scholarly journals An integrated model of seasonal changes in stock composition and abundance with an application to Chinook salmon

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11163
Author(s):  
Cameron Freshwater ◽  
Sean C. Anderson ◽  
Terry D. Beacham ◽  
Wilf Luedke ◽  
Catarina Wor ◽  
...  
Keyword(s):  
Chinook Salmon ◽  
Seasonal Changes ◽  
Anthropogenic Impacts ◽  
Spatial Scales ◽  
Integrated Model ◽  
Seasonal Abundance ◽  
Distribution Data ◽  
Sampling Effort ◽  
Catch Per Unit Effort ◽  
Marine Habitats

Population-specific spatial and temporal distribution data are necessary to identify mechanisms regulating abundance and to manage anthropogenic impacts. However the distributions of highly migratory species are often difficult to resolve, particularly when multiple populations’ movements overlap. Here we present an integrated model to estimate spatially-stratified, seasonal trends in abundance and population composition, using data from extensive genetic sampling of commercial and recreational Chinook salmon (Oncorhynchus tshawytscha) fisheries in southern British Columbia. We use the model to estimate seasonal changes in population-specific standardized catch per unit effort (a proxy for abundance) across six marine regions, while accounting for annual variability in sampling effort and uncertain genetic stock assignment. We also share this model as an R package stockseasonr for application to other regions and species. Even at the relatively small spatial scales considered here, we found that patterns in seasonal abundance differed among regions and stocks. While certain locations were clearly migratory corridors, regions within the Salish Sea exhibited diverse, and often weak, seasonal patterns in abundance, emphasizing that they are important, year-round foraging habitats. Furthermore, we found evidence that stocks with similar freshwater life histories and adult run timing, as well as relatively proximate spawning locations, exhibited divergent distributions. Our findings highlight subtle, but important differences in how adult Chinook salmon use marine habitats. Down-scaled model outputs could be used to inform ecosystem-based management efforts by resolving the degree to which salmon overlap with other species of concern, as well as specific fisheries. More broadly, variation in stock-specific abundance among regions indicates efforts to identify mechanisms driving changes in size-at-maturity and natural mortality should account for distinct marine distributions.

Synchrony of frond dynamics among patches of the clonal seaweed Mazzaella parksii (Rhodophyta) at local spatial scale

2004 ◽  
Vol 84 (5) ◽  
pp. 883-886 ◽  
Author(s):  
Ricardo Scrosati
Keyword(s):  
Spatial Scale ◽  
Seasonal Changes ◽  
Pacific Coast ◽  
Spatial Scales ◽  
Sampling Effort ◽  
Confidence Limits ◽  
Seasonal Trends ◽  
Intertidal Seaweed ◽  
The Mean

This study investigated the synchrony of frond dynamics among patches of the intertidal seaweed Mazzaella parksii (=M. cornucopiae; Rhodophyta: Gigartinales) at local spatial scale. At Prasiola Point (Pacific coast of Canada), the mean synchrony of the seasonal changes in frond density among seven permanent, 100-cm2 quadrats was significant (mean Pearson's r=0·73, with 0·65–0·81 as 95% confidence limits) between 1993 and 1995. This indicates that predicting seasonal trends for non-monitored patches at local spatial scale can be done relatively well based on observations on a limited number of quadrats. The identification of the spatial scales at which seaweed populations covary synchronously will permit minimizing sampling effort while retaining the ability to make valid predictions for non-monitored sites.

scholarly journals Novel approach to enhance coastal habitat and biotope mapping with drone aerial imagery analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
João Gama Monteiro ◽  
Jesús L. Jiménez ◽  
Francesca Gizzi ◽  
Petr Přikryl ◽  
Jonathan S. Lefcheck ◽  
...  
Keyword(s):  
Anthropogenic Impacts ◽  
Spatial Scales ◽  
Low Cost ◽  
Human Populations ◽  
Coastal Habitat ◽  
Coastal Monitoring ◽  
Monitoring Programs ◽  
Novel Approach ◽  
Aerial Platforms ◽  
Rocky Habitats

AbstractUnderstanding the complex factors and mechanisms driving the functioning of coastal ecosystems is vital towards assessing how organisms, ecosystems, and ultimately human populations will cope with the ecological consequences of natural and anthropogenic impacts. Towards this goal, coastal monitoring programs and studies must deliver information on a range of variables and factors, from taxonomic/functional diversity and spatial distribution of habitats, to anthropogenic stress indicators such as land use, fisheries use, and pollution. Effective monitoring programs must therefore integrate observations from different sources and spatial scales to provide a comprehensive view to managers. Here we explore integrating aerial surveys from a low-cost Remotely Piloted Aircraft System (RPAS) with concurrent underwater surveys to deliver a novel approach to coastal monitoring. We: (i) map depth and substrate of shallow rocky habitats, and; (ii) classify the major biotopes associated with these environmental axes; and (iii) combine data from i and ii to assess the likely distribution of common sessile organismal assemblages over the survey area. Finally, we propose a general workflow that can be adapted to different needs and aerial platforms, which can be used as blueprints for further integration of remote-sensing with in situ surveys to produce spatially-explicit biotope maps.

scholarly journals Diversity and distribution patterns of the Oligocene and Miocene decapod crustaceans (Crustacea: Malacostraca) of the Western and Central Paratethys

2016 ◽  
Vol 67 (5) ◽  
pp. 471-494 ◽  
Author(s):  
Matúš Hyžný
Keyword(s):  
Spatial Scales ◽  
Three Dimensional ◽  
Decapod Crustacean ◽  
Distribution Patterns ◽  
Mediterranean Area ◽  
Homogeneous Distribution ◽  
Decapod Crustaceans ◽  
Central Paratethys ◽  
The North ◽  
Marine Habitats

AbstractDecapod associations have been significant components of marine habitats throughout the Cenozoic when the major diversification of the group occurred. In this respect, the circum-Mediterranean area is of particular interest due to its complex palaeogeographic history. During the Oligo-Miocene, it was divided in two major areas, Mediterranean and Paratethys. Decapod crustaceans from the Paratethys Sea have been reported in the literature since the 19thcentury, but only recent research advances allow evaluation of the diversity and distribution patterns of the group. Altogether 176 species-level taxa have been identified from the Oligocene and Miocene of the Western and Central Paratethys. Using the three-dimensional NMDS analysis, the composition of decapod crustacean faunas of the Paratethys shows significant differences through time. The Ottnangian and Karpatian decapod associations were similar to each other both taxonomically and in the mode of preservation, and they differed taxonomically from the Badenian ones. The Early Badenian assemblages also differed taxonomically from the Late Badenian ones. The time factor, including speciation, immigration from other provinces and/or (local or global) extinction, can explain temporal differences among assemblages within the same environment. High decapod diversity during the Badenian was correlated with the presence of reefal settings. The Badenian was the time with the highest decapod diversity, which can, however, be a consequence of undersampling of other time slices. Whereas the Ottnangian and Karpatian decapod assemblages are preserved virtually exclusively in the siliciclastic “Schlier”-type facies that originated in non-reefal offshore environments, carbonate sedimentation and the presence of reefal environments during the Badenian in the Central Paratethys promoted thriving of more diverse reef-associated assemblages. In general, Paratethyan decapods exhibited homogeneous distribution during the Oligo-Miocene among the basins in the Paratethys. Based on the co-occurrence of certain decapod species, migration between the Paratethys and the North Sea during the Early Miocene probably occurred via the Rhine Graben. At larger spatial scales, our results suggest that the circum-Mediterranean marine decapod taxa migrated in an easterly direction during the Oligocene and/or Miocene, establishing present-day decapod communities in the Indo-West Pacific.

scholarly journals Factors affecting relative abundance of low-mobility fishing resources: spiny lobster in the Galapagos Marine Reserve

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7278 ◽  
Author(s):  
Juan Carlos Murillo-Posada ◽  
Silvia Salas ◽  
Iván Velázquez-Abunader
Keyword(s):  
Monitoring System ◽  
Relative Abundance ◽  
Spatial Scales ◽  
Marine Reserve ◽  
Spiny Lobster ◽  
Fishing Effort ◽  
Additive Models ◽  
Catch Per Unit Effort ◽  
Monthly Basis ◽  
Galapagos Marine Reserve

Management of low-mobility or benthic fisheries is a difficult task because variation in the spatial distribution and population dynamics of the resources make the monitoring and assessment of these fisheries challenging. We assumed that environmental, spatial, and temporal factors can contribute to the variability of the relative abundance of such species; we used Generalized Additive Models for Location Scale and Shape (GAMLSS) to test this hypothesis using as a case study the lobster fishery (targeting two species) in the Galapagos Marine Reserve, Ecuador. We gathered data on each of the two species of lobster on a monthly basis over seven years, including: (a) onboard observers’ records of catch data, fishing effort, and ground location by trip, and (b) data from interviews undertaken with fishers at their arrival to port, recording the same type of information as obtained from onboard observers. We use this information to analyze the effect of the measured variables and to standardize the Catch per Unit Effort (CPUE) in each case, using the GAMLSS. For both species, the temperature, region, fishing schedule, month, distance, and the monitoring system were significant variables of the selected models associated with the variability of the catch rate. ForPanulirus penicillatus, CPUE was higher at night than during the day, and forPanulirus gracilisit was higher during the day. Increased temperature resulted in a decrease of CPUE values. It was evident that temporal, spatial scales and monitoring system can influence the variability of this indicator. We contend that the identification of drivers of change of relative abundance in low-mobility species can help to support the development of monitoring and assessment programs for this type of fisheries.

scholarly journals Investigation and Development of Post-Season Modelling of Arrow Squid in the Snares and Auckland Islands

2021 ◽  
Author(s):  
◽  
Vidette Louise McGregor
Keyword(s):  
Automatic Differentiation ◽  
Integrated Model ◽  
Current Data ◽  
Management Approach ◽  
Frequency Data ◽  
Catch Per Unit Effort ◽  
Length Frequency ◽  
Model Builder ◽  
Set Up ◽  
Length Frequency Data

<p>Squid fisheries require a different management approach to most fish species which are much longer living. Most squid live for around one year, spawn and then die. The result of this is an entirely new stock each year with little or no relationship of stock sizes between the years. Hence, it is difficult to set appropriate catch limits prior to the season. Currently, there is nothing set up for modelling the New Zealand squid fishery in-season or post-season. In-season management would allow for adjustments of catch limits during a season. Post-season management would provide information on how much the stock was exploited during a season (described as the escapement). I have produced an integrated model using ADMB (Automatic Differentiation Model Builder) (Fournier et al., 2011) which models length frequency data, CPUE (Catch Per Unit Effort) indices and catch weights from a season. It calculates escapement which indicates how much the fishery is currently being exploited. In running the model against data from four area and year combinations, I found the escapement calculation to be stable. The results suggest this modelling approach could be used with the current data collected for post-season modelling of the fishery. I am less confident about in-season modelling with the current data collected. The integrated model fits quite poorly to the CPUE data, suggesting some discrepancy either between the data or the assumptions made of them. Sampling from a greater number of tows is recommended to improve the length frequency data and this may also improve the ability of the model to fit both to these and the CPUE.</p>

scholarly journals Investigation and Development of Post-Season Modelling of Arrow Squid in the Snares and Auckland Islands

2021 ◽  
Author(s):  
◽  
Vidette Louise McGregor
Keyword(s):  
Automatic Differentiation ◽  
Integrated Model ◽  
Current Data ◽  
Management Approach ◽  
Frequency Data ◽  
Catch Per Unit Effort ◽  
Length Frequency ◽  
Model Builder ◽  
Set Up ◽  
Length Frequency Data

<p>Squid fisheries require a different management approach to most fish species which are much longer living. Most squid live for around one year, spawn and then die. The result of this is an entirely new stock each year with little or no relationship of stock sizes between the years. Hence, it is difficult to set appropriate catch limits prior to the season. Currently, there is nothing set up for modelling the New Zealand squid fishery in-season or post-season. In-season management would allow for adjustments of catch limits during a season. Post-season management would provide information on how much the stock was exploited during a season (described as the escapement). I have produced an integrated model using ADMB (Automatic Differentiation Model Builder) (Fournier et al., 2011) which models length frequency data, CPUE (Catch Per Unit Effort) indices and catch weights from a season. It calculates escapement which indicates how much the fishery is currently being exploited. In running the model against data from four area and year combinations, I found the escapement calculation to be stable. The results suggest this modelling approach could be used with the current data collected for post-season modelling of the fishery. I am less confident about in-season modelling with the current data collected. The integrated model fits quite poorly to the CPUE data, suggesting some discrepancy either between the data or the assumptions made of them. Sampling from a greater number of tows is recommended to improve the length frequency data and this may also improve the ability of the model to fit both to these and the CPUE.</p>

Testing the effects of durability (shell thickness) on species over-representation in death assemblages, a taphonomic baseline for conservation paleobiology

2021 ◽  
Author(s):  
Adam Tomašových ◽  
Susan M. Kidwell
Keyword(s):  
Southern California ◽  
Anthropogenic Impacts ◽  
Spatial Scales ◽  
Organic Content ◽  
Time Averaging ◽  
Shell Size ◽  
Interspecific Differences ◽  
Conservation Paleobiology ◽  
Death Assemblages ◽  
Species Abundances

&lt;p&gt;Differences in the taxonomic or functional composition of living and death assemblages is a key means of identifying the magnitude and drivers of past ecological changes in conservation paleobiology, especially when assessing the effects of anthropogenic impacts. However, such live-dead differences in species abundances can arise not only from ecological (stochastic or deterministic) changes in abundance over the duration of time averaging but also from interspecific differences in the postmortem durability of skeletal remains or from the lifespan of the individuals. Here, we attempt to directly incorporate the effects of durability on species abundances in death assemblages by modeling dead abundance as a function of species&amp;#8217; durability traits and using abundances in living assemblages as a prior. Species inferred to be negatively affected by anthropogenic impacts should be over-represented in death assemblages relative to their abundance in death assemblages predicted by the durability model (rather than just relative to their abundance in living assemblages). Using species-level durability trait data for bivalves (shell size, thickness, mineralogy, shell organic content, and life habit) from the southern California shelf, we find that, among these traits, valve thickness correlates consistently positively and at multiple spatial scales with the log of the dead:live ratio of species abundances, and accounts for ~20-30% of live-dead mismatch. Using this benchmark for the discordance that might be taphonomic in origin, we confirm that the over-representation of epifaunal suspension-feeders and siphonate deposit-feeders in death assemblages of the southern California shelf owes in fact to their ecological decline in recent centuries, even when accounting for their greater durability.&lt;/p&gt;

Growth rings across the Tree of Life: demographic insights from biogenic time series data

2021 ◽  
pp. 77-96
Author(s):  
Margaret E. K. Evans ◽  
Bryan A. Black ◽  
Donald A. Falk ◽  
Courtney L. Giebink ◽  
Emily L. Schultz
Keyword(s):  
Time Series ◽  
Time Series Data ◽  
Spatial Scales ◽  
Ocean Dynamics ◽  
Individual Growth ◽  
Series Data ◽  
Rate Variation ◽  
Sampling Effort ◽  
Growth Rings ◽  
Demographic Processes

Biogenic time series data can be generated in a single sampling effort, offering an appealing alternative to the slow process of revisiting or recapturing individuals to measure demographic rates. Annual growth rings formed by trees and in the ear bones of fish (i.e. otoliths) are prime examples of such biogenic time series. They offer insight into not only the process of growth but also birth, death, movement, and evolution, sometimes at uniquely deep temporal and large spatial scales, well beyond 5–30 years of data collected in localised study areas. This chapter first reviews the fundamentals of how tree-ring and otolith time series data are developed and analysed (i.e. dendrochronology and sclerochronology), then surveys growth rings in other organisms, along with microstructural or microcompositional variation in growth rings, and other records of demographic processes. It highlights the answers to demographic questions revealed by these time series data, such as the influence of environmental (atmospheric or ocean) conditions, competition, and disturbances on demographic processes, and the genetic versus plastic basis of individual growth and traits that influence growth. Lastly, it considers how spatial networks of biogenic, annually resolved time series data can offer insights into the importance of macrosystem atmospheric and ocean dynamics on multispecies, trophic dynamics. The authors encourage demographers to integrate the complementary information contained in biogenic time series data into population models to better understand the drivers of vital rate variation and predict the impacts of global change.

scholarly journals Missing links in the study of solute and particle exchange between the sea floor and water column

2020 ◽  
Vol 77 (5) ◽  
pp. 1602-1616 ◽  
Author(s):  
Saskia Rühl ◽  
Charlie Thompson ◽  
Ana M Queirós ◽  
Stephen Widdicombe
Keyword(s):  
Water Column ◽  
Current Knowledge ◽  
Anthropogenic Impacts ◽  
Future Research ◽  
Sea Floor ◽  
Marine Habitats ◽  
Exchange Processes ◽  
Ecosystem Level ◽  
Particle Exchange

Abstract Exchanges of solutes and solids between the sea floor and water column are a vital component of ecosystem functioning in marine habitats around the globe. This review explores particle and solute exchange processes, the different mechanisms through which they interact at the ecosystem level, as well as their interdependencies. Solute and particle exchange processes are highly dependent on the characteristics of the environment within which they takes place. Exchange is driven directly by a number of factors, such as currents, granulometry, nutrient, and matter inputs, as well as living organisms. In turn, the occurrence of exchanges can influence adjacent environments and organisms. Major gaps in the present knowledge include the temporal and spatial variation in many of the processes driving benthic/pelagic exchange processes and the variability in the relative importance of individual processes caused by this variation. Furthermore, the accurate assessment of some anthropogenic impacts is deemed questionable due to a lack of baseline data and long-term effects of anthropogenic actions are often unknown. It is suggested that future research should be transdisciplinary and at ecosystem level wherever possible and that baseline surveys should be implemented and long-term observatories established to fill the current knowledge gaps.

scholarly journals Geomagnetic field influences upward movement of young Chinook salmon emerging from nests

2018 ◽  
Vol 14 (2) ◽  
pp. 20170752 ◽  
Author(s):  
Nathan F. Putman ◽  
Michelle M. Scanlan ◽  
Amanda M. Pollock ◽  
Joseph P. O'Neil ◽  
Ryan B. Couture ◽  
...  
Keyword(s):  
Magnetic Field ◽  
Chinook Salmon ◽  
Geomagnetic Field ◽  
Oncorhynchus Tshawytscha ◽  
Dimensional Space ◽  
Spatial Scales ◽  
Vertical Component ◽  
Life Cycles ◽  
Upward Movement ◽  
The Magnetic Field

Organisms use a variety of environmental cues to orient their movements in three-dimensional space. Here, we show that the upward movement of young Chinook salmon ( Oncorhynchus tshawytscha ) emerging from gravel nests is influenced by the geomagnetic field. Fish in the ambient geomagnetic field travelled farther upwards through substrate than did fish tested in a field with the vertical component inverted. This suggests that the magnetic field is one of several factors that influences emergence from the gravel, possibly by serving as an orientation cue that helps fish determine which way is up. Moreover, our work indicates that the Oncorhynchus species are sensitive to the magnetic field throughout their life cycles, and that it guides their movements across a range of spatial scales and habitats.

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