Use of the Abundance Spectrum and Relative‐Abundance Distributions to Analyze Assemblage Change in Massively Altered Landscapes

Population abundance estimates in conservation and biodiversity research

Measuring and tracking biodiversity from local to global scales is challenging due to its multifaceted nature and the range of metrics used to describe spatial and temporal patterns. Abundance can be used to describe how a population changes across space and time, but it can be measured in different ways, with consequences for the interpretation and communication of spatiotemporal patterns. We differentiate between relative and absolute abundance, and discuss the advantages and disadvantages of each for biodiversity monitoring, conservation, and ecological research. We highlight when absolute abundance can be advantageous and should be prioritized in biodiversity monitoring and research, and conclude by providing avenues for future research directions to better assess the necessity of absolute abundance in biodiversity monitoring.

Effects of crowding due to habitat loss on species assemblage patterns

Terrestrial animals are negatively affected by habitat loss, which is assessed on a landscape scale, whereas secondary effects of habitat loss, such as crowding, are usually disregarded. Such impacts are inherently hard to address and poorly understood, and there is a growing concern that they could have dire consequences. We sampled birds throughout a deforestation process to assess crowding stress in an adjacent habitat remnant in the southern Brazilian Atlantic Forest. Crowding is expected of highly mobile taxa, especially given the microhabitat heterogeneity of Neotropical forests, and we hypothesized that the arrival of new individuals or species in refuges shifts assemblage patterns. We used point counts to obtain bird abundances in a before-after-control-impact design sampling of a deforestation event. Temporal changes in taxonomic and functional diversity were examined with metrics used to assess alpha and beta diversity, turnover of taxonomic and functional similarity, and taxonomic and functional composition. Over time increased abundance of some species altered the Simpson index and affected the abundance-distribution of traits in the habitat remnant. Taxonomic composition and functional composition changed in the remnant, and thus bird assemblages changed over time. Taxonomic and functional metrics indicated that fugitives affected resident assemblages in refuges, and effects endured >2 years after the deforestation processes had ceased. Dissimilarity of taxonomic composition between pre- and postdeforestation assemblages increased, whereas functional composition reverted to preimpact conditions. We found that ecological disruptions resulted from crowding and escalated into disruptions of species' assemblages and potentially compromising ecosystem functioning. It is important to consider crowding effects of highly mobile taxa during impact assessments, especially in large-scale infrastructure projects that may affect larger areas than is assumed.

Using avian functional traits to assess the impact of land-cover change on ecosystem processes linked to resilience in tropical forests

Vertebrates perform key roles in ecosystem processes via trophic interactions with plants and insects, but the response of these interactions to environmental change is difficult to quantify in complex systems, such as tropical forests. Here, we use the functional trait structure of Amazonian forest bird assemblages to explore the impacts of land-cover change on two ecosystem processes: seed dispersal and insect predation. We show that trait structure in assemblages of frugivorous and insectivorous birds remained stable after primary forests were subjected to logging and fire events, but that further intensification of human land use substantially reduced the functional diversity and dispersion of traits, and resulted in communities that occupied a different region of trait space. These effects were only partially reversed in regenerating secondary forests. Our findings suggest that local extinctions caused by the loss and degradation of tropical forest are non-random with respect to functional traits, thus disrupting the network of trophic interactions regulating seed dispersal by forest birds and herbivory by insects, with important implications for the structure and resilience of human-modified tropical forests. Furthermore, our results illustrate how quantitative functional traits for specific guilds can provide a range of metrics for estimating the contribution of biodiversity to ecosystem processes, and the response of such processes to land-cover change.

The control of rank-abundance distributions by a competitive despotic species

Accounting for differences in abundances among species remains a high priority for community ecology. While there has been more than 80 years of work on trying to explain the characteristic S shape of rank-abundance distributions (RADs), there has been recent conjecture that the form may not depend on ecological processes per se but may be a general phenomenon arising in many unrelated disciplines. We show that the RAD shape can be influenced by an ecological process, namely, interference competition. The noisy miner (Manorina melanocephala) is a hyperaggressive, 'despotic' bird that occurs over much of eastern Australia (>10(6) km(2)). We compiled data for bird communities from 350 locations within its range, which were collected using standard avian survey methods. We used hierarchical Bayesian models to show that the RAD shape was much altered when the abundance of the strong interactor exceeded a threshold density; RADs consistently were steeper when the density of the noisy miner ≥2.5 birds ha(-1). The structure of bird communities at sites where the noisy miner exceeded this density was very different from that at sites where the densities fell below the threshold: species richness and Shannon diversity were much reduced, but mean abundances and mean avian biomass per site did not differ substantially.

Is there an ecological basis for species abundance distributions?

Community ecologists have attempted to explain species abundance distribution (SAD) shape for more than 80 years, but usually without relating SAD shape explicitly to ecological variables. We explored whether the scale (total assemblage abundance) and shape (assemblage evenness) of avifaunal SADs were related to ecological covariates. We used data on avifaunas, in-site habitat structure and landscape context that were assembled from previous studies; this amounted to 197 transects distributed across 16,000 km(2) of the box-ironbark forests of southeastern Australia. We used Bayesian conditional autoregressive models to link SAD scale and shape to these ecological covariates. Variation in SAD scale was relatable to some ecological covariates, especially to landscape vegetation cover and to tree height. We could not find any relationships between SAD shape and ecological covariates. SAD shape, the core component in SAD theory, may hold little information about how assemblages are governed ecologically and may result from statistical processes, which, if general, would indicate that SAD shape is not useful for distinguishing among theories of assemblage structure.

Temporal turnover and the maintenance of diversity in ecological assemblages

Temporal variation in species abundances occurs in all ecological communities. Here, we explore the role that this temporal turnover plays in maintaining assemblage diversity. We investigate a three-decade time series of estuarine fishes and show that the abundances of the individual species fluctuate asynchronously around their mean levels. We then use a time-series modelling approach to examine the consequences of different patterns of turnover, by asking how the correlation between the abundance of a species in a given year and its abundance in the previous year influences the structure of the overall assemblage. Classical diversity measures that ignore species identities reveal that the observed assemblage structure will persist under all but the most extreme conditions. However, metrics that track species identities indicate a narrower set of turnover scenarios under which the predicted assemblage resembles the natural one. Our study suggests that species diversity metrics are insensitive to change and that measures that track species ranks may provide better early warning that an assemblage is being perturbed. It also highlights the need to incorporate temporal turnover in investigations of assemblage structure and function.

Linking species abundance distributions in numerical abundance and biomass through simple assumptions about community structure

Species abundance distributions (SADs) are widely used as a tool for summarizing ecological communities but may have different shapes, depending on the currency used to measure species importance. We develop a simple plotting method that links SADs in the alternative currencies of numerical abundance and biomass and is underpinned by testable predictions about how organisms occupy physical space. When log numerical abundance is plotted against log biomass, the species lie within an approximately triangular region. Simple energetic and sampling constraints explain the triangular form. The dispersion of species within this triangle is the key to understanding why SADs of numerical abundance and biomass can differ. Given regular or random species dispersion, we can predict the shape of the SAD for both currencies under a variety of sampling regimes. We argue that this dispersion pattern will lie between regular and random for the following reasons. First, regular dispersion patterns will result if communities are comprised groups of organisms that use different components of the physical space (e.g. open water, the sea bed surface or rock crevices in a marine fish assemblage), and if the abundance of species in each of these spatial guilds is linked to the way individuals of varying size use the habitat. Second, temporal variation in abundance and sampling error will tend to randomize this regular pattern. Data from two intensively studied marine ecosystems offer empirical support for these predictions. Our approach also has application in environmental monitoring and the recognition of anthropogenic disturbance, which may change the shape of the triangular region by, for example, the loss of large body size top predators that occur at low abundance.

Where and when to revegetate: a quantitative method for scheduling landscape reconstruction

Restoration of native vegetation is required in many regions of the world, but determining priority locations for revegetation is a complex problem. We consider the problem of determining spatial and temporal priorities for revegetation to maximize habitat for 62 bird species within a heavily cleared agricultural region, 11000 km2 in area. We show how a reserve-selection framework can be applied to a complex, large-scale restoration-planning problem to account for multi-species objectives and connectivity requirements at a spatial extent and resolution relevant to management. Our approach explicitly accounts for time lags in planting and development of habitat resources, which is intended to avoid future population bottlenecks caused by delayed provision of critical resources, such as tree hollows. We coupled species-specific models of expected habitat quality and fragmentation effects with the dynamics of habitat suitability following replanting to produce species-specific maps for future times. Spatial priorities for restoration were determined by ranking locations (150-m grid cells) by their expected contribution to species habitat through time using the conservation planning tool, "Zonation." We evaluated solutions by calculating expected trajectories of habitat availability for each species. We produced a spatially explicit revegetation schedule for the region that resulted in a balanced increase in habitat for all species. Priority areas for revegetation generally were clustered around existing vegetation, although not always. Areas on richer soils and with high rainfall were more highly ranked, reflecting their potential to support high-quality habitats that have been disproportionately cleared for agriculture. Accounting for delayed development of habitat resources altered the rank-order of locations in the derived revegetation plan and led to improved expected outcomes for fragmentation-sensitive species. This work demonstrates the potential for systematic restoration planning at large scales that accounts for multiple objectives, which is urgently needed by land and natural resource managers.

The analysis of biodiversity using rank abundance distributions

Biodiversity is an important topic of ecological research. A common form of data collected to investigate patterns of biodiversity is the number of individuals of each species at a series of locations. These data contain information on the number of individuals (abundance), the number of species (richness), and the relative proportion of each species within the sampled assemblage (evenness). If there are enough sampled locations across an environmental gradient then the data should contain information on how these three attributes of biodiversity change over gradients. We show that the rank abundance distribution (RAD) representation of the data provides a convenient method for quantifying these three attributes constituting biodiversity. We present a statistical framework for modeling RADs and allow their multivariate distribution to vary according to environmental gradients. The method relies on three models: a negative binomial model, a truncated negative binomial model, and a novel model based on a modified Dirichlet-multinomial that allows for a particular type of heterogeneity observed in RAD data. The method is motivated by, and applied to, a large-scale marine survey off the coast of Western Australia, Australia. It provides a rich description of biodiversity and how it changes with environmental conditions.

Measuring the response of animals to contemporary drivers of fragmentationThis review is one of a series dealing with some aspects of the impact of habitat fragmentation on animals and plants. This series is one of several virtual symposia focussing on ecological topics that will be published in the Journal from time to time

From the perspective of most animals, fragmentation is a landscape-scale process in which habitat is separated into many smaller patches that have less total area. Here, we examine how two contemporary drivers of fragmentation, anthropogenic climate change and exurbanization, affect movement and responses of animal species to new environmental conditions. We address the definition of fragmentation and how the spatial patterns created by fragmentation can be measured at the scales at which different species of animals respond to their environments. We discuss tools, such as satellite remote sensing, that increasingly make it possible to identify and quantify changes in land cover and vegetation structure across extensive areas. We also describe a range of methods that are available to guide decisions about faunal surveys and monitoring programs in fragments or reference areas. Examination of stochastic changes in land cover and species occurrence over time is important because these shifts can confound detection of systematic responses to fragmentation. Careful evaluation of fragmentation and its influence on the distribution and viability of fauna may help to identify underlying mechanisms and to develop effective strategies for conservation and land use.