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1.
  1. Decades of environmental DNA (eDNA) method application, spanning a wide variety of taxa and habitats, has advanced our understanding of eDNA and underlined its value as a tool for conservation practitioners. The general consensus is that eDNA methods are more accurate and cost‐effective than traditional survey methods. However, they are formally approved for just a few species globally (e.g., Bighead Carp, Silver Carp, Great Crested Newt). We conducted a meta‐analysis of studies that directly compare eDNA with traditional surveys to evaluate the assertion that eDNA methods are consistently “better.”
  2. Environmental DNA publications for multiple species or single macro‐organism detection were identified using the Web of Science, by searching “eDNA” and “environmental DNA” across papers published between 1970 and 2020. The methods used, focal taxa, habitats surveyed, and quantitative and categorical results were collated and analyzed to determine whether and under what circumstances eDNA outperforms traditional surveys.
  3. Results show that eDNA methods are cheaper, more sensitive, and detect more species than traditional methods. This is, however, taxa‐dependent, with amphibians having the highest potential for detection by eDNA survey. Perhaps most strikingly, of the 535 papers reviewed just 49 quantified the probability of detection for both eDNA and traditional survey methods and studies were three times more likely to give qualitative statements of performance.
  4. Synthesis and applications: The results of this meta‐analysis demonstrate that where there is a direct comparison, eDNA surveys of macro‐organisms are more accurate and efficient than traditional surveys. This conclusion, however, is based on just a fraction of available eDNA papers as most do not offer this granularity. We recommend that conclusions are substantiated with comparable and quantitative data. Where a direct comparison has not been made, we caution against the use of qualitative statements about relative performance. This consistency and rigor will simplify how the eDNA research community tracks methods‐based advances and will also provide greater clarity for conservation practitioners. To this end suggest reporting standards for eDNA studies.
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2.
  1. Mutual reinforcement between abiotic and biotic factors can drive small populations into a catastrophic downward spiral to extinction—a process known as the “extinction vortex.” However, empirical studies investigating extinction dynamics in relation to species'' traits have been lacking.
  2. We assembled a database of 35 vertebrate populations monitored to extirpation over a period of at least ten years, represented by 32 different species, including 25 birds, five mammals, and two reptiles. We supplemented these population time series with species‐specific mean adult body size to investigate whether this key intrinsic trait affects the dynamics of populations declining toward extinction.
  3. We performed three analyses to quantify the effects of adult body size on three characteristics of population dynamics: time to extinction, population growth rate, and residual variability in population growth rate.
  4. Our results provide support for the existence of extinction vortex dynamics in extirpated populations. We show that populations typically decline nonlinearly to extinction, while both the rate of population decline and variability in population growth rate increase as extinction is approached. Our results also suggest that smaller‐bodied species are particularly prone to the extinction vortex, with larger increases in rates of population decline and population growth rate variability when compared to larger‐bodied species.
  5. Our results reaffirm and extend our understanding of extinction dynamics in real‐life extirpated populations. In particular, we suggest that smaller‐bodied species may be at greater risk of rapid collapse to extinction than larger‐bodied species, and thus, management of smaller‐bodied species should focus on maintaining higher population abundances as a priority.
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3.
4.
  1. Many animal personality traits have implicit movement‐based definitions and can directly or indirectly influence ecological and evolutionary processes. It has therefore been proposed that animal movement studies could benefit from acknowledging and studying consistent interindividual differences (personality), and, conversely, animal personality studies could adopt a more quantitative representation of movement patterns.
  2. Using high‐resolution tracking data of three‐spined stickleback fish (Gasterosteus aculeatus), we examined the repeatability of four movement parameters commonly used in the analysis of discrete time series movement data (time stationary, step length, turning angle, burst frequency) and four behavioral parameters commonly used in animal personality studies (distance travelled, space use, time in free water, and time near objects).
  3. Fish showed repeatable interindividual differences in both movement and behavioral parameters when observed in a simple environment with two, three, or five shelters present. Moreover, individuals that spent less time stationary, took more direct paths, and less commonly burst travelled (movement parameters), were found to travel farther, explored more of the tank, and spent more time in open water (behavioral parameters).
  4. Our case study indicates that the two approaches—quantifying movement and behavioral parameters—are broadly equivalent, and we suggest that movement parameters can be viewed as “micropersonality” traits that give rise to broad‐scale consistent interindividual differences in behavior. This finding has implications for both personality and movement ecology research areas. For example, the study of movement parameters may provide a robust way to analyze individual personalities in species that are difficult or impossible to study using standardized behavioral assays.
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5.
  1. Spatial capture–recapture (SCR) models have increasingly been used as a basis for combining capture–recapture data types with variable levels of individual identity information to estimate population density and other demographic parameters. Recent examples are the unmarked SCR (or spatial count model), where no individual identities are available and spatial mark–resight (SMR) where individual identities are available for only a marked subset of the population. Currently lacking, though, is a model that allows unidentified samples to be combined with identified samples when there are no separate classes of “marked” and “unmarked” individuals and when the two sample types cannot be considered as arising from two independent observation models. This is a common scenario when using noninvasive sampling methods, for example, when analyzing data on identified and unidentified photographs or scats from the same sites.
  2. Here we describe a “random thinning” SCR model that utilizes encounters of both known and unknown identity samples using a natural mechanistic dependence between samples arising from a single observation model. Our model was fitted in a Bayesian framework using NIMBLE.
  3. We investigate the improvement in parameter estimates by including the unknown identity samples, which was notable (up to 79% more precise) in low‐density populations with a low rate of identified encounters. We then applied the random thinning SCR model to a noninvasive genetic sampling study of brown bear (Ursus arctos) density in Oriental Cantabrian Mountains (North Spain).
  4. Our model can improve density estimation for noninvasive sampling studies for low‐density populations with low rates of individual identification, by making use of available data that might otherwise be discarded.
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6.
  1. Hormones are extensively known to be physiological mediators of energy mobilization and allow animals to adjust behavioral performance in response to their environment, especially within a foraging context.
  2. Few studies, however, have narrowed focus toward the consistency of hormonal patterns and their impact on individual foraging behavior. Describing these relationships can further our understanding of how individuals cope with heterogeneous environments and exploit different ecological niches.
  3. To address this, we measured between‐ and within‐individual variation of basal cortisol (CORT), thyroid hormone T3, and testosterone (TEST) levels in wild adult female Galápagos sea lions (Zalophus wollebaeki) and analyzed how these hormones may be associated with foraging strategies. In this marine predator, females exhibit one of three spatially and temporally distinct foraging patterns (i.e., “benthic,” “pelagic,” and “night” divers) within diverse habitat types.
  4. Night divers differentiated from other strategies by having lower T3 levels. Considering metabolic costs, night divers may represent an energetically conservative strategy with shorter dive durations, depths, and descent rates to exploit prey which migrate up the water column based on vertical diel patterns.
  5. Intriguingly, CORT and TEST levels were highest in benthic divers, a strategy characterized by congregating around limited, shallow seafloors to specialize on confined yet reliable prey. This pattern may reflect hormone‐mediated behavioral responses to specific risks in these habitats, such as high competition with conspecifics, prey predictability, or greater risks of predation.
  6. Overall, our study highlights the collective effects of hormonal and ecological variation on marine foraging. In doing so, we provide insights into how mechanistic constraints and environmental pressures may facilitate individual specialization in adaptive behavior in wild populations.
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7.
8.
  1. Restoration ecology has historically focused on reconstructing communities of highly visible taxa while less visible taxa, such as invertebrates and microbes, are ignored. This is problematic as invertebrates and microbes make up the vast bulk of biodiversity and drive many key ecosystem processes, yet they are rarely actively reintroduced following restoration, potentially limiting ecosystem function and biodiversity in these areas.
  2. In this review, we discuss the current (limited) incorporation of invertebrates and microbes in restoration and rewilding projects. We argue that these groups should be actively rewilded during restoration to improve biodiversity, ecosystem function outcomes, and highlight how they can be used to greater effect in the future. For example, invertebrates and microbes are easily manipulated, meaning whole communities can potentially be rewilded through habitat transplants in a practice that we refer to as “whole‐of‐community” rewilding.
  3. We provide a framework for whole‐of‐community rewilding and describe empirical case studies as practical applications of this under‐researched restoration tool that land managers can use to improve restoration outcomes.
  4. We hope this new perspective on whole‐of‐community restoration will promote applied research into restoration that incorporates all biota, irrespective of size, while also enabling a better understanding of fundamental ecological theory, such as colonization and competition trade‐offs. This may be a necessary consideration as invertebrates that are important in providing ecosystem services are declining globally; targeting invertebrate communities during restoration may be crucial in stemming this decline.
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9.
  1. The early detection of invasive non‐native species (INNS) is important for informing management actions. Established monitoring methods require the collection or observation of specimens, which is unlikely at the beginning of an invasion when densities are likely to be low. Environmental DNA (eDNA) analysis is a highly promising technique for the detection of INNS—particularly during the early stages of an invasion.
  2. Here, we compared the use of traditional kick‐net sampling with two eDNA approaches (targeted detection using both conventional and quantitative PCR and passive detection via metabarcoding with conserved primers) for detection of quagga mussel, Dreissena rostriformis bugensis, a high priority INNS, along a density gradient on the River Wraysbury, UK.
  3. All three molecular tools outperformed traditional sampling in terms of detection. Conventional PCR and qPCR both had 100% detection rate in all samples and outperformed metabarcoding when the target species was at low densities. Additionally, quagga mussel DNA copy number (qPCR) and relative read count (metabarcoding) were significantly influenced by both mussel density and distance from source population, with distance being the most significant predictor.
  4. Synthesis and application. All three molecular approaches were more sensitive than traditional kick‐net sampling for the detection of the quagga mussel in flowing water, and both qPCR and metabarcoding enabled estimates of relative abundance. Targeted approaches were more sensitive than metabarcoding, but metabarcoding has the advantage of providing information on the wider community and consequently the impacts of INNS.
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10.
  1. We contrast the response of arthropod abundance and composition to bison grazing lawns during a drought and non‐drought year, with an emphasis on acridid grasshoppers, an important grassland herbivore.
  2. Grazing lawns are grassland areas where regular grazing by mammalian herbivores creates patches of short‐statured, high nutrient vegetation. Grazing lawns are predictable microsites that modify microclimate, plant structure, community composition, and nutrient availability, with likely repercussions for arthropod communities.
  3. One year of our study occurred during an extreme drought. Drought mimics some of the effects of mammalian grazers: decreasing above‐ground plant biomass while increasing plant foliar percentage nitrogen.
  4. We sampled arthropods and nutrient availability on and nearby (“off”) 10 bison‐grazed grazing lawns in a tallgrass prairie in NE Kansas. Total grasshopper abundance was higher on grazing lawns and the magnitude of this difference increased in the wetter year of 2019 compared to 2018, when drought led to high grass foliar nitrogen concentrations on and off grazing lawns. Mixed‐feeding grasshopper abundances were consistently higher on grazing lawns while grass‐feeder and forb‐feeder abundances were higher on lawns only in 2019, the wetter year. In contrast, the abundance of other arthropods (e.g., Hemiptera, Hymenoptera, and Araneae) did not differ on and off lawns, but increased overall in 2019, relative to the drought of 2018.
  5. Understanding these local scale patterns of abundances and community composition improves predictability of arthropod responses to ongoing habitat change.
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11.
12.
  1. Saltmarsh‐mangrove ecotones occur at the boundary of the natural geographic distribution of mangroves and salt marshes. Climate warming and species invasion can also drive the formation of saltmarsh‐mangrove mixing communities. How these coastal species live together in a “new” mixed community is important in predicting the dynamic of saltmarsh‐mangrove ecosystems as affected by ongoing climate change or human activities. To date, the understanding of species interactions has been rare on adult species in these ecotones.
  2. Two typical coastal wetlands were selected as cases to understand how mangrove and saltmarsh species living together in the ecotones. The leaves of seven species were sampled from these coastal wetlands based on their distribution patterns (living alone or coexisting) in the high tidal zone, and seven commonly used functional traits of these species were analyzed.
  3. We found niche separation between saltmarsh and mangrove species, which is probably due to the different adaptive strategies they adopted to deal with intertidal environments.
  4. Weak interactions between coexisting species were dominated in the high tidal zone of the two saltmarsh‐mangrove communities, which could be driven by both niche differentiation and neutral theory.
  5. Synthesis. Our field study implies a potential opportunity to establish a multispecies community in the high tidal zone of saltmarsh‐mangrove ecotones, where the sediment was characterized by low salinity and high nitrogen.
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13.
  1. We investigated some aspects of hawkmoth community assembly at 13 elevations along a 200‐ to 2770‐m transect in the eastern Himalayas, a little studied biodiversity hot spot of global importance. We measured the morphological traits of body mass, wing loading, and wing aspect ratio of 3,301 free‐ranging individuals of 76 species without having to collect or even constrain them. We used these trait measurements and T‐statistic metrics to assess the strength of intracommunity (“internal") and extra‐community (“external”) filters which determine the composition of communities vis‐a‐vis the regional pool of species.
  2. The trait distribution of constituent species turned out to be nonrandom subsets of the community‐trait distribution, providing strong evidence for internal filtering in all elevational communities. The external filter metric was more ambiguous. However, the elevational dependence of many metrics including that of the internal filter provided evidence for external (i.e., environmental) filtering. On average, a species occupied as much as 50%–75% of the total community‐trait space, yet the T‐statistic metric for internal filter was sufficiently sensitive to detect a strong nonrandom structure in the trait distribution.
  3. We suggest that the change in T‐statistic metrics along the environmental gradient may provide more clues to the process of community assembly than previously envisaged. A large, smoothly varying and well‐sampled environmental span would make it easier to discern them. Developing T‐statistics for combined analysis of multiple traits will perhaps provide a more accurate picture of internal/filtering and niche complementarity. Moths are a hyperdiverse taxon and a very important component of many ecosystems. Our technique for accurately measuring body and wing dimensions of free‐ranging moths can generate trait database for a large number of individuals in a time‐ and resource‐efficient manner for a variety of community assembly studies using this important taxon.
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14.
  1. Biodiversity in freshwater habitats is decreasing faster than in any other type of environment, mostly as a result of human activities. Monitoring these losses can help guide mitigation efforts. In most studies, sampling strategies predominantly rely on collecting animal and vegetal specimens. Although these techniques produce valuable data, they are invasive, time-consuming and typically permit only limited spatial and temporal replication. There is need for the development of complementary methods.
  2. As observed in other ecosystems, freshwater environments host animals that emit sounds, either to communicate or as a by-product of their activity. The main freshwater soniferous groups are amphibians, fish, and macroinvertebrates (mainly Coleoptera and Hemiptera, but also some Decapoda, Odonata, and Trichoptera). Biophysical processes such as flow or sediment transport also produce sounds, as well as human activities within aquatic ecosystems.
  3. Such animals and processes can be recorded, remotely and autonomously, and provide information on local diversity and ecosystem health. Passive acoustic monitoring (PAM) is an emerging method already deployed in terrestrial environments that uses sounds to survey environments. Key advantages of PAM are its non-invasive nature, as well as its ability to record autonomously and over long timescales. All these research topics are the main aims of ecoacoustics, a new scientific discipline investigating the ecological role of sounds.
  4. In this paper, we review the sources of sounds present in freshwater environments. We then underline areas of research in which PAM may be helpful emphasising the role of PAM for the development of ecoacoustics. Finally, we present methods used to record and analyse sounds in those environments.
  5. Passive acoustics represents a potentially revolutionary development in freshwater ecology, enabling continuous monitoring of dynamic bio-physical processes to inform conservation practitioners and managers.
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15.
  1. Caves and other subterranean habitats fulfill the requirements of experimental model systems to address general questions in ecology and evolution. Yet, the harsh working conditions of these environments and the uniqueness of the subterranean organisms have challenged most attempts to pursuit standardized research.
  2. Two main obstacles have synergistically hampered previous attempts. First, there is a habitat impediment related to the objective difficulties of exploring subterranean habitats and our inability to access the network of fissures that represents the elective habitat for the so‐called “cave species.” Second, there is a biological impediment illustrated by the rarity of most subterranean species and their low physiological tolerance, often limiting sample size and complicating laboratory experiments.
  3. We explore the advantages and disadvantages of four general experimental setups (in situ, quasi in situ, ex situ, and in silico) in the light of habitat and biological impediments. We also discuss the potential of indirect approaches to research. Furthermore, using bibliometric data, we provide a quantitative overview of the model organisms that scientists have exploited in the study of subterranean life.
  4. Our over‐arching goal is to promote caves as model systems where one can perform standardized scientific research. This is important not only to achieve an in‐depth understanding of the functioning of subterranean ecosystems but also to fully exploit their long‐discussed potential in addressing general scientific questions with implications beyond the boundaries of this discipline.
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16.
  1. Animal movement studies are conducted to monitor ecosystem health, understand ecological dynamics, and address management and conservation questions. In marine environments, traditional sampling and monitoring methods to measure animal movement are invasive, labor intensive, costly, and limited in the number of individuals that can be feasibly tracked. Automated detection and tracking of small‐scale movements of many animals through cameras are possible but are largely untested in field conditions, hampering applications to ecological questions.
  2. Here, we aimed to test the ability of an automated object detection and object tracking pipeline to track small‐scale movement of many individuals in videos. We applied the pipeline to track fish movement in the field and characterize movement behavior. We automated the detection of a common fisheries species (yellowfin bream, Acanthopagrus australis) along a known movement passageway from underwater videos. We then tracked fish movement with three types of tracking algorithms (MOSSE, Seq‐NMS, and SiamMask) and evaluated their accuracy at characterizing movement.
  3. We successfully detected yellowfin bream in a multispecies assemblage (F1 score =91%). At least 120 of the 169 individual bream present in videos were correctly identified and tracked. The accuracies among the three tracking architectures varied, with MOSSE and SiamMask achieving an accuracy of 78% and Seq‐NMS 84%.
  4. By employing this integrated object detection and tracking pipeline, we demonstrated a noninvasive and reliable approach to studying fish behavior by tracking their movement under field conditions. These cost‐effective technologies provide a means for future studies to scale‐up the analysis of movement across many visual monitoring systems.
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17.
  1. A central theme for conservation is understanding how animals differentially use, and are affected by change in, the landscapes they inhabit. However, it has been challenging to develop conservation schemes for habitat‐specific behaviors.
  2. Here we use behavioral change point analysis to identify behavioral states of golden eagles (Aquila chrysaetos) in the Sonoran and Mojave Deserts of the southwestern United States, and we identify, for each behavioral state, conservation‐relevant habitat associations.
  3. We modeled behavior using 186,859 GPS points from 48 eagles and identified 2,851 distinct segments comprising four behavioral states. Altitude above ground level (AGL) best differentiated behavioral states, with two clusters of short‐distance movement behaviors characterized by low AGL (state 1 AGL = 14 m (median); state 2 AGL = 11 m) and two associated with longer‐distance movement behaviors and characterized by higher AGL (state 3 AGL = 108 m; state 4 AGL = 450 m).
  4. Behaviors such as perching and low‐altitude hunting were associated with short‐distance movements in updraft‐poor environments, at higher elevations, and over steeper and more north‐facing terrain. In contrast, medium‐distance movements such as hunting and transiting were over gentle and south‐facing slopes. Long‐distance transiting occurred over the desert habitats that generate the best updraft.
  5. This information can guide management of this species, and our approach provides a template for behavior‐specific habitat associations for other species of management concern.
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18.
  1. Current understanding on the exposure of freshwater organisms to microplastics (plastics sized between 1 µm and 5 mm) has arisen mostly from laboratory experiments—often conducted under artificial circumstances and with unrealistic concentrations. In order to improve scientific links through real ecosystem exposure, we review field data on the exposure of free‐living organisms to microplastics.
  2. We highlight that the main outputs provided by field research are an assessment of the occurrence and, at times, the quantification of microplastics in different animal taxa. Topics of investigation also include the causes of contamination and the development of biological monitoring tools. With regard to taxa, fish, mollusks, and arthropods are at the center of the research, but birds and amphibians are also investigated. The ingestion or occurrence of microplastics in organs and tissues, such as livers and muscles, are the main data obtained. Microorganisms are studied differently than other taxa, highlighting interesting aspects on the freshwater plastisphere, for example, related to the structure and functionality of communities. Many taxa, that is, mammals, reptiles, and plants, are still under‐examined with regard to exposure to microplastics; this is surprising as they are generally endangered.
  3. As biota contamination is acknowledged, we contribute to an interdisciplinary scientific discussion aimed at a better assessment of knowledge gaps on methodology, impact assessment, and monitoring.
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19.
  1. Anthropogenic climate change is altering every ecosystem on Earth. Understanding these changes requires quality baseline measurements of ecosystem states. While satellite imagery provides a coarse baseline for regional‐scale changes in vegetation, landscape‐scale observations are lacking. Ground‐based repeat photographic points (RPP) can provide this finer baseline. As precise visual records of ecosystems at a particular time, RPP provide rich data for diverse uses. Current methodology for establishing RPP, developed in the era of film cameras, requires placement of permanent markers in a landscape to provide accurate repeats over time. Another form of RPP involves relocating sites of historic photographs, to assess change between historic and present‐day photographs. Through a three‐year field survey, we synthesized these techniques to modernize repeat photography for the 21st century ecologist.
  2. We established 100 RPP in the Peloncillo Mountains of New Mexico, recapturing 86 RPP in the three years (2015–2017) of the study. During our study, a large (>16,000 ha) complex of wildfires burned more than half of the RPP sites we established in the prior month, providing a unique opportunity to assess method accuracy after dramatic landscape disturbance by comparing burned, unburned, pre‐, and post‐fire RPP image recapture precision.
  3. Our method produced 92% mean similarity for 86 RPP between original and repeated photographs, with no difference between burned and unburned sites. Interval between photographs did not cause a decline in similarity.
  4. Our updated methods can be practically applied to nearly all terrestrial study systems. Landscape changes driven by human (e.g., effects of anthropogenic climate change, land use) and natural activities (e.g., wildfires, phenology, and hydrologic events) are especially well suited to our updated methods. Modern smartphones include the technology necessary (e.g., camera, GPS, and compass) to employ our method and provide a means for low‐cost deployment of the technique in diverse landscapes. We encourage broad adoption of this technique to establish baseline RPP of ecosystems across the globe, and the formation of a centralized database for repeat photography.
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20.
  1. Community scientists have illustrated rapid declines of several aphidophagous lady beetle (Coccinellidae) species. These declines coincide with the establishment of alien coccinellids. We established the Buckeye Lady Beetle Blitz program to measure the seasonal occupancy of coccinellids within gardens across a wide range of landscape contexts. Following the Habitat Compression Hypothesis, we predicted that gardens within agricultural landscapes would be alien‐dominated, whereas captures of natives would be higher within landscapes encompassing a high concentration of natural habitat.
  2. Within the state of Ohio, USA, community scientists collected lady beetles for a 7‐day period across 4 years in June and August using yellow sticky card traps. All identifications were verified by professional scientists and beetles were classified by three traits: status (alien or native), mean body length, and primary diet. We compared the relative abundance and diversity of coccinellids seasonally and determined if the distribution of beetles by size, status, and diet was related to landscape features.
  3. Alien species dominated the aphidophagous fauna. Native aphidophagous coccinellid abundance was positively correlated with forest habitat while alien species were more common when gardens were embedded within agricultural landscapes. Urbanization was negatively associated with both aphidophagous alien and native coccinellids.
  4. Synthesis and Applications: Our census of native coccinellid species within residential gardens—a widespread and understudied habitat—was enabled by volunteers. These data will serve as an important baseline to track future changes within coccinellid communities within this region. We found that native coccinellid species richness and native aphidophagous coccinellid abundance in gardens were positively associated with forest habitat at a landscape scale of 2 km. However, our understanding of when and why (overwintering, summer foraging, or both) forest habitats are important remains unclear. Our findings highlight the need to understand how declining aphidophagous native species utilize forest habitats as a conservation priority.
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