There is ongoing debate concerning whether there exists a generalizable effect of land-use change on biodiversity and consequently zoonotic disease risk. Strong data informing this debate is sparse because ecological and sampling complexities make it challenging to establish direct links between vertebrate hosts (and non-hosts), vectors, and pathogens across landscapes. However, emerging molecular methods using invertebrate-derived DNA (iDNA) can now measure species diversity and interactions from vector bloodmeals, which has the potential to improve mechanistic understanding of the effects of land-use change on zoonotic disease risk. Here, we used iDNA metabarcoding of vectors and their bloodmeals to disentangle the complex relationships between Leishmania parasites, known sandfly vectors, and potential wildlife hosts. We collected 56,775 sandflies during 3,159 trap nights at 39 forested sites across the southern Amazon ‘Arc of Deforestation’, which exemplifies global patterns of deforestation and fragmentation at the borders of tropical forest ecosystems due to agricultural expansion. We found that vector community composition was influenced by forest cover and pasture cover, and the most common vector, Nyssomia spp., was encountered less frequently in forests surrounded by pasture. Sandflies fed on a diversity of vertebrates, but the edge-loving nine-banded armadillo, Dasypus novemcinctus, was overwhelmingly the most prevalent host, followed by the greater long-nosed armadillo, Dasypus kappleri. The probability of a host being detected in sandfly bloodmeals was lower at sites with higher forest cover, which was overwhelmingly due to reduced bloodmeals arising from D. novemcinctus. Armadillos were also the most prevalent sylvatic vertebrate taxon in sandfly pools that were positive for Leishmania, further suggesting that these xenarthrans are a key host pathway for zoonotic disease transmission.

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.

Organisms leave traces of DNA as they move through their environments. The extraction of these DNA traces is known as environmental DNA (eDNA). eDNA provides scientists and researchers a non-invasive, rapid, cost-effective and sensitive way to detect and quantify species. Traditional eDNA sampling consists of manually filtering water, which is labor and cost-intensive for remote locations. Furthermore, commercialized solutions are expensive and require a field operator. This eDNA sampler project aims to provide an affordable, open-sourced, remotely deployable, fully automated, and customizable alternative. The PolyWAG (Water Acquired Genomics) system can run up to 24 inline filter units with support for different conditions including pressure, time and volume limit. The pumps deliver maximum 400mL/min with solenoid valves separating each inline filter to minimize cross-contamination. At the end of each sample, the desired stabilizing solution can be injected to fully submerge the filter for preservation. An optional river depth sensor can provide a proxy for flow to correct eDNA concentrations to allow for improved quantification of organisms. Data acquired during operation including water depth, pressure, temperature, and flow rate will be stored on microSD card in CSV format, which allows easier data export and analysis. A web application provides an intuitive UI for in-field programming, real-time sensor updates, scheduling tasks, and manual operations. We present data from multiple tests showing the length of the preservation period and the contamination level between samples. The PolyWAG system is estimated to be $3000 each, with add-on river depth sensor and 10ah 12V battery.

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.