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 A sparse observation model to quantify species interactions in time and space

2019 ◽  
Author(s):  
Sadoune Ait Kaci Azzou ◽  
Liam Singer ◽  
Thierry Aebischer ◽  
Madleina Caduff ◽  
Beat Wolf ◽  
...  
Keyword(s):  
Species Interactions ◽  
Activity Patterns ◽  
Niche Partitioning ◽  
Camera Trap ◽  
Camera Traps ◽  
Observation Model ◽  
Occupancy Models ◽  
Time And Space ◽  
Imperfect Detection ◽  
Mobile Species

SummaryCamera traps and acoustic recording devices are essential tools to quantify the distribution, abundance and behavior of mobile species. Varying detection probabilities among device locations must be accounted for when analyzing such data, which is generally done using occupancy models. We introduce a Bayesian Time-dependent Observation Model for Camera Trap data (Tomcat), suited to estimate relative event densities in space and time. Tomcat allows to learn about the environmental requirements and daily activity patterns of species while accounting for imperfect detection. It further implements a sparse model that deals well will a large number of potentially highly correlated environmental variables. By integrating both spatial and temporal information, we extend the notation of overlap coefficient between species to time and space to study niche partitioning. We illustrate the power of Tomcat through an application to camera trap data of eight sympatrically occurring duiker Cephalophinae species in the savanna - rainforest ecotone in the Central African Republic and show that most species pairs show little overlap. Exceptions are those for which one species is very rare, likely as a result of direct competition.

The effect of camera-trap viewshed obstruction on wildlife detection: implications for inference

2020 ◽  
Vol 47 (2) ◽  
pp. 158 ◽  
Author(s):  
Remington J. Moll ◽  
Waldemar Ortiz-Calo ◽  
Jonathon D. Cepek ◽  
Patrick D. Lorch ◽  
Patricia M. Dennis ◽  
...  
Keyword(s):  
Image Data ◽  
Camera Trap ◽  
Camera Traps ◽  
Mammal Species ◽  
Ecological Processes ◽  
Detection Rates ◽  
Management Application ◽  
Efficiency And Effectiveness ◽  
Steep Slopes ◽  
Wildlife Detection

Abstract ContextCamera traps are one of the most popular tools used to study wildlife worldwide. Numerous recent studies have evaluated the efficiency and effectiveness of camera traps as a research tool. Nonetheless, important aspects of camera-trap methodology remain in need of critical investigation. One such issue relates to camera-trap viewshed visibility, which is often compromised in the field by physical obstructions (e.g. trees) or topography (e.g. steep slopes). The loss of visibility due to these obstructions could affect wildlife detection rates, with associated implications for study inference and management application. AimsWe aimed to determine the effect of camera-trap viewshed obstruction on wildlife detection rates for a suite of eight North American species that vary in terms of ecology, commonness and body size. MethodsWe deployed camera traps at 204 sites throughout an extensive semi-urban park system in Cleveland, Ohio, USA, from June to September 2016. At each site, we quantified camera-trap viewshed obstruction by using a cover-board design. We then modelled the effects of obstruction on wildlife detection rates for the eight focal species. Key resultsWe found that detection rates significantly decreased with an increasing viewshed obstruction for five of the eight species, including both larger and smaller mammal species (white-tailed deer, Odocoileus virginianus, and squirrels, Sciurus sp., respectively). The number of detections per week per camera decreased two- to three-fold as visibility at a camera site decreased from completely free of obstruction to mostly obstructed. ConclusionsThese results imply that wildlife detection rates are influenced by site-level viewshed obstruction for a variety of species, and sometimes considerably so. ImplicationsResearchers using camera traps should address the potential for this effect to ensure robust inference from wildlife image data. Accounting for viewshed obstruction is critical when interpreting detection rates as indices of abundance or habitat use because variation in detection rate could be an artefact of site-level viewshed obstruction rather than due to underlying ecological processes.

scholarly journals A dynamic occupancy model for interacting species with two spatial scales

2020 ◽  
Author(s):  
Eivind Flittie Kleiven ◽  
Frederic Barraquand ◽  
Olivier Gimenez ◽  
John-André Henden ◽  
Rolf Anker Ims ◽  
...  
Keyword(s):  
Spatial Structure ◽  
Species Interactions ◽  
Spatial Scales ◽  
Species Interaction ◽  
Camera Traps ◽  
Occupancy Models ◽  
Occupancy Model ◽  
Interacting Species ◽  
Multi Scale ◽  
Extinction Probabilities

1AbstractOccupancy models have been developed independently to account for multiple spatial scales and species interactions in a dynamic setting. However, as interacting species (e.g., predators and prey) often operate at different spatial scales, including nested spatial structure might be especially relevant in models of interacting species. Here we bridge these two model frameworks by developing a multi-scale two-species occupancy model. The model is dynamic, i.e. it estimates initial occupancy, colonization and extinction probabilities - including probabilities conditional to the other species’ presence. With a simulation study, we demonstrate that the model is able to estimate parameters without bias under low, medium and high average occupancy probabilities, as well as low, medium and high detection probabilities. We further show the model’s ability to deal with sparse field data by applying it to a multi-scale camera trapping dataset on a mustelid-rodent predator-prey system. The field study illustrates that the model allows estimation of species interaction effects on colonization and extinction probabilities at two spatial scales. This creates opportunities to explicitly account for the spatial structure found in many spatially nested study designs, and to study interacting species that have contrasted movement ranges with camera traps.

scholarly journals Dominance hierarchy on palm resource partitioning among Neotropical frugivorous mammals

2020 ◽  
Vol 101 (3) ◽  
pp. 697-709 ◽  
Author(s):  
Paula Akkawi ◽  
Nacho Villar ◽  
Calebe P Mendes ◽  
Mauro Galetti
Keyword(s):  
Body Mass ◽  
Behavioral Plasticity ◽  
Interaction Strength ◽  
Camera Traps ◽  
Close Relative ◽  
Occupancy Models ◽  
Mammal Species ◽  
Resource Overlap ◽  
Pecari Tajacu ◽  
Temporal Overlap

Abstract In tropical forests, the diets of many frugivorous mammals overlap, yet how hyper-diverse assemblages of consumers exploit resources and coexist remains poorly understood. We evaluated competitive interactions among three species of terrestrial frugivorous mammals, the ungulate Tayassu pecari (white-lipped peccary), its close relative Pecari tajacu (collared peccary), and a large rodent (Dasyprocta azarae, agouti), in their exploitation strategies of palm resources of different quality. We conducted the study in a large isolated fragment at the tropical Atlantic Forest of Brazil, where these mammal species show high spatial and temporal overlap. We evaluated if body mass and foraging group size define a hierarchy in exploitation of preferentially richer palm resources. We used camera traps and two-species occupancy models to examine patterns of co-occurrence and variable interaction strength between these consumers and three species of palms. Our analyses supported the hypothesis of partial resource overlap but no competition among frugivores, and a body mass dominance hierarchical exploitation of resources. The larger frugivore (white-lipped peccary) dominated patches of the lipid-rich palm Euterpe edulis, where the smallest frugivore (agouti) was absent. Instead, the smallest frugivore concentrated its foraging in areas with the poorest palm resource, Syagrus oleracea. Collared peccaries preferred areas of high abundance of Syagrus romanzoffiana when the other two mammal species were rarely detected or absent, strongly avoided patches of E. edulis, and showed higher average detection probabilities when agoutis were present. Our study highlights the important role of behavioral plasticity in promoting coexistence and indicates that through context-dependent interactions and hierarchical partitioning of resources, consumers can avoid strong competition, even under conditions of high spatial and temporal overlap and high levels of habitat fragmentation and isolation.

scholarly journals Mammal diversity among vertical strata and the evaluation of a survey technique in a central Amazonian forest

2021 ◽  
Vol 61 ◽  
pp. e20216133
Author(s):  
Alexander Roldán Arévalo-Sandi ◽  
André Luis Sousa Gonçalves ◽  
Kota Onizawa ◽  
Tsuneaki Yabe ◽  
Wilson Roberto Spironello
Keyword(s):  
Camera Trap ◽  
Camera Traps ◽  
Sampling Effort ◽  
Mammal Species ◽  
Lowland Forest ◽  
Survey Technique ◽  
Terrestrial Habitats ◽  
Common Technique ◽  
The Difference ◽  
Mammal Diversity

Mammal groups have a vast variety of habitats, which include aquatic, aerial, arboreal, and terrestrial. For terrestrial habitats, camera traps are used as a common technique to record mammals and other vertebrates and have been recently utilized to observe arboreal animals as well. Here, we compare the difference in mammal diversity between floor and canopy strata and evaluate the use of camera trapping in a lowland forest in central Amazon. We installed nine paired camera traps, one in the canopy stratum and other in the floor stratum, in the Alto Cuieiras Biological Reserve (Brazilian Amazon). With a sampling effort of 720 camera-days, we recorded 30 mammal species: nine in canopy strata, 14 in floor strata, and seven in scansorial strata (sharing both strata). On the forest floor, the species with the greatest abundance was Myoprocta acouchy; in the canopy, Isothrix paguros had the greatest abundance; and among the scansorial species, Proechymis sp. was the most abundant. Our results show the differences in mammal diversity between floor and canopy strata; canopy strata contained more small and frugivorous mammals. Although we obtained a relatively low sampling effort with the camera-trap method compared with other studies utilizing different techniques, our results were especially similar to those of previous studies that worked with canopy and floor strata. Thus, camera trap can be very effective for recording short periods of time, and this method is less physically exhaustive and expensive for researchers to study vertical strata.

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.

scholarly journals Occupancy rate and observations of Baird’s tapir (Tapirella bairdii) near waterholes in the Maya forest corridor, Belize

Therya ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 37-43
Author(s):  
Wilber E. Martinez ◽  
Rafael A. Reyna-Hurtado ◽  
Eduardo J. Naranjo ◽  
Daniel Thornton ◽  
Reynold N. Cal ◽  
...  
Keyword(s):  
At Risk ◽  
Nature Reserve ◽  
Essential Element ◽  
Camera Trap ◽  
Probability Of Detection ◽  
Sampling Effort ◽  
Occupancy Models ◽  
Probability Models ◽  
Mammal Species ◽  
Risk Of Extinction

It is estimated that 25 % of the mammal species in the world are at risk of extinction due to habitat loss, fragmentation, farming, and overexploitation. Baird’s tapir (Tapirella bairdii), an ungulate with part of its distribution within the Maya Forest, is at risk of extinction. Waterholes, a primary source for water and an essential element for the survival of tapirs, were the target of this study design. We used a camera-trap survey to determine tapir occupancy and detection rate probability models at seven survey stations at Runaway Creek Nature Reserve which is located within the Maya Forest Corridor in central Belize. The survey was carried out from March to September 2015 and from January 2017 to October 2019 with a total sampling effort of 8,932 camera-trap nights. Our results indicated a cumulative naïve occupancy estimate of 85.7 %, a rate probability of occupancy of 0.97 +/- 0.15 (SE), and a probability of detection of 0.14 +/- 0.01 for all sites and years. The results of occupancy models with human infrastructure covariate showed that the distance to roads model had the highest influence on tapir occurrence (β = -0.95 +/- 0.87), followed by the village covariate model (β = 0.77 +/- 0.99). The topographic covariate of river model (β = 0.47 +/- 0.85) had minimal support. This study highlights the critical importance of waterholes for survival of tapirs, and the influence of roads on tapir occurrence at Runaway Creek Nature Reserve.

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 Buffer zone use by mammals in a Cerrado protected area

2016 ◽  
Vol 16 (2) ◽  
Author(s):  
Roberta Montanheiro Paolino ◽  
Natalia Fraguas Versiani ◽  
Nielson Pasqualotto ◽  
Thiago Ferreira Rodrigues ◽  
Victor Gasperotto Krepschi ◽  
...  
Keyword(s):  
Protected Areas ◽  
Puma Concolor ◽  
Buffer Zone ◽  
Camera Traps ◽  
Imperfect Detection ◽  
Mammal Species ◽  
Buffer Zones ◽  
Terrestrial Mammals ◽  
External Threats ◽  
The Impact

Habitat loss and degradation is threatening mammals worldwide. Therefore, Protected Areas (PA) are of utmost importance to preserve biodiversity. Their effectiveness, however, depends on some management strategies such as buffer zones, which prevent/mitigate the impact of external threats and might increase the amount of available habitat for wildlife existing within reserves. Nevertheless, how intensively terrestrial mammals use buffer zones remains little studied, particularly in the Neotropical region. Aiming to analyse the use of a buffer zone (5 km wide) by medium and large-sized mammals, we modelled the occupancy probabilities of five species of conservation concern including local (interior and buffer zone) as a site covariate, simultaneously controlling for imperfect detection. Data collection was made with camera traps from April to September 2013 in a 9000 ha Cerrado PA (“interior”) and in its surrounding area (39721.41 ha; “buffer zone”). This PA (Jataí Ecological Station) is immersed in a landscape where sugarcane plantations predominate in the northeastern of the state of São Paulo. We also conducted an inventory to compare the number and composition of species between interior and buffer zone. A total of 31 mammal species (26 natives) was recorded via camera traps and active search for sightings, vocalizations, tracks and signs. Occupancy estimates for Myrmecophaga tridactyla, Leopardus pardalis and Pecari tajacu were numerically higher in interior. On the other hand, Chrysocyon brachyurus had the highest occupancy in buffer zone, while the largest predator, Puma concolor, used both areas similarly. However, as the confidence intervals (95%) overlapped, the differences in occupancy probabilities between interior and buffer were weak for all these species. Additionally, regarding only the species recorded by cameras, the observed and estimated richness were similar between interior and buffer zone of the PA. Our data demonstrated that the buffer zone is indeed used by medium and large-sized mammals, including conservation-dependent ones. The lack of enforcement of current legislation regarding buffer zones is therefore a real threat for mammals, even when protection is guaranteed in the interior of protected areas.

scholarly journals Influence of camera-trap sampling design on mammal species capture rates and community structures in southeastern Brazil

2013 ◽  
Vol 13 (2) ◽  
pp. 51-62 ◽  
Author(s):  
Ana Carolina Srbek-Araujo ◽  
Adriano Garcia Chiarello
Keyword(s):  
Activity Patterns ◽  
Camera Trap ◽  
Camera Traps ◽  
Southeastern Brazil ◽  
Sampling Point ◽  
Community Structures ◽  
Mammal Species ◽  
Forest Interior ◽  
Trap Location ◽  
Capture Rates

The distribution of species and population attributes are critical data for biodiversity conservation. As a tool for obtaining such data, camera traps have become increasingly common throughout the world. However, there are disagreements on how camera-trap records should be used due to imperfect species detectability and limitations regarding the use of capture rates as surrogates for abundance. We evaluated variations in the capture rates and community structures of mammals in camera-trap surveys using four different sampling designs. The camera traps were installed on internal roads (in the first and fourth years of the study), at 100-200 m from roads (internal edges; second year) and at 500 m from the nearest internal road (forest interior; third year). The mammal communities sampled in the internal edges and forest interior were similar to each other but differed significantly from those sampled on the roads. Furthermore, for most species, the number of records and the capture success varied widely among the four sampling designs. A further experiment showed that camera traps placed on the same tree trunk but facing in opposing directions also recorded few species in common. Our results demonstrated that presence or non-detection and capture rates vary among the different sampling designs. These differences resulted mostly from the habitat use and behavioral attributes of species in association with differences in sampling surveys, which resulted in differential detectability. We also recorded variations in the distribution of records per sampling point and at the same spot, evidencing the stochasticity associated with the camera-trap location and orientation. These findings reinforce that for species whose specimens cannot be individually identified, the capture rates should be best used as inputs for presence and detection analyses and for behavior inferences (regarding the preferential use of habitats and activity patterns, for example). Comparisons between capture rates or among relative abundance indices, even for the same species, should be made cautiously.

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