Showing papers in "Ecological Monographs in 2014"

Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies

Abstract: Quantifying and assessing changes in biological diversity are central aspects of many ecological studies, yet accurate methods of estimating biological diversity from sampling data have been elusive. Hill numbers, or the effective number of species, are increasingly used to characterize the taxonomic, phylogenetic, or functional diversity of an assemblage. However, empirical estimates of Hill numbers, including species richness, tend to be an increasing function of sampling effort and, thus, tend to increase with sample completeness. Integrated curves based on sampling theory that smoothly link rarefaction (interpolation) and prediction (extrapolation) standardize samples on the basis of sample size or sample completeness and facilitate the comparison of biodiversity data. Here we extended previous rarefaction and extrapolation models for species richness (Hill number q D, where q ¼ 0) to measures of taxon diversity incorporating relative abundance (i.e., for any Hill number q D, q . 0) and present a unified approach for both individual-based (abundance) data and sample- based (incidence) data. Using this unified sampling framework, we derive both theoretical formulas and analytic estimators for seamless rarefaction and extrapolation based on Hill numbers. Detailed examples are provided for the first three Hill numbers: q ¼ 0 (species richness), q ¼ 1 (the exponential of Shannon's entropy index), and q ¼ 2 (the inverse of Simpson's concentration index). We developed a bootstrap method for constructing confidence intervals around Hill numbers, facilitating the comparison of multiple assemblages of both rarefied and extrapolated samples. The proposed estimators are accurate for both rarefaction and short-range extrapolation. For long-range extrapolation, the performance of the estimators depends on both the value of q and on the extrapolation range. We tested our methods on simulated data generated from species abundance models and on data from large species inventories. We also illustrate the formulas and estimators using empirical data sets from biodiversity surveys of temperate forest spiders and tropical ants.

A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning

Abstract: Fungi play key roles in ecosystems as mutualists, pathogens, and decomposers. Current estimates of global species richness are highly uncertain, and the importance of stochastic vs. deterministic forces in the assembly of fungal communities is unknown. Molecular studies have so far failed to reach saturated, comprehensive estimates of fungal diversity. To obtain a more accurate estimate of global fungal diversity, we used a direct molecular approach to census diversity in a boreal ecosystem with precisely known plant diversity, and we carefully evaluated adequacy of sampling and accuracy of species delineation. We achieved the first exhaustive enumeration of fungi in soil, recording 1002 taxa in this system. We show that the fungus : plant ratio in Picea mariana forest soils from interior Alaska is at least 17:1 and is regionally stable. A global extrapolation of this ratio would suggest 6 million species of fungi, as opposed to leading estimates ranging from 616 000 to 1.5 million. We also find that clos...

The spatial structure of Antarctic biodiversity

Abstract: Patterns of environmental spatial structure lie at the heart of the most fundamental and familiar patterns of diversity on Earth. Antarctica contains some of the strongest environmental gradients on the planet and therefore provides an ideal study ground to test hypotheses on the relevance of environmental variability for biodiversity. To answer the pivotal question, “How does spatial variation in physical and biological environmental properties across the Antarctic drive biodiversity?” we have synthesized current knowledge on environmental variability across terrestrial, freshwater, and marine Antarctic biomes and related this to the observed biotic patterns. The most important physical driver of Antarctic terrestrial communities is the availability of liquid water, itself driven by solar irradiance intensity. Patterns of biota distribution are further strongly influenced by the historical development of any given location or region, and by geographical barriers. In freshwater ecosystems, free water is also crucial, with further important influences from salinity, nutrient availability, oxygenation, and characteristics of ice cover and extent. In the marine biome there does not appear to be one major driving force, with the exception of the oceanographic boundary of the Polar Front. At smaller spatial scales, ice cover, ice scour, and salinity gradients are clearly important determinants of diversity at habitat and community level. Stochastic and extreme events remain an important driving force in all environments, particularly in the context of local extinction and colonization or recolonization, as well as that of temporal environmental variability. Our synthesis demonstrates that the Antarctic continent and surrounding oceans provide an ideal study ground to develop new biogeographical models, including life history and physiological traits, and to address questions regarding biological responses to environmental variability and change.

On tests of spatial pattern based on simulation envelopes

Abstract: In the analysis of spatial point patterns, an important role is played by statistical tests based on simulation envelopes, such as the envelope of simulations of Ripley's K function. Recent ecological literature has correctly pointed out a common error in the interpretation of simulation envelopes. However, this has led to a widespread belief that the tests themselves are invalid. On the contrary, envelope-based statistical tests are correct statistical procedures, under appropriate conditions. In this paper, we explain the principles of Monte Carlo tests and their correct interpretation, canvas the benefits of graphical procedures, measure the statistical performance of several popular tests, and make practical recommendations. There are several caveats including the under-recognized problem that Monte Carlo tests of goodness of fit are probably conservative if the model parameters have to be estimated from data. Finally, we discuss whether graphs of simulation envelopes can be used to infer the scale of...

Biodiversity declines due to abandonment and intensification of agricultural lands: patterns and mechanisms

Abstract: Declines in plants and herbivorous insects due to land use abandonment and intensification have been studied in agricultural areas worldwide. We tested four hypotheses, which were complementary rather than mutually exclusive, to understand the mechanisms driving biodiversity declines due to abandonment and intensification. These predict that biodiversity decline is caused by a decline in resource diversity, changes in disturbance regime, surrounding landscape conversion, and a decrease in biomass production. We compared plant richness and butterfly and orthopteran richness and diversity among three land use types in seminatural grasslands: abandoned, traditional, and intensified terraces. Then, we examined effects of changes in resource (plant) richness, frequency of disturbance (mowing), and surrounding landscapes on butterfly and orthopteran diversity to understand the mechanisms driving decline after land abandonment and intensification. Plant and herbivore richness and diversity were significantly lower in abandoned and intensified grasslands than in traditional grasslands. This trend was consistent throughout the seasons in both years of the study. Changes in mowing frequency and surrounding landscape explained plant richness declines as a consequence of land abandonment and intensification. Declines in herbivorous insects were explained by plant richness declines and changes in mowing frequency, but not by landscape changes. Plant and herbivore richness were maximized at an intermediate mowing frequency (approximately twice per year), which is typical practice on traditional terraces. This is the first report demonstrating that the intermediate disturbance hypothesis explained well the biodiversity declines in agricultural ecosystems. The richness and diversity responses of herbivore functional groups to plant richness, mowing frequency, and surrounding landscapes were generally inconsistent with predictions. We found significant trends in which butterfly and orthopteran species with low abundance in traditional terraces were lost in abandoned and/or intensive terraces. This may suggest that the number of individuals of most herbivorous species decreased randomly with respect to life-history traits following a decline in plant richness after changes in disturbance frequency. This study demonstrates that declines in herbivorous insects can be explained by multiple factors, and provides a unified explanation for biodiversity declines in both abandoned and intensified use of agricultural lands, which have often been studied separately.

Biophysical forcings of land‐use changes from potential forestry activities in North America

Abstract: Land-use changes through forestry and other activities alter not just carbon storage, but biophysical properties, including albedo, surface roughness, and canopy conductance, all of which affect temperature. This study assessed the biophysical forcings and climatic impact of vegetation replacement across North America by comparing satellite-derived albedo, land surface temperature (LST), and evapotranspiration (ET) between adjacent vegetation types. We calculated radiative forcings (RF) for potential local conversions from croplands (CRO) or grasslands (GRA) to evergreen needleleaf (ENF) or deciduous broadleaf (DBF) forests. Forests generally had lower albedo than adjacent grasslands or croplands, particularly in locations with snow. They also had warmer nighttime LST, cooler daily and daytime LST in warm seasons, and smaller daily LST ranges. Darker forest surfaces induced positive RFs, dampening the cooling effect of carbon sequestration. The mean (±SD) albedo-induced RFs for each land conversion were e...

The Legacy of Episodic Climatic Events in Shaping Temperate, Broadleaf Forests

Abstract: In humid, broadleaf-dominated forests where gap dynamics and partial canopy mortality appears to dominate the disturbance regime at local scales, paleoecological evidence shows alteration at regional-scales associated with climatic change. Yet, little evidence of these broad-scale events exists in extant forests. To evaluate the potential for the occurrence of large-scale disturbance, we used 76 tree-ring collections spanning approx. 840 000 sq km and 5327 tree recruitment dates spanning approx. 1.4 million sq km across the humid eastern United States. Rotated principal component analysis indicated a common growth pattern of a simultaneous reduction in competition in 22 populations across 61 000 km2. Growth-release analysis of these populations reveals an intense and coherent canopy disturbance from 1775 to 1780, peaking in 1776. The resulting time series of canopy disturbance is so poorly described by a Gaussian distribution that it can be described as ''heavy tailed,'' with most of the years from 1775 to 1780 comprising the heavy-tail portion of the distribution. Historical documents provide no evidence that hurricanes or ice storms triggered the 1775-1780 event. Instead, we identify a significant relationship between prior drought and years with elevated rates of disturbance with an intense drought occurring from 1772 to 1775. We further find that years with high rates of canopy disturbance have a propensity to create larger canopy gaps indicating repeated opportunities for rapid change in species composition beyond the landscape scale. Evidence of elevated, regional-scale disturbance reveals how rare events can potentially alter system trajectory: a substantial portion of old-growth forests examined here originated or were substantially altered more than two centuries ago following events lasting just a few years. Our recruitment data, comprised of at least 21 species and several shade-intolerant species, document a pulse of tree recruitment at the subcontinental scale during the late-1600s suggesting that this event was severe enough to open large canopy gaps. These disturbances and their climatic drivers support the hypothesis that punctuated, episodic, climatic events impart a legacy in broadleaf-dominated forests centuries after their occurrence. Given projections of future drought, these results also reveal the potential for abrupt, meso- to large-scale forest change in broadleaf-dominated forests over future decades.

Under niche construction: an operational bridge between ecology, evolution, and ecosystem science

Abstract: All living organisms modify their biotic and abiotic environment. Niche construction theory posits that organism-mediated modifications to the environment can change selection pressures and influence the evolutionary trajectories of natural populations. While there is broad support for this proposition in general, there is considerable uncertainty about how niche construction is related to other similar concepts in ecology and evolution. Comparative studies dealing with certain aspects of niche construction are increasingly common, but there is a troubling lack of experimental tests of the core concepts of niche construction theory. Here, we propose an operational framework to evaluate comparative and experimental evidence of the evolutionary consequences of niche construction, and suggest how such research can improve our understanding of ecological and evolutionary dynamics in ecosystems. We advocate for a shift toward explicit experimental tests of how organism-mediated environmental change can influence the selection pressures underlying evolutionary responses, as well as targeted field-based comparative research to identify the mode of evolution by niche construction and assess its importance in natural populations.

Behavior and nutritional condition buffer a large‐bodied endotherm against direct and indirect effects of climate

Abstract: Temporal changes in net energy balance of animals strongly influence fitness; consequently, natural selection should favor behaviors that increase net energy balance by buffering individuals against negative effects of environmental variation. The relative importance of behavioral responses to climate-induced variation in costs vs. supplies of energy, however, is uncertain, as is the degree to which such responses are mediated by current stores of energy. We evaluated relationships among behavior, nutritional condition (i.e., energy state), and spatiotemporal variation in costs vs. supplies of energy available to a large- bodied endotherm, the North American elk (Cervus elaphus), occupying two ecosystems with contrasting climates and energy landscapes: a temperate, montane forest and an arid, high- elevation desert. We hypothesized that during spring through autumn, behavioral responses to the energy landscape would be both context dependent (i.e., would vary as a function of the contrasting environmental conditions experienced by elk in the forest vs. the desert), and state dependent (i.e., would vary as a function of the energy balance of an individual). We tested several predictions derived from that hypothesis by combining output from a biophysical model of the thermal environment with data on forage quality, animal locations, and nutritional condition of individuals. At the population level, elk in the desert selected areas that reduced costs of thermoregulation over those that provided the highest-quality forage. In the forest, however, costs imposed by the thermal environment were less pronounced, and elk selected areas that increased access to high-quality forage over those that reduced costs of thermoregulation. At the individual level, nutritional condition did not influence strength of selection for low-cost areas or high-quality forage among elk in the forest. In the desert, however, strength of selection for low-cost areas (but not forage quality) was state dependent; individuals in the poorest condition at the end of winter showed the strongest selection for areas that reduced costs of thermoregulation during spring and summer, and also expended the least amount of energy on locomotion. Our results highlight the importance of understanding the roles of behavior and nutritional condition in buffering endotherms against direct and indirect effects of climate on fitness.

Phylogenetic beta diversity, similarity, and differentiation measures based on Hill numbers

Abstract: Until now, decomposition of abundance-sensitive gamma (regional) phylogenetic diversity measures into alpha and beta (within- and between-group) components has been based on an additive partitioning of phylogenetic generalized entropies, especially Rao's quadratic entropy. This additive approach led to a phylogenetic measure of differentiation between assemblages: (gamma − alpha)/gamma. We show both empirically and theoretically that this approach inherits all of the problems recently identified in the additive partitioning of non-phylogenetic generalized entropies. When within-assemblage (alpha) quadratic entropy is high, the additive beta and the differentiation measure (gamma − alpha)/gamma always tend to zero (implying no differentiation) regardless of phylogenetic structures and differences in species abundances across assemblages. Likewise, the differentiation measure based on the phylogenetic generalization of Shannon entropy always approaches zero whenever gamma phylogenetic entropy is high. Such ...

EcoVeg: a new approach to vegetation description and classification

Abstract: A vegetation classification approach is needed that can describe the diversity of terrestrial ecosystems and their transformations over large time frames, span the full range of spatial and geographic scales across the globe, and provide knowledge of reference conditions and current states of ecosystems required to make decisions about conservation and resource management. We summarize the scientific basis for EcoVeg, a physiognomic-floristic-ecological classification approach that applies to existing vegetation, both cultural (planted and dominated by human processes) and natural (spontaneously formed and dominated by nonhuman ecological processes). The classification is based on a set of vegetation criteria, including physiognomy (growth forms, structure) and floristics (compositional similarity and characteristic species combinations), in conjunction with ecological characteristics, including site factors, disturbance, bioclimate, and biogeography. For natural vegetation, the rationale for the upper le...

Competition, predation, and migration: Individual choice patterns of Serengeti migrants captured by hierarchical models

Abstract: Large-herbivore migrations occur across gradients of food quality or food abundance that are generally determined by underlying geographic patterns in rainfall, elevation, or latitude, in turn causing variation in the degree of interspecific competition and the exposure to predators. However, the role of top-down effects of predation as opposed to the bottom-up effects of competition for resources in shaping migrations is not well understood. We studied 30 GPS radio-collared wildebeest and zebra migrating seasonally in the Serengeti-Mara ecosystem to ask how predation and food availability differentially affect the individual movement patterns of these co-migrating species. A hierarchical analysis of movement trajectories (directions and distances) in relation to grass biomass, high-quality food patches, and predation risk show that wildebeest tend to move in response to food quality, with little attention to predation risk. In contrast, individual zebra movements reflect a balance between the risk of predation and the access to high-quality food of sufficient biomass. Our analysis shows how two migratory species move in response to different attributes of the same landscape. Counterintuitively and in contrast to most other animal movement studies, we find that both species move farther each day when resources are locally abundant than when they are scarce. During the wet season when the quality of grazing is at its peak, both wildebeest and zebra move the greatest distances and do not settle in localized areas to graze for extended periods. We propose that this punctuated movement in high-quality patches is explained by density dependency, whereby large groups of competing individuals (up to 1.65 million grazers) rapidly deplete the localized grazing opportunities. These findings capture the roles of predation and competition in shaping animal migrations, which are often claimed but rarely measured.

Resource competition across habitat boundaries: asymmetric interactions between benthic and pelagic producers

Abstract: In shallow aquatic systems, benthic and pelagic primary producers typically compete for light and nutrients along opposing vertical supply axes: pelagic algae shade the benthic habitat; conversely, ...

How climate extremes—not means—define a species' geographic range boundary via a demographic tipping point

Abstract: Species' geographic range limits interest biologists and resource managers alike; however, scientists lack strong mechanistic understanding of the factors that set geographic range limits in the field, especially for animals. There exists a clear need for detailed case studies that link mechanisms to spatial dynamics and boundaries because such mechanisms allow us to predict whether climate change is likely to change a species' geographic range and, if so, how abundance in marginal populations compares to the core. The bagworm Thyridopteryx ephemeraeformis (Lepidoptera: Psychidae) is a major native pest of cedars, arborvitae, junipers, and other landscape trees throughout much of North America. Across dozens of bagworm populations spread over six degrees of latitude in the American Midwest we find latitudinal declines in fecundity and egg and pupal survivorship as one proceeds toward the northern range boundary. A spatial gradient of bagworm reproductive success emerges, which is associated with a progres...

Dispersal potential and population genetic structure in the marine intertidal of the eastern North Pacific

Abstract: Population genetic theory and empirical comparisons of sister and sympatric marine species show that life history traits related to dispersal, such as pelagic duration (PD), should affect the frequency and spatial scale of migration, and thus influence population genetic structure. However, recent global analyses have concluded that PD is poorly correlated with marine population genetic structure. Here, we identify and compare genetic structure between four pairs of synchronously diverging co-distributed (SDC) species, drawn from standardized analyses of eight eastern North Pacific rocky intertidal invertebrates and one macrophyte. We test two hypotheses: H0, that species with similar dispersal potential have similar population genetic structure, and H1, that species with higher dispersal potential have lower population genetic differentiation. We find that differences in census population size (Nc), fecundity (F), and PD are sufficient to explain measured differences in population genetic structure (ϕST,...

Responses of a tundra system to warming using SCAMPS: a stoichiometrically coupled, acclimating microbe–plant–soil model

Abstract: Author Posting. © Ecological Society of America, 2014. This article is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Ecological Monographs 84 (2014): 151-170, doi:10.1890/12-2119.1.

Logging-induced changes in habitat network connectivity shape behavioral interactions in the wolf–caribou–moose system

Abstract: Habitat connectivity influences the distribution dynamics of animals. Connectivity can therefore shape trophic interactions, but little empirical evidence is available, especially for large mammals. In forest ecosystems, logging alters functional connectivity among habitat patches, and such activities can affect the spatial game between large herbivores and their predators. We used graph theory to evaluate how harvesting-induced changes in habitat connectivity influence patch choice and residency time of GPS-collared caribou (Rangifer tarandus caribou) and moose (Alces alces) in winter in the boreal forest. We then investigated the predator–prey game by assessing how GPS-collared wolves (Canis lupus) adjusted their movements to changes in landscape properties and in the networks of their prey species. We built prey habitat networks using minimum planar graphs organized around species-specific, highly selected habitat patches (i.e., network nodes). We found that spatial dynamics of large herbivores were in...

Pulsing hydrology determines top‐down control of basal resources in a tropical river–floodplain ecosystem

Abstract: Variable hydrology of rivers strongly affects biophysical factors that influence primary production and population densities, thereby affecting the relative influence of bottom-up and top-down processes in trophic networks. Many tropical floodplain rivers have sustained seasonal flood pulses driven by precipitation patterns of the Intertropical Convergence Zone. These changes in flow alter concentrations of dissolved nutrients, aquatic primary productivity, and per-unit-area densities of aquatic organisms. Therefore, one would predict that the strength of top-down effects of animals on basal resources should shift as the annual flood pulse progresses. We conducted a series of field experiments in a Neotropical lowland river to test for effects of hydrologic phase, habitat (in-channel vs. floodplain aquatic habitat), and benthic-feeding fish and meiofauna on particulate organic matter, chlorophyll, and benthic microalgae. Net ecosystem productivity of this oligotrophic river is higher during the low phase ...

Intercontinental comparison of fish ecomorphology: null model tests of community assembly at the patch scale in rivers

Abstract: Community assembly is affected by environmental filtering that restricts viable phenotypes and by species interactions that impose limits on interspecific trait similarity. Relative influences of these processes should vary according to habitat features and dispersal. Species dispersion within assemblage trait space also should vary in relation to species richness, strength of competition, and the spatiotemporal scale of analysis. We examined ecomorphological diversity of two freshwater fish families (Neotropical Cichlidae, Nearctic Centrarchidae) to test theories of local assembly from regional species pools and theories of species packing within mesohabitat patches. Cichlid and centrarchid assemblages were surveyed in four floodplain rivers (two in South America and two in North America) during low-water periods when fish densities are highest. Surveys were conducted in four mesohabitat types (submerged wood, leaf litter, rocks, sand bank) within river channels and floodplain lakes. We measured 23 morph...

Oceanographic and climatic variation drive top-down/bottom-up coupling in the Galapagos intertidal meta-ecosystem

Abstract: The impact of herbivores on primary producers in differing oceanographic regimes is a matter of intense ecological interest due to ongoing changes in their abundance, that of their predators, and anthropomorphic alteration of nutrient cycles and climatic patterns. Interactions between productivity and herbivory in marine habitats have been studied on temperate rocky shores, coral reefs, mangroves, and salt marshes, but less so at tropical latitudes. To determine how herbivore-alga dynamics varied with oceanographic regime, we used the comparative-experimental approach in rocky intertidal communities on the Galapagos Islands from January 2006 to January 2009. This setting was selected because strongly contrasting oceanographic conditions occurred within a range of ;181 km, with significant differences in temperature, nutrients, phytoplankton productivity, and intertidal communities, and in abundance of macro-herbivores, including marine iguanas. Experiments and measurements were conducted at two sites in each of three oceanographic regimes characterized by low, intermediate, and high bottom-up inputs. At sites of low inputs, macro- herbivores (fish, crabs, iguanas) had a consistent top-down effect, reducing algal abundance, and leaving a few grazer-resistant varieties. At sites of intermediate and high inputs, consumer impacts were stronger during La Ni˜ na (cool phase) than during El Ni˜ no (warm phase). At sites of high inputs, algal biomass was naturally relatively high and was dominated by the edible algae Ulva spp. Macro-grazers reduced algal biomass, but their primary effect was indirect, as articulated corallines displaced other species of algae in their absence. Prior results from the tropics had revealed dominant effects of top-down interactions and recruitment in structuring intertidal communities. Our results suggest that, when a broader oceanographic scenario is taken into account, the relative importance of top-down and bottom-up forces are context dependent, varying with oceanographic regime and climatic variability.

Modeling emergent patterns of dynamic desert ecosystems

Abstract: In many desert ecosystems, vegetation is both patchy and dynamic: vegetated areas are interspersed with patches of bare ground, and both the positioning and the species composition of the vegetated areas exhibit change through time. These characteristics lead to the emergence of multi-scale patterns in vegetation that arise from complex relationships between plants, soils, and transport processes. Previous attempts to probe the causes of spatial complexity and predict responses of desert ecosystems tend to be limited in their focus: models of dynamics have been developed with no consideration of the inherent patchiness in the vegetation, or else models have been developed to generate patterns with no consideration of the dynamics. Here we develop a general modelling framework for the analysis of ecosystem change in deserts that is rooted in the concept of connectivity and is derived from a detailed process-based understanding. We explicitly consider spatial interactions among multiple vegetation types and multiple resources, and our model is formulated to predict responses to a variety of endogenous and exogenous disturbances. The model is implemented in the deserts of the American Southwest both to test hypotheses of the causes of the invasion of woody shrubs, and to test its ability to reproduce observed spatial differences in response to drought in the 20th century. The model's performance leads us to argue that vertical and lateral connectivity are key emergent properties of the ecosystem, which both control its behavior and provide indicators of its state. If this argument is shown to be compatible with field observations, the model presented here will provide a more certain approach toward preventing further degradation of semiarid grasslands. © 2014 by the Ecological Society of America.

Temperature effects on long-term population dynamics in a parasitoid–host system

Abstract: Long-term environmental changes will likely alter the strengths of interactions between species and consequently their population dynamics, leading to changes in the stability of ecological systems. While an increasing number of empirical studies have shown that environmental changes can alter the strengths of species interactions, these studies are typically short (<1–2 generations) and therefore give only partial information about longer term population dynamics. To focus on longer term dynamics, we investigated population cycles of pea aphids and their most common parasitoid, Aphidius ervi, in Wisconsin, USA. Data collected over three years in alfalfa fields showed an apparent host–parasitoid population cycle. Furthermore, higher pea aphid population growth rates and increased parasitism were correlated with higher naturally occurring temperatures. While these effects were observed with seasonal fluctuations in temperature, they beg the question of how long-term changes in mean annual temperature might...

Consensus RDA across dissimilarity coefficients for canonical ordination of community composition data

Abstract: Understanding how habitat structures species assemblages in a community is one of the main goals of community ecology. To relate community patterns to particular factors defining habitat conditions, ecologists often use canonical ordinations such as canonical redundancy analysis (RDA). It is a common practice to use dissimilarity coefficients to perform canonical ordinations through distance-based RDA (db-RDA) or transformation-based RDA (tb-RDA). Dissimilarity coefficients are measures of resemblance where the information about species communities is condensed into a symmetric square matrix of dissimilarities among sites. In this study, we compared 16 of the most commonly used dissimilarity coefficients to evaluate if the species-abundance distribution (SAD) of a community can be used to select an appropriate coefficient. Of these, 11 are designed to be used primarily with abundance data, although they can also be used with presence–absence data, whereas five can only be applied to presence–absence data....

Broad‐scale geographic variation in the organization of rocky intertidal communities in the Gulf of Maine

Abstract: A major challenge facing ecology is to better understand how large-scale processes modify local-scale processes to shape the organization of ecological communities. Although the results of ecological experiments are repeatable on local scales, different results often emerge across broad scales, which can hinder the development of general predictions that apply across the geographical range of a community. Numerous studies in the southern Gulf of Maine have shaped our understanding of community organization and dynamics on New England rocky intertidal shores, where consumers strongly control recovery from disturbance on sheltered shores, and high invertebrate recruitment and competition for space dictate recovery on wave-exposed shores. It is unclear, however, whether the effects of consumers and recruitment variation on resulting community organization in this region apply more broadly to rocky intertidal habitats throughout the Gulf. We characterized variation in rocky intertidal community structure at 34 sites throughout the Gulf of Maine and experimentally examined the influence of consumers (present, absent) and wave energy (wave-exposed, sheltered) on community recovery from disturbance in the northern and southern Gulf. Our results reinforced previous work in the southern Gulf, because consumers dictated the recovery of fucoid algae and mussels on sheltered shores, whereas high barnacle and mussel recruitment and competition for space shaped recovery on wave-exposed shores. However, on sheltered shores in the northern Gulf, neither consumers nor barnacle and mussel recruitment impacted recovery, which was dominated by fucoid algae. Moreover, recovery on wave-exposed shores in the northern Gulf was quite distinct from that observed in the southern Gulf; barnacle and mussel recruitment was negligible and fucoid algae dominated recovery, including the long-term establishment of Ascophyllum nodosum, which is largely absent from wave-exposed shores in the southern Gulf. Thus, distinct community types emerged in the northern and southern Gulf despite their sharing of many of the same species. These patterns likely emerged because of regional differences in coastal oceanography that modulate the recruitment of barnacles and mussels. Hence, increased attention to regional factors should provide key insight into how rocky-shore communities are organized in the Gulf of Maine and elsewhere.

Global approaches to addressing biofuel-related invasive species risks and incorporation into U.S. laws and policies

Abstract: Biofuels are being pursued for their potential greenhouse gas (GHG) emissions benefits, among other reasons. In order to maximize productivity, avoid food–fuel conflicts, and minimize GHG emissions, many advanced biofuel feedstock crops, such as those desired by the aviation community, are under consideration based on traits, such as high biomass and/or seed production, tolerance of marginal cultivation conditions, and short generation times, that may also be predictors of potential invasiveness risk. Biofuel-related invasion risks can be mitigated through careful feedstock crop selection and cultivation techniques developed from the invasion science literature. Existing voluntary best practices and some state and federal regulatory requirements in the United States recommend and/or require the use of such risk mitigation strategies. However, other policies and programs allow or provide incentives for biofuel production without conditions requiring the use of these strategies. We have synthesized informat...

Stochastic models reveal conditions for cyclic dominance in sockeye salmon populations

Abstract: The cause of population cycles is a common question in ecology, and one especially puzzling case is the cycles over the past century in populations of sockeye salmon, Oncorhyncus nerka. Some populations of this semelparous species in British Columbia, Canada, exhibit a phenomenon termed cyclic dominance: every four years there is a dominant cohort of primarily four-year-old spawners, orders of magnitude more abundant than other cohorts, producing a distinctive four-year cycle. In some populations, these cycles stop, start, or shift phase. We used a stochastic age-structured model to investigate the conditions allowing cycles and the events that could cause them to move in and out of cyclic dominance. We first defined cyclic dominance as high values of cyclicity, the fraction of time the population is cyclic, and dominance, the difference in abundance between the dominant cohort and the other three cohorts. We then used simulations to determine the values of (1) relative population persistence (i.e., proxi...

Individual, population, and ecosystem effects of hypoxia on a dominant benthic bivalve in Chesapeake Bay

Abstract: Hypoxia is an environmental stressor that affects abundance, biomass, diversity, and ecosystem function of benthic assemblages worldwide, yet its collective impact at individual, population, and ecosystem levels has rarely been investigated. We examined the effects of hypoxia on the biomass-dominant clam, Macoma balthica, in the York and Rappahannock Rivers (Chesapeake Bay, USA). We (1) surveyed the M. balthica populations in both rivers in 2003 and 2004, (2) determined the effects of low dissolved oxygen (DO) on M. balthica fecundity in a laboratory experiment, and (3) employed a predator-exclusion field experiment to establish the effects of hypoxia and prey density on predation upon M. balthica. The resultant data were used to parameterize a matrix model, which was analyzed to define potential effects of hypoxia at the population level. In both rivers, hypoxia decreased individual clam growth and caused local extinction of populations. Hypoxia reduced egg production of M. balthica by 40% and increased ...

Postglacial reorganization of a small-mammal paleocommunity in southern Australia reveals thresholds of change

Abstract: Natural variation describes the normal fluctuations that occur in ecosystems over time in the absence of significant human-driven disturbance, providing a buffer that facilitates ecological resilience. Long-term data on ecosystems are useful in developing baselines of natural variation and identifying the limits to resilience within different ecosystems. Here, we examined two contemporaneous vertebrate fossil assemblages of the Naracoorte Caves in southern Australia to determine the magnitude and extent of natural variation and resilience exhibited by a small-mammal paleocommunity through the last glacial cycle (c. 50–10 kyr BP). We also investigated the effect of sampling the assemblages at different timescales on observed patterns of variability and quantified sampling effects to test the robustness of the temporal trends. Our results show that the paleocommunity was structurally and compositionally stable through the early glacial period and last glacial maximum (LGM), with variability exhibited only i...

Carbon transit through degradation networks

Abstract: The decay of organic matter in natural ecosystems is controlled by a network of biologically, physically, and chemically driven processes. Decomposing organic matter is often described as a continuum that transforms and degrades over a wide range of rates, but it is difficult to quantify this heterogeneity in models. Most models of carbon degradation consider a network of only a few organic matter states that transform homogeneously at a single rate. These models may fail to capture the range of residence times of carbon in the soil organic matter continuum. Here we assume that organic matter is distributed among a continuous network of states that transform with stochastic, heterogeneous kinetics. We pose and solve an inverse problem in order to identify the rates of carbon exiting the underlying degradation network (exit rates) and apply this approach to plant matter decay throughout North America. This approach provides estimates of carbon retention in the network without knowing the details of underlying state transformations. We find that the exit rates are approximately lognormal, suggesting that carbon flow through a complex degradation network can be described with just a few parameters. These results indicate that the serial and feedback processes in natural degradation networks can be well approximated by a continuum of parallel decay rates.