SNP Panel and Genomic Sex Identification in Atlantic Halibut (Hippoglossus hippoglossus).

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.

The associations of implant and patient factors with migration of the tibial component differ by sex : a radiostereometric study on more than 400 total knee arthroplasties.

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.

Estimating minke whale relative abundance in the North Atlantic using passive acoustic sensors.

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.

Early Identification of Patient Satisfaction Two Years After Total Knee Arthroplasty.

BACKGROUND: There are numerous reports of poor satisfaction after total knee arthroplasty (TKA), yet there is little known about when to use evidence-based models of care to improve patient outcomes. OBJECTIVE: This study aimed to characterize longitudinal changes in patient-reported satisfaction after TKA and to identify factors for early identification of poor satisfaction. METHODS: For a cohort of primary TKA surgeries (n = 86), patient-reported outcomes were captured one week before TKA and 6 weeks, 12 weeks, 6 months, and 1 and 2 years after TKA. "Satisfied" versus "not fully satisfied" patients were defined using a binary response (≥90 vs <90) from a 100-point scale. Wilcoxon signed-rank tests identified changes in satisfaction between follow-up times, and longitudinal analyses examined demographic and questionnaire factors associated with satisfaction. RESULTS: Improvements in satisfaction occurred within the first 6 months after TKA (P ≤ 0.01). Preoperative patient-reported outcome measures alone were not predictive of satisfaction. Key factors that improved longitudinal satisfaction included higher Oxford Knee Scores (odds ratio (OR) = 2.1, P < .001), general health (EQ-VAS, OR = 1.3, P = .03), and less visual analog scale pain (VAS; OR = 1.7, P < .001). Differences in these factors between satisfied and not fully satisfied patients were identified as early as 6 weeks after surgery. CONCLUSION: Visibly different satisfaction profiles were captured among satisfied and not fully satisfied patient responses, with differences in patient-perceived joint function, general health, and pain severity occurring as early as 6 weeks after surgery. This study provides metrics to support early identification of patients at risk of poor TKA satisfaction, enabling clinicians to apply timely targeted treatment and support interventions, with the aim of improving patient outcomes.

Equivalent 2-year stabilization of uncemented tibial component migration despite higher early migration compared with cemented fixation: an RSA study on 360 total knee arthroplasties.

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.

Stable isotopes can be used to infer the overwintering locations of prebreeding marine birds in the Canadian Arctic.

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.

Local overfishing may be avoided by examining parameters of a spatio-temporal model.

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.

A hidden Markov movement model for rapidly identifying behavioral states from animal tracks.

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' dirty little secrets: even simple linear Gaussian models can have estimation problems.

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.

A novel approach to quantifying the spatiotemporal behavior of instrumented grey seals used to sample the environment.

BACKGROUND: Paired with satellite location telemetry, animal-borne instruments can collect spatiotemporal data describing the animal's movement and environment at a scale relevant to its behavior. Ecologists have developed methods for identifying the area(s) used by an animal (e.g., home range) and those used most intensely (utilization distribution) based on location data. However, few have extended these models beyond their traditional roles as descriptive 2D summaries of point data. Here we demonstrate how the home range method, T-LoCoH, can be expanded to quantify collective sampling coverage by multiple instrumented animals using grey seals (Halichoerus grypus) equipped with GPS tags and acoustic transceivers on the Scotian Shelf (Atlantic Canada) as a case study. At the individual level, we illustrate how time and space-use metrics quantifying individual sampling coverage may be used to determine the rate of acoustic transmissions received. RESULTS: Grey seals collectively sampled an area of 11,308 km (2) and intensely sampled an area of 31 km (2) from June-December. The largest area sampled was in July (2094.56 km (2)) and the smallest area sampled occurred in August (1259.80 km (2)), with changes in sampling coverage observed through time. CONCLUSIONS: T-LoCoH provides an effective means to quantify changes in collective sampling effort by multiple instrumented animals and to compare these changes across time. We also illustrate how time and space-use metrics of individual instrumented seal movement calculated using T-LoCoH can be used to account for differences in the amount of time a bioprobe (biological sampling platform) spends in an area.

ECOLOGY. Aquatic animal telemetry: A panoramic window into the underwater world.

The distribution and interactions of aquatic organisms across space and time structure our marine, freshwater, and estuarine ecosystems. Over the past decade, technological advances in telemetry have transformed our ability to observe aquatic animal behavior and movement. These advances are now providing unprecedented ecological insights by connecting animal movements with measures of their physiology and environment. These developments are revolutionizing the scope and scale of questions that can be asked about the causes and consequences of movement and are redefining how we view and manage individuals, populations, and entire ecosystems. The next advance in aquatic telemetry will be the development of a global collaborative effort to facilitate infrastructure and data sharing and management over scales not previously possible.

Observer aging and long-term avian survey data quality.

Long-term wildlife monitoring involves collecting time series data, often using the same observers over multiple years. Aging-related changes to these observers may be an important, under-recognized source of error that can bias management decisions. In this study, we used data from two large, independent bird surveys, the Atlas of the Breeding Birds of Ontario ("OBBA") and the North American Breeding Bird Survey ("BBS"), to test for age-related observer effects in long-term time series of avian presence and abundance. We then considered the effect of such aging phenomena on current population trend estimates. We found significantly fewer detections among older versus younger observers for 13 of 43 OBBA species, and declines in detection as an observer ages for 4 of 6 vocalization groups comprising 59 of 64 BBS species. Consistent with hearing loss influencing this pattern, we also found evidence for increasingly severe detection declines with increasing call frequency among nine high-pitched bird species (OBBA); however, there were also detection declines at other frequencies, suggesting important additional effects of aging, independent of hearing loss. We lastly found subtle, significant relationships between some species' published population trend estimates and (1) their corresponding vocalization frequency (n ≥ 22 species) and (2) their estimated declines in detectability among older observers (n = 9 high-frequency, monotone species), suggesting that observer aging can negatively bias long-term monitoring data for some species in part through hearing loss effects. We recommend that survey designers and modelers account for observer age where possible.

Probability of detecting marine predator-prey and species interactions using novel hybrid acoustic transmitter-receiver tags.

Understanding the nature of inter-specific and conspecific interactions in the ocean is challenging because direct observation is usually impossible. The development of dual transmitter/receivers, Vemco Mobile Transceivers (VMT), and satellite-linked (e.g. GPS) tags provides a unique opportunity to better understand between and within species interactions in space and time. Quantifying the uncertainty associated with detecting a tagged animal, particularly under varying field conditions, is vital for making accurate biological inferences when using VMTs. We evaluated the detection efficiency of VMTs deployed on grey seals, Halichoerus grypus, off Sable Island (NS, Canada) in relation to environmental characteristics and seal behaviour using generalized linear models (GLM) to explore both post-processed detection data and summarized raw VMT data. When considering only post-processed detection data, only about half of expected detections were recorded at best even when two VMT-tagged seals were estimated to be within 50-200 m of one another. At a separation of 400 m, only about 15% of expected detections were recorded. In contrast, when incomplete transmissions from the summarized raw data were also considered, the ratio of complete transmission to complete and incomplete transmissions was about 70% for distances ranging from 50-1000 m, with a minimum of around 40% at 600 m and a maximum of about 85% at 50 m. Distance between seals, wind stress, and depth were the most important predictors of detection efficiency. Access to the raw VMT data allowed us to focus on the physical and environmental factors that limit a transceiver's ability to resolve a transmitter's identity.

Recovery trends in marine mammal populations.

Marine mammals have greatly benefitted from a shift from resource exploitation towards conservation. Often lauded as symbols of conservation success, some marine mammal populations have shown remarkable recoveries after severe depletions. Others have remained at low abundance levels, continued to decline, or become extinct or extirpated. Here we provide a quantitative assessment of (1) publicly available population-level abundance data for marine mammals worldwide, (2) abundance trends and recovery status, and (3) historic population decline and recent recovery. We compiled 182 population abundance time series for 47 species and identified major data gaps. In order to compare across the largest possible set of time series with varying data quality, quantity and frequency, we considered an increase in population abundance as evidence of recovery. Using robust log-linear regression over three generations, we were able to classify abundance trends for 92 spatially non-overlapping populations as Significantly Increasing (42%), Significantly Decreasing (10%), Non-Significant Change (28%) and Unknown (20%). Our results were comparable to IUCN classifications for equivalent species. Among different groupings, pinnipeds and other marine mammals (sirenians, polar bears and otters) showed the highest proportion of recovering populations, likely benefiting from relatively fast life histories and nearshore habitats that provided visibility and protective management measures. Recovery was less frequent among cetaceans, but more common in coastal than offshore populations. For marine mammals with available historical abundance estimates (n = 47), larger historical population declines were associated with low or variable recent recoveries so far. Overall, our results show that many formerly depleted marine mammal populations are recovering. However, data-deficient populations and those with decreasing and non-significant trends require attention. In particular, increased study of populations with major data gaps, including offshore small cetaceans, cryptic species, and marine mammals in low latitudes and developing nations, is needed to better understand the status of marine mammal populations worldwide.

Overestimating fish counts by non-instantaneous visual censuses: consequences for population and community descriptions.

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.

Hierarchical state-space estimation of leatherback turtle navigation ability.

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.