scholarly journals Seasonal monitoring of Hida salamander Hynobius kimurae using environmental DNA with a genus-specific primer set

2020 ◽  
Vol 43 ◽  
pp. 341-352
Author(s):  
T Jo ◽  
S Tomita ◽  
Y Kohmatsu ◽  
M Osathanunkul ◽  
A Ushimaru ◽  
...  
Keyword(s):  
Detection Rate ◽  
Habitat Restoration ◽  
Site Occupancy ◽  
Environmental Dna ◽  
Taqman Probe ◽  
Morphological Identification ◽  
Target Species ◽  
Amphibian Species ◽  
Detection Rates ◽  
Occupancy Probability

The diversity and the abundance of amphibians have dramatically declined globally over the past 30 years, and the monitoring and conservation of their habitats is essential. However, traditional methods such as bait trapping and mark-recapture are costly, and morphological identification usually requires a high level of taxonomic expertise. Here, seasonal surveillances of Hida salamander Hynobius kimurae were performed by means of environmental DNA (eDNA) analysis with Hynobius-specific primers and a species-specific TaqMan probe. Water sampling and visual surveys were conducted seasonally in a stream in Kyoto Prefecture, Japan. Detection rates of eDNA were then calculated by real-time PCR, and eDNA site occupancy probability was estimated by multi-scale occupancy modeling. The eDNA-based detection rate of Hida salamander was 76.7%, whereas the visual survey-based detection rate was 23.3%, and target eDNA was detected at almost all sites where the presence of target species was visually confirmed. Moreover, factors relating to the site- and sample-level occurrence probabilities of the target eDNA differed depending on the developmental stage of the target species. Our findings support previous studies showing that eDNA analysis enables an effective assessment of amphibian distributions without damaging the organisms or their habitat, and we compare for the first time the site occupancy probability of amphibian eDNA throughout the life cycle of an amphibian species. The present study contributes to the development of eDNA analysis as a tool for understanding the distribution and seasonal activity of amphibian species and will thus aid in the planning of conservation measures and habitat restoration for these species.

Detection of medium-sized ground-dwelling mammals using infrared digital cameras: an alternative way forward?

2010 ◽  
Vol 32 (2) ◽  
pp. 165 ◽  
Author(s):  
Andrew W. Claridge ◽  
David J. Paull ◽  
Simon C. Barry
Keyword(s):  
Detection Rate ◽  
Detection Efficiency ◽  
Digital Cameras ◽  
Target Species ◽  
Detection Rates ◽  
Reporting Rates ◽  
Swamp Wallaby ◽  
Over Time

Infrared digital cameras were used to examine temporal detection rates of medium-sized ground-dwelling mammals in a coastal woodland landscape. From three successive deployments at fixed stations, a range of mammals was detected, including three target species: the long-nosed bandicoot, the long-nosed potoroo and the southern brown bandicoot. Reporting rates of target species were largely consistent and in some cases high. The swamp wallaby was the most commonly detected species, ranging from 47–67% of cameras on any given deployment. Long-nosed bandicoots were detected at 37–53% of cameras, long-nosed potoroos 13–23% and southern brown bandicoots 10–17%. In total, bandicoots and potoroos were detected at 23 of 30 sites (77%) while forage-diggings of these mammals were universally present. There were differences in the detection rate of bandicoots and potoroos in relation to 24-hourly cycles: all three species were less likely to be detected between dawn and dusk than dusk and dawn. Otherwise, with few exceptions, the rate at which bandicoots and potoroos were detected over time within a deployment did not vary markedly. Infrared digital cameras offer great potential as sampling devices for bandicoots and potoroos because of their greater detection efficiency relative to other techniques.

scholarly journals Distribution and seasonal differences in Pacific Lamprey andLampetraspp eDNA across 18 Puget Sound watersheds

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4496 ◽  
Author(s):  
Carl O. Ostberg ◽  
Dorothy M. Chase ◽  
Michael C. Hayes ◽  
Jeffrey J. Duda
Keyword(s):  
North America ◽  
Detection Rate ◽  
Puget Sound ◽  
Environmental Dna ◽  
Probe Design ◽  
Significant Finding ◽  
Ecological Communities ◽  
Detection Rates ◽  
Pacific Lamprey ◽  
The Pacific

Lampreys have a worldwide distribution, are functionally important to ecological communities and serve significant roles in many cultures. In Pacific coast drainages of North America, lamprey populations have suffered large declines. However, lamprey population status and trends within many areas of this region are unknown and such information is needed for advancing conservation goals. We developed two quantitative PCR-based, aquatic environmental DNA (eDNA) assays for detection of Pacific Lamprey (Entosphenus tridentatus) andLampetraspp, using locked nucleic acids (LNAs) in the probe design. We used these assays to characterize the spatial distribution of lamprey in 18 watersheds of Puget Sound, Washington, by collecting water samples in spring and fall. Pacific Lamprey andLampetraspp were each detected in 14 watersheds and co-occurred in 10 watersheds. Lamprey eDNA detection rates were much higher in spring compared to fall. Specifically, the Pacific Lamprey eDNA detection rate was 3.5 times higher in spring and theLampetraspp eDNA detection rate was 1.5 times higher in spring even though larval lamprey are present in streams year-round. This significant finding highlights the importance of seasonality on eDNA detection. Higher stream discharge in the fall likely contributed to reduced eDNA detection rates, although seasonal life history events may have also contributed. These eDNA assays differentiate Pacific Lamprey andLampetraspp across much of their range along the west coast of North America. Sequence analysis indicates the Pacific Lamprey assay also targets otherEntosphenusspp and indicates theLampetraspp assay may have limited or no capability of detectingLampetrain some locations south of the Columbia River Basin. Nevertheless, these assays will serve as a valuable tool for resource managers and have direct application to lamprey conservation efforts, such as mapping species distributions, occupancy modeling, and monitoring translocations and reintroductions.

scholarly journals Assessment of Environmental DNA for Detecting Presence of Imperiled Aquatic Amphibian Species in Isolated Wetlands

2015 ◽  
Vol 6 (2) ◽  
pp. 498-510 ◽  
Author(s):  
Anna M. McKee ◽  
Daniel L. Calhoun ◽  
William J. Barichivich ◽  
Stephen F. Spear ◽  
Caren S. Goldberg ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Water Samples ◽  
Survey Methods ◽  
Pinus Palustris ◽  
Environmental Dna ◽  
Breeding Habitat ◽  
Target Species ◽  
Amphibian Species ◽  
Ambystoma Bishopi ◽  
Ambystoma Cingulatum

Abstract Environmental DNA (eDNA) is an emerging tool that allows low-impact sampling for aquatic species by isolating DNA from water samples and screening for DNA sequences specific to species of interest. However, researchers have not tested this method in naturally acidic wetlands that provide breeding habitat for a number of imperiled species, including the frosted salamander (Ambystoma cingulatum), reticulated flatwoods salamanders (Ambystoma bishopi), striped newt (Notophthalmus perstriatus), and gopher frog (Lithobates capito). Our objectives for this study were to develop and optimize eDNA survey protocols and assays to complement and enhance capture-based survey methods for these amphibian species. We collected three or more water samples, dipnetted or trapped larval and adult amphibians, and conducted visual encounter surveys for egg masses for target species at 40 sites on 12 different longleaf pine (Pinus palustris) tracts. We used quantitative PCRs to screen eDNA from each site for target species presence. We detected flatwoods salamanders at three sites with eDNA but did not detect them during physical surveys. Based on the sample location we assumed these eDNA detections to indicate the presence of frosted flatwoods salamanders. We did not detect reticulated flatwoods salamanders. We detected striped newts with physical and eDNA surveys at two wetlands. We detected gopher frogs at 12 sites total, three with eDNA alone, two with physical surveys alone, and seven with physical and eDNA surveys. We detected our target species with eDNA at 9 of 11 sites where they were present as indicated from traditional surveys and at six sites where they were not detected with traditional surveys. It was, however, critical to use at least three water samples per site for eDNA. Our results demonstrate eDNA surveys can be a useful complement to traditional survey methods for detecting imperiled pond-breeding amphibians. Environmental DNA may be particularly useful in situations where detection probability using traditional survey methods is low or access by trained personnel is limited.

Estimating tadpole-detection rates using visual field surveys: effects of survey time, tadpole species and tadpole density

2017 ◽  
Vol 44 (2) ◽  
pp. 147 ◽  
Author(s):  
N. Iwai
Keyword(s):  
Visual Field ◽  
Detection Probability ◽  
Detection Rate ◽  
Negative Relationship ◽  
Visual Observation ◽  
Target Species ◽  
Detection Rates ◽  
Field Surveys ◽  
Detection Probabilities ◽  
Species Occupancy

Context When understanding species occupancy, estimation of detection probability for the target species is often required, provided by repeated surveys. However, if the actual detection probability of the species is determined experimentally, such estimates are not required, and the reliability of the occupancy data obtained by a particular survey effort can be determined. Aims The aim of this study was to determine the detection rate of tadpoles using visual field surveys, as well as to explore the effects of survey time, species and tadpole density on the tadpole-detection rate. The suitability of visual surveys for detecting tadpole occupancy was also assessed. Methods Batch-identified tadpoles were released into several pools and repeatedly counted over successive days to calculate detection rates using visual observation. In Experiment 1, the effects of tag colour, survey time (morning vs night) and species on the detection rates of two species of tadpoles (Babina subaspera and Odorrana splendida) were examined. In Experiment 2, the effects of tadpole density on O. splendida were examined. Key results Detection rates varied by survey time, species and tadpole density; mean rates ranged from 0.2 to 0.6 for B. subaspera and 0.4 to 0.8 for O. splendida, with higher rates at night. There was a negative relationship between detection rate and tadpole density. Based on these detection rates, it was calculated that single visual surveys of O. splendida tadpoles can achieve detection probabilities near 1.0 when more than four individuals occur in a patch. Conclusions Variations in detection probability should be considered in field surveys. If the factors that cause variations in detection rates are controlled, visual surveys of tadpoles should, at least in some species, provide detection probabilities near 1.0. Implications When repeated surveys to estimate species occupancy are not practicable, determination of the actual detection probability of the target species using real detection rates provides a robust alternative approach.

scholarly journals Training: improving antenatal detection and outcomes of congenital heart disease

2018 ◽  
Vol 7 (4) ◽  
pp. e000276 ◽  
Author(s):  
Orhan Uzun ◽  
Julia Kennedy ◽  
Colin Davies ◽  
Anthony Goodwin ◽  
Nerys Thomas ◽  
...  
Keyword(s):  
Congenital Heart Disease ◽  
Detection Rate ◽  
Congenital Heart ◽  
Training Programme ◽  
Referral Rate ◽  
Cardiac Anomaly ◽  
Cardiac Ultrasound ◽  
Detection Rates ◽  
Antenatal Detection ◽  
The Uk

ObjectivesThis study describes the design, delivery and efficacy of a regional fetal cardiac ultrasound training programme. This programme aimed to improve the antenatal detection of congenital heart disease (CHD) and its effect on fetal and postnatal outcomes.Design setting and participantsThis was a prospective study that compared antenatal CHD detection rates by professionals from 13 hospitals in Wales before and after engaging in our ‘skills development programme’. Existing fetal cardiac practice and perinatal outcomes were continuously audited and progressive targets were set. The work was undertaken by the Welsh Fetal Cardiovascular Network, Antenatal Screening Wales (ASW), a superintendent sonographer and a fetal cardiologist.InterventionsA core professional network was established, engaging all stakeholders (including patients, health boards, specialist commissioners, ASW, ultrasonographers, radiologists, obstetricians, midwives and paediatricians). A cardiac educational lead (midwife, superintendent sonographer, radiologist, obstetrician, or a fetal medicine specialist) was established in each hospital. A new cardiac anomaly screening protocol (‘outflow tract view’) was created and training on the new protocol was systematically delivered at each centre. Data were prospectively collected and outcomes were continuously audited: locally by the lead fetal cardiologist; regionally by the Congenital Anomaly Register and Information Service in Wales; and nationally by the National Institute for Cardiac Outcomes and Research (NICOR) in the UK.Main outcome measuresPatient satisfaction; improvements in individual sonographer skills, confidence and competency; true positive referral rate; local hospital detection rate; national detection rate of CHD; clinical outcomes of selected cardiac abnormalities; reduction of geographical health inequality; cost efficacy.ResultsHigh levels of patient satisfaction were demonstrated and the professional skill mix in each centre was improved. The confidence and competency of sonographers was enhanced. Each centre demonstrated a reduction in the false-positive referral rate and a significant increase in cardiac anomaly detection rate. According to the latest NICOR data, since implementing the new training programme Wales has sustained its status as UK lead for CHD detection. Health outcomes of children with CHD have improved, especially in cases of transposition of the great arteries (for which no perinatal mortality has been reported since 2008). Standardised care led to reduction of geographical health inequalities with substantial cost saving to the National Health Service due to reduced false-positive referral rates. Our successful model has been adopted by other fetal anomaly screening programmes in the UK.ConclusionsAntenatal cardiac ultrasound mass training programmes can be delivered effectively with minimal impact on finite healthcare resources. Sustainably high CHD detection rates can only be achieved by empowering the regional screening workforce through continuous investment in lifelong learning activities. These should be underpinned by high quality service standards, effective care pathways, and robust clinical governance and audit practices.

scholarly journals Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tatsuhiko Hoshino ◽  
Ryohei Nakao ◽  
Hideyuki Doi ◽  
Toshifumi Minamoto
Keyword(s):  
Fish Species ◽  
High Throughput Sequencing ◽  
Correlation Coefficients ◽  
Environmental Dna ◽  
Digital Pcr ◽  
Absolute Quantification ◽  
Taqman Probe ◽  
Individual Species ◽  
Natural Environments ◽  
Target Sequence

AbstractThe combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in natural environments, we have to obtain quantitative eDNA data, usually via individual assays for each species. The recently developed quantitative sequencing (qSeq) technique enables simultaneous phylogenetic identification and quantification of individual species by counting random tags added to the 5′ end of the target sequence during the first DNA synthesis. Here, we applied qSeq to eDNA analysis to test its effectiveness in biodiversity monitoring. eDNA was extracted from water samples taken over 4 days from aquaria containing five fish species (Hemigrammocypris neglectus, Candidia temminckii, Oryzias latipes, Rhinogobius flumineus, and Misgurnus anguillicaudatus), and quantified by qSeq and microfluidic digital PCR (dPCR) using a TaqMan probe. The eDNA abundance quantified by qSeq was consistent with that quantified by dPCR for each fish species at each sampling time. The correlation coefficients between qSeq and dPCR were 0.643, 0.859, and 0.786 for H. neglectus, O. latipes, and M. anguillicaudatus, respectively, indicating that qSeq accurately quantifies fish eDNA.

scholarly journals Mortality due to primary brain tumours in China and detection rate in people with suspected symptoms: a nationally representative cross-sectional survey

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Bin Jiang ◽  
Hongmei Liu ◽  
Dongling Sun ◽  
Haixin Sun ◽  
Xiaojuan Ru ◽  
...  
Keyword(s):  
Brain Tumour ◽  
Brain Tumours ◽  
Detection Rate ◽  
Epidemiological Data ◽  
Cross Sectional Survey ◽  
Cross Sectional ◽  
Detection Rates ◽  
Primary Brain Tumours ◽  
Symptom Screening ◽  
Nationally Representative

Abstract Background and purpose Epidemiological data on primary brain tumours (PBTs) are lacking due to the difficulty in case ascertainment among the population. Thus, we aimed to estimate mortality due to PBTs in China nationwide and the detection rate in people with suspected symptoms. Methods A multistage, complex sampling survey regarding mortality due to PBTs in Chinese individuals was carried out by reviewing all causes of death within a year. The detection rates in people with suspected symptoms were estimated based on PBT symptom screening and neurologist reviews and compared between groups by logistic regression analysis. Results Weighted mortality due to PBT was 1.6 (0.8–3.3) per 100,000 population in Chinese individuals, 1.8 (0.7–4.6) per 100,000 population in men, and 1.5 (0.5–4.5) per 100,000 population in women. Among 14,990 people with suspected symptoms, the PBT detection rate was 306.9 (95% CI 224.7–409.3) per 100,000 population in the total population, 233.0 (95% CI 135.7–373.1) per 100,000 population in men, and 376.9 (95% CI 252.4–546.3) per 100,000 population in women. People with an unsteady gait (OR 2.46; 95% CI 1.09–5.51; P=0.029), visual anomalies (3.84; 1.88–7.85; P<0.001), and headache (2.06; 1.10–3.86; P=0.023) were more likely to have a brain tumour than those without corresponding symptoms, while people with dizziness/vertigo were less likely to have a brain tumour than those without corresponding symptoms (0.45; 0.23–0.87; P=0.017). Conclusions Mortality due to PBT in China was low, with a nationwide estimate of 21,215 (10,427–43,165) deaths attributable to PBTs annually. However, the detection rate of PBTs can be greatly improved based on symptom screening in the population.

scholarly journals Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mizuki Ogata ◽  
Reiji Masuda ◽  
Hiroya Harino ◽  
Masayuki K. Sakata ◽  
Makoto Hatakeyama ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Oil Spills ◽  
Sediment Cores ◽  
Environmental Dna ◽  
Target Species ◽  
Tank Experiment ◽  
Polycyclic Aromatic ◽  
Flow Through ◽  
High Concentrations ◽  
One Year

AbstractEnvironmental DNA (eDNA) can be a powerful tool for detecting the distribution and abundance of target species. This study aimed to test the longevity of eDNA in marine sediment through a tank experiment and to use this information to reconstruct past faunal occurrence. In the tank experiment, juvenile jack mackerel (Trachurus japonicus) were kept in flow-through tanks with marine sediment for two weeks. Water and sediment samples from the tanks were collected after the removal of fish. In the field trial, sediment cores were collected in Moune Bay, northeast Japan, where unusual blooms of jellyfish (Aurelia sp.) occurred after a tsunami. The samples were analyzed by layers to detect the eDNA of jellyfish. The tank experiment revealed that after fish were removed, eDNA was not present in the water the next day, or subsequently, whereas eDNA was detectable in the sediment for 12 months. In the sediment core samples, jellyfish eDNA was detected at high concentrations above the layer with the highest content of polycyclic aromatic hydrocarbons, reflecting tsunami-induced oil spills. Thus, marine sediment eDNA preserves a record of target species for at least one year and can be used to reconstruct past faunal occurrence.

scholarly journals The Effects of Social Distancing Policies on non-SARS-CoV-2 Respiratory Pathogens

2021 ◽  
Author(s):  
Jeff Nawrocki ◽  
Katherine Olin ◽  
Martin C Holdrege ◽  
Joel Hartsell ◽  
Lindsay Meyers ◽  
...  
Keyword(s):  
Public Health ◽  
Influenza A ◽  
Detection Rate ◽  
Respiratory Illness ◽  
Respiratory Pathogens ◽  
Public Health Response ◽  
Mixed Effect ◽  
Detection Rates ◽  
Social Distancing ◽  
The Impact

Abstract Background The initial focus of the US public health response to COVID-19 was the implementation of numerous social distancing policies. While COVID-19 was the impetus for imposing these policies, it is not the only respiratory disease affected by their implementation. This study aimed to assess the impact of social distancing policies on non-SARS-CoV-2 respiratory pathogens typically circulating across multiple US states. Methods Linear mixed-effect models were implemented to explore the effects of five social distancing policies on non-SARS-CoV-2 respiratory pathogens across nine states from January 1 through May 1, 2020. The observed 2020 pathogen detection rates were compared week-by-week to historical rates to determine when the detection rates were different. Results Model results indicate that several social distancing policies were associated with a reduction in total detection rate, by nearly 15%. Policies were associated with decreases in pathogen circulation of human rhinovirus/enterovirus and human metapneumovirus, as well as influenza A, which typically decrease after winter. Parainfluenza viruses failed to circulate at historical levels during the spring. Total detection rate in April 2020 was 35% less than historical average. Many of the pathogens driving this difference fell below historical detection rate ranges within two weeks of initial policy implementation. Conclusion This analysis investigated the effect of multiple social distancing policies implemented to reduce transmission of SARS-CoV-2 on non-SARS-CoV-2 respiratory pathogens. These findings suggest that social distancing policies may be used as an impactful public health tool to reduce communicable respiratory illness.

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