scholarly journals Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: a case study using coastal marine eDNA

2019 ◽  
Author(s):  
Beverly McClenaghan ◽  
Zacchaeus G. Compson ◽  
Mehrdad Hajibabaei
Keyword(s):  
Model Comparison ◽  
Environmental Dna ◽  
Model Assessment ◽  
Occupancy Models ◽  
Ecological Inference ◽  
Biodiversity Data ◽  
Imperfect Detection ◽  
Coastal Marine ◽  
Species Occupancy

AbstractEnvironmental DNA (eDNA) metabarcoding is an increasingly popular method for rapid biodiversity assessment. As with any ecological survey, false negatives can arise during sampling and, if unaccounted for, lead to biased results and potentially misdiagnosed environmental assessments. We developed a multi-scale, multi-species occupancy model for the analysis of community biodiversity data resulting from eDNA metabarcoding; this model accounts for imperfect detection and additional sources of environmental and experimental variation. We present methods for model assessment and model comparison and demonstrate how these tools improve the inferential power of eDNA metabarcoding data using a case study in a coastal, marine environment. Using occupancy models to account for factors often overlooked in the analysis of eDNA metabarcoding data will dramatically improve ecological inference, sampling design, and methodologies, empowering practitioners with an approach to wield the high-resolution biodiversity data of next-generation sequencing platforms.

scholarly journals Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: A case study using coastal marine eDNA

PLoS ONE ◽  
2020 ◽  
Vol 15 (3) ◽  
pp. e0224119 ◽  
Author(s):  
Beverly McClenaghan ◽  
Zacchaeus G. Compson ◽  
Mehrdad Hajibabaei
Keyword(s):  
Occupancy Models ◽  
Coastal Marine ◽  
Species Occupancy

Predicting fish species richness and habitat relationships using Bayesian hierarchical multispecies occupancy models

2020 ◽  
Vol 77 (3) ◽  
pp. 602-610
Author(s):  
Shannon White ◽  
Evan Faulk ◽  
Caleb Tzilkowski ◽  
Andrew Weber ◽  
Matthew Marshall ◽  
...  
Keyword(s):  
Species Richness ◽  
Fish Community ◽  
Fish Assemblages ◽  
Similar Species ◽  
Occupancy Models ◽  
Imperfect Detection ◽  
Modeling Framework ◽  
Bayesian Hierarchical ◽  
Recreation Area ◽  
Species Occupancy

Understanding how stream fishes respond to changes in habitat availability is complicated by low occurrence rates of many species, which in turn reduces the ability to quantify species–habitat relationships and account for imperfect detection in estimates of species richness. Multispecies occupancy models have been used sparingly in the analysis of fisheries data, but address the aforementioned deficiencies by allowing information to be shared among ecologically similar species, thereby enabling species–habitat relationships to be estimated for entire fish communities, including rare species. Here, we highlight the utility of hierarchical multispecies occupancy models for the analysis of fish community data and demonstrate the modeling framework on a stream fish community dataset collected in the Delaware Water Gap National Recreation Area, USA. In particular, we demonstrate the ability of the modeling framework to make inferences at the species-, guild-, and community-levels, thereby making it a powerful tool for understanding and predicting how environmental variables influence species occupancy probabilities and structure fish assemblages.

scholarly journals Site occupancy models in the analysis of environmental DNA presence/absence surveys: a case study of an emerging amphibian pathogen

2013 ◽  
Vol 4 (7) ◽  
pp. 646-653 ◽  
Author(s):  
Benedikt R. Schmidt ◽  
Marc Kéry ◽  
Sylvain Ursenbacher ◽  
Oliver J. Hyman ◽  
James P. Collins
Keyword(s):  
Site Occupancy ◽  
Environmental Dna ◽  
Occupancy Models ◽  
Amphibian Pathogen

Distribution of tiger salamanders in northern Sonora, Mexico: comparison of sampling methods and possible implications for an endangered subspecies

2021 ◽  
pp. 1-11
Author(s):  
Blake R. Hossack ◽  
Julio Alberto Lemos-Espinal ◽  
Brent H. Sigafus ◽  
Erin Muths ◽  
Gerardo Carreón Arroyo ◽  
...  
Keyword(s):  
Management Practices ◽  
Introgressive Hybridization ◽  
Environmental Dna ◽  
Tiger Salamander ◽  
Limited Information ◽  
Occupancy Models ◽  
Imperfect Detection ◽  
Tiger Salamanders ◽  
Land And Water Management ◽  
The Usa

Abstract Many aquatic species in the arid USA-Mexico borderlands region are imperiled, but limited information on distributions and threats often hinders management. To provide information on the distribution of the Western Tiger Salamander (Ambystoma mavortium), including the USA-federally endangered Sonoran Tiger Salamander (Ambystoma mavortium stebbinsi), we used traditional (seines, dip-nets) and modern (environmental DNA [eDNA]) methods to sample 91 waterbodies in northern Sonora, Mexico, during 2015-2018. The endemic Sonoran Tiger Salamander is threatened by introgressive hybridization and potential replacement by another sub-species of the Western Tiger Salamander, the non-native Barred Tiger Salamander (A. m. mavortium). Based on occupancy models that accounted for imperfect detection, eDNA sampling provided a similar detection probability (0.82 [95% CI: 0.56-0.94]) as seining (0.83 [0.46-0.96]) and much higher detection than dip-netting (0.09 [0.02-0.23]). Volume of water filtered had little effect on detection, possibly because turbid sites had greater densities of salamanders. Salamanders were estimated to occur at 51 sites in 3 river drainages in Sonora. These results indicate tiger salamanders are much more widespread in northern Sonora than previously documented, perhaps aided by changes in land and water management practices. However, because the two subspecies of salamanders cannot be reliably distinguished based on morphology or eDNA methods that are based on mitochondrial DNA, we are uncertain if we detected only native genotypes or if we documented recent invasion of the area by the non-native sub-species. Thus, there is an urgent need for methods to reliably distinguish the subspecies so managers can identify appropriate interventions.

A field ecologist's guide to environmental DNA sampling in freshwater environments

2020 ◽  
Vol 40 (4) ◽  
pp. 641-651
Author(s):  
Emily F. McColl-Gausden ◽  
Andrew R. Weeks ◽  
Reid Tingley
Keyword(s):  
Environmental Samples ◽  
Environmental Dna ◽  
Single Species ◽  
Freshwater Ecosystems ◽  
False Positives ◽  
Imperfect Detection ◽  
Occupancy Detection ◽  
Multiple Species ◽  
Methodological Considerations ◽  
Species Occupancy

Environmental DNA, or eDNA—DNA shed from organisms and extracted from environmental samples—is an emerging survey technique that has the potential to transform biodiversity monitoring in freshwater ecosystems. We provide a brief overview of the primary methodological aspects of eDNA sampling that ecologists should consider before taking environmental samples in the field. We outline five key methodological considerations: (i) targeting single species vs multiple species; (ii) where and when to sample; (iii) how much water to collect; (iv) how many samples to take; and (v) recognising potential sources of false positives. The need to account for false negatives and false positives in eDNA surveys, and the power of species occupancy detection models in accounting for imperfect detection, is also discussed.

scholarly journals Shifting up a gear with iDNA: from mammal detection events to standardized surveys

2018 ◽  
Author(s):  
Jesse F Abrams ◽  
Lisa Hoerig ◽  
Robert Brozovic ◽  
Jan Axtner ◽  
Alex Crampton-Platt ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Ad Hoc ◽  
Environmental Dna ◽  
Camera Trap ◽  
Camera Traps ◽  
Occupancy Models ◽  
Imperfect Detection ◽  
Mammal Species ◽  
Occupancy Model ◽  
Cost Efficient

Invertebrate-derived DNA (iDNA), in combination with high throughput sequencing, has been proposed as a cost-efficient and powerful tool to survey vertebrate species. Previous studies, however, have only provided evidence that vertebrates can be detected using iDNA, but have not taken the next step of placing these detection events within a statistical framework that allows for robust biodiversity assessments. Here, we compare concurrent iDNA and camera-trap surveys. Leeches were repeatedly collected in close vicinity to 64 camera-trap stations in Sabah, Malaysian Borneo. We analyze iDNA-derived mammalian detection events in a modern occupancy model that accounts for imperfect detection and compare the results with those from occupancy models parameterized with camera-trap-derived detection events. We also combine leech-iDNA and camera-trap data in a single occupancy model. We found consistent estimates of occupancy probabilities produced by our camera-trap and leech datasets. This indicates that the metabarcoding of leech-iDNA method provides reasonable estimates of occupancy and can be a suitable method for studying and monitoring mammal species in tropical rainforests. However, we also show that a more extensive collection of leeches would be needed to assess mammal biodiversity with a similar robustness as with camera traps. As certain taxa were only detected in leeches, we see great potential in complementing camera-trap studies with the iDNA approach, as long as the collection of leeches follows a similar robust and standardized sampling scheme. Synthesis and applications: The approach we describe here is not restricted to the processing of leech samples, but can be used for the analysis of other iDNA and environmental DNA (eDNA) data. Our study is the first step to shift the application of e/iDNA studies from opportunistic ad-hoc collections to systematic surveys required for long-term wildlife populations and biodiversity monitoring programs.

scholarly journals Using areas of known occupancy to identify sources of variation in detection probability of raptors: taking time lowers replication effort for surveys

2016 ◽  
Vol 3 (10) ◽  
pp. 160368 ◽  
Author(s):  
Campbell Murn ◽  
Graham J. Holloway
Keyword(s):  
Detection Probability ◽  
Spatial Scales ◽  
Survey Methods ◽  
A Priori ◽  
Low Density ◽  
Occupancy Models ◽  
Imperfect Detection ◽  
Factors Affecting ◽  
Sources Of Variation ◽  
Time Of Year

Species occurring at low density can be difficult to detect and if not properly accounted for, imperfect detection will lead to inaccurate estimates of occupancy. Understanding sources of variation in detection probability and how they can be managed is a key part of monitoring. We used sightings data of a low-density and elusive raptor (white-headed vulture Trigonoceps occipitalis ) in areas of known occupancy (breeding territories) in a likelihood-based modelling approach to calculate detection probability and the factors affecting it. Because occupancy was known a priori to be 100%, we fixed the model occupancy parameter to 1.0 and focused on identifying sources of variation in detection probability. Using detection histories from 359 territory visits, we assessed nine covariates in 29 candidate models. The model with the highest support indicated that observer speed during a survey, combined with temporal covariates such as time of year and length of time within a territory, had the highest influence on the detection probability. Averaged detection probability was 0.207 (s.e. 0.033) and based on this the mean number of visits required to determine within 95% confidence that white-headed vultures are absent from a breeding area is 13 (95% CI: 9–20). Topographical and habitat covariates contributed little to the best models and had little effect on detection probability. We highlight that low detection probabilities of some species means that emphasizing habitat covariates could lead to spurious results in occupancy models that do not also incorporate temporal components. While variation in detection probability is complex and influenced by effects at both temporal and spatial scales, temporal covariates can and should be controlled as part of robust survey methods. Our results emphasize the importance of accounting for detection probability in occupancy studies, particularly during presence/absence studies for species such as raptors that are widespread and occur at low densities.

scholarly journals Environmental DNA as a ‘Snapshot’ of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan

PLoS ONE ◽  
2016 ◽  
Vol 11 (3) ◽  
pp. e0149786 ◽  
Author(s):  
Satoshi Yamamoto ◽  
Kenji Minami ◽  
Keiichi Fukaya ◽  
Kohji Takahashi ◽  
Hideki Sawada ◽  
...  
Keyword(s):  
Sea Of Japan ◽  
Environmental Dna ◽  
Fish Distribution ◽  
Jack Mackerel ◽  
Japanese Jack Mackerel

A penalized likelihood for multi‐species occupancy models improves predictions of species interactions

Ecology ◽  
2021 ◽  
Author(s):  
Hannah L. Clipp ◽  
Amber L. Evans ◽  
Brin E. Kessinger ◽  
Kenneth Kellner ◽  
Christopher T. Rota
Keyword(s):  
Species Interactions ◽  
Penalized Likelihood ◽  
Occupancy Models ◽  
Species Occupancy
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