Influence of accuracy, repeatability and detection probability in the reliability of species-specific eDNA based approaches.
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ABSTRACT:
SUBMITTER: Mauvisseau Q
PROVIDER: S-EPMC6345946 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Environmental DNA (eDNA) holds great promise for conservation applications like the monitoring of invasive or imperiled species, yet this emerging technique requires ongoing testing in order to determine the contexts over which it is effective. For example, little research to date has evaluated how seasonality of organism behavior or activity may influence detection probability of eDNA. We applied eDNA to survey for two highly imperiled species endemic to the upper Black Warrior River basin in Alabama, US: the Black Warrior Waterdog (Necturus alabamensis) and the Flattened Musk Turtle (Sternotherus depressus). Importantly, these species have contrasting patterns of seasonal activity, with N. alabamensis more active in the cool season (October-April) and S. depressus more active in the warm season (May-September). We surveyed sites historically occupied by these species across cool and warm seasons over two years with replicated eDNA water samples, which were analyzed in the laboratory using species-specific quantitative PCR (qPCR) assays. We then used occupancy estimation with detection probability modeling to evaluate both the effects of landscape attributes on organism presence and season of sampling on detection probability of eDNA. Importantly, we found that season strongly affected eDNA detection probability for both species, with N. alabamensis having higher eDNA detection probabilities during the cool season and S. depressus have higher eDNA detection probabilities during the warm season. These results illustrate the influence of organismal behavior or activity on eDNA detection in the environment and identify an important role for basic natural history in designing eDNA monitoring programs.
| S-EPMC5077074 | biostudies-literature
Project description:The effectiveness and accuracy of detection using environmental DNA (eDNA) is dependent on understanding the influence laboratory methods such as DNA extraction and PCR strategies have on detection probability. Ideally choice of sampling and extraction method will maximize eDNA yield and detection probability. Determining the survey effort required to reach a satisfactory detection probability (via increased PCR replicates or more sampling) could compensate for a lower eDNA yield if the sampling and extraction method has other advantages for a study, species or system. I analysed the effect of three different sampling and extraction methods on eDNA yield, detection probability and PCR replication for detecting the endangered freshwater fish Macquaria australasica from water samples. The impact of eDNA concentration, PCR strategy, target amplicon size and two marker regions: 12S (a mitochondrial gene) and 18S (a nuclear gene) was also assessed. The choice of sampling and extraction method and PCR strategy, rather than amplicon size and marker region, had the biggest effect on detection probability and PCR replication. The PCR replication effort required to achieve a detection probability of 0.95, ranged from 2 to 6 PCR replicates depending on the laboratory method used. As all methods yielded eDNA from which M. australasica was detected using the three target amplicons, differences in eDNA yield and detection probability between the three methods could be mitigated by determining the appropriate PCR replication effort. Evaluating the effect sampling and extraction methods will have on the detection probability and determining the laboratory protocols and PCR replication required to maximize detection and minimize false positives and negatives is a useful first step for eDNA occupancy studies.
| S-EPMC4798829 | biostudies-literature
Project description:BackgroundOver the past decade, environmental DNA (eDNA) has become a resourceful tool in conservation and biomonitoring. Environmental DNA has been applied in a variety of environments, but the application to studies of marine fish, particularly at tropical latitudes, are limited. Since many commercially important Caribbean fishes are overexploited, these species are optimal candidates to explore the use of this method as a biomonitoring tool. Specifically, for many of these species, the formation of fish spawning aggregations (FSAs) marks a critical life history event where fishes will gather in large numbers for reproduction. These FSAs are ephemeral in nature, lasting only a few days, but are predictable in time and space which makes them susceptible to overfishing.MethodsIn this study, we test the feasibility of using an eDNA sampling approach (water and sediment collection) to detect the presence of known FSAs off the west coast of Puerto Rico, with cytochrome c oxidase subunit 1 (CO1) and 12S rRNA (12S) primers designed to target specific species. A total of 290 eDNA samples were collected and, of those, 206 eDNA samples were processed. All eDNA samples varied in DNA concentration, both between replicates and collection methods. A total of 12 primer sets were developed and tested using traditional PCR and qPCR.ResultsDespite validation of primer accuracy and sample collection during known peak spawning times, the use of traditional PCR and qPCR with both molecular markers failed to produce species-specific amplification. Thus, a trial test was conducted using the CO1 primers in which target fish DNA was 'spiked' at various concentrations into the respective eDNA samples to determine the target species DNA concentration limit of detection. Upon successful amplification of the trial, results indicated that eDNA samples were below the detection threshold of our methods, suggesting that the number of fish present at the spawning aggregations was inadequate for single-species detection methods. In addition, elements such as the unavoidable presence of non-target DNA, oceanic environmental conditions, shedding rates of target fish, among other biotic and abiotic factors could have affected DNA persistence and degradation rates at the sites.ConclusionWe provide recommendations for species-specific fish detection in lower latitudes, and suggestions for studies aiming to monitor or detect fish spawning aggregations using eDNA sampling.
| S-EPMC9899429 | biostudies-literature
Project description:Genetic analysis of airborne plant material has historically focused (generally implicitly rather than as a stated goal) on pollen from anemophilous (wind-pollinated) species, such as in multiple studies examining the relationship of allergens to human health. Inspired by the recent influx of literature applying environmental DNA (eDNA) approaches to targeted-species and whole-ecosystem study, we conducted a proof-of-concept experiment to determine whether airborne samples reliably detect genetic material from non-anemophilous species that may not be releasing large plumes of pollen. We collected airborne eDNA using Big Spring Number Eight dust traps and quantified the amount of eDNA present for a flowering wind-pollinated genus (Bouteloua) and insect-pollinated honey mesquite (Prosopis glandulosa) that was not flowering at the time of the study. We were able to detect airborne eDNA from both species. Since honey mesquite is insect-pollinated and was not flowering during the time of this study, our results confirm that airborne eDNA consists of and can detect species through more than just pollen. Additionally, we were able to detect temporal patterns reflecting Bouteloua reproductive ecology and suggest that airborne honey mesquite eDNA responded to weather conditions during our study. These findings suggest a need for more study of the ecology of airborne eDNA to uncover its potential for single-species and whole-community research and management in terrestrial ecosystems.
| S-EPMC6867632 | biostudies-literature
Project description:PURPOSE:Corneal and anterior segment diseases cause most of the urgent visits to eye care professionals. We evaluated the diagnostic accuracy of detecting corneal diseases using external photographs from 2 portable cameras for telemedicine purposes. METHODS:This is a prospective study of adults with a clinical diagnosis of corneal pathology including corneal abrasions, ulcers, scars, and pterygia. A cornea specialist provided the gold standard diagnosis by slit-lamp examination. Images of both eyes were obtained using iTouch 5S and Nidek VersaCam cameras in multiple gazes and interpreted by 3 cornea specialists for the presence of pathology. Accuracy to detect disease was compared with gold standard diagnosis, stratified by the camera and grader. Reliability was evaluated with weighted kappa statistics. Graders assessed image quality on a Likert scale from 1 (poor) to 9 (optimal). RESULTS:A total of 198 eyes (110 subjects) were photographed. By gold standard diagnosis, 59 eyes (30%) had corneal scars, 34 (17%) had ulcers, 13 (7%) had abrasions, 10 (5%) had pterygia, and 82 (41%) were normal. Sensitivity to detect AS pathology ranged from 54% to 71% for the iTouch and 66% to 75% for the Nidek, across graders; specificity ranged from 82% to 96% for the iTouch and 91% to 98% for the Nidek. The intergrader reliability was moderate to strong (kappa ranges: 0.54-0.71 for the iTouch; 0.75-0.76 for the Nidek). Quality ratings were variable between graders. CONCLUSIONS:External photographs taken by standard, nonenhanced portable cameras and interpreted remotely by ophthalmologist graders yielded sensitivity values that are not yet suitable for telemedicine applications. Additional work is needed to improve the ability to detect AS pathology remotely.
| S-EPMC5646384 | biostudies-literature
Project description:Reliability of data has become a major concern in the course of the reproducibility crisis. Especially when studying animal behavior, confounding factors such as novelty of the test apparatus can lead to a wide variability of data which may mask treatment effects and consequently lead to misinterpretation. Habituation to the test situation is a common practice to circumvent novelty induced increases in variance and to improve the reliability of the respective measurements. However, there is a lack of published empirical knowledge regarding reasonable habituation procedures and a method validation seems to be overdue. This study aimed at setting up a simple strategy to increase reliability of behavioral data measured in a familiar test apparatus. Therefore, exemplary data from mice tested in an Open Field (OF) arena were used to elucidate the potential of habituation and how reliability of measures can be confirmed by means of a repeatability analysis using the software R. On seven consecutive days, male C57BL/6J, BALB/cJ and 129S1/SvImJ mice were tested in an OF arena once daily and individual mouse behavior was recorded. A repeatability analysis was conducted with regard to repeated trials of habituation. Our data analysis revealed that monitoring animal behavior during habituation is important to determine when individual differences of the measurements are stable. Repeatability values from distance travelled and average activity increased over the habituation period, revealing that around 60% of the variance of the data can be explained by individual differences between mice. The first day of habituation was significantly different from the following 6 days. A three-day habituation period appeared to be sufficient in this study. Overall, these results emphasize the importance of habituation and in depth analysis of habituation data to define the correct starting point of the experiment for improving the reliability and reproducibility of experimental data.
| S-EPMC7117744 | biostudies-literature
Project description:Detection of Plasmodium ovale by use of a nested PCR assay with a novel Plasmodium ovale primer set was superior to detection of Plasmodium ovale by real-time PCR assays. Nested PCR was also better at detecting P. malariae. The detection of P. ovale in many patients first admitted >2 months following their return to Italy indicated that P. ovale relapses are common.
| S-EPMC1865880 | biostudies-literature
Project description:Purpose:Researchers have long noted speech recognition variability that is not explained by the pure-tone audiogram. Previous work (Souza, Wright, Blackburn, Tatman, & Gallun, 2015) demonstrated that a small number of listeners with sensorineural hearing loss utilized different types of acoustic cues to identify speechlike stimuli, specifically the extent to which the participant relied upon spectral (or temporal) information for identification. Consistent with recent calls for data rigor and reproducibility, the primary aims of this study were to replicate the pattern of cue use in a larger cohort and to verify stability of the cue profiles over time. Method:Cue-use profiles were measured for adults with sensorineural hearing loss using a syllable identification task consisting of synthetic speechlike stimuli in which spectral and temporal dimensions were manipulated along continua. For the first set, a static spectral shape varied from alveolar to palatal, and a temporal envelope rise time varied from affricate to fricative. For the second set, formant transitions varied from labial to alveolar and a temporal envelope rise time varied from approximant to stop. A discriminant feature analysis was used to determine to what degree spectral and temporal information contributed to stimulus identification. A subset of participants completed a 2nd visit using the same stimuli and procedures. Results:When spectral information was static, most participants were more influenced by spectral than by temporal information. When spectral information was dynamic, participants demonstrated a balanced distribution of cue-use patterns, with nearly equal numbers of individuals influenced by spectral or temporal cues. Individual cue profile was repeatable over a period of several months. Conclusion:In combination with previously published data, these results indicate that listeners with sensorineural hearing loss are influenced by different cues to identify speechlike sounds and that those patterns are stable over time.
| S-EPMC6198918 | biostudies-other
Project description:Surveying terrestrial species across diverse habitats is important for predicting species' distributions and implementing conservation actions. For vocalising species, passive acoustic monitoring (PAM) is increasing in popularity; however, survey design rarely considers the factors influencing the timing and occurrence of vocalisations and in turn, how they may influence detectability of the species. Here, we use the koala (Phascolarctos cinereus) as a case study to show how PAM can be used to first examine the factors influencing vocalisations, and then use occupancy modelling to make recommendations on survey design for the species. We used automated recording units to monitor koala vocalisations at ten sites between August 2016 and January 2017. The timing of male koala vocalisations was linked to time of sunset with vocalisations increasing two hours prior to sunset and peaking at four hours after sunset. Vocalisations had a seasonal trend, increasing from the early to middle stage of the breeding season. Koala population density and stage of the breeding season had more influence on detection probability than daily sampling schedule. Where population density was low, and during the early stage of the breeding season, 7 survey nights (recording for 6 hours from 20:00h to 02:00h; i.e. the period of peak bellowing activity) were required to be 95% confident of a site-specific absence. Our study provides an approach for designing effective passive acoustic surveys for terrestrial species.
| S-EPMC6051584 | biostudies-literature
Project description:OBJECTIVE: The aim of the present study was to evaluate the reliability of scout CT (sCT) lateral radiograph, in terms of diagnostic accuracy and intra- and interobserver agreement in the detection of vertebral fractures (VFs). METHODS: 300 CT examinations of the thoracic and/or lumbar spine were collected and independently analysed by 3 musculoskeletal radiologists in 2 different sessions. A semi-quantitative approach was used for VF assessment on sCT, and morphometric analysis was performed when a VF was suspected. Results of multiplanar sagittal CT reconstructions interpreted by the most expert radiologist were considered as gold standard. Arthrosis was also scored. Only vertebral bodies assessable by both sCT and gold standard were considered for the analysis. Area under the receiver operating characteristic curve (AUROC), Cohen's kappa statistic and linear-by-linear association were used for statistical analysis. RESULTS: 1522 vertebrae were considered (130 males and 170 females; ages, 73.0±2.8 years). 73 of 1522 (4.8%) VFs were identified in 34/300 patients (11.3%). In the detection of VFs, the sensitivity and specificity of sCT were 98.7% and 99.7%, respectively. Accuracy (AUROC=0.992±0.008), as well as interobserver agreement (k=0.968±0.008), was excellent. Intra-observer agreement was perfect (k=1.000). Performance of this method was independent of arthrosis, vertebral level and type and grade of VFs. CONCLUSION: sCT is a simple but very accurate method for the detection of VFs. It should be introduced as a spine evaluation tool for the detection of VFs in examinations that are performed for other diagnostic purposes. ADVANCES IN KNOWLEDGE: sCT lateral radiograph is an accurate tool for the detection of VFs. This technique may be used with several advantages in clinical practice.
| S-EPMC3854570 | biostudies-other