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Recent declines of Yukon River Chinook salmon (Oncorhynchus tshawytscha) populations have severely impacted people residing in the Yukon and Alaska. Evidence-based conservation strategies focused on stock recovery and adaptation are urgently needed but are limited by our understanding of what is driving declines, particularly in Canadian portions of the Yukon River basin. We examined how multiple environmental drivers may be influencing Canadian-origin Yukon River Chinook salmon productivity for eight populations over a 28-year period. We found that productivity was related to various environmental and ecosystem processes acting cumulatively over multiple life stages and across broad geographic scales. Productivity decreased in association with warmer upriver migration temperatures, wetter freshwater juvenile rearing habitats, and increasing abundances of potential marine competitors. In contrast, productivity increased in years with warmer and snowier winters and earlier spring onset. We found that different populations had similar relationships with environmental drivers, with potentially negative implications for regional fisheries stability. Our findings provide insight into how Chinook salmon are responding to rapid environmental change and can help inform salmon conservation initiatives and sustainable harvest strategies. [ABSTRACT FROM AUTHOR]

Longitudinal models are commonly used for studying data collected on individuals repeatedly through time. While there are now a variety of such models available (marginal models, mixed effects models, etc.), far fewer options exist for the closely related issue of variable selection. In addition, longitudinal data typically derive from medical or other large-scale studies where often large numbers of potential explanatory variables and hence even larger numbers of candidate models must be considered. Cross-validation is a popular method for variable selection based on the predictive ability of the model. Here, we propose a cross-validation Markov chain Monte Carlo procedure as a general variable selection tool which avoids the need to visit all candidate models. Inclusion of a 'one-standard error' rule provides users with a collection of good models as is often desired. We demonstrate the effectiveness of our procedure both in a simulation setting and in a real application. Copyright © 2006 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

State-space models have recently been shown to effectively model animal movement. In this paper we illustrate how such models can be used to improve our knowledge of animal navigation ability, something which is poorly understood. This work is of great interest when modeling the behavior of animals that are migrating, often over tremendously large distances. We use the term circle of confusion, first proposed by Kendall (1974), to describe the general inability of an animal to know its location precisely. Our modeling strategy enables us to statistically describe the circle of confusion associated with any animal movements where departure and destination points are known. For illustration, we use ARGOS satellite telemetry of leatherback turtles migrating over a distance of approximately 4000 km in the Atlantic Ocean. Robust features of the model enable one to deal with outlying observations, highly characteristic of these types of data. Although specifically designed for data obtained using satellite telemetry, our approach is generalizable to other common kinds of movement data such as archival tag data. [ABSTRACT FROM AUTHOR]

The ability to identify sex is necessary in population biology for a proper understanding of the dynamics of a population. In Atlantic halibut, phenotypic sex identification is not possible due to the lack of significant external morphological differences. We developed an Illumina SNP panel for Atlantic halibut with 4000 SNPs spread evenly throughout the genome with a minor allele frequency MAF ≥ 0.4, except for N = 249 SNPs located in a sex-determining region on chromosome 12, N = 176 of these SNPs were selected to genetically identify male and female individuals using a DAPC analysis. The genomic identification of sex allows for non-lethal sex determination and validation of sex identification in the field. The SNP panel is a new genomic resource for Atlantic halibut that will make it possible to generate the genotypic data for the large number of individuals needed to estimate population abundance using genomics and the Close Kin Mark Recapture (CKMR) approach, an emerging component of fisheries management and stock monitoring., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Aims: Thresholds of acceptable early migration of the components in total knee arthroplasty (TKA) have traditionally ignored the effects of patient and implant factors that may influence migration. The aim of this study was to determine which of these factors are associated with overall longitudinal migration of well-fixed tibial components following TKA., Methods: Radiostereometric analysis (RSA) data over a two-year period were available for 419 successful primary TKAs (267 cemented and 152 uncemented in 257 female and 162 male patients). Longitudinal analysis of data using marginal models was performed to examine the associations of patient factors (age, sex, BMI, smoking status) and implant factors (cemented or uncemented, the size of the implant) with maximum total point motion (MTPM) migration. Analyses were also performed on subgroups based on sex and fixation., Results: In the overall group, only fixation was significantly associated with migration (p < 0.001). For uncemented tibial components in males, smoking was significantly associated with lower migration (p = 0.030) and BMI approached significance (p = 0.061). For females with uncemented components, smoking (p = 0.081) and age (p = 0.063) approached significance and were both associated with increased migration. The small number of self-reported smokers in this study warrants cautious interpretation and further investigation. For cemented components in females, larger sizes of tibial component were significantly associated with increased migration (p = 0.004). No factors were significant for cemented components in males., Conclusion: The migration of uncemented tibial components was more sensitive to patient factors than cemented implants. These differences were not consistent by sex, suggesting that it may be of value to evaluate female and male patients separately following TKA. Cite this article: Bone Joint J  2022;104-B(4):444-451.

Estimates of abundance and their changes through time are key elements of marine mammal conservation and management. Absolute marine mammal abundance in a region of the open ocean is often difficult to attain. However, methods of estimating their abundance based on passive acoustic recordings are becoming increasingly employed. This study shows that passive acoustic monitoring of North Atlantic minke whales with a single hydrophone provides sufficient information to estimate relative population abundance. An automated detector was developed for minke whale pulse trains and an approach for converting its output into a relative abundance index is proposed by accounting for detectability as well as false positives and negatives. To demonstrate this technique, a 2 y dataset from the seven sites of the Atlantic Deepwater Ecosystem Observatory Network project on the U.S. east coast was analyzed. Resulting relative abundance indices confirm pulse train-calling minke whale presence in the deep waters of the outer continental shelf. The minkes are present December through April annually with the highest abundance near the site offshore of Savannah, Georgia.

Background and purpose - Thresholds of implant migration for predicting long-term successful fixation of tibial components in total knee arthroplasty have not separated cemented and uncemented fixation. We compared implant migration of cemented and uncemented components at 1 year and as the change in migration from 1 to 2 years. Patients and methods - Implant migration of 360 tibial components measured using radiostereometric analysis was compared at 1 year and as the change in migration from 1 to 2 years in 222 cemented components (3 implant designs) and 138 uncemented components (5 implant designs). Results - 1-year maximum total point motion was lower for the cemented tibial components compared with the uncemented components (median = 0.31 mm [0.03-2.98] versus 0.63 mm [0.11-5.19] respectively, p < 0.001, mixed model). The change in migration from 1 to 2 years, however, was equivalent for cemented and uncemented components (mean [SD] 0.06 mm [0.19] and 0.07 mm [0.27] mm respectively, p = 0.6, mixed model). Interpretation - These findings suggest that current thresholds of acceptable migration at 1 year may be better optimized by considering cemented and uncemented tibial components separately as higher early migration of uncemented components was not associated with decreased stability from 1 to 2 years.

Although assessments of winter carryover effects on fitness-related breeding parameters are vital for determining the links between environmental variation and fitness, direct methods of determining overwintering distributions (e.g., electronic tracking) can be expensive, limiting the number of individuals studied. Alternatively, stable isotope analysis in specific tissues can be used as an indirect means of determining individual overwintering areas of residency. Although increasingly used to infer the overwintering distributions of terrestrial birds, stable isotopes have been used less often to infer overwintering areas of marine birds. Using Arctic-breeding common eiders, we test the effectiveness of an integrated stable isotope approach (13-carbon, 15-nitrogen, and 2-hydrogen) to infer overwintering locations. Knowing the overwinter destinations of eiders from tracking studies at our study colony at East Bay Island, Nunavut, we sampled claw and blood tissues at two known overwintering locations, Nuuk, Greenland, and Newfoundland, Canada. These two locations yielded distinct tissue-specific isotopic profiles. We then compared the isotope profiles of tissues collected from eiders upon their arrival at our breeding colony, and used a k -means cluster analysis approach to match arriving eiders to an overwintering group. Samples from the claws of eiders were most effective for determining overwinter origin, due to this tissue's slow growth rate relative to the 40-day turnover rate of blood. Despite taking an integrative approach using multiple isotopes, k -means cluster analysis was most effective when using 13-carbon alone to assign eiders to an overwintering group. Our research demonstrates that it is possible to use stable isotope analysis to assign an overwintering location to a marine bird. There are few examples of the effective use of this technique on a marine bird at this scale; we provide a framework for applying this technique to detect changes in the migration phenology of birds' responses to rapid changes in the Arctic.

Spatial erosion of stock structure through local overfishing can lead to stock collapse because fish often prefer certain locations, and fisheries tend to focus on those locations. Fishery managers are challenged to maintain the integrity of the entire stock and require scientific approaches that provide them with sound advice. Here we propose a Bayesian hierarchical spatio-temporal modelling framework for fish abundance data to estimate key parameters that define spatial stock structure: persistence (similarity of spatial structure over time), connectivity (coherence of temporal pattern over space), and spatial variance (variation across the seascape). The consideration of these spatial parameters in the stock assessment process can help identify the erosion of structure and assist in preventing local overfishing. We use Atlantic cod (Gadus morhua) in eastern Canada as a case study an examine the behaviour of these parameters from the height of the fishery through its collapse. We identify clear signals in parameter behaviour under circumstances of destructive stock erosion as well as for recovery of spatial structure even when combined with a non-recovery in abundance. Further, our model reveals the spatial pattern of areas of high and low density persists over the 41 years of available data and identifies the remnant patches. Models of this sort are crucial to recovery plans if we are to identify and protect remaining sources of recolonization for Atlantic cod. Our method is immediately applicable to other exploited species.

Electronic telemetry is frequently used to document animal movement through time. Methods that can identify underlying behaviors driving specific movement patterns can help us understand how and why animals use available space, thereby aiding conservation and management efforts. For aquatic animal tracking data with significant measurement error, a Bayesian state-space model called the first-Difference Correlated Random Walk with Switching (DCRWS) has often been used for this purpose. However, for aquatic animals, highly accurate tracking data are now becoming more common. We developed a new hidden Markov model (HMM) for identifying behavioral states from animal tracks with negligible error, called the hidden Markov movement model (HMMM). We implemented as the basis for the HMMM the process equation of the DCRWS, but we used the method of maximum likelihood and the R package TMB for rapid model fitting. The HMMM was compared to a modified version of the DCRWS for highly accurate tracks, the DCRWSNOME, and to a common HMM for animal tracks fitted with the R package moveHMM. We show that the HMMM is both accurate and suitable for multiple species by fitting it to real tracks from a grey seal, lake trout, and blue shark, as well as to simulated data. The HMMM is a fast and reliable tool for making meaningful inference from animal movement data that is ideally suited for ecologists who want to use the popular DCRWS implementation and have highly accurate tracking data. It additionally provides a groundwork for development of more complex modeling of animal movement with TMB. To facilitate its uptake, we make it available through the R package swim.

State-space models (SSMs) are increasingly used in ecology to model time-series such as animal movement paths and population dynamics. This type of hierarchical model is often structured to account for two levels of variability: biological stochasticity and measurement error. SSMs are flexible. They can model linear and nonlinear processes using a variety of statistical distributions. Recent ecological SSMs are often complex, with a large number of parameters to estimate. Through a simulation study, we show that even simple linear Gaussian SSMs can suffer from parameter- and state-estimation problems. We demonstrate that these problems occur primarily when measurement error is larger than biological stochasticity, the condition that often drives ecologists to use SSMs. Using an animal movement example, we show how these estimation problems can affect ecological inference. Biased parameter estimates of a SSM describing the movement of polar bears (Ursus maritimus) result in overestimating their energy expenditure. We suggest potential solutions, but show that it often remains difficult to estimate parameters. While SSMs are powerful tools, they can give misleading results and we urge ecologists to assess whether the parameters can be estimated accurately before drawing ecological conclusions from their results.

Remotely sensed tracking technology has revealed remarkable migration patterns that were previously unknown; however, models to optimally use such data have developed more slowly. Here, we present a hierarchical Bayes state-space framework that allows us to combine tracking data from a collection of animals and make inferences at both individual and broader levels. We formulate models that allow the navigation ability of animals to be estimated and demonstrate how information can be combined over many animals to allow improved estimation. We also show how formal hypothesis testing regarding navigation ability can easily be accomplished in this framework. Using Argos satellite tracking data from 14 leatherback turtles, 7 males and 7 females, during their southward migration from Nova Scotia, Canada, we find that the circle of confusion (the radius around an animal's location within which it is unable to determine its location precisely) is approximately 96 km. This estimate suggests that the turtles' navigation does not need to be highly accurate, especially if they are able to use more reliable cues as they near their destination. Moreover, for the 14 turtles examined, there is little evidence to suggest that male and female navigation abilities differ. Because of the minimal assumptions made about the movement process, our approach can be used to estimate and compare navigation ability for many migratory species that are able to carry electronic tracking devices.

Background: Increasingly, underwater visual censuses (UVC) are used to assess fish populations. Several studies have demonstrated the effectiveness of protected areas for increasing fish abundance or provided insight into the natural abundance and structure of reef fish communities in remote areas. Recently, high apex predator densities (>100,000 individuals x km(-2)) and biomasses (>4 tonnes x ha(-1)) have been reported for some remote islands suggesting the occurrence of inverted trophic biomass pyramids. However, few studies have critically evaluated the methods used for sampling conspicuous and highly mobile fish such as sharks. Ideally, UVC are done instantaneously, however, researchers often count animals that enter the survey area after the survey has started, thus performing non-instantaneous UVC., Methodology/principal Findings: We developed a simulation model to evaluate counts obtained by divers deploying non-instantaneous belt-transect and stationary-point-count techniques. We assessed how fish speed and survey procedure (visibility, diver speed, survey time and dimensions) affect observed fish counts. Results indicate that the bias caused by fish speed alone is huge, while survey procedures had varying effects. Because the fastest fishes tend to be the largest, the bias would have significant implications on their biomass contribution. Therefore, caution is needed when describing abundance, biomass, and community structure based on non-instantaneous UVC, especially for highly mobile species such as sharks., Conclusions/significance: Based on our results, we urge that published literature state explicitly whether instantaneous counts were made and that survey procedures be accounted for when non-instantaneous counts are used. Using published density and biomass values of communities that include sharks we explore the effect of this bias and suggest that further investigation may be needed to determine pristine shark abundances and the existence of inverted biomass pyramids. Because such studies are used to make important management and conservation decisions, incorrect estimates of animal abundance and biomass have serious and significant implications.