Resolving the global distribution of sawfishes (family Pristidae) using environmental DNA

The imperiled status of sawfishes globally has warranted the development of robust and reliable tools to study them. Madalyn Cooper developed a non-invasive detection method harnessing environmental DNA and applied the method in a survey of coastal and riverine habitats in the global tropics and subtropics where the sawfishes face risk of extinction. The methods and findings of Madalyn's PhD are significant for agencies and practitioners working toward the management and conservation of sawfish populations, and furthers the application of eDNA methods for rare and threatened species

Practical eDNA sampling methods inferred from particle size distribution and comparison of capture techniques for a Critically Endangered elasmobranch

Environmental DNA (eDNA) methods are increasingly applied in the marine environment to identify species and community structure. To establish widely applicable eDNA techniques for elasmobranchs, we used the Critically Endangered largetooth sawfish (Pristis pristis Linnaeus, 1758) as a model species for: (1) assessing eDNA particle size distribution; (2) assessing the efficiency of long-term preservation of water samples; and (3) comparing the efficiency and detection sensitivity of filtration and precipitation methods. Water samples (1 L) collected from a tank containing one largetooth sawfish specimen were sequentially filtered through five filter membranes of decreasing pore size (20, 10, 5, 1.2, and 0.45 μm). The proportion of sawfish eDNA retained within each size class was determined through quantitative real-time PCR (qPCR) using a species-specific TaqMan probe assay. A linear mixed-effects model (lme) showed that the 1.2 and 20 μm filters captured most of the eDNA particles present in the sampled water. Additionally, whole water samples (0.375 L) were preserved in Longmire's buffer, stored at tropical ambient temperatures (26.3°C ± 3.0 SD) and extracted at five time points: immediately, one, two, and three months after collection, as well as frozen and extracted three months later, to assess the preservation efficiency of Longmire's buffer via qPCR analysis. A linear mixed-effects model showed that samples maintained maximal eDNA yield for at least three months after collection at ambient storage. Lastly, when comparing the filtration and precipitation methods, filtration using 0.45 μm pore size was more sensitive to capture of large-tooth sawfish eDNA than filtration with 20 μm filter or water precipitation. However, water precipitation was more efficient when accounting for volume of water processed. These results provide options for best capture and preservation of elasmobranch eDNA

First detection of critically endangered scalloped hammerhead sharks (Sphyrna lewini) in Guam, Micronesia, in five decades using environmental DNA

Among the hammerhead sharks, scalloped hammerheads (Sphyrna lewini) have undergone the steepest population declines worldwide. Due to their high susceptibility to exploitation, the species is now classified as ‘critically endangered’, the most threatened category listed by the International Union for Conservation of Nature. There is an urgent need for data on the distribution of S. lewini to inform the design and implementation of effective conservation management strategies, and mitigate the risk of global extinction. Environmental DNA (eDNA) is emerging as a powerful method to monitor the geographic distribution, population trends, and habitat usage of rare and endangered species. In comparison to traditional survey methods, eDNA methods offer lower cost, higher detection rates, and are non-invasive. At present, there is no targeted eDNA assay for the detection of S. lewini and existing methods to assess their distribution are either fisheries-dependent, leading to bias, or costly and laborious, leading to impracticality in regions of low or unknown abundance. Here we present an optimised workflow for the detection of S. lewini presence using eDNA methods, and apply these to successfully detect scalloped hammerhead sharks in Guam, of the western Pacific Ocean, where their presence has not been scientifically reported since the 1970s. The detection of S. lewini by eDNA survey methods was achieved from a single-day sampling effort, demonstrating the efficacy of the technique and workflow. If implemented, the eDNA survey methods developed here will enable the rapid generation of information on the distribution of scalloped hammerhead sharks in the western Pacific, and likely globally, and assist in the accurate placement of no-take reserves to best enable the species’ recovery

Best practice guidelines for environmental DNA biomonitoring in Australia and New Zealand

Environmental DNA (eDNA)- based methods are increasingly used by government agencies to detect pests and threatened species, and for broader biodiversity monitor-ing. Given rapid technological advances and a growing number of commercial service providers, there is a need to standardize methods for quality assurance and to main-tain confidence in eDNA- based results. Here, we introduce two documents to pro-vide best- practice guidelines for Australian and New Zealand eDNA researchers and end- users (available from https://sedna socie ty.com/publications ): the Environmental DNA protocol development guide for biomonitoring provides minimum standard consid-erations for eDNA and environmental RNA projects across the complete workflow, from ethical considerations and experimental design to interpreting and communicat-ing results. The Environmental DNA test validation guidelines outline key steps to be used in assay development and validation for species-specific testing and metabar-coding. Both guidelines were developed as an initiative of the Australian Government Department of Agriculture, Fisheries and Forestry and led by the Southern eDNA Society in a collaborative process including multiple consultation rounds with eDNA experts, end-users, and stakeholders to adapt the guidelines to Australian and New Zealand needs. The aim of these guidelines is not to be prescriptive, but to set mini-mum standards to support a consistent and best- practice approach to eDNA testing. We anticipate that the guidelines will be reviewed and regularly updated as required. Our aspiration is that these best- practice guidelines will ensure environmental man-agers are provided with robust scientific evidence to support decision- making

Environmental DNA (eDNA): a valuable tool for ecological inference and management of sharks and their relatives

Knowledge of spatial and temporal variation in abundance is critical for the implementation of effective protective measures for organisms that are both naturally rare and vulnerable to exploitation. The development of management and conservation strategies for elasmobranchs depends on accurate assessment and monitoring of the distribution and abundance of target species in the field, but detecting species occurrences is often even more challenging in the aquatic environment than on land (Webb and Mindel, 2015). Consequently, as is the case for many large, mobile and rare vertebrates, shark detection is inherently difficult. All organisms continuously leave traces of themselves behind in the environment in the form of shed skin cells, bodily fluids, metabolic waste, gametes, or blood. Any of these materials can contain pieces of the organism's DNA. Environmental DNA (eDNA) analysis is based on the retrieval of this naturally released genetic material from the environment. It generally refers to bulk DNA extracted from an environmental sample such as water but also from soil, sediment, snow, or even from air (Taberlet et al., 2012a). In aquatic systems, macroorganismal-derived eDNA can be present as free DNA, cellular debris, or particle-bound DNA and is mostly present in small fragments, due to rapid degradation (Barnes et al., 2014); however, much of the eDNA is retrieved from cellular material and may therefore contain still relatively undamaged nucleic acid molecules. Nevertheless, eDNA studies focus primarily on the detection of short fragments, as currently available parallel sequencing and qPCR platforms have short-read capabilities limited to a few hundred base pairs. When DNA is present at low concentrations, mitochondrial DNA (mtDNA) is often targeted, as there are substantially more mitochondrial than nuclear DNA copies per cell (Wilcox et al., 2013). Commonly employed mtDNA genes include cytochrome b, cytochrome c oxidase subunit 1 (COI), 12S rRNA, and 16S rRNA (Kelly et al., 2014; Thomsen et al., 2012b; Valentini et al., 2016), and targeted fragments typically fall within the range of 79 to 285 bp (Ficetola et al., 2008; Minamoto et al., 2012). The level of target specificity is often the main determining factor when choosing or designing primers for eDNA analysis

Improved detection sensitivity using an optimal eDNA preservation and extraction workflow and its application to threatened sawfishes

Pressures on coastal ecosystems are increasing and aquatic species that are restricted to these habitats are facing the threat of extinction. However, the true extent of many threatened and rare aquatic species, especially elasmobranchs, remains unclear due to high levels of data deficiency and poor efficacy of traditional survey methods. Sawfishes (Pristidae), a family of shark-like rays, are among the most threatened and rare elasmobranch species and are difficult to detect in turbid, coastal habitats. Reliable cost-effective tools to detect these species are urgently needed to increase their conservation potential. Characterization of environmental DNA (eDNA) extracted from water samples has garnered significant appeal for detection of rare and threatened species. To assist conservation and monitoring efforts for sawfishes using eDNA, species-specific TaqMan quantitative polymerase chain reaction assays were developed and validated to detect 1.25–5 copies of a 12S rRNA gene fragment. Filter samples were collected in Northern Territory, Australia to assess the utility of the developed eDNA assays and compare the efficacy of preservation and extraction workflows for detecting rare species. Dwarf sawfish (Pristis clavata) were detected in three of 20 sites, and there was a significant effect of preservation and extraction workflow on total eDNA yield and subsequent detection success. Longmire's preserved samples extracted using glycogen-aided precipitation yielded a significantly higher concentration of total eDNA (n = 60; β = 1.27, t(95) = 8.172, P < 0.0001) and yielded positive P. clavata eDNA detections compared to ethanol preserved samples extracted using QIAGEN DNeasy kit, which did not yield any positive detections. The optimized eDNA assays were developed to support monitoring efforts for endangered sawfishes. Importantly, this study demonstrates that choice of preservation and extraction workflow requires careful consideration, especially when detection of rare or threatened species can have important management and conservation outcomes

Monitoring threatened species with environmental DNA and open ecological data: Local distribution and habitat preferences of scalloped hammerhead sharks (Sphyrna lewini)

Evidence-based environmental management is urgently required to enable progress towards global conservation commitments. To fill large-scale biodiversity knowledge gaps, governments, organisations and communities must adopt innovative ecological monitoring techniques. The emergence of environmental DNA (eDNA) survey methods, as well as the increased availability of in situ ocean observation and satellite remote sensing data, offers opportunities to overcome significant logistic and financial challenges previously associated with traditional biodiversity monitoring. Here, a 1.5 year-long eDNA survey reveals the spatial and temporal presence of 'criti-cally endangered' scalloped hammerhead sharks (Sphyrna lewini) in Apra Harbor, Guam. The survey confirms the presence of S. lewini in the region, and shows eDNA detections are most frequent at the beginning of the dry season, in January. Combined analysis of eDNA results with open (freely available) ecological data identifies that S. lewini presence is associated with increases in water velocity, turbidity and wind direction, as well as decreases in temperature and wind speed. Additionally, the data indicate S. lewini are most frequent at sampling sites characterised by high turbidity, shallow depths, and large distances from the harbor entrance. Information on local distribution and habitat preferences generated here is fundamental to the establishment of management protocols that aim to minimise negative anthropogenic impacts on S. lewini in Apra Harbor. The work provides an example of contemporary marine monitoring for the efficient generation of biodiversity data; an approach that will enable informed management decisions and help to reduce the risk and rate of species extinctions throughout the next decade

Coronal Heating as Determined by the Solar Flare Frequency Distribution Obtained by Aggregating Case Studies

Flare frequency distributions represent a key approach to addressing one of the largest problems in solar and stellar physics: determining the mechanism that counter-intuitively heats coronae to temperatures that are orders of magnitude hotter than the corresponding photospheres. It is widely accepted that the magnetic field is responsible for the heating, but there are two competing mechanisms that could explain it: nanoflares or Alfv\'en waves. To date, neither can be directly observed. Nanoflares are, by definition, extremely small, but their aggregate energy release could represent a substantial heating mechanism, presuming they are sufficiently abundant. One way to test this presumption is via the flare frequency distribution, which describes how often flares of various energies occur. If the slope of the power law fitting the flare frequency distribution is above a critical threshold, $\alpha=2$ as established in prior literature, then there should be a sufficient abundance of nanoflares to explain coronal heating. We performed $>$600 case studies of solar flares, made possible by an unprecedented number of data analysts via three semesters of an undergraduate physics laboratory course. This allowed us to include two crucial, but nontrivial, analysis methods: pre-flare baseline subtraction and computation of the flare energy, which requires determining flare start and stop times. We aggregated the results of these analyses into a statistical study to determine that $\alpha = 1.63 \pm 0.03$. This is below the critical threshold, suggesting that Alfv\'en waves are an important driver of coronal heating.Comment: 1,002 authors, 14 pages, 4 figures, 3 tables, published by The Astrophysical Journal on 2023-05-09, volume 948, page 7