Individual identification in acoustic recordings.

Recent advances in bioacoustics combined with acoustic individual identification (AIID) could open frontiers for ecological and evolutionary research because traditional methods of identifying individuals are invasive, expensive, labor-intensive, and potentially biased. Despite overwhelming evidence that most taxa have individual acoustic signatures, the application of AIID remains challenging and uncommon. Furthermore, the methods most commonly used for AIID are not compatible with many potential AIID applications. Deep learning in adjacent disciplines suggests opportunities to advance AIID, but such progress is limited by training data. We suggest that broadscale implementation of AIID is achievable, but researchers should prioritize methods that maximize the potential applications of AIID, and develop case studies with easy taxa at smaller spatiotemporal scales before progressing to more difficult scenarios.

Audio tagging of avian dawn chorus recordings in California, Oregon and Washington.

Background: Declines in biodiversity and ecosystem health due to climate change are raising urgent concerns. In response, large-scale multispecies monitoring programmes are being implemented that increasingly adopt sensor-based approaches such as acoustic recording. These approaches rely heavily on ecological data science. However, developing reliable algorithms for processing sensor-based data relies heavily on labelled datasets of sufficient quality and quantity. We present a dataset of 1,575 dawn chorus soundscape recordings, 141 being fully annotated (n = 32,994 annotations) with avian, mammalian and amphibian vocalisations. The remaining recordings were included to facilitate novel research applications. These recordings are paired with 48 site-level climatic, forest structure and topographic covariates. This dataset provides a valuable resource to researchers developing acoustic classification algorithms or studying biodiversity and wildlife behaviour and its relationship to environmental gradients. The dawn chorus recordings were collected as part of a long-term Northern Spotted Owl monitoring program; this demonstrates the complementary value of harnessing existing monitoring efforts to strengthen biodiversity sampling. New information: This dataset of dawn chorus soundscape recordings is one of the few open-access acoustic datasets annotated with non-biotic and both interspecific (across species) and intraspecific (within species) bird, mammal and amphibian sonotypes and the first that is paired with climatic, forest structure and topographical covariates extracted at recorder locations. This makes it a valuable resource for researchers studying the dawn chorus and its relationship to the environment.

Combining environmental DNA and remote sensing for efficient, fine-scale mapping of arthropod biodiversity.

Arthropods contribute importantly to ecosystem functioning but remain understudied. This undermines the validity of conservation decisions. Modern methods are now making arthropods easier to study, since arthropods can be mass-trapped, mass-identified, and semi-mass-quantified into 'many-row (observation), many-column (species)' datasets, with homogeneous error, high resolution, and copious environmental-covariate information. These 'novel community datasets' let us efficiently generate information on arthropod species distributions, conservation values, uncertainty, and the magnitude and direction of human impacts. We use a DNA-based method (barcode mapping) to produce an arthropod-community dataset from 121 Malaise-trap samples, and combine it with 29 remote-imagery layers using a deep neural net in a joint species distribution model. With this approach, we generate distribution maps for 76 arthropod species across a 225 km2 temperate-zone forested landscape. We combine the maps to visualize the fine-scale spatial distributions of species richness, community composition, and site irreplaceability. Old-growth forests show distinct community composition and higher species richness, and stream courses have the highest site-irreplaceability values. With this 'sideways biodiversity modelling' method, we demonstrate the feasibility of biodiversity mapping at sufficient spatial resolution to inform local management choices, while also being efficient enough to scale up to thousands of square kilometres. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

Range-wide sources of variation in reproductive rates of northern spotted owls.

We conducted a range-wide investigation of the dynamics of site-level reproductive rate of northern spotted owls using survey data from 11 study areas across the subspecies geographic range collected during 1993-2018. Our analytical approach accounted for imperfect detection of owl pairs and misclassification of successful reproduction (i.e., at least one young fledged) and contributed further insights into northern spotted owl population ecology and dynamics. Both nondetection and state misclassification were important, especially because factors affecting these sources of error also affected focal ecological parameters. Annual probabilities of site occupancy were greatest at sites with successful reproduction in the previous year and lowest for sites not occupied by a pair in the previous year. Site-specific occupancy transition probabilities declined over time and were negatively affected by barred owl presence. Overall, the site-specific probability of successful reproduction showed substantial year-to-year fluctuations and was similar for occupied sites that did or did not experience successful reproduction the previous year. Site-specific probabilities for successful reproduction were very small for sites that were unoccupied the previous year. Barred owl presence negatively affected the probability of successful reproduction by northern spotted owls in Washington and California, as predicted, but the effect in Oregon was mixed. The proportions of sites occupied by northern spotted owl pairs showed steep, near-monotonic declines over the study period, with all study areas showing the lowest observed levels of occupancy to date. If trends continue it is likely that northern spotted owls will become extirpated throughout large portions of their range in the coming decades.

Asymmetrical intraguild interactions with coyotes, red foxes, and domestic dogs may contribute to competitive exclusion of declining gray foxes.

Species coexistence is governed by availability of resources and intraguild interactions including strategies to reduce ecological overlap. Gray foxes are dietary generalist mesopredators expected to benefit from anthropogenic disturbance, but populations have declined across the midwestern USA, including severe local extirpation rates coinciding with high coyote and domestic dog occurrence and low red fox occurrence. We used data from a large-scale camera trap survey in southern Illinois, USA to quantify intraguild spatial and temporal interactions among the canid guild including domestic dogs. We used a two-species co-occurrence model to make pairwise assessments of conditional occupancy and detection rates. We also estimated temporal activity overlap among species and fit a fixed-effects hierarchical community occupancy model with the four canid species. We partitioned the posterior distributions to compare gray fox occupancy probabilities conditional on estimated state of combinations of other species to assess support for hypothesized interactions. We found no evidence of broadscale avoidance among native canids and conclude that spatial and temporal segregation were limited by ubiquitous human disturbance. Mean guild richness was two canid species at a site and gray fox occupancy was greater when any combination of sympatric canids was also present, setting the stage for competitive exclusion over time. Domestic dogs may amplify competitive interactions by increasing canid guild size to the detriment of gray foxes. Our results suggest that while human activities can benefit some mesopredators, other species such as gray foxes may serve as bellwethers for habitat degradation with trophic downgrading and continued anthropogenic homogenization.

Emigration effects on estimates of age- and sex-specific survival of two sciurids.

Age- and sex-specific survival estimates are crucial to understanding important life history characteristics, and variation in these estimates can be a key driver of population dynamics. When estimating survival using Cormack-Jolly-Seber (CJS) models, emigration is typically unknown but confounded with apparent survival. Consequently, especially for populations or age classes with high dispersal rates, apparent survival estimates are often biased low and temporal patterns in survival might be masked when site fidelity varies temporally. We used 9 years of annual mark-recapture data to estimate age-, sex-, and time-specific apparent survival of Humboldt's flying squirrels (Glaucomys oregonensis) and Townsend's chipmunks (Neotamias townsendii). For Humboldt's flying squirrels, these estimates support a small body of research investigating potential variation in survival among age and sex classes, but age- and sex-specific survival has not been evaluated for Townsend's chipmunks. We also quantified the effects of age- and sex-specific emigration on confounded estimates of apparent survival. Our estimates of juvenile flying squirrel survival were high relative to other small mammal species and estimates for both species were variable among years. We found survival differed moderately among age and sex classes for Humboldt's flying squirrels, but little among age and sex classes for Townsend's chipmunks, and that the degree to which emigration confounded apparent survival estimates varied substantially among years. Our results demonstrate that emigration can influence commonly used estimates of apparent survival. Unadjusted estimates confounded the interpretation of differences in survival between age and sex classes and masked potential temporal patterns in survival because the magnitude of adjustment varied among years. We conclude that apparent survival estimators are robust during some time periods; however, when emigration rates vary in time, the effects of emigration should be carefully considered and accounted for.

Conspecific and congeneric interactions shape increasing rates of breeding dispersal of northern spotted owls.

Breeding dispersal, the movement from one breeding territory to another, is rare for philopatric species that evolved within relatively stable environments, such as the old-growth coniferous forests of the Pacific Northwest. Although dispersal is not inherently maladaptive, the consequences of increased dispersal on population dynamics in populations whose historical dispersal rates are low could be significant, particularly for a declining species. We examined rates and possible causes of breeding dispersal based on a sample of 4,118 northern spotted owls (Strix occidentalis caurina) monitored in seven study areas over 28 yr, 1990-2017, in Oregon and Washington, USA. Using a multistate mark-resight analysis, we investigated the potential impacts of an emergent congeneric competitor (barred owl Strix varia) and forest alteration (extrinsic factors), and social and individual conditions (intrinsic factors) on 408 successive and 1,372 nonsuccessive dispersal events between years. The annual probability of breeding dispersal increased for individual owls that had also dispersed in the previous year and decreased for owls on territories with historically high levels of reproduction. Intrinsic factors including pair status, prior reproductive success, and experience at a site, were also associated with breeding dispersal movements. The percent of monitored owls dispersing each year increased from ˜7% early in the study to ˜25% at the end of the study, which coincided with a rapid increase in numbers of invasive and competitively dominant barred owls. We suggest that the results presented here can inform spotted owl conservation efforts as we identify factors contributing to changing rates of demographic parameters including site fidelity and breeding dispersal. Our study further shows that increasing rates of breeding dispersal associated with population declines contribute to population instability and vulnerability of northern spotted owls to extinction, and the prognosis is unlikely to change unless active management interventions are undertaken.

Invader removal triggers competitive release in a threatened avian predator.

Changes in the distribution and abundance of invasive species can have far-reaching ecological consequences. Programs to control invaders are common but gauging the effectiveness of such programs using carefully controlled, large-scale field experiments is rare, especially at higher trophic levels. Experimental manipulations coupled with long-term demographic monitoring can reveal the mechanistic underpinnings of interspecific competition among apex predators and suggest mitigation options for invasive species. We used a large-scale before-after control-impact removal experiment to investigate the effects of an invasive competitor, the barred owl (Strix varia), on the population dynamics of an iconic old-forest native species, the northern spotted owl (Strix occidentalis caurina). Removal of barred owls had a strong, positive effect on survival of sympatric spotted owls and a weaker but positive effect on spotted owl dispersal and recruitment. After removals, the estimated mean annual rate of population change for spotted owls stabilized in areas with removals (0.2% decline per year), but continued to decline sharply in areas without removals (12.1% decline per year). The results demonstrated that the most substantial changes in population dynamics of northern spotted owls over the past two decades were associated with the invasion, population expansion, and subsequent removal of barred owls. Our study provides experimental evidence of the demographic consequences of competitive release, where a threatened avian predator was freed from restrictions imposed on its population dynamics with the removal of a competitively dominant invasive species.

Mesocarnivore landscape use along a gradient of urban, rural, and forest cover.

Mesocarnivores fill a vital role in ecosystems through effects on community health and structure. Anthropogenic-altered landscapes can benefit some species and adversely affect others. For some carnivores, prey availability increases with urbanization, but landscape use can be complicated by interactions among carnivores as well as differing human tolerance of some species. We used camera traps to survey along a gradient of urban, rural, and forest cover to quantify how carnivore landscape use varies among guild members and determine if a species was a human exploiter, adapter, or avoider. Our study was conducted in and around Corvallis, Oregon from April 2018 to February 2019 (11,914 trap nights) using 47 camera trap locations on a gradient from urban to rural. Our focal species were bobcat (Lynx rufus), coyote (Canis latrans), gray fox (Urocyon cinereoargenteus), opossum (Didelphis virginiana), raccoon (Procyon lotor), and striped skunk (Mephitis mephitis). Raccoon and opossum were human exploiters with low use of forest cover and positive association with urban and rural developed areas likely due to human-derived resources as well as some refugia from larger predators. Coyote and gray fox were human adapters with high use of natural habitats while the effects of urbanization ranged from weak to indiscernible. Bobcat and striped skunk appeared to be human avoiders with negative relationship with urban cover and higher landscape use of forest cover. We conducted a diel temporal activity analysis and found mostly nocturnal activity within the guild, but more diurnal activity by larger-bodied predators compared to the smaller species. Although these species coexist as a community in human-dominated landscapes throughout much of North America, the effects of urbanization were not equal across species. Our results, especially for gray fox and striped skunk, are counter to research in other regions, suggesting that mesopredator use of urbanized landscapes can vary depending on the environmental conditions of the study area and management actions are likely to be most effective when decisions are based on locally derived data.

Predator-prey interactions in the canopy.

Small mammal abundances are frequently limited by resource availability, but predators can exert strong lethal (mortality) and nonlethal (e.g., nest abandonment) limitations. Artificially increasing resource availability for uncommon small mammals provides a unique opportunity to examine predator-prey interactions. We used remote cameras to monitor 168 nest platforms placed in the live tree canopy (n = 23 young forest stands), primarily for arboreal red tree voles (tree voles; Arborimus longicaudus), over 3 years (n = 15,510 monitoring-weeks). Tree voles frequently built nests and were detected 37% of monitoring-weeks, whereas flying squirrels (Glaucomys oregonensis) built nests infrequently but were detected 45% of monitoring-weeks. Most nest predators were detected infrequently (<1% of monitoring-weeks) and were positively correlated with tree vole presence. Weasels (Mustela spp.) were highly effective predators of tree voles (n = 8 mortalities; 10% of detections) compared to owls (n = 1), flying squirrels (n = 2), and Steller's jays (n = 1). Tree vole activity decreased from 84.1 (95% confidence interval [CI]: 56.2, 111.9) detections/week 1-week prior to a weasel detection to 4.7 detections/week (95% CI: 1.7, 7.8) 1-week postdetection and remained low for at least 12 weeks. Interpretations of predator-prey interactions were highly sensitive to how we binned continuously collected data and model results from our finest bin width were biologically counter-intuitive. Average annual survival of female tree voles was consistent with a previous study (0.14; 95% CI: -0.04 [0.01], 0.32) and high compared to many terrestrial voles. The relative infrequency of weasel detections and inefficiency of other predators did not provide strong support for the hypothesis that predation per se limited populations. Rather, predation pressure, by reducing occupancy of already scarce nest sites through mortality and nest abandonment, may contribute to long-term local instability of tree vole populations in young forests. Additional monitoring would be needed to assess this hypothesis.

Effects of trapping effort and trap placement on estimating abundance of Humboldt's flying squirrels.

Live trapping is a common tool used to assess demography of small mammals. However, live-trapping is often expensive and stressful to captured individuals. Thus, assessing the relative tradeoffs among study goals, project expenses, and animal well-being is necessary. Here, we evaluated how apparent bias and precision of estimates for apparent annual survival, abundance, capture probability, and recapture probability of Humboldt's flying squirrels (Glaucomys oregonensis) varied with the number of secondary trapping occasions. We used data from forested sites trapped on 12 consecutive occasions annually in the HJ Andrews Experimental Forest (9 sites, 6 years) and the Siuslaw National Forest (seven sites, three years) in Oregon. We used Huggins robust design models to estimate parameters of interest for the first 4, 8, and 12 trapping occasions. We also estimated the effect of attaching Tomahawk traps to tree boles on site- and year-specific flying squirrel capture frequencies. Our estimates with 12 occasions were similar to those from previous studies. Abundances and capture probabilities were variable among years on both sites; however, variation was much lower on the Siuslaw sites. Reducing the length of primary trapping occasions from 12 to 8 nights had very little impact on parameter estimates, but further reducing the length of primary trapping occasions to four nights caused substantial apparent bias in parameter estimates and decreased precision. We found that attaching Tomahawk traps to tree boles increased the site- and year-specific capture frequency of flying squirrels. Our results suggest that live-trapping studies targeting Humboldt's flying squirrels in the Pacific Northwest of the United States could reduce per-site costs and stress to captured individuals without biasing estimates by reducing the length of primary trapping occasions to 8 nights. We encourage similar analyses for other commonly-trapped species in these and other ecosystems.

Three-dimensional partitioning of resources by congeneric forest predators with recent sympatry.

Coexistence of ecologically similar species can be maintained by partitioning along one or more niche axes. Three-dimensional structural complexity is central to facilitating resource partitioning between many forest species, but is underrepresented in field-based studies. We examined resource selection by sympatric northern spotted owls (Strix occidentalis caurina), a threatened species under the US Endangered Species Act, and nonnative barred owls (S. varia) in western Oregon, USA to explore the relative importance of canopy heterogeneity, vertical complexity of forest, and abiotic features to resource selection and identify potential differences that may facilitate long-term coexistence. We predicted that within home range selection of understory densities, measured with airborne lidar, would differ between species based on proportional differences in arboreal and terrestrial prey taken by each owl species. We used discrete choice models and telemetry data from 41 spotted owls and 38 barred owls monitored during 2007-2009 and 2012-2015. Our results suggested that while both species used tall canopy areas more often than low canopy areas, spotted owls were more commonly found in areas with lower tree cover, more developed understory, and steeper slopes. This is the first evidence of fine-scale partitioning based on structural forest properties by northern spotted owls and barred owls.

Nest trees of northern spotted owls (Strix occidentalis caurina) in Washington and Oregon, USA.

The northern spotted owl (Strix occidentalis caurina) is a federally-threatened subspecies in the United States associated with late-successional forests. In mesic forests it nests primarily in tree cavities, but also uses various types of external platform nests in drier forests. We describe 1717 northern spotted owl nests in 16 different tree species in five study areas in Washington and Oregon in the Pacific Northwest, USA. The vast majority of nests (87%) were in Douglas-fir (Pseudotsuga menziesii) trees, except on the Olympic Peninsula, Washington, where nests were about equally abundant in Douglas-fir, western red cedar (Thuja plicata), and western hemlock (Tsuga heterophylla) trees. Distribution of nests was 57.9% in top cavities of trees with broken tops, 20.3% in side cavities of hollow tree trunks, and 21.8% on external platforms of trees. Platforms were most common in the two driest study areas in the Eastern Cascades Physiographic Province, Washington (89% of nests), and the Klamath Province, Oregon (32%). The vast majority (89%) of nests were in trees with intact or declining crowns. Nests in dead trees were most common on the Olympic Peninsula. Nest trees with top and side cavities were larger and much more prevalent in study areas where annual precipitation was highest (Olympic Peninsula, Oregon Coast Range). Large nest cavities and platforms used by northern spotted owls occur almost exclusively in old forest. Managing for the retention of such forests and for their replacement is a significant challenge for land managers, especially in the face of climate change and an increasing human population, but will likely be required for the persistence of viable populations of northern spotted owls.

Differential Habitat Use or Intraguild Interactions: What Structures a Carnivore Community?

Differential habitat use and intraguild competition are both thought to be important drivers of animal population sizes and distributions. Habitat associations for individual species are well-established, and interactions between particular pairs of species have been highlighted in many focal studies. However, community-wide assessments of the relative strengths of these two factors have not been conducted. We built multi-scale habitat occupancy models for five carnivore taxa of New York's Adirondack landscape and assessed the relative performance of these models against ones in which co-occurrences of potentially competing carnivore species were also incorporated. Distribution models based on habitat performed well for all species. Black bear (Ursus americanus) and fisher (Martes pennanti) distribution was similar in that occupancy of both species was negatively associated with paved roads. However, black bears were also associated with larger forest fragments and fishers with smaller forest fragments. No models with habitat features were more supported than the null habitat model for raccoons (Procyon lotor). Martens (Martes americana) were most associated with increased terrain ruggedness and elevation. Weasel (Mustela spp.) occupancy increased with the cover of deciduous forest. For most species dyads habitat-only models were more supported than those models with potential competitors incorporated. The exception to this finding was for the smallest carnivore taxa (marten and weasel) where habitat plus coyote abundance models typically performed better than habitat-only models. Assessing this carnivore community as whole, we conclude that differential habitat use is more important than species interactions in maintaining the distribution and structure of this carnivore guild.

A survey of parasites identified in the feces of eastern spotted skunks (Spilogale putorius) in western Arkansas.

The endoparasite community of the eastern spotted skunk (Spilogale putorius) is poorly known. We surveyed parasites found in the feces of 29 eastern spotted skunks captured between March 2005 and January 2007 from a population in west-central Arkansas as part of a broader study of the ecology of the species. We identified 13 species (nine nematodes, four protozoa) from 82 fecal samples. Mean (+/-SD) number of species per individual skunk was 4.1+/-2.1, although this is likely an underestimate because some individuals were sampled more intensively than others. Most of the identified parasite species were also found in other skunk species or in other small carnivore species.