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There is increasing awareness of the negative ecological and environmental effects of widespread use of pesticides on the landscape. Spillover or drift of pesticides from agricultural areas has been shown to impact species health, reproduction, and trophic dynamics through both direct and indirect mechanisms. Neonicotinoid insecticides are associated with observed declines of insectivorous and grassland birds, and these environmental pollutants are a significant conservation concern for many species that have experienced past or current population declines. Due to the high efficacy of these modern insecticides in depressing local insect populations, insectivorous birds can be negatively impacted by a pesticide-mediated reduction in food supply. Neonicotinoids may act synergistically with other stressors, such as habitat loss, to exacerbate threats to species or population viability. The Tricolored Blackbird is an insectivorous grassland bird of conservation concern in California, USA. Due to the high association of this species with agricultural habitats, we sought to quantify the amount of neonicotinoid residues in Tricolored Blackbird carcasses as a first step in assessing how this species may be impacted by pesticides. Out of 85 salvaged carcasses sampled (N = 24 adults, N = 3 fledglings, and N = 58 nestlings), only two contained detectable levels of target compounds. These were an adult and one nestling that contained clothianidin residue (40 ppb and 7 ppb, respectively); both of these birds were salvaged from breeding colonies associated with dairy farms in Kern County, California. We suggest that further work is needed to assess neonicotinoid exposure of Tricolored Blackbirds in dairy-associated breeding colonies.

Understanding how non-trophic social systems respond to environmental gradients is still a challenge in animal ecology, particularly in comparing changes in species composition to changes in interspecific interactions. Here, we combined long-term monitoring of mixed-species bird flocks, data on participating species evolutionary history and traits, to test how elevation affected community assemblages and interspecific interactions in flock social networks. Elevation primarily affected flocks through reassembling interspecific associations rather than modifying community assemblages. Specifically, flock networks at higher elevations (compared to low elevations) had stronger interspecific associations (larger average weighted degree), network connectivity (enhanced network density) and fewer subnetworks. A phylogenetic and functional perspective revealed that associations between similar species weakened, whereas connections between dissimilar and/or random species were unchanged or strengthened with elevation. Likewise, network assortativity for the traits of vertical stratum and breeding period declined with elevation. The overall pattern is a change from modular networks in the lowlands, where species join flocks with other species that have matching traits, to a more open, random system at high elevations. Collectively, this rewiring of interspecific networks across elevational gradients imparts network stability and resiliency and makes mixed-species flocks less sensitive to local extinctions caused by harsh environments.

Nuanced understanding of seasonal movements of partially migratory birds is paramount to species and habitat conservation. Using nascent statistical methods, we identified migratory strategies of birds outfitted with radio-frequency identification (RFID) tags detected at RFID feeders in two sites in California, USA. We quantified proportions of migrants and residents and the seasonal phenology for each movement strategy in Allen's and Anna's hummingbirds; we also validated our methodology by fitting our model to obligate migratory black-chinned hummingbirds. Allen's and Anna's hummingbirds exhibited characteristics of facultative migratory behaviour. We also quantified apparent annual survival for each migratory strategy and found that residents had significantly higher probabilities of apparent survival. Low survival estimates for migrants suggest that a high proportion of birds in the migrant group permanently emigrated from our study sites. Considered together, our analyses suggest that hummingbirds in both northern and southern California sites partake in diverse and highly plastic migratory behaviours. Our assessment elucidates the dynamics underlying idiosyncratic migratory behaviours of two species of hummingbirds, in addition to describing a framework for similar assessments of migratory behaviours using the multi-state open robust design with state uncertainty model and single-site dynamics.

Dispersal is a key driver of spatial population dynamics. Dispersal behaviour may be shaped by many factors, such as mate-finding, the spatial distribution of resources, or wind and currents, yet most models of spatial dynamics assume random dispersal. We examined the spatial dynamics of a day-flying moth species (Arctia virginalis) that forms mating aggregations on hilltops (hilltopping) based on long-term adult and larval population censuses. Using time-series models, we compared spatial population dynamics resulting from empirically founded hilltop-based connectivity indices and modelled the interactive effects of temperature, precipitation and density dependence. Model comparisons supported hilltop-based connectivity metrics including hilltop elevation over random connectivity, suggesting an effect of hilltopping behaviour on dynamics. We also found strong interactive effects of temperature and precipitation on dynamics. Simulations based on fitted time-series models showed lower patch occupancy and regional synchrony, and higher colonization and extinction rates when hilltopping was included, with potential implications for the probability of persistence of the patch network. Overall, our results show the potential for dispersal behaviour to have important effects on spatial population dynamics and persistence, and we advocate the inclusion of such non-random dispersal in metapopulation models.

The influenza virus mutates and spreads rapidly, making it suitable for studying evolutionary and ecological processes. The ecological factors and processes by which different lineages of influenza compete or coexist within hosts through time and across geographical space are poorly known. We hypothesized that competition would be stronger for influenza viruses infecting the same host compared to different hosts (the Host Barrier Hypothesis), and for those with a higher cross-region transmission intensity (the Geographic Barrier Hypothesis). Using available sequences of the influenza A (H1N1) virus in GenBank, we identified six lineages, twelve clades, and several replacement events. We found that human-hosted lineages had a higher cross-region transmission intensity than swine-hosted lineages. Co-occurrence probabilities of lineages infecting the same host were lower than those infecting different hosts, and human-hosted lineages had lower co-occurrence probabilities and genetic diversity than swine-hosted lineages. These results show that H1N1 lineages infecting the same host or with high cross-region transmission rates experienced stronger competition and extinction pressures than those infecting different hosts or with low cross-region transmission. Our study highlights how host and geographic barriers shape the competition, extinction, and coexistence patterns of H1N1 lineages and clades.

The number of breeding pairs of crested ibis (Nipponia nippon) in Hanzhong, China has recovered remarkably from 2 to 511 from 1981 to 2019. Although the crested ibis has been closely monitored, the habitat preference of the bird has not been well studied despite the extensive increase in abundance. We used nest site data from the past 39 years and 30 environmental variables to develop species distribution models for each year. We applied random forest to select important environmental variables, and used logistic regressions to quantify the changes in habitat preferences in 39 years, taking into account the effects of interaction and quadratic terms. We found that six variables had strong impacts on nest site selection. The interaction term of rice paddies and waterbodies, and the quadratic term of precipitation of the wettest quarter of the year were the most important correlates of nest presence. Human impact at nest sites changed from low to high as birds increased their use of ancestral habitats with abundant rice paddies. We concluded that during the population recovery, the crested ibises retained their dependence on wetlands, yet moved from remote areas to populated rural regions where food resources had recovered due to the ban of pesticide use.

The ecological threshold concept describes how changes in one or more factors at thresholds can result in a large shift in the state of an ecosystem. This concept focuses attention on limiting factors that affect the tolerance of systems or organisms and changes in them. Accumulating empirical evidence for the existence of ecological thresholds has created favorable conditions for practical application to wildlife conservation. Applying the concept has the potential to enhance conservation of two large carnivores, Amur tiger and leopard, and the knowledge gained could guide the construction of a proposed national park. In this review, ecological thresholds that result from considering a paradigm of bottom-up control were evaluated for their potential to contribute to the conservation of Amur tiger and leopard. Our review highlights that large carnivores, as top predators, are potentially affected by ecological thresholds arising from changes in climate (or weather), habitat, vegetation, prey, competitors, and anthropogenic disturbances. What's more, interactions between factors and context dependence need to be considered in threshold research and conservation practice, because they may amplify the response of ecosystems or organisms to changes in specific drivers. Application of the threshold concept leads to a more thorough evaluation of conservation needs, and could be used to guide future Amur tiger and leopard research and conservation in China. Such application may inform the conservation of other large carnivores worldwide.

The valley elderberry longhorn beetle (VELB), Desmocerus californicus dimorphus (Coleoptera: Cerambycidae), is a federally threatened subspecies endemic to the Central Valley of California. The VELB range partially overlaps with that of its morphologically similar sister taxon, the California elderberry longhorn beetle (CELB), Desmocerus californicus californicus (Coleoptera: Cerambycidae). Current surveying methods are limited to visual identification of larval exit holes in the VELB/CELB host plant, elderberry (Sambucus spp.), into which larvae bore and excavate feeding galleries. Unbiased genetic approaches could provide a much-needed complementary approach that has more precision than relying on visual inspection of exit holes. In this study we developed a DNA sequencing-based method for indirect detection of VELB/CELB from frass (insect fecal matter), which can be easily and non-invasively collected from exit holes. Frass samples were collected from 37 locations and the 12S and 16S mitochondrial genes were partially sequenced using nested PCR amplification. Three frass-derived sequences showed 100% sequence identity to VELB/CELB barcode references from museum specimens sequenced for this study. Database queries of frass-derived sequences also revealed high similarity to common occupants of old VELB feeding galleries, including earwigs, flies, and other beetles. Overall, this non-invasive approach is a first step towards a genetic assay that could augment existing VELB monitoring and accurately discriminate between VELB, CELB, and other insects. Furthermore, a phylogenetic analysis of 12S and 16S data from museum specimens revealed evidence for the existence of a previously unrecognized, genetically distinct CELB subpopulation in southern California.

In multiple regression Y ~ β0 + β1X1 + β2X2 + β3X1 X2 + ɛ., the interaction term is quantified as the product of X1 and X2. We developed fractional-power interaction regression (FPIR), using βX1 M X2 N as the interaction term. The rationale of FPIR is that the slopes of Y-X1 regression along the X2 gradient are modeled using the nonlinear function (Slope = β1 + β3MX1 M-1 X2 N), instead of the linear function (Slope = β1 + β3X2) that regular regressions normally implement. The ranges of M and N are from -56 to 56 with 550 candidate values, respectively. We applied FPIR using a well-studied dataset, nest sites of the crested ibis (Nipponia nippon).We further tested FPIR by other 4692 regression models. FPIRs have lower AIC values (-302 ± 5003.5) than regular regressions (-168.4 ± 4561.6), and the effect size of AIC values between FPIR and regular regression is 0.07 (95% CI: 0.04-0.10). We also compared FPIR with complex models such as polynomial regression, generalized additive model, and random forest. FPIR is flexible and interpretable, using a minimum number of degrees of freedom to maximize variance explained. We have provided a new R package, interactionFPIR, to estimate the values of M and N, and suggest using FPIR whenever the interaction term is likely to be significant. • Introduced fractional-power interaction regression (FPIR) as Y ~ β0 + β1X1 + β2X2 + β3X1 M X2 N + ɛ to replace the current regression model Y ~ β0 + β1X1 + β2X2 + β3X1 X2 + ɛ; • Clarified the rationale of FPIR, and compared it with regular regression model, polynomial regression, generalized additive model, and random forest using regression models for 4692 species; • Provided an R package, interactionFPIR, to calculate the values of M and N, and other model parameters.

SADIE (Spatial Analysis by Distance Indices) is designed specifically to quantify patterns in spatially-referenced count-based data. It was developed for dealing with data that can be considered ‘patchy’. Such distributions are commonly found, for example, in insect populations where discrete patches of individuals are often evident. The distributions of such populations have ‘hard edges’, with patches and gaps occurring spatially. In these cases variance of abundance does not vary smoothly, but discontinuously. In this paper we outline the use of SADIE and provide free access to the SADIE software suite, establishing Rethinking Ecology as its permanent home. Finally, we review the use of SADIE and demonstrate its use in a wide variety of sub-disciplines within the general field of ecology.

Climate change can have strong effects on species interactions and community structure. Temperature-dependent effects on predator-prey interactions are a major mechanism through which these effects occur. To understand the net effects of predator attack rates and dynamic windows of prey vulnerability, we examined the impacts of temperature on the interaction of a caterpillar (Arctia virginalis) and its ant predator (Formica lasioides). We conducted field experiments to examine attack rates on caterpillars relative to temperature, ant abundance, and body size, and laboratory experiments to determine the effects of temperature on caterpillar growth. We modeled temperature-dependent survival based on the integrated effects of temperature-dependent growth and temperature- and size-dependent predation. Attack rates on caterpillars increased with warming and ant recruitment, but decreased with caterpillar size. Caterpillar growth rates increased with temperature, narrowing the window of vulnerability. The model predicted that net caterpillar survival would decrease with temperature, suggesting that A. virginalis populations could be depressed with future climate warming. Theoretical work suggests that the net outcome of predator-prey interactions with increasing temperature depends on the respective responses of interacting species in terms of velocity across space, whereas the present study suggests the importance of effects of temperature on prey window of vulnerability, or "velocity" across time.

Aim: We tested the effects of season and migratory status (residents-versus-seasonal migrants) on island biogeography of bird assemblages through partitioning beta diversity into richness and turnover components and community nestedness metrics. We predicted that total beta diversity, the richness component of beta diversity and community nestedness will be lower for bird assemblages in winter than in summer, and lowest of all for winter visitors. These predictions were derived from published ideas about resource availability, movement and habitat choice in birds in different seasons. Location: Thousand Island Lake, China. Methods: Bird species were sampled using line transects on 36 islands during five breeding and winter seasons (2009−2014). Birds were grouped into assemblages of winter residents, winter visitors and summer residents. Associations between beta diversity partitioning, island area, isolation and habitat richness were tested using partial Mantel correlations. We complemented these tests with measures of nestedness and null model approaches. Results: Contrary to expectation, beta diversity, nestedness and difference of beta diversity or its components from null models were higher for winter residents than either summer resident or winter visitor assemblages. As predicted, winter visitors showed little association with habitat richness, and beta diversity was rarely different from null communities. Summer residents had the highest correlations of beta diversity components with habitat richness, but showed the lowest level of total beta diversity, a low richness component and were anti-nested (less nested than random). Main conclusions: Substantial differences were found in the biogeography of winter-versus-summer residents, and seasonal visitor (migratory)-versus-resident bird assemblages, which match expectations derived from bird biology and population ecology. Summer residents highlighted the role of habitat-related niche differences, whereas winter residents showed area-related selective extinction. By contrast, winter visitors appeared to be more randomly distributed.

Human-induced environmental and climate change are widely blamed for causing rapid global biodiversity loss, but direct estimation of the proportion of biodiversity lost at local or regional scales are still infrequent. This prevents us from quantifying the main and interactive effects of anthropogenic environmental and climate change on species loss. Here, we demonstrate that the estimated proportion of species loss of 252 key protected vertebrate species at a county level of China during the past half century was 27.2% for all taxa, 47.7% for mammals, 28.8% for amphibians and reptiles and 19.8% for birds. Both human population increase and species richness showed significant positive correlations with species loss of all taxa combined, mammals, birds, and amphibians and reptiles. Temperature increase was positively correlated with all-taxa and bird species loss. Precipitation increase was negatively correlated with species loss of birds. Human population change and species richness showed more significant interactions with the other correlates of species loss. High species richness regions had higher species loss under the drivers of human environmental and climate change than low-richness regions. Consequently, ongoing human environmental and climate changes are expected to perpetuate more negative effects on the survival of key vertebrate species, particularly in high-biodiversity regions.

Global biodiversity conservation has recently focused on the roles of land management strategies of land sharing vs. land sparing. However, few studies have evaluated the roles of social and ecological interactions in modifying the effectiveness of land management for top predator conservation. Using a 65-year dataset from northeastern China, we evaluated the roles of government social policies in resolving human-wildlife conflicts and improving human livelihood. From 1998 to 2015, both big cat populations and their habitats have increased. Concurrently, regional human population density decreased by 59.6%, forest volume logged was reduced by 62.6%. Consequently, increases of key prey species were observed during the same periods. Although populations remained small, the annual finite rate of increase was 1.04 for the Amur tiger population and 1.08 for Amur leopards from 1999 to 2015. Habitat areas occupied by big cats increased significantly. Overexploitation of forest resources and big cat declines under previous unsustainable land use are progressively being reversed under land sparing. Large economic investment and intense human-relocation projects coupled with efforts to reduce poaching and illegal hunting and trapping demonstrate a complex social and ecological synergy in big cat conservation in China.

Background and aimsThe Janzen-Connell model predicts that common species suffer high seed predation from specialized natural enemies as a function of distance from parent trees, and consequently as a function of conspecific density, whereas the predator satiation hypothesis predicts that seed attack is reduced due to predator satiation at high seed densities. Pre-dispersal predation by insects was studied while seeds are still on parent trees, which represents a frequently overlooked stage in which seed predation occurs.MethodsReproductive tree density and seed production were investigated from ten Quercus serrata populations located in south-west China, quantifying density-dependent pre-dispersal seed predation over two years by three insect groups.Key resultsAcorn infestation was nearly twice as high in the low-seed year as that in the high-seed year, with considerable spatio-temporal variation in the direction and magnitude of density-dependent pre-dispersal seed predation evident. Across whole populations of trees, a high density of reproductive trees caused predator satiation and reduced insect attack in the high-seed year. Within individual trees, and consistent with the Janzen-Connell model, overall insect seed predation was positively correlated with seed production in the low-seed year. In addition, there was variation among insect taxa, with positive density-dependent seed predation by Curculio weevils in the high-seed year and moths in the low-seed year, but apparent density independence by Cyllorhynchites weevils in both years.ConclusionsThe overall trend of negative density-dependent, pre-dispersal seed predation suggests that predator satiation limited the occurrence of Janzen-Connell effects across Q. serrata populations. Such effects may have large impacts on plant population dynamics and tree diversity, depending on the extent to which they are reduced by counteracting positive density-dependent predation for seeds on individual trees and other factors affecting successful recruitment.

The performance and population dynamics of insect herbivores depend on the nutritive and defensive traits of their host plants. The literature on plant-herbivore interactions focuses on plant trait mean values, but recent studies showing the importance of plant genetic diversity for herbivores suggest that plant trait variance may be equally important. The consequences of plant trait variance for herbivore performance, however, have been largely overlooked. Here we report an extensive assessment of the effects of within-population plant trait variance on herbivore performance using 457 performance datasets from 53 species of insect herbivores. We show that variance in plant nutritive traits substantially reduces mean herbivore performance via non-linear averaging of performance relationships that were overwhelmingly concave down. By contrast, relationships between herbivore performance and plant defence levels were typically linear, with variance in plant defence not affecting herbivore performance via non-linear averaging. Our results demonstrate that plants contribute to the suppression of herbivore populations through variable nutrient levels, not just by having low average quality as is typically thought. We propose that this phenomenon could play a key role in the suppression of herbivore populations in natural systems, and that increased nutrient heterogeneity within agricultural crops could contribute to the sustainable control of insect pests in agroecosystems.

Aim: To determine how taxonomic level and spatial scale affect the phylogenetic structure of species assemblages across four classes of terrestrial vertebrates. Location: Mainland China. Methods: Using species distribution data from Mammalia, Aves, Reptilia and Amphibia, including 2153 species from 2105 counties and 1632 species from 295 nature reserves across mainland China, we analysed the phylogenetic structure of co-occurring species at multiple taxonomic levels (class, order, family and genus) and spatial scales. Results: We found that phylogenetic clustering and unstructured patterns were more frequent than phylogenetic overdispersion in all groups. There was a higher frequency of phylogenetic clustering within classes and orders than within families and genera, while spatial scale had little effect on the frequency of phylogenetic clustering. Birds and mammals showed less frequent clustering patterns than amphibians and reptiles. Main conclusions: Phylogenetic clustering in terrestrial vertebrates was predominant over overdispersion at regional scales and higher taxonomic levels. Our results suggest that regional ecological and evolutionary factors, such as environmental filtering and speciation relative to extinction or colonization rates, are important in determining species assemblages of animals.

A growing number of studies have looked at how climate change alters the effects of habitat fragmentation and degradation on both single and multiple species; some raise concern that biodiversity loss and its effects will be exacerbated. The published literature on spatial dynamics (such as dispersal and metapopulation dynamics), habitat fragmentation and climate change requires synthesis and a conceptual framework to simplify thinking. We propose a framework that integrates how climate change affects spatial population dynamics and the effects of habitat fragmentation in terms of: (i) habitat quality, quantity and distribution; (ii) habitat connectivity; and (iii) the dynamics of habitat itself. We use the framework to categorize existing autecological studies and investigate how each is affected by anthropogenic climate change. It is clear that a changing climate produces changes in the geographic distribution of climatic conditions, and the amount and quality of habitat. The most thorough published studies show how such changes impact metapopulation persistence, source-sink dynamics, changes in species' geographic range and community composition. Climate-related changes in movement behavior and quantity, quality and distribution of habitat have also produced empirical changes in habitat connectivity for some species. An underexplored area is how habitat dynamics that are driven by climatic processes will affect species that live in dynamic habitats. We end our discussion by suggesting ways to improve current attempts to integrate climate change, spatial population dynamics and habitat fragmentation effects, and suggest distinct areas of study that might provide opportunities for more fully integrative work.

Amphibians are important indicators of environmental health, and their populations are in worldwide decline. The causes of these declines are diverse and not well understood. In some cases multiple stressors and complex causal mechanisms have been identified. Experimental studies have shown that contaminants can cause the failure of Lithobates sylvaticus tadpoles to initiate predator avoidance behaviors, potentially leading to increased tadpole capture and injury. Copper is a contaminant known to negatively affect amphibians and other aquatic organisms at sub-lethal levels. Mining waste, certain pesticides, vehicle exhaust and brake pad dust are sources of copper, which can enter hydrologic systems through runoff. Additionally, temperature is known to influence predator-prey interactions of ectotherms and is predicted to rise in some areas as climate changes. We examined how copper and temperature affected behavior and predation dynamics between an odonate predator (Aeshna sitchensis) and larval L. sylvaticus prey. We found that sublethal concentrations of copper near the analytical detection limits for this element (1.85 μg Cu/L) significantly reduced tadpole and odonate activity. Above-average temperatures (22°C) significantly increased tadpole activity and decreased dragonfly activity, compared with ambient-temperature treatments (17°). These behavioral responses culminated in an approximately three-fold increase in the number of dragonfly attacks on tadpoles in the elevated-temperature, copper-exposed treatments. We suggest that increased concentrations of dissolved copper and elevated water temperatures are harmful to amphibian prey through maladaptive behavioral responses in the presence of predators.

A challenge for conservation management is to understand how population and habitat dynamics interact to affect species persistence. In real landscapes, timing and duration of disturbances can vary, and species' responses to habitat changes will depend on how timing of dispersal and reproduction events relate to the landscape temporal structure. For instance, increasing disturbance frequency may promote extinction of species that are unable to appropriately time their reproduction in an ever-changing habitat and favor species that are able to track habitat changes. We developed a mathematical model to compare the effects of pulsed dispersal, initiated by shifts in habitat quality, with temporally continuous dispersal. We tested the effects of habitat (and population) turnover rates on metapopulation establishment, persistence, and long-term patch occupancy. Pulsed dispersal reduced patch occupancy and metapopulation longevity when habitat patches are relatively permanent. In such cases, demographic extinction was the primary form of local extinction. Conversely, when habitat patches are short-lived and new ones are frequently formed, pulsed dispersal promoted rapid colonization, increased occupancy, and prolonged metapopulation persistence. Our results show that species responsiveness to habitat disturbance is critical to metapopulation persistence, having profound implications for the species likely to persist in landscapes with altered disturbance regimes.

Despite the ubiquity of ontogenetic niche shifts, their drivers and consequences are poorly understood. Different nutritional requirements and stage-specific physiological limitations have often been offered as explanations for these life history features, but emerging work has demonstrated that top-down factors may also be important. We studied the roles of predation and associational refuge in ontogenetic niche shifts for a holometabolous insect (Platyprepia virginalis), which shifts habitats and host plants to pupate. We examined the effect of pupation site selection across habitats and host plants by late-instar caterpillars on the rate of predation during the relatively vulnerable pupal stage. Studying the ontogenetic transition from mobile caterpillar to non-feeding, sessile pupa allows isolation of top-down effects from bottom-up, nutritional effects. An observational study supported previous findings that feeding caterpillars preferred marsh habitats, but pupating caterpillars preferred prairie habitats. Experiments demonstrated that caterpillars preferred to pupate within a physically defended plant species. Pupation within this defended plant species resulted in reduced predation (an associational refuge), and removal of the physical defense structures negated the reduced-predation effect. This experiment shows that ontogenetic niche shifts can be driven by predation and can involve facilitation by a host plant that provides a refuge to predation. The co-option of plant chemical defenses by animals is widely established. However, finding a clear example in which an animal exploits a plant's physical defense is rare, especially in the context of ontogenetic niche shifts. This work shows that facilitation mediated by refuge from predation provided by host plants and life-stage-dependent predation risk can interact to shape species' distributions.

Invasive species frequently degrade habitats, disturb ecosystem processes, and can increase the likelihood of extinction of imperiled populations. However, novel or enhanced functions provided by invading species may reduce the impact of processes that limit populations. It is important to recognize how invasive species benefit endangered species to determine overall effects on sensitive ecosystems. For example, since the 1990s, hybrid Spartina (Spartina foliosa × alterniflora) has expanded throughout South San Francisco Bay, USA, supplanting native vegetation and invading mudflats. The endangered California clapper rail (Rallus longirostris obsoletus) uses the tall, dense hybrid Spartina for cover and nesting, but the effects of hybrid Spartina on clapper rail survival was unknown. We estimated survival rates of 108 radio-marked California clapper rails in South San Francisco Bay from January 2007 to March 2010, a period of extensive hybrid Spartina eradication, with Kaplan-Meier product limit estimators. Clapper rail survival patterns were consistent with hybrid Spartina providing increased refuge cover from predators during tidal extremes which flood native vegetation, particularly during the winter when the vegetation senesces. Model averaged annual survival rates within hybrid Spartina dominated marshes before eradication (Ŝ = 0.466) were greater than the same marshes posttreatment (Ŝ = 0.275) and a marsh dominated by native vegetation (Ŝ = 0.272). However, models with and without marsh treatment as explanatory factor for survival rates had nearly equivalent support in the observed data, lending ambiguity as to whether hybrid Spartina facilitated greater survival rates than native marshland. Conservation actions to aid in recovery of this endangered species should recognize the importance of available of high tide refugia, particularly in light of invasive species eradication programs and projections of future sea-level rise. © 2014 Springer Science+Business Media Dordrecht (outside the USA).

Confronted with a rapidly changing world and limited resources for conservation, ecologists are increasingly challenged with predicting the impact of climate and land-use change on wildlife. A common approach is to use habitat-suitability models (HSMs) to explain aspects of species' occurrence, such as presence, abundance, and distribution, utilizing physical habitat characteristics. Although HSMs are useful, they are limited because they are typically created using spatial rather than temporal data, which omits temporal dynamics. We explored the value of combining spatial and temporal approaches by comparing HSMs with autoregressive population models. We investigated a 28-year period of bird community dynamics at a field site in northern California during which time the plant community has been transitioning from scrub to conifer forest.We used the two model frameworks to quantify the contribution of vegetation change, weather, and population processes (autoregressive models only) to variation in density of seven bird species over the first 23 years. Model predictive ability was then tested using the subsequent five years of population density data. HSMs explained 58% to 90% of the deviance in species' density. However, models that included density dependence in addition to vegetation covariates provided a better fit to the data for three of the seven species, Song Sparrow (Melospiza melodia), White-crowned Sparrow (Zonotrichia leucophrys), andWrentit (Chamaea fasciata). These three species have more localized dispersal compared to the other four species, suggesting that dispersal tendency may be an important life-history trait to consider when predicting the impact of climate and land-use change on population levels. Our results suggest that HSMs can effectively explain and predict variation in species' densities through time, however for species with localized dispersal, it may be especially informative to include population processes. © 2014 Porzig et al.

Understanding factors influencing survival of Pacific salmonids (Oncorhynchus spp.) is essential to species conservation, because drivers of mortality can vary over multiple spatial and temporal scales. Although recent studies have evaluated the effects of climate, habitat quality, or resource management (e.g., hatchery operations) on salmonid recruitment and survival, a failure to look at multiple factors simultaneously leaves open questions about the relative importance of different factors. We analyzed the relationship between ten factors and survival (1980-2007) of four populations of salmonids with distinct life histories from two adjacent watersheds (Salmon and Scott rivers) in the Klamath River basin, California. The factors were ocean abundance, ocean harvest, hatchery releases, hatchery returns, Pacific Decadal Oscillation, North Pacific Gyre Oscillation, El Niño Southern Oscillation, snow depth, flow, and watershed disturbance. Permutation tests and linear mixed-effects models tested effects of factors on survival of each taxon. Potential factors affecting survival differed among taxa and between locations. Fall Chinook salmon O. tshawytscha survival trends appeared to be driven partially or entirely by hatchery practices. Trends in three taxa (Salmon River spring Chinook salmon, Scott River fall Chinook salmon; Salmon River summer steelhead trout O. mykiss) were also likely driven by factors subject to climatic forcing (ocean abundance, summer flow). Our findings underscore the importance of multiple factors in simultaneously driving population trends in widespread species such as anadromous salmonids. They also show that the suite of factors may differ among different taxa in the same location as well as among populations of the same taxa in different watersheds. In the Klamath basin, hatchery practices need to be reevaluated to protect wild salmonids.

In metapopulations in which habitat patches vary in quality and occupancy it can be complicated to calculate the net time-averaged contribution to reproduction of particular populations. Surprisingly, few indices have been proposed for this purpose. We combined occupancy, abundance, frequency of occurrence, and reproductive success to determine the net value of different sites through time and applied this method to a bird of conservation concern. The Tricolored Blackbird (Agelaius tricolor) has experienced large population declines, is the most colonial songbird in North America, is largely confined to California, and breeds itinerantly in multiple habitat types. It has had chronically low reproductive success in recent years. Although young produced per nest have previously been compared across habitats, no study has simultaneously considered site occupancy and reproductive success. Combining occupancy, abundance, frequency of occurrence, reproductive success and nest failure rate we found that that large colonies in grain fields fail frequently because of nest destruction due to harvest prior to fledging. Consequently, net time-averaged reproductive output is low compared to colonies in non-native Himalayan blackberry or thistles, and native stinging nettles. Cattail marshes have intermediate reproductive output, but their reproductive output might be improved by active management. Harvest of grain-field colonies necessitates either promoting delay of harvest or creating alternative, more secure nesting habitats. Stinging nettle and marsh colonies offer the main potential sources for restoration or native habitat creation. From 2005-2011 breeding site occupancy declined 3x faster than new breeding colonies were formed, indicating a rapid decline in occupancy. Total abundance showed a similar decline. Causes of variation in the value for reproduction of nesting substrates and factors behind continuing population declines merit urgent investigation. The method we employ should be useful in other metapopulation studies for calculating time-averaged reproductive output for different sites.

Population trends represent a minimum amount of information required to assess the conservation status of a species. However, understanding and detecting trends can be complicated by variation among habitats and regions, and by dispersal connecting habitats through source-sink dynamics. We analyzed trends in breeding populations between habitats and regions to better understand the overall dynamics of a species' decline. Specifically, we analyzed historical trends in breeding populations of tricolored blackbirds (Agelaius tricolor) using breeding records from 1907 to 2009. The species breeds itinerantly and ephemerally uses multiple habitat types and breeding areas, which make interpretation of trends complex. We found overall abundance declines of 63% between 1935 and 1975. Since 1980 overall declines became nonsignificant and obscure despite large amounts of data from 1980 to 2009. Temporal trends differed between breeding habitat types and were associated with regional differences in population declines. A new habitat, triticale crops (a wheat-rye hybrid grain) produced colonies 40× larger, on average, than other breeding habitats, and contributed to a change in regional distribution since it primarily occurred in a single region. The mechanism for such an effect is not clear, but could represent the local availability of foodstuffs in the landscape rather than something specific to triticale crops. While variation in trends among habitats clearly occurred, they could not easily be ascribed to source-sink dynamics, ecological traps, habitat selection or other detailed ecological mechanisms. Nonetheless, such exchanges provide valuable information to guide management of dynamic systems.

Amphibians with missing, misshapen, and extra limbs have garnered public and scientific attention for two decades, yet the extent of the phenomenon remains poorly understood. Despite progress in identifying the causes of abnormalities in some regions, a lack of knowledge about their broader spatial distribution and temporal dynamics has hindered efforts to understand their implications for amphibian population declines and environmental quality. To address this data gap, we conducted a nationwide, 10-year assessment of 62,947 amphibians on U.S. National Wildlife Refuges. Analysis of a core dataset of 48,081 individuals revealed that consistent with expected background frequencies, an average of 2% were abnormal, but abnormalities exhibited marked spatial variation with a maximum prevalence of 40%. Variance partitioning analysis demonstrated that factors associated with space (rather than species or year sampled) captured 97% of the variation in abnormalities, and the amount of partitioned variance decreased with increasing spatial scale (from site to refuge to region). Consistent with this, abnormalities occurred in local to regional hotspots, clustering at scales of tens to hundreds of kilometers. We detected such hotspot clusters of high-abnormality sites in the Mississippi River Valley, California, and Alaska. Abnormality frequency was more variable within than outside of hotspot clusters. This is consistent with dynamic phenomena such as disturbance or natural enemies (pathogens or predators), whereas similarity of abnormality frequencies at scales of tens to hundreds of kilometers suggests involvement of factors that are spatially consistent at a regional scale. Our characterization of the spatial and temporal variation inherent in continent-wide amphibian abnormalities demonstrates the disproportionate contribution of local factors in predicting hotspots, and the episodic nature of their occurrence.

Large-scale ecosystem restoration projects seldom undergo comprehensive evaluation to determine project effectiveness. Consequently, there are missed opportunities for learning and strategy refinement. Before our study, monitoring information from California’s middle Sacramento River had not been synthesized, despite restoration having been ongoing since 1989. Our assessment was based on the development and application of 36 quantitative ecological indicators. These indicators were used to characterize the status of terrestrial and floodplain resources (e.g., flora and fauna), channel dynamics (e.g., planform, geomorphology), and the flow regime. Indicators were also associated with specific goal statements of the CALFED Ecosystem Restoration Program. A collective weight of evidence approach was used to assess restoration success. Our synthesis demonstrates good progress in the restoration of riparian habitats, birds and other wildlife, but not in restoration of streamflows and geomorphic processes. For example, from 1999 to 2007, there was a > 600% increase in forest patch core size, and a 43% increase in the area of the river bordered by natural habitat > 500 m wide. Species richness of landbirds and beetles increased at restoration sites, as did detections of bats. However, degraded post-Shasta Dam streamflow conditions continued. Relative to pre-dam conditions, the average number of years that pass between flows that are sufficient to mobilize the bed, and those that are of sufficient magnitude to inundate the floodplain, increased by over 100%. Trends in geomorphic processes were strongly negative, with increases in the amount of bank hardened with riprap, and decreases in the area of floodplain reworked. Overall the channel simplified, becoming less sinuous with reduced overall channel length. Our progress assessment presents a compelling case for what needs to be done to further advance the ecological restoration of the river. The most important actions to be taken relate to promoting river meander and floodplain connectivity, and restoring components of the natural flow regime.

Spatial dynamic theories such as source-sink models frequently describe habitat-specific demographies, yet there are surprisingly few field studies that have examined how and why interacting species vary in their dynamics across multiple habitat types. We studied the spatial pattern of interaction between a chewing herbivore and its primary larval host plant in two habitat types. We found that the interaction between an arctiid caterpillar (Platyprepia virginalis) and its host (Lupinus arboreus) differed in wet vs. upland dry habitats, as did yearly population dynamics for the caterpillar. In upland sites, there was a strong positive relationship between lupine cover and the abundance of caterpillars although this relationship was not apparent in wet sites. Additionally, in wet sites, caterpillar populations were larger and less variable across years. Caterpillars appeared to exhibit source-sink dynamics, with the time-averaged finite growth rate lamda > 1 in wet sites (sources), lamda < 1 in upland dry sites (sinks), and predominant source-to-sink movement of late-instar caterpillars. Populations in upland dry sites also went locally extinct in years of low regional abundance. Emigration from wet sites could potentially explain the lack of coupling of herbivore and host plant dynamics in these sites. These results indicate that movement and other factors affecting demography are habitat-specific and have important implications for trophic control. Acknowledging such complexity makes simple models of trophic control seem overly general but may allow us to formulate more broadly applicable ecological models.

1. Ecologists have argued about the commonness and strength of interspecific competition between insect herbivores, but facilitation between herbivores has received much less consideration. We previously found that when two species of folivorous caterpillars co-occurred on a shared host plant, feeding by early season tiger moth caterpillars reduced the growth and reproduction of later season tussock caterpillars. However, densities of tussock caterpillars in summer were positively correlated with densities of tiger moth caterpillars the following spring. 2. In this study, we experimentally manipulated numbers of feeding tussock caterpillars and found that they facilitated tiger moth caterpillars. 3. The depth of the litter layer beneath host lupine bushes was positively correlated with the number of tussock caterpillars feeding on each bush. Experimental additions of litter beneath lupine canopies during summer resulted in increased numbers of tiger moth caterpillars in the following spring, indicating a causal role of litter. Litter potentially provides food, habitat and protection from desiccation and predation. We failed to find evidence that tussock caterpillars facilitated tiger moth caterpillars by mechanisms independent of litter. 4. Our study demonstrates that facilitation may operate between insect herbivores, across life-stages through indirect interactions that are non-trophic. Facilitation operated by a novel mechanism, the accumulation of litter which was a by-product of feeding by one species was valuable to a second species. Facilitation persisted in time and space far beyond the creation of litter by tussock caterpillars which should be considered important ecosystem engineers from the point of view of tiger moths. Facilitations that involve habitat modification may generally connect species that do not interact directly or trophically, and have not previously been considered to affect one another.

Metacommunity theory poses that the occurrence and abundance of species is a product of local factors, including disturbance, and regional factors, like dispersal among patches. While metacommunity ideas have been broadly tested there is relatively little work on metacommunities subject to disturbance. We focused on how localized disturbance and dispersal interact to determine species composition in metacommunities. Experiments conducted in simple two-patch habitats containing eight protozoa and rotifer species tested how dispersal altered community composition in both communities that were disturbed and communities that connected to refuge communities not subject to disturbance. While disturbance lowered population densities, in disturbed patches connected to undisturbed patches this was ameliorated by immigration. Furthermore, species with high dispersal abilities or growth rates showed the fastest post-disturbance recovery in presence of immigration. Connectivity helped to counteract the negative effect of disturbances on local populations, allowing mass-effect-driven dispersal of individuals from undisturbed to disturbed patches. In undisturbed patches, however, local population sizes were not significantly reduced by emigration. The absence of a cost of dispersal for undisturbed source populations is consistent with a lack of complex demography in our system, such as age- or sex-specific emigration. Our approach provides an improved way to separate components of population growth from organisms' movement in post-disturbance recovery of (meta)communities. Further studies are required in a variety of ecosystems to investigate the transient dynamics resulting from disturbance and dispersal.

Habitat mitigation frequently leads to planting of new habitat, assuming that it can replace lost natural habitat. Yet this practice has rarely been examined in detail. In the USA habitat mitigation is frequently allowed under the US Endangered Species Act, providing monitoring reports which represent a potentially valuable data source for imperiled species. We used publicly available reports for the US threatened Valley elderberry longhorn beetle (Desmocerus californicus dimorphus) to assess record keeping practices used by US Fish and Wildlife Service (FWS), and the utility of such analyses for improving conservation. A large portion of mitigation reports known to exist were missing from FWS files, indicating problems with data management, and a loss of important information. Transplanted brought mature beetle host plants and beetles to sites, promoting beetle colonization. Conversely, few sites with seedlings were colonized. Results indicate a need for improved data management by FWS and longer term monitoring.