Simultaneous species detection and discovery with environmental DNA metabarcoding: A freshwater mollusk case study.

Environmental DNA (eDNA) sampling is a powerful tool for rapidly characterizing biodiversity patterns for specious, cryptic taxa with incomplete taxonomies. One such group that are also of high conservation concern are North American freshwater gastropods. In particular, springsnails of the genus (Family: Hydrobiidae) are prevalent throughout the western United States where >140 species have been described.

The unknown unknown: A framework for assessing environmental DNA assay specificity against unsampled taxa.

Taxon-specific quantitative PCR (qPCR) assays are commonly used for environmental DNA sampling-based inference of animal presence. These assays require thorough validation to ensure that amplification truly indicates detection of the target taxon, but a thorough validation is difficult when there are potentially many non-target taxa, some of which may have incomplete taxonomies. Here, we use a previously published, quantitative model of cross-amplification risk to describe a framework for assessing qPCR assay specificity when there is missing information and it is not possible to assess assay specificity for each individual non-target confamilial.

An inside "beak": Molecular analysis of swab samples reveals the seabird diet of invasive Barn Owls in Hawai'i.

Predation is an important species interaction to monitor when assessing an invasive species' impact on a particular ecosystem, but it can be difficult to observe and thus, fully understand. On Kaua'i island, invasive Barn Owls (Tyto alba) predate native seabirds, but difficult terrain in this region and the cryptic nature of owl predation make traditional monitoring of predation quite challenging. Using Barn Owls collected as part of removal efforts on Kaua'i and Lehua islands, we conducted DNA metabarcoding of owl digestive tracts to detect and determine seabird species they predate.

Drawing a line in the sand: Environmental DNA population genomics.

Environmental DNA (eDNA) sampling uses genetic material in the environment to infer species presence sight-unseen. The method has rapidly become a powerful tool for monitoring biodiversity. However, biological diversity, as per the Convention on Biological Diversity definition of "diversity within species, between species and of ecosystems" is more inclusive than most eDNA studies cover: The vast majority focus only on between-species and ecosystem-level biodiversity.

eDNAssay: A machine learning tool that accurately predicts qPCR cross-amplification.

Environmental DNA (eDNA) sampling is a highly sensitive and cost-effective technique for wildlife monitoring, notably through the use of qPCR assays. However, it can be difficult to ensure assay specificity when many closely related species co-occur. In theory, specificity may be assessed in silico by determining whether assay oligonucleotides have enough base-pair mismatches with nontarget sequences to preclude amplification.

Targeting Nitric Oxide Production in Microglia with Novel Imidazodiazepines for Nonsedative Pain Treatment.

The goal of this research is the identification of new treatments for neuropathic pain. We characterized the GABAergic system of immortalized mouse and human microglia using electrophysiology and qRT-PCR. Cells from both species exhibited membrane current changes in response to γ-aminobutyric acid, with an EC of 260 and 1940 nM, respectively.

Capture enrichment of aquatic environmental DNA: A first proof of concept.

Environmental DNA (eDNA) sampling-the detection of genetic material in the environment to infer species presence-has rapidly grown as a tool for sampling aquatic animal communities. A potentially powerful feature of environmental sampling is that all taxa within the habitat shed DNA and so may be detectable, creating opportunity for whole-community assessments. However, animal DNA in the environment tends to be comparatively rare, making it necessary to enrich for genetic targets from focal taxa prior to sequencing.

Evolutionary Community Ecology: Time to Think Outside the (Taxonomic) Box.

Ecologists and evolutionary biologists have long been interested in the role of interspecific competition in the diversification of clades. These studies often focus on a single taxonomic group, making the implicit assumption that important competitive interactions occur only between closely related taxa, despite abundant documentation of intense competition between species that are distantly related. Specifically, this assumption ignores convergence of distantly related competitors on limiting niche axes and thus may miss cryptic effects of distantly related competitors on the evolution of focal clades.

Ecological segregation moderates a climactic conclusion to trout hybridization.

For decades, it has been assumed that introgressive hybridization between introduced rainbow trout and native cutthroat trout in western North America will lead to genomic extinction of the latter. A broad-scale re-examination of their interaction indicates that ecological differences between these species and demographic processes are dictating the location and extent of their hybrid zones, and that runaway introgression between these taxa is unlikely.

Climate, Demography, and Zoogeography Predict Introgression Thresholds in Salmonid Hybrid Zones in Rocky Mountain Streams.

Among the many threats posed by invasions of nonnative species is introgressive hybridization, which can lead to the genomic extinction of native taxa. This phenomenon is regarded as common and perhaps inevitable among native cutthroat trout and introduced rainbow trout in western North America, despite that these taxa naturally co-occur in some locations. We conducted a synthetic analysis of 13,315 genotyped fish from 558 sites by building logistic regression models using data from geospatial stream databases and from 12 published studies of hybridization to assess whether environmental covariates could explain levels of introgression between westslope cutthroat trout and rainbow trout in the U.

Patterns of hybridization among cutthroat trout and rainbow trout in northern Rocky Mountain streams.

Introgressive hybridization between native and introduced species is a growing conservation concern. For native cutthroat trout and introduced rainbow trout in western North America, this process is thought to lead to the formation of hybrid swarms and the loss of monophyletic evolutionary lineages. Previous studies of this phenomenon, however, indicated that hybrid swarms were rare except when native and introduced forms of cutthroat trout co-occurred.

The Dual Challenges of Generality and Specificity When Developing Environmental DNA Markers for Species and Subspecies of Oncorhynchus.

Environmental DNA (eDNA) sampling is a powerful tool for detecting invasive and native aquatic species. Often, species of conservation interest co-occur with other, closely related taxa. Here, we developed qPCR (quantitative PCR) markers which distinguish westslope cutthroat trout (Oncorhynchus clarkii lewsi), Yellowstone cutthroat trout (O.

Distance, flow and PCR inhibition: eDNA dynamics in two headwater streams.

Environmental DNA (eDNA) detection has emerged as a powerful tool for monitoring aquatic organisms, but much remains unknown about the dynamics of aquatic eDNA over a range of environmental conditions. DNA concentrations in streams and rivers will depend not only on the equilibrium between DNA entering the water and DNA leaving the system through degradation, but also on downstream transport. To improve understanding of the dynamics of eDNA concentration in lotic systems, we introduced caged trout into two fishless headwater streams and took eDNA samples at evenly spaced downstream intervals.

Robust detection of rare species using environmental DNA: the importance of primer specificity.

Environmental DNA (eDNA) is being rapidly adopted as a tool to detect rare animals. Quantitative PCR (qPCR) using probe-based chemistries may represent a particularly powerful tool because of the method's sensitivity, specificity, and potential to quantify target DNA. However, there has been little work understanding the performance of these assays in the presence of closely related, sympatric taxa.