Showing papers in "Ecological Applications in 2019"

Considerations for maximizing the adaptive potential of restored coral populations in the western Atlantic.

Abstract: Active coral restoration typically involves two interventions: crossing gametes to facilitate sexual larval propagation; and fragmenting, growing, and outplanting adult colonies to enhance asexual propagation. From an evolutionary perspective, the goal of these efforts is to establish self-sustaining, sexually reproducing coral populations that have sufficient genetic and phenotypic variation to adapt to changing environments. Here, we provide concrete guidelines to help restoration practitioners meet this goal for most Caribbean species of interest. To enable the persistence of coral populations exposed to severe selection pressure from many stressors, a mixed provenance strategy is suggested: genetically unique colonies (genets) should be sourced both locally as well as from more distant, environmentally distinct sites. Sourcing three to four genets per reef along environmental gradients should be sufficient to capture a majority of intraspecies genetic diversity. It is best for practitioners to propagate genets with one or more phenotypic traits that are predicted to be valuable in the future, such as low partial mortality, high wound healing rate, high skeletal growth rate, bleaching resilience, infectious disease resilience, and high sexual reproductive output. Some effort should also be reserved for underperforming genets because colonies that grow poorly in nurseries sometimes thrive once returned to the reef and may harbor genetic variants with as yet unrecognized value. Outplants should be clustered in groups of four to six genets to enable successful fertilization upon maturation. Current evidence indicates that translocating genets among distant reefs is unlikely to be problematic from a population genetic perspective but will likely provide substantial adaptive benefits. Similarly, inbreeding depression is not a concern given that current practices only raise first-generation offspring. Thus, proceeding with the proposed management strategies even in the absence of a detailed population genetic analysis of the focal species at sites targeted for restoration is the best course of action. These basic guidelines should help maximize the adaptive potential of reef-building corals facing a rapidly changing environment.

Open science, reproducibility, and transparency in ecology

Abstract: Reproducibility is a key tenet of the scientific process that dictates the reliability and generality of results and methods. The complexities of ecological observations and data present novel challenges in satisfying needs for reproducibility and also transparency. Ecological systems are dynamic and heterogeneous, interacting with numerous factors that sculpt natural history and that investigators cannot completely control. Observations may be highly dependent on spatial and temporal context, making them very difficult to reproduce, but computational reproducibility can still be achieved. Computational reproducibility often refers to the ability to produce equivalent analytical outcomes from the same data set using the same code and software as the original study. When coded workflows are shared, authors and editors provide transparency for readers and allow other researchers to build directly and efficiently on primary work. These qualities may be especially important in ecological applications that have important or controversial implications for science, management, and policy. Expectations for computational reproducibility and transparency are shifting rapidly in the sciences. In this work, we highlight many of the unique challenges for ecology along with practical guidelines for reproducibility and transparency, as ecologists continue to participate in the stewardship of critical environmental information and ensure that research methods demonstrate integrity.

Forest structure and climate mediate drought-induced tree mortality in forests of the Sierra Nevada, USA.

Abstract: Extreme drought stress and associated bark beetle population growth contributed to an extensive tree mortality event in California, USA, resulting in more than 129 million trees dying between 2012 and 2016. Although drought is an important driver of this mortality event, past and ongoing fire suppression and the consequent densification of forests may have contributed. In some areas, land management agencies have worked to reduce stand density through mechanical treatments and prescribed fire to restore forests to less dense, more open conditions that are presumably more resilient to disturbance and changing climate. Here, we evaluate if stand structural conditions associated with treated (e.g., thinned and prescribed burned) forests in the Sierra Nevada of California conferred more resistance to the bark beetle epidemic and drought event of 2012-2016. We found that, compared to untreated units, treated units had lower stand densities, larger average tree diameters, and greater dominance of pines (Pinus), the historically dominant trees. For all tree species studied, mortality was substantially greater in climatically drier areas (i.e., lower elevations and latitudes). Both pine species studied (ponderosa pine [Pinus ponderosa] and sugar pine [Pinus lambertiana]) had greater mortality in areas where their diameters were larger, suggesting a size preference for their insect mortality agents. For ponderosa pine, the tree species experiencing greatest mortality, individual-tree mortality probability (for a given tree diameter) was significantly lower in treated stands. Ponderosa pine mortality was also positively related to density of medium- to large-sized conspecific trees, especially in areas with lower precipitation, suggesting that abundance of nearby host trees for insect mortality agents was an important determinant of pine mortality. Mortality of incense cedar (Calocedrus decurrens) and white fir (Abies concolor) was positively associated with basal area, suggesting sensitivity to competition during drought, but overall mortality was lower, likely because the most prevalent and effective mortality agents (the bark beetles Dendroctonus brevicomis and D. ponderosae) are associated specifically with pine species within our study region. Our findings suggest that forest thinning treatments are effective in reducing drought-related tree mortality in forests, and they underscore the important interaction between water and forest density in mediating bark beetle-caused mortality.

Autonomous sound recording outperforms human observation for sampling birds: a systematic map and user guide.

Abstract: Autonomous sound recording techniques have gained considerable traction in the last decade, but the question remains whether they can replace human observation surveys to sample sonant animals. For birds in particular, survey methods have been tested extensively using point counts and sound recording surveys. Here, we review the latest evidence for this taxon within the frame of a systematic map. We compare sampling effectiveness of these two survey methods, the output variables they produce, and their practicality. When assessed against the standard of point counts, autonomous sound recording proves to be a powerful tool that samples at least as many species. This technology can monitor birds in an exhaustive, standardized, and verifiable way. Moreover, sound recorders give access to entire soundscapes from which new data types can be derived (vocal activity, acoustic indices). Variables such as abundance, density, occupancy, or species richness can be obtained to yield data sets that are comparable to and compatible with point counts. Finally, autonomous sound recorders allow investigations at high temporal and spatial resolution and coverage, which are more cost effective and cannot be achieved by human observations alone, even though small-scale studies might be more cost effective when carried out with point counts. Sound recorders can be deployed in many places, they are more scalable and reliable, making them the better choice for bird surveys in an increasingly data-driven time. We provide an overview of currently available recorders and discuss their specifications to guide future study designs.

The importance of sample size in marine megafauna tagging studies

Abstract: Telemetry is a key, widely used tool to understand marine megafauna distribution, habitat use, behavior, and physiology; however, a critical question remains: "How many animals should be tracked to acquire meaningful data sets?" This question has wide-ranging implications including considerations of statistical power, animal ethics, logistics, and cost. While power analyses can inform sample sizes needed for statistical significance, they require some initial data inputs that are often unavailable. To inform the planning of telemetry and biologging studies of marine megafauna where few or no data are available or where resources are limited, we reviewed the types of information that have been obtained in previously published studies using different sample sizes. We considered sample sizes from one to >100 individuals and synthesized empirical findings, detailing the information that can be gathered with increasing sample sizes. We complement this review with simulations, using real data, to show the impact of sample size when trying to address various research questions in movement ecology of marine megafauna. We also highlight the value of collaborative, synthetic studies to enhance sample sizes and broaden the range, scale, and scope of questions that can be answered.

Persistent effects of fragmentation on tropical rainforest canopy structure after 20 yr of isolation.

Abstract: Assessing the persistent impacts of fragmentation on aboveground structure of tropical forests is essential to understanding the consequences of land use change for carbon storage and other ecosystem functions. We investigated the influence of edge distance and fragment size on canopy structure, aboveground woody biomass (AGB), and AGB turnover in the Biological Dynamics of Forest Fragments Project (BDFFP) in central Amazon, Brazil, after 22+ yr of fragment isolation, by combining canopy variables collected with portable canopy profiling lidar and airborne laser scanning surveys with long-term forest inventories. Forest height decreased by 30% at edges of large fragments (>10 ha) and interiors of small fragments (<3 ha). In larger fragments, canopy height was reduced up to 40 m from edges. Leaf area density profiles differed near edges: the density of understory vegetation was higher and midstory vegetation lower, consistent with canopy reorganization via increased regeneration of pioneers following post-fragmentation mortality of large trees. However, canopy openness and leaf area index remained similar to control plots throughout fragments, while canopy spatial heterogeneity was generally lower at edges. AGB stocks and fluxes were positively related to canopy height and negatively related to spatial heterogeneity. Other forest structure variables typically used to assess the ecological impacts of fragmentation (basal area, density of individuals, and density of pioneer trees) were also related to lidar-derived canopy surface variables. Canopy reorganization through the replacement of edge-sensitive species by disturbance-tolerant ones may have mitigated the biomass loss effects due to fragmentation observed in the earlier years of BDFFP. Lidar technology offered novel insights and observational scales for analysis of the ecological impacts of fragmentation on forest structure and function, specifically aboveground biomass storage.

Urban meadows as an alternative to short mown grassland: effects of composition and height on biodiversity.

Abstract: There are increasing calls to provide greenspace in urban areas, yet the ecological quality, as well as quantity, of greenspace is important. Short mown grassland designed for recreational use is the dominant form of urban greenspace in temperate regions but requires considerable maintenance and typically provides limited habitat value for most taxa. Alternatives are increasingly proposed, but the biodiversity potential of these is not well understood. In a replicated experiment across six public urban greenspaces, we used nine different perennial meadow plantings to quantify the relative roles of floristic diversity and height of sown meadows on the richness and composition of three taxonomic groups: plants, invertebrates, and soil microbes. We found that all meadow treatments were colonized by plant species not sown in the plots, suggesting that establishing sown meadows does not preclude further locally determined grassland development if management is appropriate. Colonizing species were rarer in taller and more diverse plots, indicating competition may limit invasion rates. Urban meadow treatments contained invertebrate and microbial communities that differed from mown grassland. Invertebrate taxa responded to changes in both height and richness of meadow vegetation, but most orders were more abundant where vegetation height was longer than mown grassland. Order richness also increased in longer vegetation and Coleoptera family richness increased with plant diversity in summer. Microbial community composition seems sensitive to plant species composition at the soil surface (0–10 cm), but in deeper soils (11–20 cm) community variation was most responsive to plant height, with bacteria and fungi responding differently. In addition to improving local residents’ site satisfaction, native perennial meadow plantings can produce biologically diverse grasslands that support richer and more abundant invertebrate communities, and restructured plant, invertebrate, and soil microbial communities compared with short mown grassland. Our results suggest that diversification of urban greenspace by planting urban meadows in place of some mown amenity grassland is likely to generate substantial biodiversity benefits, with a mosaic of meadow types likely to maximize such benefits.

A smart curtailment approach for reducing bat fatalities and curtailment time at wind energy facilities.

Abstract: The development and expansion of wind energy is considered a key global threat to bat populations. Bat carcasses are being found underneath wind turbines across North and South America, Eurasia, Africa, and the Austro-Pacific. However, relatively little is known about the comparative impacts of techniques designed to modify turbine operations in ways that reduce bat fatalities associated with wind energy facilities. This study tests a novel approach for reducing bat fatalities and curtailment time at a wind energy facility in the United States, then compares these results to operational mitigation techniques used at other study sites in North America and Europe. The study was conducted in Wisconsin during 2015 using a new system of tools for analyzing bat activity and wind speed data to make near real-time curtailment decisions when bats are detected in the area at control turbines (N = 10) vs. treatment turbines (N = 10). The results show that this smart curtailment approach (referred to as Turbine Integrated Mortality Reduction, TIMR) significantly reduced fatality estimates for treatment turbines relative to control turbines for pooled species data, and for each of five species observed at the study site: pooled data (-84.5%); eastern red bat (Lasiurus borealis, -82.5%); hoary bat (Lasiurus cinereus, -81.4%); silver-haired bat (Lasionycteris noctivagans, -90.9%); big brown bat (Eptesicus fuscus, -74.2%); and little brown bat (Myotis lucifugus, -91.4%). The approach reduced power generation and estimated annual revenue at the wind energy facility by ≤ 3.2% for treatment turbines relative to control turbines, and we estimate that the approach would have reduced curtailment time by 48% relative to turbines operated under a standard curtailment rule used in North America. This approach significantly reduced fatalities associated with all species evaluated, each of which has broad distributions in North America and different ecological affinities, several of which represent species most affected by wind development in North America. While we recognize that this approach needs to be validated in other areas experiencing rapid wind energy development, we anticipate that this approach has the potential to significantly reduce bat fatalities in other ecoregions and with other bat species assemblages in North America and beyond.

Functional responses in habitat selection: clarifying hypotheses and interpretations.

Abstract: A fundamental challenge in habitat ecology and management is understanding the mechanisms generating animal distributions. Studies of habitat selection provide a lens into such mechanisms, but are often limited by unrealistic assumptions. For example, most studies assume that habitat selection is constant with respect to the availability of resources, such that habitat use remains proportional to availability. To the contrary, a growing body of work has shown the fallacy of this assumption, indicating that animals modify their behavior depending on the context at broader scales. This has been termed a functional response in habitat selection. Furthermore, a diversity of methods is employed to model functional responses in habitat selection, with little attention to how methodology might affect scientific and conservation conclusions. Here, we first review the conceptual and statistical foundations of methods currently used to model functional responses and clarify the ecological tests evaluated within each approach. We then use a combination of simulated and empirical data sets to evaluate the similarities and differences among approaches. Importantly, we identified multiple statistical issues with the most widely applied approaches to understand functional responses, including: (1) a complex and important role of random- or individual-level intercepts in adjusting individual-level regression coefficients as resource availability changes and (2) a sensitivity of results to poorly informed individual-level coefficients estimated for animals with low availability of a given resource. Consequently, we provide guidance on applying approaches that are insensitive to these issues with the goal of advancing our understanding of animal habitat ecology and management. Finally, we characterize the management implications of assuming similarity between the current approaches to model functional responses with two empirical data sets of federally threatened species: Canada lynx (Lynx canadensis) in the United States and woodland caribou (Rangifer tarandus caribou) in Canada. Collectively, our assessment helps clarify the similarities and differences among current approaches and, therefore, assists the integration of functional responses into the mainstream of habitat ecology and management.

Northern forest winters have lost cold, snowy conditions that are important for ecosystems and human communities

Abstract: Winter is an understudied but key period for the socioecological systems of northeastern North American forests. A growing awareness of the importance of the winter season to forest ecosystems and surrounding communities has inspired several decades of research, both across the northern forest and at other mid- and high-latitude ecosystems around the globe. Despite these efforts, we lack a synthetic understanding of how winter climate change may impact hydrological and biogeochemical processes and the social and economic activities they support. Here, we take advantage of 100 years of meteorological observations across the northern forest region of the northeastern United States and eastern Canada to develop a suite of indicators that enable a cross-cutting understanding of (1) how winter temperatures and snow cover have been changing and (2) how these shifts may impact both ecosystems and surrounding human communities. We show that cold and snow covered conditions have generally decreased over the past 100 years. These trends suggest positive outcomes for tree health as related to reduced fine root mortality and nutrient loss associated with winter frost but negative outcomes as related to the northward advancement and proliferation of forest insect pests. In addition to effects on vegetation, reductions in cold temperatures and snow cover are likely to have negative impacts on the ecology of the northern forest through impacts on water, soils, and wildlife. The overall loss of coldness and snow cover may also have negative consequences for logging and forest products, vector-borne diseases, and human health, recreation, and tourism, and cultural practices, which together represent important social and economic dimensions for the northern forest region. These findings advance our understanding of how our changing winters may transform the socioecological system of a region that has been defined by the contrasting rhythm of the seasons. Our research also identifies a trajectory of change that informs our expectations for the future as the climate continues to warm.

Intensive silviculture enhances biomass accumulation and tree diversity recovery in tropical forest restoration

Abstract: Maximizing initial aboveground woody biomass (AGB) accumulation in order to obtain early payments for carbon stocking is essential for the financial viability of reforestation programs fostered by climate mitigation efforts. Intensive silviculture, i.e., silviculture traditionally used in commercial forestry to maximize productivity and gains, has recently been advocated as a promising approach to enhance AGB accumulation in restoration plantations. However, this approach may hamper natural forest regeneration and ecological succession due to high competition between colonizing plants and planted trees. We investigated the impacts of different silvicultural treatments applied to restoration plantations with 20 native tree species on AGB accumulation and spontaneous regeneration of native woody species in an experiment set up in the Atlantic Forest of Brazil. Intensive silviculture demonstrated a remarkable potential to enhance AGB accumulation in restoration plantations by increasing up to three times the AGB of tree stands (from ~25 to 75 Mg/ha in the 12th year). Intensive fertilization/weed control enhanced AGB accumulation, while higher tree density and the proportion of pioneers did not have a significant effect on AGB over the time. In spite of higher costs (cost increase of 13–19%), the cost‐effectiveness for AGB accumulation of intensive silviculture was comparable to that of traditional silviculture applied to restoration (US$50–100/Mg AGB for 3 × 2 m spacing). Contrary to our expectations, we did not find a trade‐off between AGB accumulation by planted trees and the spontaneous regeneration of tree species, since intensive silviculture enhanced the regeneration of both planted (total of 12 species) and colonizing woody species (total of 30 species) in the plantation understory. Specifically, a strong association was found between AGB stocks and the abundance and richness of colonizing species, a vast majority of which (90% of species and 95% of individuals) were dispersed by animals. We report a case of positive correlation between AGB stocking and woody species regeneration in the restoration of the Atlantic Forest. Fostering the establishment and maintenance of restoration tree plantations can, in some cases, be a win‐win strategy for climate mitigation and biodiversity conservation in human‐modified tropical landscapes.

Community structure dynamics and carbon stock change of rehabilitated mangrove forests in Sulawesi, Indonesia.

Abstract: To date, discourse associated with the potential application of "blue carbon" within real-world carbon markets has focused on blue carbon as a mitigation strategy in the context of avoided deforestation (e.g., REDD+). Here, we report structural dynamics and carbon storage gains from mangrove sites that have undergone rehabilitation to ascertain whether reforestation can complement conservation activities and warrant project investment. Replicated sites at two locations with contrasting geomorphic conditions were selected, Tiwoho and Tanakeke on the island of Sulawesi, Indonesia. These locations are representative of high (Tiwoho, deep muds and silty substrates) and low (Tanakeke, shallow, coralline sands) productivity mangrove ecosystems. They share a similar management history of clearing and conversion for aquaculture before restorative activities were undertaken using the practice of Ecological Mangrove Rehabilitation (EMR). Species diversity and mean biomass carbon storage gains after 10 yr of regrowth from the high productivity sites of Tiwoho (49.2 ± 9.1 Mg C·ha-1 ·yr-1 ) are already almost of one-third of mean biomass stocks exhibited by mature forests (167.8 ± 30.3 Mg C·ha-1 ·yr-1 ). Tiwoho's EMR sites, on average, will have offset all biomass C that was initially lost through conversion within the next 11 yr, a finding in marked contrast to the minimal carbon gains observed on the low productivity, low diversity, coral atoll EMR sites of Tanakeke (1.1 ± 0.4 Mg C·ha-1 ·yr-1 ). These findings highlight the importance of geomorphic and biophysical site selection if the primary purpose of EMR is intended to maximize carbon sequestration gains.

Changing landscapes of Southeast Asia and rodent-borne diseases: decreased diversity but increased transmission risks.

Abstract: The reduction in biodiversity from land use change due to urbanization and agricultural intensification appears to be linked to major epidemiological changes in many human diseases. Increasing disease risks and the emergence of novel pathogens result from increased contact among wildlife, domesticated animals, and humans. We investigated the relationship between human alteration of the environment and the occurrence of generalist and synanthropic rodent species in relation to the diversity and prevalence of rodent-borne pathogens in Southeast Asia, a hotspot of threatened and endangered species, and a foci of emerging infectious diseases. We used data from an extensive pathogen survey of rodents from seven sites in mainland Southeast Asia in conjunction with past and present land cover analyses. At low spatial resolutions, we found that rodent-borne pathogen richness is negatively associated with increasing urbanization, characterized by increased habitat fragmentation, agriculture cover and deforestation. However, at a finer spatial resolution, we found that some major pathogens are favored by environmental characteristics associated with human alteration including irrigation, habitat fragmentation, and increased agricultural land cover. In addition, synanthropic rodents, many of which are important pathogen reservoirs, were associated with fragmented and human-dominated landscapes, which may ultimately enhance the opportunities for zoonotic transmission and human infection by some pathogens.

Loss of functional connectivity in migration networks induces population decline in migratory birds.

Abstract: Migratory birds rely on a habitat network along their migration routes by temporarily occupying stopover sites between breeding and non-breeding grounds. Removal or degradation of stopover sites in a network might impede movement and thereby reduce migration success and survival. The extent to which the breakdown of migration networks, due to changes in land use, impacts the population sizes of migratory birds is poorly understood. We measured the functional connectivity of migration networks of waterfowl species that migrate over the East Asian-Australasian Flyway from 1992 to 2015. We analysed the relationship between changes in non-breeding population sizes and changes in functional connectivity, while taking into account other commonly considered species traits, using a phylogenetic linear mixed model. We found that population sizes significantly declined with a reduction in the functional connectivity of migration networks; no other variables were important. We conclude that the current decrease in functional connectivity, due to habitat loss and degradation in migration networks, can negatively and crucially impact population sizes of migratory birds. Our findings provide new insights into the underlying mechanisms that affect population trends of migratory birds under environmental changes. Establishment of international agreements leading to the creation of systematic conservation networks associated with migratory species' distributions and stopover sites may safeguard migratory bird populations.

Making inference with messy (citizen science) data: when are data accurate enough and how can they be improved?

Abstract: Measurement or observation error is common in ecological data: as citizen scientists and automated algorithms play larger roles processing growing volumes of data to address problems at large scales, concerns about data quality and strategies for improving it have received greater focus. However, practical guidance pertaining to fundamental data quality questions for data users or managers-how accurate do data need to be and what is the best or most efficient way to improve it?-remains limited. We present a generalizable framework for evaluating data quality and identifying remediation practices, and demonstrate the framework using trail camera images classified using crowdsourcing to determine acceptable rates of misclassification and identify optimal remediation strategies for analysis using occupancy models. We used expert validation to estimate baseline classification accuracy and simulation to determine the sensitivity of two occupancy estimators (standard and false-positive extensions) to different empirical misclassification rates. We used regression techniques to identify important predictors of misclassification and prioritize remediation strategies. More than 93% of images were accurately classified, but simulation results suggested that most species were not identified accurately enough to permit distribution estimation at our predefined threshold for accuracy ( 97% accuracy: enough to meet our accuracy threshold. Occupancy models that accounted for false-positive error provided even more accurate inference even at high rates of misclassification (30%). As simulation suggested occupancy models were less sensitive to additional false-negative error, screening models or fitting occupancy models accounting for false-positive error emerged as efficient data remediation solutions. Combining simulation-based sensitivity analysis with empirical estimation of baseline error and its variability allows users and managers of potentially error-prone data to identify and fix problematic data more efficiently. It may be particularly helpful for "big data" efforts dependent upon citizen scientists or automated classification algorithms with many downstream users, but given the ubiquity of observation or measurement error, even conventional studies may benefit from focusing more attention upon data quality.

Color, chlorophyll a, and suspended solids effects on Secchi depth in lakes: implications for trophic state assessment.

Abstract: Secchi depth (SD), a primary metric to assess trophic state, is controlled in many lakes by algal densities, measured as chlorophyll-a (chl-a) concentration. Two other optically related water quality variables also directly affect SD: non-algal suspended solids (SSNA ) and colored dissolved organic matter (CDOM, expressed as the absorption coefficient at 440 nm, a440 ). Using a database of ~1,460 samples from ~625 inland lake basins in Minnesota and two other Upper Midwest states, Wisconsin and Michigan, we analyzed relationships among these variables, with special focus on CDOM levels that influence SD values and the Minnesota SD standards used to assess eutrophication impairment of lakes. Log-transformed chl-a, total suspended solids (TSS), and SD were strongly correlated with each other; log(a440 ) had major effects on log(SD) but was only weakly correlated with log(chl-a) and log(TSS). Multiple regression models for log(SD) and 1/SD based on the three driving variables (chl-a, SSNA , and CDOM) explained ~80% of the variance in SD in the whole data set, but substantial differences in the form of the best-fit relationships were found between major ecoregions. High chl-a concentrations (> 50 μg/L) and TSS (> 20 mg/L) rarely occurred in lakes with high CDOM (a440 > ~4 m-1 ), and all lakes with a440 > 8 m-1 had SD ≤ 2.0 m despite low chl-a values ( ~ 4 m-1 . Thus, SD is not an accurate trophic state metric in moderately to highly colored lakes, and Minnesota's 2-m SD criterion should not be the sole metric to assess eutrophication impairment in warm/cool-water lakes of the Northern Lakes and Forest ecoregion. More generally, trophic state assessments using SD in regions with large landscape sources of CDOM need to account for effects of CDOM on SD.

Exploring the relationships between marine protected areas and invasive fish in the world's most invaded sea

Abstract: Marine Protected Areas (MPAs) are an essential tool for marine biodiversity conservation. Yet, their effectiveness in protecting marine ecosystems from global stressors is debated. Biological invasions are a major driver of global change, causing biodiversity loss and altering ecosystem functioning. Here, we explored the relationships between MPAs and alien/native range-expanding fishes in the Mediterranean Sea, the world's most invaded sea. We surveyed fish and benthic communities in nine MPAs and adjacent unprotected areas across six countries. In the South and Eastern Mediterranean MPAs, the biomass of alien and native range-expanding fishes often exceeded 50% of the total fish biomass. Conversely, in the North and Western Mediterranean, alien fishes were absent. A negative relationship was found between native and alien species richness. Average and minimum sea surface temperature (SST) over six consecutive years were positively correlated with the total biomass of alien species; no alien fishes were recorded below 20.5°C average SST and 13.8°C minimum SST. We also found a negative relationship between alien fishes' biomass and the distance from the Suez Canal, which is the main pathway for the introduction of alien fish in the Mediterranean Sea. The biomass of alien and native range-expanding fishes was found to be higher in the South and Eastern Mediterranean MPAs than in adjacent unprotected areas. The association of barrens (rocky reefs deprived of vegetation) and invasive herbivores was observed at all eastern sites, regardless of protection status. Currently, the level of fishing pressure exerted on alien and native range-expanding fishes seems to be the most influential factor determining the lower biomass of invasive fishes at unprotected sites compared to MPAs. Our findings suggest that complementary management actions, such as species-targeted removals, should be taken in MPAs to effectively control invasive fish populations.

Organic Farming at Local and Landscape Scales Fosters Biological Pest Control in Vineyards

Abstract: While organic farming practices, which are often promoted as models of ecological intensification, generally enhance biodiversity, their effects on the delivery of ecosystem services, such as biological pest control, are still unknown. Here, using a multi-scale hierarchical design in southwestern France, we examined the effects of organic farming and seminatural habitats at the local and landscape scales on biological control services of three pests, including weeds and insects, in 42 vineyards. Organic farming at the local and landscape scales was beneficial to the mean and temporal stability of biological control services, while the proportion of seminatural habitats in the landscape reduced the level of biological pest control potential. The effects of organic farming and seminatural habitats across spatial scales varied with the type of prey considered and with time. Egg moth removal rates were higher in fields under organic management compared to conventional management while weed seed removal rates increased with the proportion of organic farming in the landscape. Larval removal rates as well as seed removal rates were always more stable within time in organic fields than in conventional fields. Moreover, independently of farming system type, local variables describing the agricultural management intensity, such as pesticide use or crop productivity, were also found to be important variables explaining levels of biological control services. Pesticide use tended to reduce biological control potential, while crop productivity was associated with contrasting biological control responses depending on the pest type. Our study demonstrates the need to target multiple spatial scales and to consider farming practices, as well as the proportion of seminatural habitats, to design functional landscapes that optimize biological pest control services.

Beyond the model: expert knowledge improves predictions of species' fates under climate change.

Abstract: The need to proactively manage landscapes and species to aid their adaptation to climate change is widely acknowledged. Current approaches to prioritizing investment in species conservation generally rely on correlative models, which predict the likely fate of species under different climate change scenarios. Yet, while model statistics can be improved by refining modeling techniques, gaps remain in understanding the relationship between model performance and ecological reality. To investigate this, we compared standard correlative species distribution models to highly accurate, fine-scale, distribution models. We critically assessed the ecological realism of each species' model, using expert knowledge of the geography and habitat in the study area and the biology of the study species. Using interactive software and an iterative vetting with experts, we identified seven general principles that explain why the distribution modeling under- or overestimated habitat suitability, under both current and predicted future climates. Importantly, we found that, while temperature estimates can be dramatically improved through better climate downscaling, many models still inaccurately reflected moisture availability. Furthermore, the correlative models did not account for biotic factors, such as disease or competitor species, and were unable to account for the likely presence of micro refugia. Under-performing current models resulted in widely divergent future projections of species' distributions. Expert vetting identified regions that were likely to contain micro refugia, even where the fine-scale future projections of species distributions predicted population losses. Based on the results, we identify four priority conservation actions required for more effective climate change adaptation responses. This approach to improving the ecological realism of correlative models to understand climate change impacts on species can be applied broadly to improve the evidence base underpinning management responses.

A city-scale assessment reveals that native forest types and overstory species dominate New York City forests.

Abstract: Cities are increasingly focused on expanding tree canopy cover as a means to improve the urban environment by, for example, reducing heat island effects, promoting better air quality, and protecting local habitat. The majority of efforts to expand canopy cover focus on planting street trees or on planting native tree species and removing nonnatives in natural areas through reforestation. Yet many urban canopy assessments conducted at the city-scale reveal co-dominance by nonnative trees, fueling debates about the value of urban forests and native-specific management targets. In contrast, assessments within cities at site or park scales find that some urban forest stands harbor predominantly native biodiversity. To resolve this apparent dichotomy in findings, about the extent to which urban forests are native dominated, between the city-scale canopy and site-level assessments, we measure forest structure and composition in 1,124 plots across 53 parks in New York City's 2,497 ha of natural area forest. That is, we assess urban forests at the city-scale and deliberately omit sampling trees existing outside of forest stands but which are enumerated in citywide canopy assessments. We find that on average forest stand canopy is comprised of 82% native species in New York City forests, suggesting that conclusions that the urban canopy is co-dominated by nonnatives likely results from predominantly sampling street trees in prior city-scale assessments. However, native tree species' proportion declines to 75% and 53% in the midstory and understory, respectively, suggesting potential threats to the future native dominance of urban forest canopies. Furthermore, we find that out of 57 unique forest types in New York City, the majority of stands (81%) are a native type. We find that stand structure in urban forest stands is more similar to rural forests in New York State than to stand structure reported for prior assessments of the urban canopy at the city scale. Our results suggest the need to measure urban forest stands apart from the entire urban canopy. Doing so will ensure that city-scale assessments return data that align with conservation policy and management strategies that focus on maintaining and growing native urban forests rather than individual trees.

Genetic tagging in the Anthropocene: scaling ecology from alleles to ecosystems

Abstract: The Anthropocene is an era of marked human impact on the world. Quantifying these impacts has become central to understanding the dynamics of coupled human-natural systems, resource-dependent livelihoods, and biodiversity conservation. Ecologists are facing growing pressure to quantify the size, distribution, and trajectory of wild populations in a cost-effective and socially acceptable manner. Genetic tagging, combined with modern computational and genetic analyses, is an under-utilized tool to meet this demand, especially for wide-ranging, elusive, sensitive, and low-density species. Genetic tagging studies are now revealing unprecedented insight into the mechanisms that control the density, trajectory, connectivity, and patterns of human-wildlife interaction for populations over vast spatial extents. Here, we outline the application of, and ecological inferences from, new analytical techniques applied to genetically tagged individuals, contrast this approach with conventional methods, and describe how genetic tagging can be better applied to address outstanding questions in ecology. We provide example analyses using a long-term genetic tagging dataset of grizzly bears in the Canadian Rockies. The genetic tagging toolbox is a powerful and overlooked ensemble that ecologists and conservation biologists can leverage to generate evidence and meet the challenges of the Anthropocene.

Climate and lawn management interact to control C4 plant distribution in residential lawns across seven U.S. cities.

Abstract: In natural grasslands, C4 plant dominance increases with growing season temperatures and reflects distinct differences in plant growth rates and water use efficiencies of C3 vs. C4 photosynthetic pathways. However, in lawns, management decisions influence interactions between planted turfgrass and weed species, leading to some uncertainty about the degree of human vs. climatic controls on lawn species distributions. We measured herbaceous plant carbon isotope ratios (δ13 C, index of C3 /C4 relative abundance) and C4 cover in residential lawns across seven U.S. cities to determine how climate, lawn plant management, or interactions between climate and plant management influenced C4 lawn cover. We also calculated theoretical C4 carbon gain predicted by a plant physiological model as an index of expected C4 cover due to growing season climatic conditions in each city. Contrary to theoretical predictions, plant δ13 C and C4 cover in urban lawns were more strongly related to mean annual temperature than to growing season temperature. Wintertime temperatures influenced the distribution of C4 lawn turf plants, contrary to natural ecosystems where growing season temperatures primarily drive C4 distributions. C4 cover in lawns was greatest in the three warmest cities, due to an interaction between climate and homeowner plant management (e.g., planting C4 turf species) in these cities. The proportion of C4 lawn species was similar to the proportion of C4 species in the regional grass flora. However, the majority of C4 species were nonnative turf grasses, and not of regional origin. While temperature was a strong control on lawn species composition across the United States, cities differed as to whether these patterns were driven by cultivated lawn grasses vs. weedy species. In some cities, biotic interactions with weedy plants appeared to dominate, while in other cities, C4 plants were predominantly imported and cultivated. Elevated CO2 and temperature in cities can influence C3 /C4 competitive outcomes; however, this study provides evidence that climate and plant management dynamics influence biogeography and ecology of C3 /C4 plants in lawns. Their differing water and nutrient use efficiency may have substantial impacts on carbon, water, energy, and nutrient budgets across cities.

Multi-scalar drivers of biodiversity: local management mediates wild bee community response to regional urbanization

Abstract: It is critical to understand the specific drivers of biodiversity across multiple spatial scales, especially within rapidly urbanizing areas, given the distinct management recommendations that may result at each scale. However, drivers of biodiversity patterns and interactions between drivers are often only measured and modeled at a single scale. In this study, we assessed bee community composition at three time periods in 20 grassland and 20 agriculture sites located across two major metroplexes. We examined how local environmental variables and surrounding landscape composition impact bee abundance, richness, and evenness, including comparisons between groups with different nesting strategies and body sizes. We collected nearly 13,000 specimens and identified 172 species. We found that levels of regional land use differentially impacted bee abundance and diversity depending on local habitat management. Specifically, within agriculture sites, bee richness was greater with increasing landscape-level seminatural habitat, while in grassland sites, bee richness was similar across landscapes regardless of seminatural habitat cover. Bee evenness at both site types declined with increasing landscape-level habitat heterogeneity, due to an increase of rare species at the grassland sites, but not in the agricultural sites, further indicating that diversity is driven by the interaction of local habitat quality and landscape-level habitat composition. We additionally found that agriculture sites supported higher abundances, but not richness, of small-bodied and below-ground nesting bees, while grassland sites supported higher abundances of aboveground nesting bees, and higher richness of large-bodied species. Increased levels of local bare ground were significantly related to multiple metrics of bee diversity, including greater belowground nesting bee abundance and richness. Local floral richness was also significantly related to increases of overall bee abundance, as well as the abundance and richness of small bees. Overall, we suggest that local land managers can support bee abundance and diversity by conserving areas of bare soil and promoting native floral diversity, the latter especially critical in highly urban agricultural spaces. Our results provide the first documentation of significant interactions between local habitat management and landscape composition impacting insect communities in urban systems, indicating that bee conservation practices depend critically on land use interactions across multiple spatial scales.

Where to forage when afraid: Does perceived risk impair use of the foodscape?

Abstract: The availability and quality of forage on the landscape constitute the foodscape within which animals make behavioral decisions to acquire food. Novel changes to the foodscape, such as human disturbance, can alter behavioral decisions that favor avoidance of perceived risk over food acquisition. Although behavioral changes and population declines often coincide with the introduction of human disturbance, the link(s) between behavior and population trajectory are difficult to elucidate. To identify a pathway by which human disturbance may affect ungulate populations, we tested the Behaviorally Mediated Forage-Loss Hypothesis, wherein behavioral avoidance is predicted to reduce use of available forage adjacent to disturbance. We used GPS collar data collected from migratory mule deer (Odocoileus hemionus) to evaluate habitat selection, movement patterns, and time-budgeting behavior in response to varying levels of forage availability and human disturbance in three different populations exposed to a gradient of energy development. Subsequently, we linked animal behavior with measured use of forage relative to human disturbance, forage availability, and quality. Mule deer avoided human disturbance at both home range and winter range scales, but showed negligible differences in vigilance rates at the site level. Use of the primary winter forage, sagebrush (Artemisia tridentata), increased as production of new annual growth increased but use decreased with proximity to disturbance. Consequently, avoidance of human disturbance prompted loss of otherwise available forage, resulting in indirect habitat loss that was 4.6-times greater than direct habitat loss from roads, well pads, and other infrastructure. The multiplicative effects of indirect habitat loss, as mediated by behavior, impaired use of the foodscape by reducing the amount of available forage for mule deer, a consequence of which may be winter ranges that support fewer animals than they did before development.

Spatiotemporal prediction of wildfire size extremes with Bayesian finite sample maxima

Abstract: Wildfires are becoming more frequent in parts of the globe, but predicting where and when wildfires occur remains difficult. To predict wildfire extremes across the contiguous United States, we integrate a 30-yr wildfire record with meteorological and housing data in spatiotemporal Bayesian statistical models with spatially varying nonlinear effects. We compared different distributions for the number and sizes of large fires to generate a posterior predictive distribution based on finite sample maxima for extreme events (the largest fires over bounded spatiotemporal domains). A zero-inflated negative binomial model for fire counts and a lognormal model for burned areas provided the best performance. This model attains 99% interval coverage for the number of fires and 93% coverage for fire sizes over a six year withheld data set. Dryness and air temperature strongly predict extreme wildfire probabilities. Housing density has a hump-shaped relationship with fire occurrence, with more fires occurring at intermediate housing densities. Statistically, these drivers affect the chance of an extreme wildfire in two ways: by altering fire size distributions, and by altering fire frequency, which influences sampling from the tails of fire size distributions. We conclude that recent extremes should not be surprising, and that the contiguous United States may be on the verge of even larger wildfire extremes.

Warm, dry winters truncate timing and size distribution of seaward-migrating salmon across a large, regulated watershed

Abstract: Ecologists are pressed to understand how climate constrains the timings of annual biological events (phenology). Climate influences on phenology are likely significant in estuarine watersheds because many watersheds provide seasonal fish nurseries where juvenile presence is synched with favorable conditions. While ecologists have long recognized that estuaries are generally important to juvenile fish, we incompletely understand the specific ecosystem dynamics that contribute to their nursery habitat value, limiting our ability to identify and protect vital habitat components. Here we examined the annual timing of juvenile coldwater fish migrating through a seasonally warm, hydrologically managed watershed. Our goal was to (1) understand how climate constrained the seasonal timing of water conditions necessary for juvenile fish to use nursery habitats and (2) inform management decisions about (a) mitigating climate-mediated stress on nursery habitat function and (b) conserving heat-constrained species in warming environments. Cool, wet winters deposited snow and cold water into mountains and reservoirs, which kept the lower watershed adequately cool for juveniles through the spring despite the region approaching its hot, dry summers. For every 1°C waters in April were colder, the juvenile fish population (1) inhabited the watershed 4-7 d longer and (2) entered marine waters, where survival is size selective, at maximum sizes 2.1 mm larger. Climate therefore appeared to constrain the nursery functions of this system by determining seasonal windows of tolerable rearing conditions, and cold water appeared to be a vital ecosystem component that promoted juvenile rearing. Fish in this system inhabit the southernmost extent of their range and already rear during the coolest part of the year, suggesting that a warming climate will truncate rather than shift their annual presence. Our findings are concerning for coldwater diadromous species in general because warming climates may constrain watershed use and diminish viability of life histories (e.g., late springtime rearing) and associated portfolio benefits over the long term. Lower watershed nurseries for coldwater fish in warming climates may be enhanced through allocating coldwater reservoir releases to prolong juvenile rearing periods downstream or restorations that facilitate colder conditions.

The past and future roles of competition and habitat in the range-wide occupancy dynamics of Northern Spotted Owls

Abstract: Slow ecological processes challenge conservation. Short-term variability can obscure the importance of slower processes that may ultimately determine the state of a system. Furthermore, management actions with slow responses can be hard to justify. One response to slow processes is to explicitly concentrate analysis on state dynamics. Here, we focus on identifying drivers of Northern Spotted Owl (Strix occidentalis caurina) territorial occupancy dynamics across 11 study areas spanning their geographic range and forecasting response to potential management actions. Competition with Barred Owls (Strix varia) has increased Spotted Owl territory extinction probabilities across all study areas and driven recent declines in Spotted Owl populations. Without management intervention, the Northern Spotted Owl subspecies will be extirpated from parts of its current range within decades. In the short term, Barred Owl removal can be effective. Over longer time spans, however, maintaining or improving habitat conditions can help promote the persistence of northern spotted owl populations. In most study areas, habitat effects on expected Northern Spotted Owl territorial occupancy are actually greater than the effects of competition from Barred Owls. This study suggests how intensive management actions (removal of a competitor) with rapid results can complement a slower management action (i.e., promoting forest succession).

Nearshore seascape connectivity enhances seagrass meadow nursery function.

Abstract: Diverse habitats composing coastal seascapes occur in close proximity, connected by the flux of materials and fauna across habitat boundaries. Understanding how seascape connectivity alters important ecosystem functions for fish, however, is not well established. For a seagrass-dominant seascape, we predicted that configuration and composition of adjacent habitats would alter habitat access for fauna and trophic subsidies, enhancing nursery function for juvenile fish. In an extensive Zostera marina seagrass meadow, we established sites adjacent to (1) highly complex and productive kelp forests (Nereocystis luetkeana), (2) unvegetated sand habitats, and (3) in the seagrass meadow interior. Using SCUBA, we conducted underwater observations of young-of the-year (YOY) rockfish (Sebastes spp.) recruitment across sites. Using generalized linear mixed effects models, we assessed the role of seascape adjacency relative to seagrass provisions (habitat complexity and prey) on YOY recruitment. YOY rockfish collections were used to trace sources of allochthonous vs. autochthonous primary production in the seagrass food web, via a δ13 C and δ15 N isotopic mixing model, and prey consumption using stomach contents. Overall, seagrass nursery function was strongly influenced by adjacent habitats and associated subsidies. Allochthonous N. luetkeana was the greatest source of energy assimilated by YOY rockfish within seagrass sites. In seagrass sites adjacent to N. luetkeana kelp forests, YOYs consumed higher quality prey, which corresponded with better body condition relative to sites adjacent to sand. Moreover, kelp forest adjacency enhanced YOY rockfish recruitment within the seagrass meadow, suggesting that habitat complexity is a key seascape feature influencing the nursery function of nearshore habitats. In general, to promote seascape connectivity, the conservation and restoration of nursery habitats should prioritize the inclusion of habitat mosaics of high structural complexity and productivity. We illustrate and emphasize the importance of using a seascape-level approach that considers linkages among habitats for the management of important nearshore ecosystem functions.

Increased population size of fish in a lowland river following restoration of structural habitat

Abstract: Most assessments of the effectiveness of river restoration are done at small spatial scales (<10 km) over short time frames (less than three years), potentially failing to capture large-scale mechanisms such as completion of life-history processes, changes to system productivity, or time lags of ecosystem responses. To test the hypothesis that populations of two species of large-bodied, piscivorous, native fishes would increase in response to large-scale structural habitat restoration (reintroduction of 4,450 pieces of coarse woody habitat into a 110-km reach of the Murray River, southeastern Australia), we collected annual catch, effort, length, and tagging data over seven years for Murray cod (Maccullochella peelii) and golden perch (Macquaria ambigua) in a restored "intervention" reach and three neighboring "control" reaches. We supplemented mark-recapture data with telemetry and angler phone-in data to assess the potentially confounding influences of movement among sampled populations, heterogeneous detection rates, and population vital rates. We applied a Bayesian hierarchical model to estimate changes in population parameters including immigration, emigration, and mortality rates. For Murray cod, we observed a threefold increase in abundance in the population within the intervention reach, while populations declined or fluctuated within the control reaches. Golden perch densities also increased twofold in the intervention reach. Our results indicate that restoring habitat heterogeneity by adding coarse woody habitats can increase the abundance of fish at a population scale in a large, lowland river. Successful restoration of poor-quality "sink" habitats for target species relies on connectivity with high-quality "source" habitats. We recommend that the analysis of restoration success across appropriately large spatial and temporal scales can help identify mechanisms and success rates of other restoration strategies such as restoring fish passage or delivering water for environmental outcomes.

Half a century of multiple anthropogenic stressors has altered northern forest understory plant communities.

Abstract: Boreal forests form the largest and least disturbed forest biome in the northern hemisphere. However, anthropogenic pressure from intensified forest management, eutrophication, and climate change may alter the ecosystem functions of understory vegetation and services boreal forests provide. Swedish forests span long gradients of climate, nitrogen deposition, and management intensity. This makes them ideal to study how the species composition and functions of other, more pristine, boreal forests might change under increased anthropogenic pressure. Moreover, the National Forest Inventory (NFI) has collected systematic data on Swedish forest vegetation since the mid-20th century. We use this data to quantify changes in vegetation types between two periods, 1953-1962 and 2003-2012. The results show changes in forest understory vegetation since the 1950s at scales not previously documented in the boreal biome. The spatial extent of most vegetation types changed significantly. Shade-adapted and nutrient-demanding species (those with high specific leaf area) have become more common at the expense of light-demanding and nutrient-conservative (low specific leaf area) species. The cover of ericaceous dwarf shrubs decreased dramatically. These effects were strongest where anthropogenic impacts were greatest, suggesting links to drivers such as nitrogen deposition and land-use change. These changes may impact ecosystem functions and services via effects on higher trophic levels and faster plant litter decomposition in the expanding vegetation types. This, in turn, may influence nutrient dynamics, and consequently ecosystem productivity and carbon sequestration.