No abstract

Metabarcoding of environmental DNA (eDNA) provides more comprehensive, efficient, and non‐invasive sampling of biological communities than conventional methods. However, limitations of metabarcoding include taxon‐specific biases in amplification and sequencing that distort assessments of community composition. Further, hyper‐abundant species may disproportionately affect community composition assessments and impair the detection of rare species (i.e., “species masking”). In this study, we examine methodological approaches to improve eDNA metabarcoding assessments of community structure using fish community diversity in a pond in south Florida using MiFish primers modified to improve cichlid detection. Mitochondrial 12S eDNA amplicon sequencing via Illumina NovaSeq was analyzed using the DADA2 model‐based exact sequence inference. The fish species and abundances in the system were recorded during piscicide treatment and subsequent native species restocking. Our results demonstrate that (1) ultra‐high‐throughput sequencing on the newer NovaSeq patterned flow cell provided reliable detection of very rare taxa—with detections of a single individual. (2) Read numbers were significantly correlated to the total surface area of the fish population, and numerical abundance to a lesser degree; however, dominant taxa largely drove those correlations, and simulations showed that biases in the most abundant taxa will have disproportionate effects on the strength of the correlation. (3) The read number coefficient of variation for each species across spatially separated replicate samples may provide less biased abundance estimates compared with estimates based on average read counts. Finally, (4) exact sequence inference detected multiple haplotypes and population genetic diversity within a species. Our results demonstrate the real‐world metabarcoding capacity to reveal community structure and reliably detect rare species and unique haplotypes and shows that read numbers can, to a limited degree, be used to infer the size of fish populations. Careful examination of detection biases among dominant taxa and spatial variation among samples are required for rigorous eDNA‐based estimates of community structure. Our results demonstrate the capacity of NovaSeq metabarcoding to reveal freshwater fish community structure and reliably detect rare species and unique haplotypes. Metabarcoding read numbers were significantly correlated to the total surface area of the fish species' populations, allowing for conditional inferences of population sizes. However, dominant taxa largely drove those correlations, and simulations indicated that biases toward the most abundant taxa will have disproportionate effects on the strength of the correlation.

BackgroundVector-borne diseases exert a global economic impact to the livestock industry. Understanding how agriculture practices and acaricide usage affect the ecology of these diseases is important for making informed management decisions. Theileria cervi is a hemoprotozoan parasite infecting white-tailed deer (Odocoileus virginianus) and is transmitted by the lone star tick, Amblyomma americanum. The purpose of this study was to determine if acaricide treatment decreased hematozoan prevalence in farmed white-tailed deer when compared to geographically-close wild deer or altered the genotypes of T. cervi present.ResultsWe compared prevalence of T. cervi in 52 farmed adult white-tailed deer which were regularly treated with permethrin and ivermectin, 53 farmed neonates that did not receive treatment for vector control, and 42 wild deer that received no form of chemical vector control. Wild deer had significantly higher prevalence of T. cervi than farmed deer. Additionally, no neonate fawns tested positive for T. cervi, and we found that age was a significant predictor of infection status. We found no difference in genotypic variation in T. cervi isolates between adjacent herds of farmed and wild white-tailed deer, although a divergent genotype X was identified. Chronic infection with T. cervi had no significant effects on mortality in the white-tailed deer.ConclusionsWe found significantly lower prevalence of T. cervi infection in farmed (40%) compared to wild white-tailed deer (98%), which may be due to the inclusion of chemical vector control strategies. More work is needed to determine the implications, if any, of mixed genotypic infections of T. cervi, although we found no significant effect of infection with Theileria on mortality in farmed deer. Theileria infection does sometimes cause disease when an animal is stressed, immunosuppressed, or translocated from non-endemic to endemic regions.

Background: Epizootic hemorrhagic disease virus (EHDV) is a pathogen vectored by Culicoides midges that causes significant economic loss in the cervid farming industry and affects wild deer as well. Despite this, its ecology is poorly understood. Studying movement and space use by ruminant hosts during the transmission season may elucidate EHDV ecology by identifying behaviors that can increase exposure risk. Here we compared home ranges (HRs) and site fidelity metrics within HRs using the T-LoCoH R package and GPS data from collared deer.Methods: Here, we tested whether white-tailed deer (Odocoileus virginianus) roaming within a high-fenced, private deer farm (ranched) and native deer from nearby state-managed properties (wild) exhibited differences in home range (HR) size and usage during the 2016 and 2017 EHDV seasons. We captured male and female individuals in both years and derived seasonal HRs for both sexes and both groups for each year. HRs were calculated using a time-scale distance approach in T-LoCoH. We then derived revisitation and duration of visit metrics and compared between years, sexes, and ranched and wild deer.Results: We found that ranched deer of both sexes tended to have smaller activity spaces (95% HR) and revisited sites within their HR more often but stayed for shorter periods than wild deer. However, core area (25% HR) sizes did not significantly differ between these groups. Conclusions: The contrast in our findings between wild and ranched deer suggest that home range usage, rather than size, in addition to differences in population density, likely drive differences in disease exposure during the transmission period.