Etienne Rivot - Academia.edu (original) (raw)
Papers by Etienne Rivot
Restricted to other programme participants (including the Commission Services) RE Restricted to a... more Restricted to other programme participants (including the Commission Services) RE Restricted to a group specified by the consortium (including the Commission Services) CO Confidential, only for members of the consortium (including the Commission Services) X
Canadian Journal of Fisheries and Aquatic Sciences
Estimation of abundance with wide spatio-temporal coverage is essential to the assessment and man... more Estimation of abundance with wide spatio-temporal coverage is essential to the assessment and management of wild populations. But, in many cases, data available to estimate abundance time series have diverse forms, variable quality over space and time and they stem from multiple data collection procedures. We developed a Hierarchical Bayesian Modelling (HBM) approach that take full advantage of the diverse assemblage of data at hand to estimate homogeneous time series of abundances irrespective of the data collection procedure. We apply our approach to the estimation of adult abundances of 18 Atlantic salmon populations of Brittany (France) from 1987 to 2017 using catch statistics, environmental covariates and fishing effort. Additional data of total or partial abundance collected in 4 closely monitored populations are also integrated into the analysis. The HBM framework allows the transfer of information from the closely monitored populations to the others. Our results reveal no cl...
Canadian Journal of Fisheries and Aquatic Sciences
Recent decline in abundance of Atlantic salmon (Salmo salar) and concomitant changes in life hist... more Recent decline in abundance of Atlantic salmon (Salmo salar) and concomitant changes in life history may result from a decline in the growth conditions during marine migration. Available literature suggests the existence of a sex-specific reaction norm linking maturation with environmental growth conditions at sea. However, the extent to which this mechanism explains variations in age at maturity remains unclear. Using a historical collection of scales (1987–2017) from the Sélune River, France, we showed that marine growth declined over the first summer and remained stable during the subsequent periods at sea among returning salmon. Results support the hypothesis of a sex-specific probabilistic reaction norm, with individual probability to return after 1 year at sea increasing when growth increases. Females may require higher growth than males to attain their maturation threshold. This mechanism is a good candidate to explain temporal variability in sea-age at return at both the ind...
Canadian Journal of Fisheries and Aquatic Sciences
The biological status of many commercially exploited fishes remains unknown, mostly due to a lack... more The biological status of many commercially exploited fishes remains unknown, mostly due to a lack of data necessary for their assessment. Investigating the spatiotemporal dynamics of such species can lead to new insights into population processes and foster a path towards improved spatial management decisions. Here, we focused on striped red mullet (Mullus surmuletus), a widespread yet data-limited species of high commercial importance. Aiming to quantify range dynamics in this data-poor scenario, we combined fishery-dependent and -independent data sets through a series of Bayesian mixed-effects models designed to capture monthly and seasonal occurrence patterns near the species’ northern range limit across 20 years. Combining multiple data sets allowed us to cover the entire distribution of the northern population of M. surmuletus, exploring dynamics at different spatiotemporal scales and identifying key environmental drivers (i.e., sea surface temperature, salinity) that shape occ...
Canadian Journal of Fisheries and Aquatic Sciences
Successful management and protection of wild animal populations relies on good understanding of t... more Successful management and protection of wild animal populations relies on good understanding of their life cycles. Because population dynamics depends on intricate interactions of biological and ecological processes at various scales, new approaches are needed that account for the variability of demographic processes and associated parameters in a hierarchy of spatial scales. A hierarchical Bayesian model for the resident brown trout (Salmo trutta) life cycle was built to assess the relative influence of local and general determinants of mortality. The model was fitted to an extensive data set collected in 40 river reaches, combining abundance and environmental data (hydraulics, water temperature). Density-dependent mortality of juveniles increased at low water temperatures and decreased with shelter availability. High water temperature increased density-dependent mortality in adults. The model could help to predict monthly juvenile and adult mortality under scenarios of global warm...
ABSTRACT Integrated life cycle models are key tools for an ecosystem approach to fish population ... more ABSTRACT Integrated life cycle models are key tools for an ecosystem approach to fish population dynamics and stock assessment. They allow analysing ecological processes underlying the spatio-temporal variability of different life stages, together with the integration of multiple interacting sources of environmental and anthropogenic stressors along the life cycle. We developed a life cycle model for Atlantic salmon. The model captures the population dynamics of eight stocks of the eastern Atlantic Ocean over the past 42 years. The Bayesian Hierarchical Modelling structure provides a tool for separating out signals at different temporal (e.g., year, decades) and spatial (e.g., specific or shared by all the 8 stocks) scales in demographic traits. It improves the capability to identify responses to key influential stressors associated with different scales. Results show that the survival during the first months at sea and the proportion of salmon returning to freshwater after one year at sea exhibit common trends shared, supporting a response to broad scale ecosystem changes. The survival has decreased over the time series and supports the hypothesis of a synchronous collapse of marine survival with ecosystem changes observed in the North Atlantic in the early 1990s. Simultaneously, the proportion of early maturing salmon has increased.
Estuarine, Coastal and Shelf Science, 2016
Fisheries Research, Feb 1, 2007
Fisheries research often involves a repetitive sampling protocol for multiple ecological units (o... more Fisheries research often involves a repetitive sampling protocol for multiple ecological units (our example is gillnetting of lakes). Estimates of abundance based on catch per unit effort can be erroneous due to lake effects on sampling efficiency. Conversely dividing data into individual lakes may lead to poor inference due to sparse data. Hierarchical Bayesian analysis compromises between these two extreme methods by estimating parameters for an individual lake, but borrowing information from other lakes. We estimated size-selective gillnet efficiency with mark-recapture data across a series of lakes subject to a constant netting effort. Hierarchical Bayesian analysis was able to prevent unrealistic selectivity functions that arose from individual lake analysis. Furthermore, the hierarchical approach was able to derive accurate parameter estimates with very few markrecaptures in sub-sampled data trials. This paper demonstrates the hierarchical methodology for the estimation of fishery selectivity parameters. The results could be used to derive informative priors for future research which uses the proposed gillnet protocol.
Canadian Journal of Fisheries and Aquatic Sciences, 2002
We present a hierarchical Bayesian model (HBM) for capturemarkrecapture (CMR) data analysis. It... more We present a hierarchical Bayesian model (HBM) for capturemarkrecapture (CMR) data analysis. It aims at estimating the probability of capture (θi) and the total population size (Ni) in a series of I years i = 1,...,I. The HBM assumes that the θis and Nis are sampled from a common probability distribution with unknown parameters. It is compared with the model assuming independence between years in the θis and Nis (ABM). We show how a transfer of information between years is organized by the HBM. We compare the merits of HBM vs. ABM to estimate the spawning run and smolt run of an Atlantic salmon (Salmo salar) population of the River Oir (France) over a period of 17 years. In the spawners case, yearly data are poorly informative. Consequently, the HBM greatly improves posterior inferences compared with the ABM in terms of dispersion and robustness to the choice of prior. In the smolts case, the HBM does not significantly improve inferences compared with the ABM because data are more informative. We discuss why hierarchical modeling should be recommended in any ecological study where the data are collected on several sampling units that share some common features.
International Statistical Review, 2013
ICES Journal of Marine Science, 2012
Rougier, T., Lambert, P., Drouineau, H., Girardin, M., Castelnaud, G., Carry, L., Aprahamian, M.,... more Rougier, T., Lambert, P., Drouineau, H., Girardin, M., Castelnaud, G., Carry, L., Aprahamian, M., Rivot, E., and Rochard, E. 2012. Collapse of allis shad, Alosa alosa, in the Gironde system (southwest France): environmental change, fishing mortality, or Allee effect? – ICES Journal of Marine Science, 69: 1802–1811. At the end of the 20th century the allis shad population in the Gironde was the largest in Europe. During the first decade of the 21st century, catches declined dramatically by two orders of magnitude, and a fishery moratorium was implemented in 2008. This deterioration in the status of the stock was confirmed by three independent assessments (abundance of juveniles and of potential and effective spawners). Three hypotheses on the cause of the collapse were examined: (i) an environmental change in freshwater and/or in the estuary; (ii) an increase in marine and/or estuarine mortality; and (iii) the presence of an Allee effect. Changes in flow, temperature, and water quali...
Restricted to other programme participants (including the Commission Services) RE Restricted to a... more Restricted to other programme participants (including the Commission Services) RE Restricted to a group specified by the consortium (including the Commission Services) CO Confidential, only for members of the consortium (including the Commission Services) X
Canadian Journal of Fisheries and Aquatic Sciences
Estimation of abundance with wide spatio-temporal coverage is essential to the assessment and man... more Estimation of abundance with wide spatio-temporal coverage is essential to the assessment and management of wild populations. But, in many cases, data available to estimate abundance time series have diverse forms, variable quality over space and time and they stem from multiple data collection procedures. We developed a Hierarchical Bayesian Modelling (HBM) approach that take full advantage of the diverse assemblage of data at hand to estimate homogeneous time series of abundances irrespective of the data collection procedure. We apply our approach to the estimation of adult abundances of 18 Atlantic salmon populations of Brittany (France) from 1987 to 2017 using catch statistics, environmental covariates and fishing effort. Additional data of total or partial abundance collected in 4 closely monitored populations are also integrated into the analysis. The HBM framework allows the transfer of information from the closely monitored populations to the others. Our results reveal no cl...
Canadian Journal of Fisheries and Aquatic Sciences
Recent decline in abundance of Atlantic salmon (Salmo salar) and concomitant changes in life hist... more Recent decline in abundance of Atlantic salmon (Salmo salar) and concomitant changes in life history may result from a decline in the growth conditions during marine migration. Available literature suggests the existence of a sex-specific reaction norm linking maturation with environmental growth conditions at sea. However, the extent to which this mechanism explains variations in age at maturity remains unclear. Using a historical collection of scales (1987–2017) from the Sélune River, France, we showed that marine growth declined over the first summer and remained stable during the subsequent periods at sea among returning salmon. Results support the hypothesis of a sex-specific probabilistic reaction norm, with individual probability to return after 1 year at sea increasing when growth increases. Females may require higher growth than males to attain their maturation threshold. This mechanism is a good candidate to explain temporal variability in sea-age at return at both the ind...
Canadian Journal of Fisheries and Aquatic Sciences
The biological status of many commercially exploited fishes remains unknown, mostly due to a lack... more The biological status of many commercially exploited fishes remains unknown, mostly due to a lack of data necessary for their assessment. Investigating the spatiotemporal dynamics of such species can lead to new insights into population processes and foster a path towards improved spatial management decisions. Here, we focused on striped red mullet (Mullus surmuletus), a widespread yet data-limited species of high commercial importance. Aiming to quantify range dynamics in this data-poor scenario, we combined fishery-dependent and -independent data sets through a series of Bayesian mixed-effects models designed to capture monthly and seasonal occurrence patterns near the species’ northern range limit across 20 years. Combining multiple data sets allowed us to cover the entire distribution of the northern population of M. surmuletus, exploring dynamics at different spatiotemporal scales and identifying key environmental drivers (i.e., sea surface temperature, salinity) that shape occ...
Canadian Journal of Fisheries and Aquatic Sciences
Successful management and protection of wild animal populations relies on good understanding of t... more Successful management and protection of wild animal populations relies on good understanding of their life cycles. Because population dynamics depends on intricate interactions of biological and ecological processes at various scales, new approaches are needed that account for the variability of demographic processes and associated parameters in a hierarchy of spatial scales. A hierarchical Bayesian model for the resident brown trout (Salmo trutta) life cycle was built to assess the relative influence of local and general determinants of mortality. The model was fitted to an extensive data set collected in 40 river reaches, combining abundance and environmental data (hydraulics, water temperature). Density-dependent mortality of juveniles increased at low water temperatures and decreased with shelter availability. High water temperature increased density-dependent mortality in adults. The model could help to predict monthly juvenile and adult mortality under scenarios of global warm...
ABSTRACT Integrated life cycle models are key tools for an ecosystem approach to fish population ... more ABSTRACT Integrated life cycle models are key tools for an ecosystem approach to fish population dynamics and stock assessment. They allow analysing ecological processes underlying the spatio-temporal variability of different life stages, together with the integration of multiple interacting sources of environmental and anthropogenic stressors along the life cycle. We developed a life cycle model for Atlantic salmon. The model captures the population dynamics of eight stocks of the eastern Atlantic Ocean over the past 42 years. The Bayesian Hierarchical Modelling structure provides a tool for separating out signals at different temporal (e.g., year, decades) and spatial (e.g., specific or shared by all the 8 stocks) scales in demographic traits. It improves the capability to identify responses to key influential stressors associated with different scales. Results show that the survival during the first months at sea and the proportion of salmon returning to freshwater after one year at sea exhibit common trends shared, supporting a response to broad scale ecosystem changes. The survival has decreased over the time series and supports the hypothesis of a synchronous collapse of marine survival with ecosystem changes observed in the North Atlantic in the early 1990s. Simultaneously, the proportion of early maturing salmon has increased.
Estuarine, Coastal and Shelf Science, 2016
Fisheries Research, Feb 1, 2007
Fisheries research often involves a repetitive sampling protocol for multiple ecological units (o... more Fisheries research often involves a repetitive sampling protocol for multiple ecological units (our example is gillnetting of lakes). Estimates of abundance based on catch per unit effort can be erroneous due to lake effects on sampling efficiency. Conversely dividing data into individual lakes may lead to poor inference due to sparse data. Hierarchical Bayesian analysis compromises between these two extreme methods by estimating parameters for an individual lake, but borrowing information from other lakes. We estimated size-selective gillnet efficiency with mark-recapture data across a series of lakes subject to a constant netting effort. Hierarchical Bayesian analysis was able to prevent unrealistic selectivity functions that arose from individual lake analysis. Furthermore, the hierarchical approach was able to derive accurate parameter estimates with very few markrecaptures in sub-sampled data trials. This paper demonstrates the hierarchical methodology for the estimation of fishery selectivity parameters. The results could be used to derive informative priors for future research which uses the proposed gillnet protocol.
Canadian Journal of Fisheries and Aquatic Sciences, 2002
We present a hierarchical Bayesian model (HBM) for capturemarkrecapture (CMR) data analysis. It... more We present a hierarchical Bayesian model (HBM) for capturemarkrecapture (CMR) data analysis. It aims at estimating the probability of capture (θi) and the total population size (Ni) in a series of I years i = 1,...,I. The HBM assumes that the θis and Nis are sampled from a common probability distribution with unknown parameters. It is compared with the model assuming independence between years in the θis and Nis (ABM). We show how a transfer of information between years is organized by the HBM. We compare the merits of HBM vs. ABM to estimate the spawning run and smolt run of an Atlantic salmon (Salmo salar) population of the River Oir (France) over a period of 17 years. In the spawners case, yearly data are poorly informative. Consequently, the HBM greatly improves posterior inferences compared with the ABM in terms of dispersion and robustness to the choice of prior. In the smolts case, the HBM does not significantly improve inferences compared with the ABM because data are more informative. We discuss why hierarchical modeling should be recommended in any ecological study where the data are collected on several sampling units that share some common features.
International Statistical Review, 2013
ICES Journal of Marine Science, 2012
Rougier, T., Lambert, P., Drouineau, H., Girardin, M., Castelnaud, G., Carry, L., Aprahamian, M.,... more Rougier, T., Lambert, P., Drouineau, H., Girardin, M., Castelnaud, G., Carry, L., Aprahamian, M., Rivot, E., and Rochard, E. 2012. Collapse of allis shad, Alosa alosa, in the Gironde system (southwest France): environmental change, fishing mortality, or Allee effect? – ICES Journal of Marine Science, 69: 1802–1811. At the end of the 20th century the allis shad population in the Gironde was the largest in Europe. During the first decade of the 21st century, catches declined dramatically by two orders of magnitude, and a fishery moratorium was implemented in 2008. This deterioration in the status of the stock was confirmed by three independent assessments (abundance of juveniles and of potential and effective spawners). Three hypotheses on the cause of the collapse were examined: (i) an environmental change in freshwater and/or in the estuary; (ii) an increase in marine and/or estuarine mortality; and (iii) the presence of an Allee effect. Changes in flow, temperature, and water quali...