Environmental DNA (eDNA) has significant potential to improve the efficiency of biological sampling and detect species that pose challenges for traditional sampling methods. However, a key obstacle in utilizing eDNA data for ecosystem management is uncertainty surrounding the ability to estimate abundance or biomass of multiple species simultaneously. In this study, we use experimental trials with known biomasses of multiple species to explore the feasibility of (1) estimating species proportions from eDNA metabarcoding data and (2) estimating absolute eDNA concentrations of multiple species by scaling metabarcoding proportions with eDNA concentrations of a single species obtained from qPCR. The focal species for this study were three gadid fishes that are key components of marine ecosystems in Alaska and vary in their distribution and habitat use: Walleye pollock (Gadus chalcogrammus), Pacific cod (Gadus macrocephalus), and Arctic cod (Boreogadus saida). After designing gadid‐specific metabarcoding primers and accounting for PCR biases in the metabarcoding data, we found corrected read proportions closely approximated the true biomass proportions of species. Furthermore, we found strong positive relationships between absolute eDNA concentration and absolute biomass for Arctic cod and Pacific cod using quantitative metabarcoding data combined with estimates of Walleye pollock eDNA concentration derived from qPCR. These findings suggest that it is possible to accurately quantify species compositions and estimate metrics of biomass for gadids in real‐world scenarios. Furthermore, this work provides a framework for developing primers and analytical approaches that can be applied to other species to improve the quantitative utility of eDNA.

Ticks are widespread parasites of vertebrates and major vectors of pathogens to humans, domestic animals, and wildlife. In southern Africa, numerous tick species transmit diseases of economic and health importance. This study aimed to describe the occurrence of ticks and tick-borne pathogens in multiple land-use types and the possible role of ticks in the transmission of pathogen species. Using molecular techniques, we screened 1716 ticks for infection by rickettsial bacteria and protozoans. To characterize pathogen identity, we sequenced multiple loci from positive samples and analyzed sequences within a phylogenetic framework. Across the seven tick species collected as nymphs or adults, we detected Rickettsia, Anaplasma, Ehrlichia, Babesia, Hepatozoon, and Theileira species. We found that some tick species and tick-borne pathogens differed according to land use. For example, we found a higher density of Haemaphysalis elliptica and higher prevalence of Rickettsia in H. elliptica collected from savanna grasses used for livestock grazing near human settlements than savanna grasses in conservation areas. These findings highlight the importance of comprehensive surveillance to achieve a full understanding of the diversity and ecology of the tick-borne pathogens that can infect humans, domestic animals, and wildlife.

In Latin America, synanthropic mammalian reservoirs maintain Trypanosoma cruzi, a parasitic protozoan, where they facilitate the transmission of the parasite to humans and other reservoir hosts in peridomestic settings. In the United States, raccoons (Procyon lotor) and Virginia opossums (Didelphis virginiana) are known synanthropic T. cruzi reservoir hosts; however, the role these species have in the peridomestic transmission cycle in the US is not well understood. This study aimed to identify the suite of mammalian reservoirs of T. cruzi in Florida. We also compared infection prevalence in raccoon populations sampled from within and outside of the estimated distribution of the common T. cruzi vector in Florida to gain insight into how the arthropod vector distribution impacts the distribution of infected reservoirs in the state. Finally, to investigate the impact of peridomestic landscapes on parasite prevalence, we compared the prevalence of T. cruzi-infected raccoons and opossums across five paired peridomestic and sylvatic sites. We live-trapped and collected peripheral blood samples from 135 raccoons, 112 opossums, 18 nine-banded armadillos (Dasypus novemcinctus), and nine species of rodents in north central Florida. Using quantitative PCR methods, we found that raccoons (42.2%, 95% CI [34.2–50.7%]) and opossums (50.9%, 95% CI [41.8–60.0%]) were infected with T. cruzi and the prevalence across habitats was similar for both raccoons (peridomestic: n = 77, 44.2%, 95% CI [33.6–55.3%], sylvatic: n = 58, 39.7%, 95% CI [28.1–52.5%]) and opossums (peridomestic: n = 66, 48.5%, 95% CI [36.8–60.3%], sylvatic: n = 46, 54.3%, 95% CI [40.2–67.8%]). Raccoons sampled outside the estimated distribution of Triatoma sanguisuga were not infected with T. cruzi (n = 73, 0.0%, 95% CI [0.0–5.0%]). Our study did not indicate that peridomestic habitats in Florida maintained a higher infection prevalence than their sylvatic counterparts; however, we did find a difference in prevalence within vs. outside the estimated vector distribution in Florida.

Tick-borne infections are an increasing medical and veterinary concern in the southeastern United States, but there is limited understanding of how recreational greenspaces influence the hazard of pathogen transmission. This study aimed to estimate the potential human and companion animal encounter risk with different questing tick species, and the bacterial or protozoal agents they carry in recreational greenspaces. We collected ticks bimonthly along trails and designated recreational areas in 17 publicly accessible greenspaces, in and around Gainesville, Florida, USA. We collected Amblyomma americanum, Ixodes scapularis, Amblyomma maculatum, Dermacentor variabilis, Ixodes affinis, and Haemaphysalis leporispalustris. Across the six tick species collected, we detected 18 species of bacteria or protozoa within the Babesia, Borrelia, Cytauxzoon, Cryptoplasma (Allocryptoplasma), Ehrlichia, Hepatozoon, Rickettsia, and Theileria genera, including pathogens of medical or veterinary importance. While tick abundance and associated microorganism prevalence and richness were the greatest in natural habitats surrounded by forests, we found both ticks and pathogenic microorganisms in manicured groundcover. This relationship is important for public health and awareness, because it suggests that the probability of encountering an infected tick is measurable and substantial even on closely manicured turf or gravel, if the surrounding landcover is undeveloped. The presence of medically important ticks and pathogenic microorganisms in recreational greenspaces indicates that public education efforts regarding ticks and tick-borne diseases are warranted in this region of the United States.

The ‘omics revolution’ has advanced scientific understanding of marine ecosystems and led to a rapid increase in data that can inform species' population structure, distribution, and abundance. Of the 'omics data types, environmental DNA (eDNA) may present the most cost‐effective opportunity for developing quantitative estimates of abundance trends, a key input for stock assessment models. However, eDNA has yet to be widely adopted for stock status determinations within regional fisheries management organisations. We review progress towards addressing key challenges that limited the application of eDNA in marine fisheries management, including advances in (1) the quantitative relationship between eDNA observations and species biomass, (2) reducing false‐negative and false‐positive detections, (3) defining the spatial scale of eDNA, (4) collecting biological data from eDNA surveys, (5) quantifying uncertainty in eDNA surveys, and (6) responding to scepticism of new survey methods. We use a case study with Pacific hake (Merluccius productus) to demonstrate the development of an eDNA index and its direct integration into an age‐structured stock assessment model. Given the many ways in which the field of eDNA has matured, we propose that eDNA can meaningfully inform a range of fisheries management needs, and outline a roadmap for using eDNA in stock assessment models in data‐limited to data‐rich species. A primary impediment to operationalising eDNA as stock assessment model inputs is the lack of interdisciplinary research teams, including geneticists, ecological modellers, and stock assessment scientists, which are necessary to interpret methods and results across scientific disciplines and ensure data are used appropriately.

Environmental DNA (eDNA) metabarcoding primers that target specific taxonomic groups can alleviate the common shortcoming of metabarcoding studies in differentiating closely related taxa of interest. Here, we describe the development and validation of an eDNA metabarcoding primer set for the diverse genus of rockfishes (Sebastes sp.), with a focus on species found in the Alaska Current—many of which are commercially and recreationally important or of conservation concern. Our results demonstrate that the Sebastes D‐loop primer set improves upon existing fish eDNA metabarcoding primer sets by providing accurate species identification for nearly all of the 42 species of rockfishes tested. Using this primer set with mock community samples resulted in substantial amplification bias across 18 rockfishes, suggesting that a quantitative metabarcoding model would be appropriate for correcting bias in future datasets. Testing the Sebastes D‐loop primers with aquarium eDNA samples containing 11 species of rockfishes (high eDNA concentration) and eDNA samples collected on a trawl survey in the Aleutian Islands (low eDNA concentration) confirmed that the primer set is robust to varying rockfish species compositions and concentrations. These findings highlight the potential of the Sebastes D‐loop primer set as a valuable tool for enhancing species identification and characterization of species assemblages in eDNA studies, and as a reliable method for rockfish population monitoring and assessment.