scholarly journals Multispecies site occupancy modeling and study design for spatially replicated environmental DNA metabarcoding

2021 ◽  
Author(s):  
Keiichi Fukaya ◽  
Natsuko Ito Kondo ◽  
Shin-Ichiro S. Matsuzaki ◽  
Taku Kadoya
Keyword(s):  
Study Design ◽  
Detection Efficiency ◽  
Site Occupancy ◽  
Environmental Dna ◽  
List Type ◽  
Bayesian Decision ◽  
Imperfect Detection ◽  
Efficient Manner ◽  
Species Detection ◽  
Multi Stage

AbstractEnvironmental DNA (eDNA) metabarcoding has become widely applied to gauge biodiversity in a noninvasive and cost-efficient manner. The detection of species using eDNA metabarcoding is, however, imperfect owing to various factors that can cause false negatives in the inherent multi-stage workflow.Imperfect detection in the multi-stage workflow of eDNA metabarcoding also raises an issue of study design: namely, how available resources should be allocated among the different stages to optimize survey efficiency.Here, we propose a variant of the multispecies site occupancy model for eDNA metabar-coding studies where samples are collected at multiple sites within a region of interest. This model describes the variation in sequence reads, the unique output of the high-throughput sequencers, in terms of the hierarchical workflow of eDNA metabarcoding and interspecific heterogeneity, allowing the decomposition of the sources of variation in the detectability of species throughout the different stages of the workflow. We also introduced a Bayesian decision analysis framework to identify the study design that optimizes the efficiency of species detection with a limited budget.An application of the model to freshwater fish communities in the Lake Kasumigaura watershed, in Japan, highlighted a remarkable inhomogeneity in the detectability of species, indicating a potential risk of the biased detection of specific species. Species with lower site occupancy probabilities tended to be difficult to detect as they had lower capture probabilities and lower dominance of the sequences. The expected abundance of sequence reads was predicted to vary by up to 23.5 times between species.An analysis of the study design suggested that ensuring multiple within-site replications of the environmental samples is preferred in order to achieve better species detection efficiency, provided that a throughput of tens of thousands of sequence reads was secured.The proposed framework makes the application of eDNA metabarcoding more error-tolerant, allowing ecologists to monitor ecological communities more efficiently.

scholarly journals The influence of dynamic environmental interactions on detection efficiency of acoustic transmitters in a large, deep, freshwater lake

2019 ◽  
Vol 7 (1) ◽  
Author(s):  
Natalie V. Klinard ◽  
Edmund A. Halfyard ◽  
Jordan K. Matley ◽  
Aaron T. Fisk ◽  
Timothy B. Johnson
Keyword(s):  
Study Design ◽  
Environmental Conditions ◽  
Power Output ◽  
Environmental Variables ◽  
Acoustic Telemetry ◽  
Detection Efficiency ◽  
Data Interpretation ◽  
Heterogeneous Environments ◽  
Depth Range ◽  
Dynamic Relationship

Abstract Background Acoustic telemetry is an increasingly common method used to address ecological questions about the movement, behaviour, and survival of freshwater and marine organisms. The variable performance of acoustic telemetry equipment and ability of receivers to detect signals from transmitters have been well studied in marine and coral reef environments to inform study design and improve data interpretation. Despite the growing use of acoustic telemetry in large, deep, freshwater systems, detection efficiency and range, particularly in relation to environmental variation, are poorly understood. We used an array of 90 69-kHz acoustic receivers and 8 sentinel range transmitters of varying power output deployed at different depths and locations approximately 100–9500 m apart for 215 days to evaluate how the detection efficiency of acoustic receivers varied spatially and temporally in relation to environmental conditions. Results The maximum distance that tags were detected ranged from 5.9 to 9.3 km. Shallow tags consistently had lower detection efficiency than deep tags of the same power output and detection efficiency declined through the winter months (December–February) of the study. In addition to the distance between tag and receiver, thermocline strength, surface water velocity, ice thickness, water temperature, depth range between tag and receiver, and number of fish detections contributed to explaining variation in detection efficiency throughout the study period. Furthermore, the most significant models incorporated interactions between several environmental variables and tag–receiver distance, demonstrating the complex temporal and spatial relationships that exist in heterogeneous environments. Conclusions Relying on individual environmental variables in isolation to interpret receiver performance, and thus animal behaviour, may be erroneous when detection efficiency varies across distances, depths, or tag types. As acoustic telemetry becomes more widely used to study ecology and inform management, it is crucial to understand its limitations in heterogeneous environments, such as freshwater lakes, to improve the quality and interpretation of data. We recommend that in situ range testing and retrospective analysis of detection efficiency be incorporated into study design for telemetry projects. Furthermore, we caution against oversimplifying the dynamic relationship between detection efficiency and environmental conditions for the sake of producing a correction that can be applied directly to detection data of tagged animals when the intended correction may not be justified.

Environmental DNA (eDNA): A Promising Biological Survey Tool for Aquatic Species Detection

2018 ◽  
Vol 72 (3) ◽  
pp. 211-228 ◽  
Author(s):  
Debabrata Senapati ◽  
Manojit Bhattacharya ◽  
Avijit Kar ◽  
Deep Sankar Chini ◽  
Basanta Kumar Das ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Aquatic Species ◽  
Species Detection ◽  
Survey Tool ◽  
Biological Survey

Effect of Sieve Unit Inclination Angle in a Rotary Cleaning Device for Barley Grain

2020 ◽  
Vol 63 (3) ◽  
pp. 609-618
Author(s):  
Zbigniew Krzysiak ◽  
Waldemar Samociuk ◽  
Janusz Zarajczyk ◽  
Karolina Beer-Lech ◽  
Grzegorz Bartnik ◽  
...  
Keyword(s):  
Inclination Angle ◽  
Barley Grain ◽  
Separation Coefficient ◽  
List Type ◽  
Technological Parameters ◽  
Cleaning Efficiency ◽  
Multi Stage ◽  
Cereal Grain ◽  
Cleaning Device

Highlights Cleaning cereal grain after harvest is very important for the quality of the product. Technological progress enables the design of new equipment for cleaning cereal grain. Grain segregation allows selecting the best grain to increase yields. The quality of segregation depends on the technological parameters of the device. Abstract. This article presents the results of laboratory tests of a new rotary cleaning device used for the separation and cleaning of barley grain. This device has the characteristics of a multi-stage screen assisted by an air stream (i.e., pneumo-separation). The prototype was constructed at the University of Life Sciences in Lublin, Poland. The tests were conducted on a test stand, which allowed changes in the operating parameters of the cleaning device and their measurement. The tests included determining the influence of the sieve drum inclination angle (a) on the effectiveness and efficiency of barley grain cleaning. The tests were carried out using two drum rotational speeds: 5 rpm and 75 rpm. The quality of the separation and cleaning of barley grain was evaluated using six cleaning process parameters: plump grain separation coefficient (Spg), fine grain separation coefficient (Sfg), fine impurities separation coefficient (Sfi), chaff separation coefficient (Sch), total coefficient of cleaning effectiveness (E), and plump grain cleaning efficiency (qpg). The results showed significant effects of the sieve drum inclination angle on the efficiency and effectiveness of barley grain cleaning. Keywords: Barley grain, Conical sieve, Grain separation, Rotary cleaning device.

Evaluation of biodiversity metrics through environmental DNA metabarcoding compared with visual and capture surveys in river fish community

2019 ◽  
Author(s):  
Hideyuki Doi ◽  
Ryutei Inui ◽  
Shunsuke Matsuoka ◽  
Yoshihisa Akamatsu ◽  
Masuji Goto ◽  
...  
Keyword(s):  
Community Dynamics ◽  
Species Turnover ◽  
Environmental Dna ◽  
List Type ◽  
Visual Capture ◽  
Gamma Diversity ◽  
Community Patterns ◽  
Community Assemblages ◽  
Study Sites ◽  
River Fish

AbstractInformation on alpha (local), beta (between habitats), and gamma (regional) diversity is fundamental to understanding biodiversity as well as the function and stability of community dynamics. The methods like environmental DNA (eDNA) metabarcoding are currently considered useful to investigate biodiversity.We compared the performance of eDNA metabarcoding with visual and capture surveys in estimating alpha/gamma diversity and the variation of the community assemblages of river fish communities, particularly considering community nestedness and turnover.In five rivers across west Japan, with comparing to visual/capture surveys, eDNA metabarcoding detected more species in the study sites, consequently the overall number of species in the region (i.e., gamma diversity) was higher. In particular, the species found by visual/capture surveys were encompassed by those by eDNA metabarcoding.With analyzing the community assemblages between the rivers, we showed the different results between the both methods. While, in the same river, the nestedness and species turnover changing from upstream to downstream did not significantly differ between the both methods. Our results suggest that eDNA metabarcoding may be suitable method, especially for understanding regional community patterns, for fish monitoring in rivers.

scholarly journals Short COI markers for freshwater macroinvertebrate metabarcoding

2017 ◽  
Author(s):  
Ecaterina Edith Vamos ◽  
Vasco Elbrecht ◽  
Florian Leese
Keyword(s):  
In Silico ◽  
Detection Efficiency ◽  
In Silico Analysis ◽  
Environmental Dna ◽  
Degraded Dna ◽  
Macroinvertebrate Communities ◽  
Universal Primer ◽  
Primer Sets ◽  
Mock Communities

Species diversity of metazoan bulk samples can be rapidly assessed using cytochrome c oxidase I (COI) metabarcoding. However, in some applications often only degraded DNA is available, e.g. from poorly conserved museum specimens, environmental DNA (eDNA) filtered from water or gut content analyses. Here universal primer sets targeting only a short COI fragment are advantageous, as they often can still amplify short DNA fragments. Using PrimerMiner, we optimised two universal primer sets targeting freshwater macroinvertebrates based on NCBI and BOLD reference sequences. The fwh1 and fwh2 primer sets targeting a 178 and 205 bp region were tested in vitro by sequencing previously used freshwater macroinvertebrate mock communities as well as three monitoring samples from Romanian streams of unknown composition. They were further evaluated in silico for their suitability to amplify other insect groups. The fwh1 primer sets showed the most consistent amplification in silico and in vitro , detecting 92% of the taxa present in the mock communities, and allowing clear differentiation between the three macroinvertebrate communities from the Romanian streams. In silico analysis indicates that the short primers are likely to perform well even for non-freshwater insects. Comparing the performance of the new fwh1 primer sets to a highly degenerate primer set targeting a longer fragment (BF2+BR2) revealed that detection efficiency is slightly lower for the new primer set. Nevertheless, the shorter new primer pairs might be useful for studies that have to rely on degraded or poorly conserved DNA and thus be of importance for biomonitoring, conservation biological or molecular ecological studies. Furthermore, our study highlights the need for in silico evaluation of primer sets in order to detect design errors in primers (fwhR2) and find optimal universal primer sets for the target taxa of interest.

scholarly journals Non-invasive surveys of mammalian viruses using environmental DNA

2020 ◽  
Author(s):  
Niccolò Alfano ◽  
Anisha Dayaram ◽  
Jan Axtner ◽  
Kyriakos Tsangaras ◽  
Marie-Louise Kampmann ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Environmental Dna ◽  
List Type ◽  
Dna Viruses ◽  
Remote Areas ◽  
Hybridization Capture ◽  
Non Invasive ◽  
Zoonotic Viruses ◽  
Wildlife Pathogens ◽  
Rna And Dna

ABSTRACTEnvironmental DNA (eDNA) and invertebrate-derived DNA (iDNA) have been used to survey biodiversity non-invasively to mitigate difficulties of obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA have been applied to monitor known wildlife pathogens, however, most wildlife pathogens are unknown and often evolutionarily divergent.To detect and identify known and novel mammalian viruses from eDNA/iDNA sources, we used a curated set of RNA oligonucleotides as viral baits in a hybridization capture system coupled with high throughput sequencing.We detected multiple known and novel mammalian RNA and DNA viruses from multiple viral families from both waterhole eDNA and leech derived iDNA. Congruence was found between detected hosts and viruses identified in leeches and waterholes.Our results demonstrate that eDNA/iDNA samples represent an effective non-invasive resource for studying wildlife viral diversity and for detecting novel potentially zoonotic viruses prior to their emergence.

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