scholarly journals Refining sampling protocols for cavefishes and cave crayfishes to account for environmental variation

2021 ◽  
Vol 39 ◽  
pp. 79-105
Author(s):  
Joshua B. Mouser ◽  
Shannon K. Brewer ◽  
Matthew L. Niemiller ◽  
Robert Mollenhauer ◽  
Ronald A. Van Den Bussche
Keyword(s):  
Environmental Conditions ◽  
Detection Probability ◽  
Survey Methods ◽  
Environmental Dna ◽  
Sampling Bias ◽  
Water Velocity ◽  
Conservation Strategies ◽  
Water Volume ◽  
Factors Affecting ◽  
Sampling Protocols

Subterranean habitats represent focal habitats in many conservation strategies; however, these environments are some of the most difficult to sample. New sampling methods, such as environmental DNA (eDNA), show promise to improve stygobiont detection, but sources of sampling bias are poorly understood. Therefore, we determined the factors affecting detection probability using traditional visual surveys and eDNA surveys for both cavefishes and cave crayfishes and demonstrated how detection affects survey efforts for these taxa. We sampled 40 sites (179 visual and 183 eDNA surveys) across the Ozark Highlands ecoregion. We estimated the detection probability of cave crayfishes and cavefishes using both survey methods under varying environmental conditions. The effectiveness of eDNA or visual surveys varied by environmental conditions (i.e., water volume, prevailing substrate, and water velocity) and the target taxa. When sampling in areas with average water velocity, no flow, and coarse substrate, eDNA surveys had a higher detection probability (0.49) than visual surveys (0.35) for cavefishes and visual surveys (0.67) had a higher detection probability than eDNA surveys (0.40) for cave crayfishes. Under the same sampling conditions, 5 visual surveys compared to 10 eDNA surveys would be needed to confidently detect cave crayfishes and 9 visual surveys compared to 4 eDNA surveys for cavefishes. Environmental DNA is a complementary tool to traditional visual surveys; however, the limitations we identified indicate eDNA currently cannot replace visual surveys in subterranean environments. Although sampling designs that account for imperfect sampling are particularly useful, they may not be practical; thus, increasing sampling efforts to offset known detection bias would benefit conservation strategies.

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 Noninvasive Method for a Statewide Survey of Eastern HellbendersCryptobranchus alleganiensisUsing Environmental DNA

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Amy J. Santas ◽  
Tyler Persaud ◽  
Barbara A. Wolfe ◽  
Jenise M. Bauman
Keyword(s):  
Population Density ◽  
Survey Methods ◽  
Aquatic Organisms ◽  
Environmental Dna ◽  
Specific Primers ◽  
Filtration Time ◽  
Sampling Protocols ◽  
Welfare Implications ◽  
Historical Accounts ◽  
Eastern Hellbender

Traditional survey methods of aquatic organisms may be difficult, lengthy, and destructive to the habitat. Some methods are invasive and can be harmful to the target species. The use of environmental DNA (eDNA) has proven to be effective at detecting low population density aquatic macroorganisms. This study refined the technique to support statewide surveys. Hellbender presence was identified by using hellbender specific primers (cytochrome b gene) to detect eDNA in water samples collected at rivers, streams and creeks in Ohio and Kentucky with historical accounts of the imperiled eastern hellbender (Cryptobranchus a. alleganiensis). Two sampling protocols are described; both significantly reduced the amount of water required for collection from the previously described 6 L collection. Two-liter samples were adequate to detect hellbender presence in natural waterways where hellbenders have been previously surveyed in both Ohio and Kentucky—1 L samples were not reliable. DNA extracted from 3 L of water collected onto multiple filters (1 L/filter) could be combined and concentrated through ethanol precipitation, supporting amplification of hellbender DNA and dramatically reducing the filtration time. This method improves the efficiency and welfare implications of sampling methods for reclusive aquatic species of low population density for statewide surveys that involve collecting from multiple watersheds.

scholarly journals Environmental DNA sampling provides new management strategies for vernal pool branchiopods in California

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0243338
Author(s):  
Shannon Rose C. Kieran ◽  
Joshua M. Hull ◽  
Amanda J. Finger
Keyword(s):  
Management Strategies ◽  
Environmental Dna ◽  
Vernal Pool ◽  
Modern Method ◽  
Conservation Strategies ◽  
Fairy Shrimp ◽  
Native Plant ◽  
Freshwater Organisms ◽  
Animal Diversity ◽  
Sampling Protocols

California’s vernal pools are declining ecosystems that support valuable native plant and animal diversity. Vernal pool branchiopods are particularly at risk from vernal pool habitat loss and conservation efforts have targeted their long-term protection through the establishment of preserves and conservation banks. These conservation strategies require repeated, perpetual monitoring of preserved habitat, which is currently carried out through dip-net surveys and visual identification of specimens. Dip-netting may be destructive and frequently requires some sacrifice of protected species. Environmental DNA offers a new, modern method to monitor many protected freshwater organisms. We designed qPCR-based species-specific assays for four of California’s vernal pool branchiopods: The Vernal Pool Fairy Shrimp Branchinecta lynchi (BRLY), the Midvalley Fairy Shrimp Branchinecta mesovallensis (BRME), and the Conservancy Fairy Shrimp Branchinecta conservatio (BRCO), and the Vernal Pool Tadpole Shrimp Lepidurus packardi (LEPA). We tested these assays using eDNA sampling protocols alongside traditional dip-net surveys to assess their viability as an alternative method to monitor vernal pool branchiopods. Based on occupancy modeling, each of our assays achieved a 95% or higher detection rate when using optimized sampling protocols.

scholarly journals Environmental DNA sampling provides new management strategies for vernal pool branchiopods in California

2020 ◽  
Author(s):  
Shannon Rose Kieran ◽  
Joshua Hull ◽  
Amanda Finger
Keyword(s):  
Management Strategies ◽  
Environmental Dna ◽  
Vernal Pool ◽  
Modern Method ◽  
Conservation Strategies ◽  
Fairy Shrimp ◽  
Native Plant ◽  
Freshwater Organisms ◽  
Animal Diversity ◽  
Sampling Protocols

ABSTRACTCalifornia’s vernal pools are declining ecosystems that support valuable native plant and animal diversity. Vernal pool branchiopods are particularly at risk from vernal pool habitat loss and conservation efforts have targeted their long-term protection through the establishment of preserves and conservation banks. These conservation strategies require repeated, perpetual monitoring of preserved habitat, which is currently carried out through dip-net surveys and visual identification of specimens. Dip-netting may be destructive and frequently requires some sacrifice of protected species. Environmental DNA offers a new, modern method to monitor many protected freshwater organisms. We designed qPCR-based species-specific assays for four of California’s vernal pool branchiopods: The Vernal Pool Fairy Shrimp Branchinecta lynchi (BRLY), the Midvalley Fairy Shrimp Branchinecta mesovallensis (BRME), and the Conservancy Fairy Shrimp Branchinecta conservatio (BRCO), and the Vernal Pool Tadpole Shrimp Lepidurus packardi (LEPA). We tested these assays using eDNA sampling protocols alongside traditional dip-net surveys to assess their viability as an alternative method to monitor vernal pool branchiopods. Based on occupancy modeling, each of our assays achieved a 95% or higher detection rate when using optimized sampling protocols.

Predicting changes in distribution of a large coastal shark in the face of the strengthening East Australian Current

2020 ◽  
Vol 642 ◽  
pp. 163-177 ◽  
Author(s):  
Y Niella ◽  
AF Smoothey ◽  
V Peddemors ◽  
R Harcourt
Keyword(s):  
Austral Summer ◽  
Conservation Strategies ◽  
Limiting Factor ◽  
Commercial Fisheries ◽  
East Australian Current ◽  
Spatial And Temporal Patterns ◽  
Marine Animals ◽  
Factors Affecting ◽  
Southeastern Australia ◽  
The Face

In the face of accelerating climate change, conservation strategies will need to consider how marine animals deal with forecast environmental change as well as ongoing threats. We used 10 yr (2009-2018) of data from commercial fisheries and a bather protection program along the coast of New South Wales (NSW), southeastern Australia, to investigate (1) spatial and temporal patterns of occurrence in bull sharks and (2) environmental factors affecting bull shark occurrence along the coast of NSW. Predicted future distribution for this species was modelled for the forecast strengthening East Australian Current. Bull sharks were mostly harvested in small to larger estuaries, with average depth and rainfall responsible for contrasting patterns for each of the fisheries. There was an increase in the occurrence of bull sharks over the last decade, particularly among coastal setline fisheries, associated with seasonal availability of thermal gradients >22°C and both westward and southward coastal currents stronger than 0.15 and 0.60 m s-1, respectively, during the austral summer. Our model predicts a 3 mo increase in the availability of favourable water temperatures along the entire coast of NSW for bull sharks by 2030. This coastline provides a uniquely favourable topography for range expansion in the face of a southerly shift of warmer waters, and habitat is unlikely to be a limiting factor for bull sharks in the future. Such a southerly shift in distribution has implications for the management of bull sharks both in commercial fisheries and for mitigation of shark-human interactions.

scholarly journals Population estimates of Antillean manatees in Puerto Rico: an analytical framework for aerial surveys using multi-pass removal sampling

2019 ◽  
Vol 100 (4) ◽  
pp. 1340-1349
Author(s):  
Jaime A Collazo ◽  
Matthew J Krachey ◽  
Kenneth H Pollock ◽  
Francisco J Pérez-Aguilo ◽  
Jan P Zegarra ◽  
...  
Keyword(s):  
Puerto Rico ◽  
Detection Probability ◽  
Analytical Framework ◽  
Population Estimates ◽  
High Concentration ◽  
Imperfect Detection ◽  
Factors Affecting ◽  
Management Actions ◽  
Aerial Surveys ◽  
Population Size Estimates

AbstractEffective management of the threatened Antillean manatee (Trichechus manatus manatus) in Puerto Rico requires reliable estimates of population size. Estimates are needed to assess population responses to management actions, and whether recovery objectives have been met. Aerial surveys have been conducted since 1976, but none adjusted for imperfect detection. We summarize surveys since 1976, report on current distribution, and provide population estimates after accounting for apparent detection probability for surveys between June 2010 and March 2014. Estimates in areas of high concentration (hotspots) averaged 317 ± 101, three times higher than unadjusted counts (104 ± 0.56). Adjusted estimates in three areas outside hotspots also differed markedly from counts (75 ± 9.89 versus 19.5 ± 3.5). Average minimum island-wide estimate was 386 ± 89, similar to the maximum estimate of 360 suggested in 2005, but fewer than the 700 recently suggested by the Puerto Rico Manatee Conservation Center. Manatees were more widespread than previously understood. Improving estimates, locally or island-wide, will require stratifying the island differently and greater knowledge about factors affecting detection probability. Sharing our protocol with partners in nearby islands (e.g., Cuba, Jamaica, Hispaniola), whose populations share genetic make-up, would contribute to enhanced regional conservation through better population estimates and tracking range expansion.El manejo efectivo del manatí antillano amenazado en Puerto Rico requiere estimados de tamaños de poblaciónes confiables. Dichas estimaciones poblacionales son necesarias para evaluar las respuestas a las acciones de manejo, y para determinar si los objetivos de recuperación han sido alcanzados. Se han realizado censos aéreos desde 1976, pero ninguno de ellos han sido ajustados para detecciones imperfectas. Aquí resumimos los censos desde 1976, actualizamos la distribución, y reportamos los primeros estimados poblacionales ajustados para la probabilidad de detección aparente en los censos de Junio 2010 a Marzo 2014. Las estimaciones poblacionales en áreas de mayor concentración del manatí promedió 317 ± 103, tres veces más abundante que los conteos sin ajuste (104 ± 0.56). Las estimaciones poblacionales en tres áreas fuera de las áreas de mayor concentración del manatí también fueron marcadamente diferentes (75 ± 9.89 vs 19.5 ± 3.5). El estimado mínimo poblacional en la isla entera fue de 386 ± 89, similar al estimado máximo de 360 sugerido en el año 2005, pero menor a los 700 sugeridos recientemente por el Centro de Conservación de Manatíes de Puerto Rico. Documentamos que el manatí tiene una distribución más amplia de lo que se sabía con anterioridad. El mejoramiento de los estimados poblacionales locales o a nivel de isla requerirá que se estratifique a la isla en forma diferente y que se investiguen los factores que influencian a la probabilidad de detección. Compartir protocolos como este con colaboradores de islas vecinas (por. ej., Cuba, Jamaica, Española), cuyas poblaciones de manatíes comparten material genético, contribuiría a la conservación regional mediante mejores estimaciones poblacionales y monitoreo de la expansión de su ámbito doméstico.

INHERITANCE OF RESISTANCE TO NET BLOTCH IN BARLEY. I. FACTORS AFFECTING THE PENETRANCE AND EXPRESSIVITY OF GENE(S) CONDITIONING HOST RESISTANCE

1969 ◽  
Vol 11 (3) ◽  
pp. 587-591 ◽  
Author(s):  
T. N. Khan
Keyword(s):  
Environmental Conditions ◽  
Net Blotch ◽  
Host Reaction ◽  
Susceptible Parent ◽  
Breeding Programs ◽  
Genetic Studies ◽  
Factors Affecting ◽  
Drechslera Teres ◽  
Resistant Varieties ◽  
High Level

Variability in the host-reaction of barley to infection by Drechslera teres was examined in the parents and progeny of selected crosses under different environmental conditions of testing.The Ethiopian variety C.I. 5791 exhibits a consistently high level of resistance under a range of environmental conditions, which is in contrast to the Manchurian variety C.I. 2330. The sensitivity of the genes for resistance possessed by these varieties to environmental modifications is considered to depend upon their respective genetic backgrounds. Furthermore, variability of host reaction in the progeny of these resistant varieties was shown to be influenced by the genetic background of the susceptible parent used.The implications of these findings in the conduct and interpretation of genetic studies and in backcross breeding programs is discussed.

scholarly journals Factors Affecting the Problem of Guidance and Counseling Service Programs in High Schools

2019 ◽  
Vol 6 (2) ◽  
pp. 99-108
Author(s):  
Dina Rahmawati Hapsyah ◽  
Herdi Herdi
Keyword(s):  
Survey Methods ◽  
Counseling Services ◽  
Guidance And Counseling ◽  
Counseling Service ◽  
Personal Factors ◽  
Counseling Program ◽  
Factors Affecting ◽  
Descriptive Research ◽  
High Category ◽  
Service Programs

The implementation of guidance and counseling services cannot be separated from various factors that can influence. The purpose of this study is to study what factors can affect the implementation of guidance and counseling program services in high school. This study uses descriptive research with survey methods. Data collection techniques used through the instrument contained a questionnaire. The results of the study show that the guidance and counseling program has been well prepared. But the implementation of guidance and counseling is still not good, and this is characterized by high factors that influence the implementation of guidance and counseling service programs. The following are the percentages obtained, among others: personal factors consisting of the competence of the counselor get a percentage of 73% according to the high category; 71% depending on the high category; homeroom teacher obtained a percentage of 79% in the high category; subject teachers earn a percentage of 75%. Non-personal factors consisting of the BK program obtained a percentage of 70 with a high category; Facilities and infrastructure have a percentage of 77% in the high category.

scholarly journals An experimental assessment of the distribution of environmental DNA along the water column

2020 ◽  
Author(s):  
André O. Agostinis ◽  
Giorgi Dal Pont ◽  
Alexandre Borio ◽  
Aline Horodesky ◽  
Ana Paula da Silva Bertão ◽  
...  
Keyword(s):  
Water Column ◽  
Environmental Dna ◽  
Aquatic Communities ◽  
Natural Conditions ◽  
Sampling Protocol ◽  
Experimental Assessment ◽  
Qpcr Analysis ◽  
Time Period ◽  
Sampling Protocols ◽  
Different Depths

AbstractThe study of environmental DNA (eDNA) is increasingly becoming a valuable tool to survey and monitor aquatic communities. However, there are important gaps in our understanding of the dynamics governing the distribution of eDNA under natural conditions. In this report we carry out controlled experiments to assess the extent and timing of eDNA distribution along the water column. A sample of known eDNA concentration was placed at the bottom of a 5-m high tube (20 cm in diameter and total volume of 160 L), and water samples were obtained at different depths over an 8 h-period. The presence of the target eDNA was assessed by qPCR analysis. This sampling protocol allowed for assessing the timescale for the diffusion of eDNA while minimizing the influence of turbulence. We demonstrate that, after a time-period of as little as 30 min, the eDNA had spread across the entire container. The implications of these results for eDNA sampling protocols in the field are discussed.

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