occupancy model
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Author(s):  
Hiroki Mizumoto ◽  
Osamu Kishida ◽  
Kotaro Takai ◽  
Naru Matsuura ◽  
Hitoshi Araki

AbstractUnderstanding the distribution of invasive species and their reproductive area is crucial for their managements after invasion. While catch and observation surveys are still embraced, environmental DNA (eDNA) has been increasingly utilized as an efficient tool for identifying these species in the wild. In this study, we developed a Bufo-specific eDNA assay for detecting an invasive, toxic, and terrestrial toad species Bufo japonicus formosus in Hokkaido, Japan, and applied it to their reproductive area at watershed scale. The eDNA assay was field-validated in ponds where B. japonicus were observed, as well as in rivers downstream of the reproductive ponds. Thus, the assay provided us an opportunity to screen watersheds that include their reproductive area by collecting downstream water samples. Applying it to the Ishikari river basin, the largest river basin in Hokkaido (c.a., 14,330 km2), we detected toad eDNA at 32 out of 73 sampling sites. They are composed of eleven sites with species observation records nearby (all the sites with observation records within a 500 m radius) and 21 sites without such records. And those eDNA detections were from twelve out of 31 river systems in the entire river basin. A Bayesian, multiscale occupancy model supported high eDNA detectability among those sites. These results suggest that the eDNA assay can efficiently estimate the presence of reproductive area of the terrestrial toad even from a distant downstream of the watershed, and that it provides a powerful means of detecting new reproductive area and monitoring further spread of invasive species.


Wanaraksa ◽  
2021 ◽  
Vol 12 (2) ◽  
Author(s):  
Feizal Tawaqal ◽  
Toto Supartono ◽  
Iing Nasihin
Keyword(s):  

Polulasi Famili Kucing (Felidae) di Asia Tenggara mengalami penurunan di alam akibat hilangnya habitat, fragmentasi satu, dan perburuan besar-besaran. Sementara itu, penelitian tentang Kucing Emas Asia, Macan Dahan Sunda, Kucing Marbled, dan Kucing Macan Tutul Asia belum banyak dilakukan. Penelitian ini bertujuan untuk mengetahui sebaran dan pemanfaatan habitat di Taman Nasional Bukit Barisan Selatan (TNBBS). Pengambilan data menggunakan Camera Trap, kemudian dianalisis model okupansi dengan musim tunggal dan spesies tunggal menggunakan software R. Ditemukan bahwa Asiatic Golden Cat Occupancy Model menghasilkan 0,75 di Zona Perlindungan Intensif atau Zona Perlindungan Intensive (IPZ) dan 0,4 nilai hunian di bagian utara Taman Nasional Sourthern Bukit Barisan (TNBBS). Selain itu, Macan Dahan Sunda menghasilkan nilai IPZ 0,50 dan okupansi 0,42 di bagian utara TNBBS. Kucing Leopard Asia-nya memiliki nilai okupansi 0,16 di IPZ dan model okupansi yang tidak dijalankan di bagian utara TNBBS karena deteksi yang sangat rendah


2021 ◽  
Vol 13 (8) ◽  
pp. 1500
Author(s):  
Juan Uribe-Toril ◽  
Alejandro C. Galindo ◽  
José A. Torres ◽  
Jaime De Pablo ◽  
José L. Ruiz-Real

The recovery of a built heritage and specifically of singular buildings is a key aspect of local development. The aim of this study was to understand the influence of these regenerations on their environment by transforming adjacent businesses and initiating parallel processes of gentrification and local development. The renewed attraction of these new businesses to the area can result in increased employment and production. The methodology used was based on self-organizing maps of neural networks with matrix architecture and competitive learning. Through the analysis of neural networks, we were able to identify common relationships and behaviors in commercial properties which are adjacent to singular buildings and that share common patterns and characteristics or attributes. The singular buildings analyzed are located along the Spanish Mediterranean coast in the cities of Almería, Barcelona, and Valencia. The results obtained were based on the following hypotheses: occupancy model and the classification based on total occupancy, total variation in occupancy, and the most common types of usage of a given ground floor commercial property. Among the conclusions, we highlight the existence of commercial premises that display anti-cyclical economic behavior and the presence of commercial premises considered to be “unfortunate” or with low potential.


2021 ◽  
Author(s):  
Anna I Spiers ◽  
J Andrew Royle ◽  
Christa L Torrens ◽  
Maxwell B Joseph

1. Large-scale, long-term biodiversity monitoring is essential to meeting conservation and land management goals and identifying threats to biodiversity. However, multispecies surveys are prone to various types of observation error, including false positive/negative detection, and misclassification, where a species is encountered but its species identity is not correctly identified. Previous methods assume an imperfect classifier produces species-level classifications, but in practice, particularly with human observers, we may end up with extraspecific classifications including "unknown", morphospecies designations, and taxonomic identifications coarser than species. Disregarding these types of species misclassification in biodiversity monitoring datasets can bias estimates of ecologically important quantities such as demographic rates, occurrence, and species richness. 2. Here we develop an occupancy model that accounts for species non-detection and misclassification. Our framework accommodates extinction and colonization dynamics, allows for additional uncertain 'morphospecies' designations in the imperfect species classifications, and makes use of individual specimen with known species identities in a semi-supervised setting. We compare the performance of our joint classification-occupancy model to a reduced classification model that discards information about occupancy and encounter rate on a withheld test set. We illustrate our model with an empirical case study of the carabid beetle (Carabidae) community at the National Ecological Observatory Network Niwot Ridge Mountain Research Station, west of Boulder, CO, USA, and quantify taxonomist identification error by accounting for classification probabilities. 3. Species occupancy varied through time and across sites and species. The model yielded high probabilities (30 to 92\% medians) of classification where the imperfect classifier matched the true species. The classification model informed by occupancy and encounter rates outperformed the classification that was not, and these differences were most pronounced for abundant species. 4. Our probabilistic framework can be applied to datasets with imperfect species detection and classification. This model can identify commonly misclassified species, helping biodiversity monitoring organizations systematically prioritize which samples need validation by an expert. Our Bayesian approach propagates classification uncertainty to offer an alternative to making conservation decisions based on point estimates


Author(s):  
Brian Mahardja ◽  
Lara Mitchell ◽  
Michael Beakes ◽  
Catherine Johnston ◽  
Cory Graham ◽  
...  

Monitoring is an essential component in ecosystem management, and leveraging existing data sources for multiple species of interest can be one effective way to enhance information for management agencies. Here, we analyzed juvenile Chinook Salmon (Oncorhynchus tshawytscha) bycatch data that has been collected by the recently established Enhanced Delta Smelt Monitoring program (EDSM), a survey designed to estimate the abundance and distribution of the San Francisco Estuary’s (estuary) endangered Delta Smelt (Hypomesus transpacificus). Two key aspects of the EDSM program distinguish it from other fish surveys in the estuary: a stratified random sampling design and the spatial scale of its sampling effort. We integrated the EDSM data set with other existing surveys in the estuary, and used an occupancy model to assess differences in the probability of detecting Delta Smelt across gear types. We saw no large-scale differences in size selectivity, and while detection probability varied among gear types, cumulative detection probability for EDSM was comparable to other surveys because of the program’s use of replicate tows. Based on our occupancy model and sampling effort in the estuary during spring of 2017 and 2018, we highlighted under-sampled regions that saw improvements in monitoring coverage from EDSM. Our analysis also revealed that each sampling method has its own benefits and constraints. Although the use of random sites with replicates, as conducted by EDSM, can provide more statistically robust abundance estimates relative to traditional methods, the use of fixed stations and simple methods such as beach seining may provide a more cost-effective way to monitor salmon occurrence in certain regions of the estuary. Leveraging the strengths of each survey’s method can enable stronger inferences on salmon abundance and distribution. Careful consideration of these trade-offs is crucial as the management agencies of the estuary continue to adapt and improve their monitoring programs.


Author(s):  
Brian Mahardja ◽  
Lara Mitchell ◽  
Michael Beakes ◽  
Catherine Johnston ◽  
Cory Graham ◽  
...  

Monitoring is an essential component in ecosystem management, and leveraging existing data sources for multiple species of interest can be one effective way to enhance information for management agencies. Here, we analyzed juvenile Chinook Salmon (Oncorhynchus tshawytscha) bycatch data that has been collected by the recently established Enhanced Delta Smelt Monitoring program (EDSM), a survey designed to estimate the abundance and distribution of the San Francisco Estuary’s (estuary) endangered Delta Smelt (Hypomesus transpacificus). Two key aspects of the EDSM program distinguish it from other fish surveys in the estuary: a stratified random sampling design and the spatial scale of its sampling effort. We integrated the EDSM data set with other existing surveys in the estuary, and used an occupancy model to assess differences in the probability of detecting Delta Smelt across gear types. We saw no large-scale differences in size selectivity, and while detection probability varied among gear types, cumulative detection probability for EDSM was comparable to other surveys because of the program’s use of replicate tows. Based on our occupancy model and sampling effort in the estuary during spring of 2017 and 2018, we highlighted under-sampled regions that saw improvements in monitoring coverage from EDSM. Our analysis also revealed that each sampling method has its own benefits and constraints. Although the use of random sites with replicates, as conducted by EDSM, can provide more statistically robust abundance estimates relative to traditional methods, the use of fixed stations and simple methods such as beach seining may provide a more cost-effective way to monitor salmon occurrence in certain regions of the estuary. Leveraging the strengths of each survey’s method can enable stronger inferences on salmon abundance and distribution. Careful consideration of these trade-offs is crucial as the management agencies of the estuary continue to adapt and improve their monitoring programs.


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