence and demonstrated that, in general, a) conspecific fleas were aggregated across their hosts; b) flea assemblages were not dominated by negative interspecific interactions; and c) the level of interspecific aggregation in flea assemblages was reduced in relation to the level of intraspecific aggregation. Intraspecific aggregation tended to be correlated positively to body mass, burrow complexity and mass-independent BMR of a host. Positive interspecific associations of fleas tended to occur more frequently in species-rich flea assemblages and/or in larger hosts possessing deep complex burrows. Intraspecific aggregation increased relative to interspecific aggregation when species richness of flea infracommunities (the flea assemblage of a host individual) and component communities increased. We conclude that the pattern of flea coexistence is related both to the structure of flea communities and affinities of host species.     

Plant–plant interactions and local patterns of diversity from semi-arid to subalpine Mediterranean plant communities

An understanding of the diversity spatial organization in plant communities provides essential information for management and conservation planning. In this study we investigated, using a multi-species approach, how plant–plant interactions determine the local structure and composition of diversity in a set of Mediterranean plant communities, ranging from semi-arid to subalpine habitats. Specifically, we evaluated the spatial pattern of diversity (i.e., diversity aggregation or segregation) in the local neighborhood of perennial plant species using the ISAR (individual species–area relationship) method. We also assessed the local pattern of beta-diversity (i.e., the spatial heterogeneity in species composition among local assemblages), including the contribution of species turnover (i.e., species replacement) and nestedness (i.e., differences in species richness) to the overall local beta-diversity. Our results showed that local diversity segregation decreased in the less productive plant communities. Also, we found that graminoids largely acted as diversity segregators, while forbs showed more diverse neighborhoods than expected in less productive study sites. Interestingly, not all shrub and dwarf shrub species aggregated diversity in their surroundings. Finally, an increase in nestedness was associated with less segregated diversity patterns in the local neighborhood of shrub species, underlining their role in creating diversity islands in less productive environmental conditions. Our results provide further insights into the effect of plant–plant interactions in shaping the structure and composition of diversity in Mediterranean plant communities, and highlight the species and groups of species that management and conservation strategies should focus on in order to prevent a loss of biodiversity.

     

Biotic homogenization and changes in species diversity across human-modified ecosystems

Changing land use and the spread of 'winning' native or exotic plants are expected to lead to biotic homogenization (BH), in which previously distinct plant communities become progressively more similar. In parallel, many ecosystems have recently seen increases in local species (alpha-) diversity, yet gamma-diversity has continued to decline at larger scales. Using national ecological surveillance data for Great Britain, we quantify relationships between change in alpha-diversity and between-habitat homogenizations at two levels of organization: species composition and plant functional traits. Across Britain both increases and decreases in alpha-diversity were observed in small random sampling plots (10-200m2) located within a national random sample of 1km square regions. As alpha-diversity declined (spatially in 1978 or temporally between 1978 and 1998), plant communities became functionally more similar, but species-compositional similarity declined. Thus, different communities converged on a narrower range of winning trait syndromes, but species identities remained historically contingent, differentiating a mosaic of residual species-poor habitat patches within each 1km square. The reverse trends in beta-diversity occurred where alpha-diversity increased. When impacted by the same type and intensity of environmental change, directions of change in alpha-diversity are likely to depend upon differences in starting productivity and disturbance. This is one reason why local diversity change and BH across habitats are not likely to be consistently coupled.     

Habitat and climate heterogeneity maintain beta-diversity of birds among landscapes within ecoregions

Aim  Habitat and climate heterogeneity may affect patterns of species diversity from the relatively local scale of communities to the broad biogeographical scale of continents. However, the effects of heterogeneity on species diversity have not been studied as widely at intermediate scales although differences among landscapes in local climate and habitat should maintain beta-diversity.
Location  Bailey ecoregions in the USA.
Methods  Using a geographically extensive dataset on bird distribution and abundance in 35 ecoregions, we tested for the effects of habitat and climate heterogeneity on beta-diversity at two discrete spatial scales: among sample points within landscapes, and among landscapes within ecoregions.
Results  Landscape-level beta-diversity typically accounted for 50% or more of gamma-diversity and was significantly and positively related to habitat heterogeneity (elevational range within an ecoregion) and climate heterogeneity (variation in potential evapotranspiration). Contrary to predictions, point-level beta-diversity was negatively related to habitat and climate heterogeneity, perhaps because heterogeneity constrains alpha-diversity at the landscape level. The geographical spatial separation of landscapes within an ecoregion did not significantly affect beta-diversity at either scale.
Main conclusions  Our results suggest that habitat selection and adaptation to local climate may be the primary processes structuring bird diversity among landscapes within ecoregions, and that dispersal limitation has a lesser role in influencing beta-diversity among landscapes.     

Species divergence and the measurement of microbial diversity

Diversity measurement is important for understanding community structure and dynamics, but has been particularly challenging for microorganisms. Microbial community characterization using small subunit rRNA (SSU rRNA) gene sequences has revealed an extensive, previously unsuspected diversity that we are only now beginning to understand, especially now that advanced sequencing technologies are producing datasets containing hundreds of thousands of sequences from hundreds of samples. Efforts to quantify microbial diversity often use taxon-based methods that ignore the fact that not all species are equally related, which can therefore obscure important patterns in the data. For example, alpha-diversity (diversity within communities) is often estimated as the number of species in a community (species richness), and beta-diversity (partitioning of diversity among communities) is often based on the number of shared species. Methods for measuring alpha- and beta-diversity that account for different levels of divergence between individuals have recently been more widely applied. These methods are more powerful than taxon-based methods because microorganisms in a community differ dramatically in sequence similarity, which also often correlates with phenotypic similarity in key features such as metabolic capabilities. Consequently, divergence-based methods are providing new insights into microbial community structure and function.     

Intraspecific phenotypic variation in a fish predator affects multitrophic lake metacommunity structure

Contemporary insights from evolutionary ecology suggest that population divergence in ecologically important traits within predators can generate diversifying ecological selection on local community structure. Many studies acknowledging these effects of intraspecific variation assume that local populations are situated in communities that are unconnected to similar communities within a shared region. Recent work from metacommunity ecology suggests that species dispersal among communities can also influence species diversity and composition but can depend upon the relative importance of the local environment. Here, we study the relative effects of intraspecific phenotypic variation in a fish predator and spatial processes related to plankton species dispersal on multitrophic lake plankton metacommunity structure. Intraspecific diversification in foraging traits and residence time of the planktivorous fish alewife (Alosa pseudoharengus) among coastal lakes yields lake metacommunities supporting three lake types which differ in the phenotype and incidence of alewife: lakes with anadromous, landlocked, or no alewives. In coastal lakes, plankton community composition was attributed to dispersal versus local environmental predictors, including intraspecific variation in alewives. Local and beta diversity of zooplankton and phytoplankton was additionally measured in response to intraspecific variation in alewives. Zooplankton communities were structured by species sorting, with a strong influence of intraspecific variation in A. pseudoharengus. Intraspecific variation altered zooplankton species richness and beta diversity, where lake communities with landlocked alewives exhibited intermediate richness between lakes with anadromous alewives and without alewives, and greater community similarity. Phytoplankton diversity, in contrast, was highest in lakes with landlocked alewives. The results indicate that plankton dispersal in the region supplied a migrant pool that was strongly structured by intraspecific variation in alewives. This is one of the first studies to demonstrate that intraspecific phenotypic variation in a predator can maintain contrasting patterns of multitrophic diversity in metacommunities.     

cati: an R package using functional traits to detect and quantify multi‐level community assembly processes

Community ecologists are active in describing species by their functional traits, quantifying the functional structure of plant and animal assemblages and inferring community assembly processes with null‐model analyses of trait distribution and functional diversity indices. Intraspecific variation in traits and effects of spatial scale are potentially important in these analyses. Here, we introduce the R package cati (Community Assembly by Traits: Individuals and beyond) available on CRAN, for the analysis of community assembly with functional traits. cati builds on a recent approach to community assembly that explicitly incorporates individual differences in community assembly analyses and decomposes phenotypic variations across scales and organizational levels, based on three phenotypic variance ratios, termed the T‐statistics. More generally, the cati package 1) calculates a variety of single‐trait and multi‐trait indices from interspecific and intraspecific trait measures; 2) it partitions functional trait variation among spatial and taxonomic levels; 3) it implements a palette of flexible null models for detecting non‐random patterns of functional traits. These patterns can be used to draw inferences about hypotheses of community assembly such as environmental filtering and species interactions. The basic input for cati is a data frame in which columns are traits, rows are species or individuals, and entries are the measured trait values. The cati package can also incorporate a square distance matrix into analyses, which could include phylogenetic or genetic distances among individuals or species. Users select from a variety of functional trait metrics and analyze these relative to a null model that specifies trait distributions in a regional source pool.     

The effect of intraspecific variation and heritability on community pattern and robustness

Intraspecific trait variation is widespread in nature, yet its effects on community dynamics are not well understood. Here we explore the consequences of intraspecific trait variation for coexistence in two‐ and multispecies competitive communities. For two species, the likelihood of coexistence is in general reduced by intraspecific variation, except when the species have almost equal trait means but different trait variances, such that one is a generalist and the other a specialist consumer. In multispecies communities, the only strong effect of non‐heritable intraspecific variation is to reduce expected species richness. However, when intraspecific variation is heritable, allowing for the possibility of trait evolution, communities are much more resilient against environmental disturbance and exhibit far more predictable trait patterns. Our results are robust to varying model parameters and relaxing model assumptions.     

Restoration of invaded Cape Floristic Region riparian systems leads to a recovery in foliage-active arthropod alpha- and beta-diversity

The Cape Floristic Region of South Africa is a global biodiversity hotspot threatened by invasive alien plants (IAPs). We assessed the effect of plant invasions, and their subsequent clearing, on riparian arthropod diversity. Foliage-active arthropod communities were collected from two native and one invasive alien tree species. Alpha- and beta-diversity of their associated arthropod communities were compared between near pristine, Acacia-invaded and restored sites. Arthropod alpha-diversity at near pristine sites was higher than at restored sites, and was lowest at invaded sites. This was true for most arthropod taxonomic groups associated with all native tree species and suggests a general trend towards recovery in arthropod alpha-diversity after IAP removal. Overall, arthropod species turnover among sites was significantly influenced by plant invasions with communities at near pristine sites having higher turnover than those at restored and invaded sites. This pattern was not evident at the level of individual tree species. Although arthropod community composition was significantly influenced by plant invasions, only a few significant differences in arthropod community composition could be detected between restored and near pristine sites for all tree species and arthropod taxonomic groups. Assemblage composition on each tree species generally differed between sites with similar degrees of plant invasion indicating a strong turnover of arthropod communities across the landscape. Results further suggest that both arthropod alpha- and beta-diversity can recover after IAP removal, given sufficient time, but catchment signatures must be acknowledged when monitoring restoration recovery.     

Diversity partitioning in Permian and Early Triassic benthic ecosystems of the Western USA: a comparison

This paper compares the relative contributions of within-habitat diversity [alpha-diversity] and between-habitat-diversity [beta-diversity] to regional diversity [gamma-diversity] in marine benthic communities of the western US before and after the end-Permian mass extinction. We found that presumably cool-water faunas from the Permian Gerster Limestone and the Park City Formation had low alpha- and beta-diversities, comparable to those of low diverse faunas of the Early Triassic. In contrast, tropical Permian faunas had much higher alpha-diversities and a variable pattern of beta-diversity: Whereas faunas of space-limited bioherms show a positive correlation between beta-diversity and gamma-diversity, beta-diversity in level-bottom faunas is elevated only when gamma-diversity is very high (>250 species). This contrasting pattern probably reflects differential effects of interspecific competition on habitat partitioning. In low-competitive level-bottom faunas, species are able to coexist until competition forces species into their ecological optima, thereby increasing beta-diversity. This effect occurs at much lower gamma-diversities in more competitive reef-bound faunas, causing the observed positive correlation between beta- and gamma-diversity. We suggest that differences in the level of interspecific competition and hence diversity partitioning between Permian and Triassic benthic communities result from the higher average metabolic rates in the Mesozoic mollusc-dominated benthos in contrast to their Permian counterparts.     

Diversity partitioning in Jurassic level-bottom communities

The analysis of diversity partitioning is a potential tool for detecting the factors that control taxonomic diversification in a given ecological context. Previously proposed models provide a theoretical framework that is herein applied to three sets of level-bottom communities representing different phases of the Jurassic diversification of marine life. The analysis shows that mean alpha-diversity remained surprisingly constant through most of the Jurassic, whereas beta-diversity increased by a factor of 2.6 during the same time interval. Diversification that is primarily driven by increasing beta-diversity is indicative of late diversification phases in ecosystems with low interspecific competition and/or high predation, as typical for marine level-bottom communities. Although generality of this conclusion is not claimed because of data limitations, the example demonstrates that the study of diversity partitioning provides a promising approach to the basic question about the factors that control the diversification of life.     

Putting beta-diversity on the map: broad-scale congruence and coincidence in the extremes

Beta-diversity, the change in species composition between places, is a critical but poorly understood component of biological diversity. Patterns of beta-diversity provide information central to many ecological and evolutionary questions, as well as to conservation planning. Yet beta-diversity is rarely studied across large extents, and the degree of similarity of patterns among taxa at such scales remains untested. To our knowledge, this is the first broad-scale analysis of cross-taxon congruence in beta-diversity, and introduces a new method to map beta-diversity continuously across regions. Congruence between amphibian, bird, and mammal beta-diversity in the Western Hemisphere varies with both geographic location and spatial extent. We demonstrate that areas of high beta-diversity for the three taxa largely coincide, but areas of low beta-diversity exhibit little overlap. These findings suggest that similar processes lead to high levels of differentiation in amphibian, bird, and mammal assemblages, while the ecological and biogeographic factors influencing homogeneity in vertebrate assemblages vary. Knowledge of beta-diversity congruence can help formulate hypotheses about the mechanisms governing regional diversity patterns and should inform conservation, especially as threat from global climate change increases.     

Assembly rules for New England ant assemblages

Community assembly rules specify patterns of species co-occurrence and morphology dictated by interspecific competition. We collected data on the occurrence of ground-foraging ant species in 22 ombrotrophic bogs and adjacent forest plots of New England to test two general assembly rules: reduced co-occurrence of species among communities, and even spacing of body sizes of species within communities. We used null models to generate random communities unstructured by competition and evaluated patterns at regional and local spatial scales. At the regional scale, species co-occurrence in forests, but not bogs, was less than expected by chance, whereas, at the local scale, co-occurrence in both habitats was not different from random. At the regional scale, spacing of body size distributions was random (in bogs) or aggregated (in forests). At the local scale, body size patterns were weakly segregated in bogs, but random or weakly aggregated in forests. In bogs, size ratio constancy was accompanied by greater generic diversity than expected. Although assembly rules were originally developed for vertebrate communities, they successfully explained some patterns in New England ant assemblages. However, the patterns were contingent on spatial scale, and were distinctly different for bog and forest communities, despite their close proximity and the presence of many shared species in both assemblages. The harsh physical conditions of bogs may act as a habitat filter that alters community assembly rules.     

Community structure of arboreal caterpillars within and among four tree species of the eastern deciduous forest

Abstract.  1. A seasonally replicated experimental design was used to address the question of how differences within and among host tree species affect arboreal caterpillar communities.
2. Seasonal variation influenced caterpillar community composition most significantly, and the similarity among caterpillar assemblages did not necessarily follow the pattern of phylogenetic relatedness among host trees.
3. Species richness and abundance of caterpillars were higher on oaks and maples than on American beech. Diversity partitioning models revealed that β diversity was only occasionally greater or less than expected by chance alone.
4. When β diversity was significant, values tended to be greater than expected by chance among replicate trees within each species and lower than expected by chance among the four tree species.
5. Differences among trees appeared important for determining patterns of species presence/absence for rare species and influencing patterns of species dominance within caterpillar assemblages. Differences among tree species had a significant effect on overall lepidopteran community composition and mean species diversity (i.e. α diversity).
6. Because β diversity of caterpillars among host trees was lower than expected by chance, host specificity within the Lepidoptera may be less prevalent than thought previously.     

The role of the floodplain gradient in structuring of testate amoebae communities in the Ilych River

Forty-two testate amoebae taxa were identified in alluvial soils of floodplain islands in the Ilych River. Among the pedo- and eurybionts, there were aquatic rhizopods. Along the floodplain transect (willow meadow ?? deciduous forest ?? coniferous forest), the testate amoebae community changed directly. There are spatially homogeneous (low beta-diversity) testacean communities but species rich on the local level (high alpha-diversity) within forests. Within willows and meadows, communities are characterized by low alpha-diversity and high heterogeneity that leads to high gamma-diversity.     

Biological diversity of fish communities: pattern and process

For over 150 years, ecologists have been striving to explain fundamental patterns of biological diversity, such as the observation that communities invariably consist of common and rare species, and to unravel the processes that underpin these patterns. This task is increasingly urgent given the accelerating loss of biological diversity. Although fishes are the most diverse vertebrate taxon and fish communities occur in a wide range of habitats, they have been relatively little studied in the quest to elucidate the processes that shape patterns of biological diversity. Here, some of the topics that investigations of fish assemblages can illuminate are highlighted. These include the characteristics of ecological communities and the role that dispersal limitation plays in structuring them, the distinction between core and occasional species, the insights that evaluating abundance in different currencies can bring and the assessment of community capacity. Questions are identified that future investigations of fish communities might tackle and a case study of a biodiverse ecoregion (Thailand and Peninsula Malaysia) is used to illustrate the need for better links between these ecological questions and effective conservation practice.     

Intraspecific variation and species coexistence

We use a two-species model of plant competition to explore the effect of intraspecific variation on community dynamics. The competitive ability ("performance") of each individual is assigned by an independent random draw from a species-specific probability distribution. If the density of individuals competing for open space is high (e.g., because fecundity is high), species with high maximum (or large variance in) performance are favored, while if density is low, species with high typical (e.g., mean) performance are favored. If there is an interspecific mean-variance performance trade-off, stable coexistence can occur across a limited range of intermediate densities, but the stabilizing effect of this trade-off appears to be weak. In the absence of this trade-off, one species is superior. In this case, intraspecific variation can blur interspecific differences (i.e., shift the dynamics toward what would be expected in the neutral case), but the strength of this effect diminishes as competitor density increases. If density is sufficiently high, the inferior species is driven to extinction just as rapidly as in the case where there is no overlap in performance between species. Intraspecific variation can facilitate coexistence, but this may be relatively unimportant in maintaining diversity in most real communities.     

Additive partitioning of reef fish diversity variation: a promising marine biodiversity management tool

Additive partitioning was applied to variation in reef fish spatial diversity at Isla Isabel National Park, Nayarit state, Mexico, and to identify the environmental and spatial variables that best explains it. Analyses included expected and observed species curves, rare species analysis, additive partitioning of alpha- and beta-diversity, and canonical redundancy analysis. A total of 10,517 individuals were recorded from 75 species and 33 reef fish families, representing 85% of expected richness. Species richness beta-diversity was dependent on the site scale, while the alpha-diversity of the Shannon diversity was most significant at the transect scale. Canonical partitioning showed species richness and Shannon diversity was explained by spatially-structured environmental components. Variation in species composition and abundance was explained by a purely environmental component. Therefore, elements of habitat structure (especially corals), topographic complexity, and refuge availability determine fish species diversity. Our results suggest that greater emphasis is required to conserve sites that promote β-diversity, increasing fish spatial diversity. In Isla Isabel, these sites would be mostly those located at eastern and southern of protected sides, where coral reef patches are well represented. The results of this multi-scale analysis are valuable and useful as an addition and complement to the holistic management strategies implemented at Isla Isabel.     

Niche versus neutrality in structuring the beta diversity of damselfly assemblages

1. Differences among communities in taxonomic composition – beta diversity – are frequently expected to result from taxon‐specific responses to spatial variation in ecological conditions, through niche partitioning. Such process‐derived patterns are in sharp contrast to arguments from neutral theory, where taxa are ecologically equivalent and beta diversity results primarily from dispersal limitation. 2. Here, we compared beta diversity among assemblages of damselflies (Odonata: Zygoptera), for which previous experiments have shown that niche differences maintain genera within a community, but patterns of relative abundance for species within each genus are shaped primarily by neutral dynamics. 3. Using null‐model and ordination‐based methods, we find that both genera and (in contrast to neutral theory) species assemblage composition vary across the landscape in a deterministic fashion, shaped by environmental and spatial factors. 4. While the observed patterns in species composition conflict with theory, we suggest that this a result of weak ecological filters acting to produce spatial variation in assemblages of ecologically similar species undergoing ecological drift within communities. Such patterns are especially likely in systems of relatively weak dispersers like damselflies.