scholarly journals Habitat suitability modeling based on a spatiotemporal model: an example for cusk in the Gulf of Maine

2018 ◽  
Vol 75 (11) ◽  
pp. 1784-1797 ◽  
Author(s):  
Jocelyn Runnebaum ◽  
Lisha Guan ◽  
Jie Cao ◽  
Loretta O’Brien ◽  
Yong Chen
Keyword(s):  
Habitat Suitability ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Gulf Of Maine ◽  
Population Decline ◽  
Monitoring Program ◽  
Marine Species ◽  
Habitat Modeling ◽  
Density Estimates ◽  
Habitat Suitability Modeling

Habitat use and distribution is a critical aspect in the management and conservation of a species, particularly for those in decline. Habitat suitability indices (HSI) are a common method of habitat mapping dependent on empirical data that can easily lead to misunderstanding the spatiotemporal dynamics of marine species experiencing population decline and density-dependent catchability within surveys. This is especially true when only a single monitoring program with limited spatiotemporal coverage is used. A delta-generalized linear mixed model was used to combine trawl and longline surveys to predict density estimates for cusk (Brosme brosme) in unsampled locations for use in HSIs. Catchability was estimated for longline and trawl gear without having an estimate of area fished for the longline survey. HSIs performed better using model-based density estimates from multiple surveys compared with sample-based abundance indices from a single survey. The increased spatial resolution can better inform the HSIs by providing information where the survey programs did not sample. This study provides a novel approach for integrating data from different monitoring programs for habitat modeling.

Predicting bycatch hotspots based on suitable habitat derived from fishery-independent data

2020 ◽  
Vol 641 ◽  
pp. 159-175
Author(s):  
J Runnebaum ◽  
KR Tanaka ◽  
L Guan ◽  
J Cao ◽  
L O’Brien ◽  
...  
Keyword(s):  
Habitat Suitability ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Gulf Of Maine ◽  
Homarus Americanus ◽  
Management Tool ◽  
American Lobster ◽  
Suitable Habitat ◽  
Climate Conditions ◽  
Suitability Index

Bycatch remains a global problem in managing sustainable fisheries. A critical aspect of management is understanding the timing and spatial extent of bycatch. Fisheries management often relies on observed bycatch data, which are not always available due to a lack of reporting or observer coverage. Alternatively, analyzing the overlap in suitable habitat for the target and non-target species can provide a spatial management tool to understand where bycatch interactions are likely to occur. Potential bycatch hotspots based on suitable habitat were predicted for cusk Brosme brosme incidentally caught in the Gulf of Maine American lobster Homarus americanus fishery. Data from multiple fisheries-independent surveys were combined in a delta-generalized linear mixed model to generate spatially explicit density estimates for use in an independent habitat suitability index. The habitat suitability indices for American lobster and cusk were then compared to predict potential bycatch hotspot locations. Suitable habitat for American lobster has increased between 1980 and 2013 while suitable habitat for cusk decreased throughout most of the Gulf of Maine, except for Georges Basin and the Great South Channel. The proportion of overlap in suitable habitat varied interannually but decreased slightly in the spring and remained relatively stable in the fall over the time series. As Gulf of Maine temperatures continue to increase, the interactions between American lobster and cusk are predicted to decline as cusk habitat continues to constrict. This framework can contribute to fisheries managers’ understanding of changes in habitat overlap as climate conditions continue to change and alter where bycatch interactions could occur.

scholarly journals Spatiotemporal variation in size-structured populations using fishery data: an application to shortfin mako (Isurus oxyrinchus) in the Pacific Ocean

2017 ◽  
Vol 74 (11) ◽  
pp. 1765-1780 ◽  
Author(s):  
Mikihiko Kai ◽  
James T. Thorson ◽  
Kevin R. Piner ◽  
Mark N. Maunder
Keyword(s):  
Coastal Waters ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Marine Species ◽  
Structured Populations ◽  
Spatiotemporal Model ◽  
The North ◽  
Isurus Oxyrinchus ◽  
Shortfin Mako ◽  
Catch Rates

We develop a length-disaggregated, spatiotemporal, delta-generalized linear mixed model (GLMM) and apply the method to fishery-dependent catch rates of shortfin mako sharks (Isurus oxyrinchus) in the North Pacific. The spatiotemporal model may provide an improvement over conventional time-series and spatially stratified models by yielding more precise and biologically interpretable estimates of abundance. Including length data may provide additional information to better understand life history and habitat partitioning for marine species. Nominal catch rates were standardized using a GLMM framework with spatiotemporal and length composition data. The best-fitting model showed that most hotspots for “immature” shortfin mako occurred in the coastal waters of Japan, while hotspots for “subadult and adult” occurred in the offshore or coastal waters of Japan. We also found that size-specific catch rates provide an indication that there has been a recent increasing trend in stock abundance since 2008.

scholarly journals Robots Versus Humans: Automated Annotation Accurately Quantifies Essential Ocean Variables of Rocky Intertidal Functional Groups and Habitat State

2021 ◽  
Vol 8 ◽  
Author(s):  
Gonzalo Bravo ◽  
Nicolas Moity ◽  
Edgardo Londoño-Cruz ◽  
Frank Muller-Karger ◽  
Gregorio Bigatti ◽  
...  
Keyword(s):  
Machine Learning ◽  
Functional Groups ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Visual Analysis ◽  
Gulf Of Maine ◽  
The United States ◽  
Marine Biodiversity ◽  
Percent Cover ◽  
Automated Annotation

Standardized methods for effectively and rapidly monitoring changes in the biodiversity of marine ecosystems are critical to assess status and trends in ways that are comparable between locations and over time. In intertidal and subtidal habitats, estimates of fractional cover and abundance of organisms are typically obtained with traditional quadrat-based methods, and collection of photoquadrat imagery is a standard practice. However, visual analysis of quadrats, either in the field or from photographs, can be very time-consuming. Cutting-edge machine learning tools are now being used to annotate species records from photoquadrat imagery automatically, significantly reducing processing time of image collections. However, it is not always clear whether information is lost, and if so to what degree, using automated approaches. In this study, we compared results from visual quadrats versus automated photoquadrat assessments of macroalgae and sessile organisms on rocky shores across the American continent, from Patagonia (Argentina), Galapagos Islands (Ecuador), Gorgona Island (Colombian Pacific), and the northeast coast of the United States (Gulf of Maine) using the automated software CoralNet. Photoquadrat imagery was collected at the same time as visual surveys following a protocol implemented across the Americas by the Marine Biodiversity Observation Network (MBON) Pole to Pole of the Americas program. Our results show that photoquadrat machine learning annotations can estimate percent cover levels of intertidal benthic cover categories and functional groups (algae, bare substrate, and invertebrate cover) nearly identical to those from visual quadrat analysis. We found no statistical differences of cover estimations of dominant groups in photoquadrat images annotated by humans and those processed in CoralNet (binomial generalized linear mixed model or GLMM). Differences between these analyses were not significant, resulting in a Bray-Curtis average distance of 0.13 (sd 0.11) for the full label set, and 0.12 (sd 0.14) for functional groups. This is the first time that CoralNet automated annotation software has been used to monitor “Invertebrate Abundance and Distribution” and “Macroalgal Canopy Cover and Composition” Essential Ocean Variables (EOVs) in intertidal habitats. We recommend its use for rapid, continuous surveys over expanded geographical scales and monitoring of intertidal areas globally.

scholarly journals Effect of PRRSV stability on productive parameters in breeding herds of a swine large integrated group in Spain

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
D Torrents ◽  
J Miranda ◽  
PC Gauger ◽  
A Ramirez ◽  
DCL Linhares
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
Monitoring Program ◽  
Direct Consequence ◽  
Weaned Piglets ◽  
Total Period ◽  
Prrs Virus ◽  
Productivity Data ◽  
Production Improvement ◽  
One Year

Abstract Background In breeding herds, porcine reproductive and respiratory syndrome (PRRS) clinically manifests as increased abortions, number of stillbirths, and pre-weaning mortality, and as a direct consequence, results in a decrease of the number of piglets weaned per sow per year. Breeding farm classification according the PRRS virus (PRRSV) status (unstable or stable) is a key control strategy for this disease. The aim of this study was to evaluate the production improvement related to achieving a PRRSV stable status in breeding herds in Spain. For this purpose, epidemiological and productivity data were collected from a systematic PRRSV monitoring program in 35 breeding herds from a large integrated swine group in Spain. A comparative statistical analysis was conducted using four key production indicators (KPI) between different PRRSV status and a generalized linear mixed model: weekly abortions/1000 sows (ABTHS), born-alive rate (BAR), pre-weaning mortality rate (PWMR), and number of weaned piglets per 1000 sows (WPTHS). Results From the 35 monitored farms during a total period of 58 weeks, we collected 49 to 58 weeks of production data and PRRSV classification status for each study farm. This represented a total of 1997 (741 unstable and 1256 stable) weekly data collected that was eligible for the KPI comparative study. PRRSV stability was associated with significant improvement in BAR (+ 1.10 %, p < 0.001), PWMR (-0.88 %, p < 0.002) and WPTHS (+ 24.52, p < 0.0001). Conclusions These results demonstrate for the first time the improved production due to achieving PRRSV stability in breeding herds under field conditions in a European country. Increased number of born-alive piglets and a reduction of piglet pre-weaning mortality represents an increase of 1.28 weaned piglets per sow per year if PRRSV stability was achieved and maintained for one-year period in a breeding farm.

scholarly journals Dramatic decline and limited recovery of a green crab (Carcinus maenas) population in the Minas Basin, Canada after the summer of 2013

2018 ◽  
Author(s):  
Brady K. Quinn
Keyword(s):  
Gulf Of Maine ◽  
Carcinus Maenas ◽  
Monitoring Program ◽  
Marine Species ◽  
Bay Of Fundy ◽  
Catch Per Unit Effort ◽  
Spring Precipitation ◽  
Spring Temperature ◽  
Wind Speeds ◽  
Causative Agents

This paper reports the results of a ten-year monitoring program of an Atlantic Canadian population of green crabs, Carcinus maenas, in the Minas Basin of the Bay of Fundy. Intertidal densities, sex and reproductive ratios, juvenile recruitment, subtidal catch-per-unit-effort (CPUE), and sizes of crabs in this population were recorded from 2008 to 2017. In 2013 intertidal densities, mean crab sizes, subtidal CPUE, and proportions of crabs mature and reproducing all dramatically decreased to all-time lows, and large crabs virtually disappeared from the population. From 2014 to 2017 the population partially recovered but remained in an altered state. Potential causes of interannual changes to this population were investigated by correlating intertidal densities to 67 seasonal environmental variables. Crab densities in a given year were best explained by potential settlement, mean and variability of autumn, spring, and summer wind speeds, winter and spring temperature, and spring precipitation. However, potential roles of other factors (e.g., summer temperatures, North Atlantic Oscillation index) could not be ruled out. Changes in abundances of other species in the region, particularly predators and prey of green crabs, have also been observed and present possible alternative causative agents that should be investigated. Populations of other marine species in the Gulf of Maine-Bay of Fundy region within which the Minas Basin is situated have also been reported to have undergone dramatic changes in and after 2013, suggesting the occurrence of some oceanographic event or regime shift in the region. Declines to the monitored crab population in this study may have resulted from this same 2013 event. These observations have implications for recruitment to marine populations in this region.

scholarly journals Dramatic decline and limited recovery of a green crab (Carcinus maenas) population in the Minas Basin, Canada after the summer of 2013

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5566 ◽  
Author(s):  
Brady K. Quinn
Keyword(s):  
Gulf Of Maine ◽  
Carcinus Maenas ◽  
Monitoring Program ◽  
Marine Species ◽  
Stepwise Multiple Regression ◽  
Bay Of Fundy ◽  
Catch Per Unit Effort ◽  
Canadian Population ◽  
Dramatic Decline ◽  
Causative Agents

This paper reports the results of a ten-year monitoring program of an Atlantic Canadian population of green crabs, Carcinus maenas, in the Minas Basin of the Bay of Fundy. Intertidal densities, sex and reproductive ratios, juvenile recruitment, subtidal catch-per-unit-effort (CPUE), and sizes of crabs in this population were recorded from 2008 to 2017. In 2013 intertidal densities, mean crab sizes, subtidal CPUE, and proportions of crabs mature and reproducing all dramatically decreased to all-time lows, and large crabs virtually disappeared from the population. From 2014 to 2017 the population partially recovered but remained in an altered state. Potential causes of interannual changes to this population were investigated by correlating intertidal densities to 257 monthly environmental variables and performing stepwise multiple regression analyses. Crab densities in a given year were best explained by potential settlement during the summer and the maximum sea-surface temperature during March of the same year. However, potential roles of other factors (e.g., autumn winds, summer temperatures, North Atlantic Oscillation index) could not be ruled out. Changes in abundances of other species in the area, particularly predators and prey of green crabs, have also been observed and present possible alternative causative agents that should be investigated. Populations of other marine species in the Gulf of Maine-Bay of Fundy region within which the Minas Basin is situated have also been reported to have undergone dramatic changes in and after 2013, suggesting the occurrence of some oceanographic event or regime shift in the region. Declines to the monitored crab population in this study may have resulted from this same 2013 event. These observations have implications for recruitment to marine populations in this region.

scholarly journals Investigating face veneer check development in decorative plywood panels: the impact of four common manufacturing factors

2019 ◽  
Vol 77 (6) ◽  
pp. 961-979
Author(s):  
Michael Burnard ◽  
Scott Leavengood ◽  
Lech Muszyński ◽  
Lisa Ganio
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
Urea Formaldehyde ◽  
Image Correlation ◽  
Future Research ◽  
Medium Density Fibreboard ◽  
Density Estimates ◽  
Drying Conditions ◽  
Lathe Check ◽  
The Impact

Abstract An optical method based on digital image correlation was used to investigate the impact of four decorative plywood manufacturing factors (core type, veneer type, adhesive type and lathe check orientation) on face veneer checking. The four core types were: combination core, medium density fibreboard, particleboard, and veneer core. The four veneer types were: peeled 0.604 mm, peeled 0.706 mm, sliced 0.508 mm, and sliced 0.564 mm. Both loose-side out and tight-side out lathe check orientations were used. The adhesive systems were urea–formaldehyde, polyvinyl acetate, and soy-protein based. 96 treatment combinations with 8 replicates were tested. All specimens were exposed to harsh but realistic drying conditions (approximately 30°C and 26% relative humidity) for 4 h during inspection. Checks were detected on 428 out of a total of 765 specimens (56%). The estimated mean check densities (area of checking per unit area) indicated some unfavourable factor combinations. All factors had some degree of interaction with one another and check development could not be attributed to a single factor examined in this study. The data were fit to a generalized linear mixed model based on Tweedie’s compound Poisson distribution. Confidence intervals were calculated via bootstrapping. The check density estimates produced by this model can be used to cautiously guide manufacturers as they decide on panel components. The broader use of the model is to highlight the complexity of the problem and guide future research in this area.

The influence of complex structure on the spatial dynamics of Atlantic cod (Gadus morhua) in the Gulf of Maine

2017 ◽  
Vol 74 (9) ◽  
pp. 2379-2388 ◽  
Author(s):  
Lisha Guan ◽  
Yong Chen ◽  
Kevin W Staples ◽  
Jie Cao ◽  
Bai Li
Keyword(s):  
Gadus Morhua ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Gulf Of Maine ◽  
Atlantic Cod ◽  
Complex Structure ◽  
Spatial Dynamics ◽  
Trawl Survey ◽  
Marine Fishery ◽  
Density Dependent Habitat Selection

Abstract Atlantic cod (Gadus morhua) in the Gulf of Maine (GOM) is an iconic marine fishery stock that has experienced a substantial distributional shift since the mid-1990s. A geostatistical delta-generalized linear mixed model was utilized to hindcast yearly season-specific distributions of GOM cod. These distributions were calculated using the spring and fall bottom trawl survey data for the stock, along with cell-based bathymetry and bottom temperature data for the study area for the years 1982–2013. The centre of stock distribution (the centre of gravity), spatial extent in latitude and longitude, area occupied and median habitat temperature were estimated annually to quantify changes in the spatial dynamics of GOM cod. Time series of these distributional metrics were then used to evaluate the influences of climate change and density-dependent habitat selection on GOM cod’s distribution. Results showed that the rapid southwestward shift in the stock distribution after the late 1990s could not simply be attributed to decreasing stock abundance or warming bottom temperatures. The observed shift in cod distribution requires further investigation on whether it is possibly a result of other factors, like fluctuating productivity among subpopulations.

scholarly journals The use of linear mixed effects models to investigate local adaptation in marine fish subpopulations: case study, changing spawning times of common sole (Solea solea)

2019 ◽  
Vol 76 (7) ◽  
pp. 2297-2304
Author(s):  
Jennifer I Fincham ◽  
Jon Barry
Keyword(s):  
Local Adaptation ◽  
Fisheries Management ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Environmental Gradients ◽  
Management Strategies ◽  
Marine Species ◽  
Window Analysis ◽  
North East ◽  
The North

Abstract Populations along environmental gradients have the potential to adapt to their own local environments. It is important to understand these adaptations in fisheries stocks to fully inform fisheries management strategies. With this is mind, sea temperatures are an important cue in timing for many marine species, including sole in the North-East Atlantic Ocean. We used spawning data and modelled sea surface temperature (SST) data from sole subpopulations to examine the possibility of local adaptation of their spawning times to rising temperature. Climate window analysis was used, in a linear mixed model using mean spawning week and SST, to investigate statistically significant differences between subpopulations of sole. There was no evidence of local adaptation to changing temperatures for these subpopulations. This suggests that their spawning-time reaction to changing temperatures is currently due to their subpopulation’s mean plasticity. Using climate window analysis and modelled temperature data we have demonstrated a method of examining spawning changes in marine populations along a temperature gradient. Recruitment and spawning success are key elements of fisheries population models which contribute to fisheries management. Further understanding of the influence of temperature on recruitment will help inform future modelling.

scholarly journals Dramatic decline and limited recovery of a green crab (Carcinus maenas) population in the Minas Basin, Canada after the summer of 2013

2018 ◽  
Author(s):  
Brady K. Quinn
Keyword(s):  
Gulf Of Maine ◽  
Carcinus Maenas ◽  
Monitoring Program ◽  
Marine Species ◽  
Bay Of Fundy ◽  
Catch Per Unit Effort ◽  
Spring Precipitation ◽  
Spring Temperature ◽  
Wind Speeds ◽  
Causative Agents

This paper reports the results of a ten-year monitoring program of an Atlantic Canadian population of green crabs, Carcinus maenas, in the Minas Basin of the Bay of Fundy. Intertidal densities, sex and reproductive ratios, juvenile recruitment, subtidal catch-per-unit-effort (CPUE), and sizes of crabs in this population were recorded from 2008 to 2017. In 2013 intertidal densities, mean crab sizes, subtidal CPUE, and proportions of crabs mature and reproducing all dramatically decreased to all-time lows, and large crabs virtually disappeared from the population. From 2014 to 2017 the population partially recovered but remained in an altered state. Potential causes of interannual changes to this population were investigated by correlating intertidal densities to 67 seasonal environmental variables. Crab densities in a given year were best explained by potential settlement, mean and variability of autumn, spring, and summer wind speeds, winter and spring temperature, and spring precipitation. However, potential roles of other factors (e.g., summer temperatures, North Atlantic Oscillation index) could not be ruled out. Changes in abundances of other species in the region, particularly predators and prey of green crabs, have also been observed and present possible alternative causative agents that should be investigated. Populations of other marine species in the Gulf of Maine-Bay of Fundy region within which the Minas Basin is situated have also been reported to have undergone dramatic changes in and after 2013, suggesting the occurrence of some oceanographic event or regime shift in the region. Declines to the monitored crab population in this study may have resulted from this same 2013 event. These observations have implications for recruitment to marine populations in this region.

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