Forecasting species’ responses to long-term trends of ecosystem degradation is paramount in shifting disturbance regimes, especially for forest-associated species undergoing steep, range-wide population declines. Large-scale passive acoustic monitoring (PAM) networks provide an unprecedented opportunity to predict how such species may respond to environmental and management pressures through time and over broad spatial scales. Using detections from an extensive PAM network spanning over 4,000 autonomous recording units, we predict the distribution and drivers of habitat use for the varied thrush (Ixoreus naevius), a widespread but declining temperate forest-interior songbird species. We employ boosted regression trees to create fine-scale, range-wide distribution maps of the varied thrush under current and future climate and habitat conditions, providing a strong test case for evaluating how acoustic data, particularly from bycatch recordings, can forecast shifts in habitat suitability. Despite incidental data collection, we detected 5.6 million apparent instances of the varied thrush and manually validated presence at 2,595 automated recording units, with our final model achieving high predictive performance with low deviance (AUC = 0.92). Climatic water deficit emerged as the strongest predictor of occurrence, underscoring the species’ vulnerability to warming and drying conditions. Projected distributions of varied thrush under future high- and intermediate-warming climatic scenarios (simulating RCP8.5 and RCP4.5) revealed broad-scale contractions of suitable habitat by the year 2100, with 70% and 63% of current habitat decreasing in suitability, respectively. Low elevation, vertical forest structure, and dense canopy cover were also strong predictors of occurrence, though to a lesser degree. These results highlight the power of passive acoustic monitoring to guide regional adaptation and forest management frameworks for maximizing biodiversity inference amid rapid ecosystem change.

1) Effective conservation of the northern spotted owl (Strix occidentalis caurina) requires accurate occupancy and space use information, especially as passive acoustic monitoring becomes the primary population assessment method. Spotted owls actively vocalize in core use areas during the breeding season, but interpreting acoustic data is complicated by variable detectability—particularly for females—and interference from invasive barred owls (S. varia). 2) Using a dense network of autonomous recording units deployed 0–3 km from known activity centers, we quantified spotted owl vocal activity by sex and context. We additionally analyzed detection patterns from regional monitoring sites overlapping our study area to refine our understanding of detectability. 3) Male four-note calls were detected more frequently and consistently than female calls, and detection rates decreased with barred owl presence. Female calls were infrequent and restricted to the activity center and immediately adjacent areas, especially if nesting. 4) Vocal space use areas were similar in size but smaller than published home ranges, reinforcing that territorial calls represent high-use areas, not full spatial use. Synthesis and applications 5) We propose a detection-based spectrum of weeks with detection for inferring site occupancy that accounts for calling rate, caller sex, and project objectives. Stricter thresholds can minimize false positives in population assessments, while inclusive thresholds reduce false negatives in habitat protection. Our results support nuanced, objective-based thresholds for interpreting spotted owl detections from passive acoustic monitoring. This approach balances accuracy with conservation risk tolerance, demonstrating that suitable habitat extends beyond acoustically inferred territories. By clarifying vocal behavior, this study advances the application of passive acoustic monitoring for habitat management and occupancy estimation amid invasive species pressures and ongoing landscape change.

Montane red foxes (Vulpes vulpes ssp.) native to western North America are of broad conservation interest, occupying a narrow ecological niche and restricted to small, isolated populations across much of their distribution. Despite the need for robust information in guiding effective carnivore conservation, many aspects of montane red fox ecology are poorly understood due to their rarity. To improve ecological knowledge of Sierra Nevada red fox (V. v. necator), a montane red fox subspecies, we examined fox diet in an unstudied portion of their range in the central Cascades of Oregon, USA. In addition, we evaluated dietary overlap between montane red foxes and coyotes (Canis latrans), a presumably dominant carnivore that is expected to increase distributional overlap with montane red foxes under changing climatic regimes. We collected Sierra Nevada red fox and coyote scats via detection dog team surveys during 2017 in Oregon and used DNA metabarcoding to determine scat composition. Sierra Nevada red fox and coyote diets differed with respect to the most frequently occurring prey species and prey species that comprised the largest proportions of their diets (golden-mantled ground squirrel [Callospermophilus lateralis] and snowshoe hare [Lepus americanus], respectively). Despite some differences, Sierra Nevada red fox and coyote diets exhibited similar taxonomic richness and their dietary overlap was high (Pianka’s index = 0.74 via weighted percent occurrence, 0.69 via frequency of occurrence), with golden-mantled ground squirrel appearing to be an important prey item for both species. High dietary overlap suggests potential for competition between Sierra Nevada red foxes and coyotes where the two species occur sympatrically, which could be consequential for foxes in the future if spatial overlap indeed increases and results in niche compression. Our work addresses an aspect of data insufficiency for an imperiled species that can inform conservation strategies and species management.

Background: There is debate concerning whether there exists a generalizable effect of land-use change on zoonotic disease risk. Strong data informing this debate are sparse because it is challenging to establish direct links between hosts, vectors, and pathogens. However, molecular methods using invertebrate-derived DNA (iDNA) can now measure species composition and interactions from vector samples at landscape scales, which has the potential to improve mechanistic understanding of the effects of land-use change on zoonotic disease risk. Methodology/Principal Findings: We used iDNA metabarcoding of sandflies to disentangle the relationships between Leishmania parasites, sandfly vectors, and vertebrate hosts. We paired these samples with iDNA metabarcoding of carrion flies to survey vertebrates independent of sandfly feeding preferences. We collected sandflies and carrion flies at forest sites across a deforestation gradient in the southern Amazon ‘Arc of Deforestation’, which exemplifies global patterns of deforestation due to agricultural expansion. We used a series of models to test whether sandflies and the vertebrate they feed upon were influenced by deforestation, which we measured using percent forest cover, percent pasture cover, and distance to the major urban center. We found that vectors were encountered less frequently in forests surrounded by pasture. We also found that the probability of a Leishmania host/reservoir being detected in sandfly bloodmeals was quadratically related to local forest cover, with the highest probability found at sites with intermediate levels of deforestation. Hosts were also detected most often with carrion flies at sites with intermediate forest cover, suggesting that increased host availability rather than feeding preferences was responsible for this result. Domestic dogs and the nine-banded armadillo, Dasypus novemcinctus, were the most prevalent hosts found in the sandfly iDNA data.Conclusions/Significance: Our results did not support the generality of the ‘dilution effect’ hypothesis. However, important vectors and hosts showed consistent responses to deforestation and our findings suggest that interactions between domestic dogs and sylvatic hosts are a pathway for zoonotic disease transmission in human impacted tropical forests.

Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information—especially sequence information that includes intraspecific variation—creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error-free mitogenomic sequences for all of Oregon’s fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous, and estuarine fishes representing 24 families, 55 genera, and 128 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial “barcode” regions typically used for eDNA assays do not consistently diagnose for species, and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon’s fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences, and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.

How changes in biodiversity affect disease, particularly in the face of large-scale land-use change, is a contentious topic in disease ecology that has implications for public health and conservation policy. The ‘dilution effect’ hypothesis argues that declines in biodiversity are associated with increased disease risk, but this can be challenging to demonstrate because many pathogens have complex life cycles such that changes to the species composition and abundance of hosts can influence the density and infection prevalence of vectors via multiple mechanisms. Key to addressing this debate is a quantification of interactions between hosts, vectors, and pathogens. In their recent study published in Molecular Ecology, Kocher et al. (2022) captured thousands of sandflies, some species of which are vectors for the Leishmania protozoan that causes Leishmaniasis, across a human footprint gradient in French Guiana (Fig. 1). By implementing DNA metabarcoding of vectors combined with an innovative modeling approach, they effectively quantified the nuanced relationships between changes in land-use, mammalian host diversity, vector abundance, and parasite prevalence. In support of the dilution effect hypothesis, Kocher et al. found that sites with higher mammal diversity were associated with lower relative abundance of reservoir hosts and higher Leishmania infection prevalence in sandflies. However, while infection prevalence was lower when mammal diversity was high, the density of sandfly vectors was higher, which resulted in a weak overall effect of mammal diversity on the density of infected vectors, the most important indicator of Leishmania transmission risk.

Understanding the extent to which predators engage in active search for prey versus incidentally encountering them is important because active search can exert a stabilizing force on prey populations by alleviating predation pressure on low-density prey and increasing it for high-density prey. Parturition of many large herbivores occurs during a short and predictable temporal window in which young are highly vulnerable to predation. Our study aims to determine how a suite of carnivores responds to the seasonal pulse of newborn ungulates using contemporaneous GPS locations of four species of predators and two species of prey. We used step-selection functions to assess whether coyotes, cougars, black bears, and bobcats actively searched for parturient females in a low-density population of mule deer and a high-density population of elk. We then assessed whether searching carnivores shifted their habitat use toward areas exhibiting a high probability of encountering neonates. None of the four carnivore species encountered parturient mule deer more often than expected by chance suggesting that predation of young resulted from incidental encounters. By contrast, we determined that cougar and male bear movements positioned them in proximity of parturient elk more often than expected by chance which is evidence of searching behavior. Although both male bears and cougars searched for neonates, only male bears used elk parturition habitat in a way that dynamically tracked the phenology of the elk birth pulse suggesting that maximizing encounters with juvenile elk was a motivation when selecting resources. Our results support the existence of a stabilizing mechanism to prey populations through active search behavior by predators because carnivores in our study searched for the high-density prey species (elk) but ignored the low-density species (mule deer). We conclude that prey density must be high enough to warrant active search, and that there is high interspecific and intersexual variability in foraging strategies among large mammalian predators and their prey.

Species detection using eDNA is revolutionizing the global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information—especially sequence information that includes intraspecific variation—creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of complete mitogenomic sequence information to evaluate the effectiveness of such data to differentiate, identify and detect taxa. We created the Oregon Biodiversity Genome Project working group to utilize recent advances in sequencing technology to create a database of complete, near error-free mitogenomic sequences for all of Oregon’s resident freshwater fishes. So far, we have successfully assembled the complete mitogenomes of 313 specimens of freshwater fish representing 7 families, 55 genera, and 129 (88%) of the 146 resident species and lineages. Our comparative analyses of these sequences illustrate that the short (~150 bp) mitochondrial “barcode” regions typically used for eDNA assays are not consistently diagnostic for species-level identification and that no single region is best for metabarcoding Oregon’s fishes. However, often-overlooked intergenic regions of the mitogenome such as the D-loop have the potential to reliably diagnose and differentiate species. This project provides a blueprint for other researchers to follow as they build regional databases. It also illustrates the taxonomic value and limits of complete mitogenomic sequences, and how current eDNA assays and the “PCR-free” environmental genomics methods of the future can best leverage this information.

Metabarcoding of environmental DNA (eDNA) is now widely used to build diversity profiles from DNA that has been shed by species into the environment. There is substantial interest in the expansion of eDNA approaches for improved detection of terrestrial vertebrates using invertebrate-derived DNA (iDNA) in which hematophagous, sarcophagous, and coprophagous invertebrates sample vertebrate blood, carrion, or feces. Here, we use metabarcoding and multiple iDNA samplers (carrion flies, sandflies, and mosquitos) to profile gamma and alpha diversity in a dry, tropical forest in the southern Amazon. Our main objectives were to (1) compare diversity found with iDNA to camera trapping, which is the conventional method of vertebrate diversity surveillance and (2) compare each of the iDNA samplers to assess the effectiveness, efficiency, and potential biases associated with each sampler. Carrion flies were the most effective sampler, despite the least amount of sampling effort and the fewest number of individuals captured for metabarcoding, in describing vertebrate biodiversity followed by sandflies. Camera traps had the highest median species richness at the site-level but showed strong bias towards carnivore and ungulate species and missed much of the diversity described by iDNA methods. Mosquitos showed a strong feeding preference for humans as did sandflies for armadillos, thus presenting potential utility to further study related to host-vector interactions.