Cohort and tag-site-specific tag-loss rates in mark–recapture studies: A southern elephant seal cautionary case

Marker-loss is a common feature of mark–recapture studies and important as it may bias parameter estimation. A slight alteration in tag-site of double tagged southern elephant seals (Mirounga leonina), marked at Marion Island from 1983 to 2005 in an ongoing mark–recapture program, had important consequences for tag-loss. We calculated age-specific tag-retention rates and cumulative tag-retention probabilities using a maximum likelihood model selection approach in the software application TAG_LOSS 3.2.0. Under the tag-loss independence assumption, double tag-loss of inner interdigital webbing tags (IIT; 17 cohorts) remained below 1% in the first 5 yr and increased monotonically as seals aged, with higher tag-loss in males. Lifetime cumulative IIT tag-loss was 11.9% for females and 18.4% for males, and equivalent for all cohorts. Changing the tag-site to the outer interdigital webbing (OIT; 6 cohorts) resulted in increased and cohort-dependent tag-loss, although the variation (mean ± 95% CI) in cumulative tag-loss probabilities never exceeded 5.3% between cohorts at similar age. Although different studies may homogenize techniques, we advocate the importance of data set-specific assessment of tag-loss rates to ensure greatest confidence in population parameters obtained from mark–recapture experiments. Permanent marking should be implemented where feasible.     

Retention of plastic-tipped dart tags in African tigerfish Hydrocynus vittatus

Estimates of tag retention and tagging-related mortality are essential for mark-recapture experiments. Mortality and tag loss were estimated from 15 tigerfish Hydrocynus vittatus marked using Hallmark model PDL plastic-tipped dart tags released into a 1 730 m² pond at Kamutjonga Inland Fisheries Institute, Namibia, and inspected bi-monthly for the presence or absence of tags. No mortality was observed during the experiment. All marked fish had lost their tags after 10 months and 50% tag loss was estimated at 3.9 months. The high tag loss rate indicates that PDL plastic-tipped dart tags are not suitable for long-term studies on this species.     

Long-term retention of internal elastomer tags in a wild population of painted crayfish (Panulirus versicolor [Latreille]) on the Great Barrier Reef

Many crustaceans are highly exploited fisheries species, but determining the population parameters of these animals via mark-recapture techniques is problematic, primarily due to tag-loss during moulting of the exoskeleton. Recently developed internal elastomer tags may overcome this challenging problem, since they are completely encased in the tissues beneath the exoskeleton. In this study, we evaluated the effectiveness of internal elastomer tags in a wild population of painted crayfish (Panulirus versicolor) over an 18-month period. Seventy animals were double-tagged in the abdominal musculature, with individuality obtained using different combinations of tag colour and tag location. Forty individuals were recaptured after 6, 12 and (or) 18 months, giving an overall recapture rate of 57%. Annual tag retention was estimated to be 98%, since only one instance of tag-loss was observed, despite numerous episodes of moulting among tagged individuals. The majority of tags (95%) were easily visible, even after 18 months at liberty. Nonetheless, small reductions in tag condition were observed after the first six months (mostly due to fading and [or] fragmentation), but this did not interfere with overall tag readability. Tag condition did not decline in the following 12 months, nor did it vary with gender or tag location. It is concluded that internal elastomer tags are an effective method for marking wild crayfish over long-term periods. Given the durability of elastomer, and the capacity for individual identification of large numbers of animals, such tags may be suitable for commercial-scale fishery applications.     

EFFECTIVENESS OF VARIOUS CATTLE EAR TAGS AS MARKERS FOR WEDDELL SEALS

Methods for estimating tag loss and sightability of tags are presented. Rates of tag loss were estimated for metal and several varieties of plastic cattle ear tags in a long-term population study of Weddell seals. Tags were lost at a higher rate in the first year after application than in subsequent years, and pups lost tags at a higher rate than older seals given the same tag types. Medium-sized plastic tags (Dalton, Allflex and Fearing) were retained at higher rates and were overlooked less frequently than metal tags on adult seals. Dalton Jumbo Rototags showed the lowest loss rates on pups in comparison to larger, flexible plastic tags, but were harder to read in the field.     

Marking hard-shelled gastropods: tag loss, impact on life-history traits, and perspectives in biology

Abstract. Individual marking has long been used in many fields of biology. However, capture–mark–recapture (CMR) studies are not evenly distributed among taxonomic groups, with most studies focusing on vertebrates. For example, a limited number of studies have been conducted in gastropods, in sharp contrast to their important role as biological models or exploited natural resources. The lack of standard, validated marking techniques certainly contributes to the limited use of CMR. In this article, we evaluate two fundamental requirements for a marking technique to be suitable, i.e., tag loss (two experiments) and impact on life-history traits (survival, growth, and fecundity, in three experiments). Five marking techniques for hard-shelled gastropods were tested in the freshwater snail Physa acuta (Pulmonata). The tag-loss rate per month was lower for glued plastic marks (0.01) than for paint marks (0.03–0.07), and the tag-loss rate varied among colors (gouache paint). Under laboratory conditions, the life-history traits were not significantly affected by marking. We thus recommend using glued plastic marks for long-term studies, and paint marks for mass marking, with double marking to account for tag-loss rate. Based on an extensive literature survey, we also review current CMR practices in gastropod studies and suggest general improvements that would prove useful in both this group and invertebrates in general.     

Low Rates of PIT-Tag Loss in an Insectivorous Bat Species

The rate of loss of tags used to mark individuals is an important consideration in wildlife research and monitoring. Passive integrated transponder (PIT) tags (or microchips) generally have high retention rates; however, tag loss rates for small mammals such as insectivorous bats are poorly understood. We double-marked a population of Gould's wattled bats (Chalinolobus gouldii) with forearm bands and PIT tags (with the injection site sealed with surgical adhesive) in January and February 2020 to determine rates of subsequent tag loss over the short- (1–2 months) and medium- (13–14 months) term. Loss of PIT tags occurred in 4 (2.7%) of 146 recaptured individuals, all within 2 months of microchipping. We also recorded 1 occurrence of band loss 11 months after banding. Our study supports assertions that PIT-tag retention rates in small mammals are high, and suggests that rates of tag loss in small bat species are low when surgical adhesive is applied. Quantifying the rate of tag loss enables this variable to be incorporated into mark-recapture models. © 2021 The Wildlife Society.     

An easy way to reduce PIT-tag loss in rodents

Passive integrated transponders (PIT-tags) have been shown to be a reliable method for individually marking rodents in field studies. The loss rates of PIT-tags vary, depending on the species, from 3.6 to 7.2%. We used PIT-tags to individually mark a population of edible dormice. Due to a relatively high loss rate of transponders in the first year (7.4%) we used a tissue adhesive to seal the punctuation wound in the second year. With this method we could reduce the tag-loss rate to 2.2%. We therefore recommend using a tissue adhesive, which is easy and fast to apply, after injecting a transponder.     

A Field Evaluation of an External and Neutrally Buoyant Acoustic Transmitter for Juvenile Salmon: Implications for Estimating Hydroturbine Passage Survival

Turbine-passed fish are exposed to rapid decreases in pressure which can cause barotrauma. The presence of an implanted telemetry tag increases the likelihood of injury or death from exposure to pressure changes, thus potentially biasing studies evaluating survival of turbine-passed fish. Therefore, a neutrally buoyant externally attached tag was developed to eliminate this bias in turbine passage studies. This new tag was designed not to add excess mass in water or take up space in the coelom, having an effective tag burden of zero with the goal of reducing pressure related biases to turbine survival studies. To determine if this new tag affects fish performance or susceptibility to predation, it was evaluated in the field relative to internally implanted acoustic transmitters (JSATS; Juvenile Salmon Acoustic Telemetry System) used widely for survival studies of juvenile salmonids. Survival and travel time through the study reach was compared between fish with either tag type in an area of high predation in the Snake and Columbia rivers, Washington. An additional group of fish affixed with neutrally-buoyant dummy external tags were implanted with passive integrated transponder (PIT) tags and recovered further downstream to assess external tag retention and injury. There were no significant differences in survival to the first detection site, 12 river kilometers (rkm) downstream of release. Travel times were also similar between groups. Conversely, externally-tagged fish had reduced survival (or elevated tag loss) to the second detection site, 65 rkm downstream. In addition, the retention study revealed that tag loss was first observed in fish recaptured approximately 9 days after release. Results suggest that this new tag may be viable for short term (<8 days) single-dam turbine-passage studies and under these situations, may alleviate the turbine passage-related bias encountered when using internal tags, however further research is needed to confirm this.     

Growth, survival, and tag retention of steelhead trout (Oncorhynchus mykiss) and its application to survival estimates

Steelhead trout, Oncorhynchus mykiss, are known to expel acoustic tags which can negatively bias population survival estimates. Tag burden may also affect the development and behavior of smolts, thereby impacting the results of population and behavioral studies. We monitored the growth, condition, and tag expulsion rate of steelhead trout in similar-sized individuals and used these data to adjust survival rates from an acoustic telemetry study conducted in the Sacramento River. Eighty fish were surgically implanted with tags—40 with cylindrical tags of 9 mm diameter and 21 or 24 mm length (V9, Vemco Ltd) and 40 with a 7 mm diameter and 20 mm length tag (V7, Vemco Ltd)—to examine the impact of tag size on peritoneal retention and survival rate of juvenile steelhead trout. A total of 20 % (16/80) of all tags were expelled by smolts during the 143-day study. Ten V9 tags were expelled between day 18 and day 66. Six V7 tags were expelled between day 21 and day 143. A statistical difference was found for retention rate by surgeon even though the surgeons were of equal experience and received the same training. There were no significant differences in the tag retention rate in relation to the tag/body weight ratio, or in growth (weight or fork length) among the control, V7 or V9 treatment groups over the duration of the study. All individuals survived throughout the experiment. Two methods were used to adjust the survival estimates of an acoustic telemetry data set from the Sacramento River based on the tag retention study. First, a simple individual censorship approach in Program MARK was utilized and next ATLAS, a software program designed to compensate for bias in survival estimates caused by tag failures was used. The results of the adjusted survival estimates were not significantly different from the unadjusted rates suggesting that it may be more important to focus on improving surgical techniques to reduce tag expulsion rather than adjusting survival estimates dependent on the study. The surgical techniques utilized in this study did not have significant impacts on the growth rates of either of the tag treatment groups compared to the control. However, tag retention was an issue regardless of the size and weight of the implanted tag and the size of the steelhead.     

Retention of loop,monel, and passive integrated transponder tags by wild,free‐ranging Lake Sturgeon (Acipenser fulvescens Rafinesque, 1817)

Tagging or marking of fish is instrumental to fisheries biologists and managers seeking to distinguish groups of fish, track movement or migration patterns, and monitor population characteristics. However, tag loss can inhibit the ability of biologists and managers to reach these objectives. The ability of Lake Sturgeon to live for long periods of time and reach large sizes, in combination with their dynamic spawning activity, requires tags to be retained under a variety of environmental and physically demanding conditions. This study evaluated tag retention of loop, monel, and passive integrated transponder (PIT) tags on wild, free‐ranging Lake Sturgeon in Lake Huron and the St. Clair – Detroit River System. Lake Sturgeon in this study were double‐tagged with both a PIT tag under one of the three anterior‐most dorsal scutes and an external tag (loop or monel) at the base of the dorsal fin. Fish were at large for up to 16 years. Overall, tag loss for PIT tags was 1% followed by monel tags at 12% and loop tags at 36%. Tag loss for loop tags was higher when the initial length of Lake Sturgeon tagged was smaller. Tag loss for monel tags increased with time at large but was not related to length at initial tagging. Monel tags left behind abrasion marks when attached to smaller Lake Sturgeon. PIT tag retention was higher than reported in previous studies that tagged other sturgeon species in different body locations. Monel tag retention was higher than other external tag types evaluated in previous studies while loop tags had similar retention rates to external tag types. Most previous studies on tag retention of sturgeon species were of shorter duration and conducted in laboratory settings, therefore loop tags may have performed more favorably during studies under short term laboratory settings. Results of this study suggest that PIT tags inserted below dorsal scutes represent a viable option for long‐term tracking of Lake Sturgeon. Monel tags attached at the base of the dorsal fin also seem to be a viable option relative to other external tag types, but should be limited to larger sturgeon as they can leave behind abrasion marks.     

Growth,survival, and tag retention of steelhead trout (<Emphasis Type="Italic">O. mykiss</Emphasis>) surgically implanted with dummy acoustic tags

Recent advances in micro-electronics make the study of the migration of even small marine animals (>12 cm) over many 1000s of kilometres a serious possibility. Important assumptions in long-term studies are that rates of tag loss caused by mortality or tag shedding are low, and that the tagging procedure does not have an unacceptable negative effect on the animal. This paper reports results from a study to examine the retention of relatively large (24 × 8 mm) surgically-implanted dummy acoustic tags over a 7-month period in steelhead pre-smolts (O. mykiss), and the effects of implantation on growth and survival. Although there was some influence on growth to week 12, survival was high for animals > 13 cm FL. In the following 16-week period, growth of surgically implanted pre-smolts was the same as the control population and there was little tag loss from mortality or shedding. Currently available acoustic tags can be implanted in salmonid fish ≥12 cm FL, although combined losses from mortality and tag shedding were 33–40% for animals in the 12 and 13 cm FL size classes. By 14 cm FL, combined rates of tag loss (mortality plus tag shedding) for surgically implanted tags dropped to <15% and growth following surgery was close to that of the controls. Our results suggest that studies of ocean migration and survival over periods of many months are now feasible even for animals as small as salmon smolts. Surgically implanted salmon smolts are therefore good candidates for freshwater and coastal ocean-tracking studies on relatively long time scales (months). On such time scales, even relatively small salmon smolts may move thousands of kilometers in the ocean.     

Long-term retention of dummy acoustic transmitters in adult brown trout

A group of 36 1+ age class Salmo trutta were surgically implanted with dummy acoustic tags and monitored for 370 days. In total 13 tags were expelled throughout the experiment with an overall tag loss rate of c. 0^.035 tags per day. Fish length was the only explanatory variable which had a significant association with subsequent tag expulsion. The estimated probability of retaining a tag for a year for a fish of length 32 cm was 0.76, 34 cm was 0.60 and 36 cm was 0.38. The long-term tag loss patterns were examined and discussed.     

An investigation of the advantages of autumn and spring stocking with brown trout Salmo trutta L. in a Yorkshire reservoir

Batches of trout have been introduced into Chelker Reservoir in Yorkshire in the autumn and spring since the 1870's for angling purposes. Six batches of tagged, hatchery-reared brown trout Salmo trutta L. were introduced from autumn 1966 to spring 1969. During the angling season fish introduced in the spring give better catches than those stocked in the autumn. At the beginning of the season the larger fish in the spring batch are caught more often than the smaller fish from the same batch. The larger fish in the autumn batch are caught more often than the smaller fish from that batch throughout the season. The population, available to the angler from the shore was estimated to be 1491 in 1968, with 722 fish/km of shoreline. More fish survive to a second year in the reservoir than is apparent from the number of tags returned. Fish introduced in the spring usually begin growing before those introduced in the autumn, thereafter growth rates varied. The growth rate was independent of the number offish stocked up to the numbers put in.
Batches of tagged trout were retained at the hatchery up to nine months to gain relevant experience of post-tagging mortalities, tag loss rate and effect of tags on growth.     

Adjusting survival estimates for premature transmitter failure: a case study from the Sacramento-San Joaquin Delta

In telemetry studies, premature tag failure causes negative bias in fish survival estimates because tag failure is interpreted as fish mortality. We used mark-recapture modeling to adjust estimates of fish survival for a previous study where premature tag failure was documented. High rates of tag failure occurred during the Vernalis Adaptive Management Plan’s (VAMP) 2008 study to estimate survival of fall-run Chinook salmon (Oncorhynchus tshawytscha) during migration through the San Joaquin River and Sacramento-San Joaquin Delta, California. Due to a high rate of tag failure, the observed travel time distribution was likely negatively biased, resulting in an underestimate of tag survival probability in this study. Consequently, the bias-adjustment method resulted in only a small increase in estimated fish survival when the observed travel time distribution was used to estimate the probability of tag survival. Since the bias-adjustment failed to remove bias, we used historical travel time data and conducted a sensitivity analysis to examine how fish survival might have varied across a range of tag survival probabilities. Our analysis suggested that fish survival estimates were low (95% confidence bounds range from 0.052 to 0.227) over a wide range of plausible tag survival probabilities (0.48–1.00), and this finding is consistent with other studies in this system. When tags fail at a high rate, available methods to adjust for the bias may perform poorly. Our example highlights the importance of evaluating the tag life assumption during survival studies, and presents a simple framework for evaluating adjusted survival estimates when auxiliary travel time data are available.     

Accounting for tagging‐to‐harvest mortality in a Brownie tag‐recovery model by incorporating radio‐telemetry data

The Brownie tag‐recovery model is useful for estimating harvest rates but assumes all tagged individuals survive to the first hunting season; otherwise, mortality between time of tagging and the hunting season will cause the Brownie estimator to be negatively biased. Alternatively, fitting animals with radio transmitters can be used to accurately estimate harvest rate but may be more costly. We developed a joint model to estimate harvest and annual survival rates that combines known‐fate data from animals fitted with transmitters to estimate the probability of surviving the period from capture to the first hunting season, and data from reward‐tagged animals in a Brownie tag‐recovery model. We evaluated bias and precision of the joint estimator, and how to optimally allocate effort between animals fitted with radio transmitters and inexpensive ear tags or leg bands. Tagging‐to‐harvest survival rates from >20 individuals with radio transmitters combined with 50–100 reward tags resulted in an unbiased and precise estimator of harvest rates. In addition, the joint model can test whether transmitters affect an individual's probability of being harvested. We illustrate application of the model using data from wild turkey, Meleagris gallapavo, to estimate harvest rates, and data from white‐tailed deer, Odocoileus virginianus, to evaluate whether the presence of a visible radio transmitter is related to the probability of a deer being harvested. The joint known‐fate tag‐recovery model eliminates the requirement to capture and mark animals immediately prior to the hunting season to obtain accurate and precise estimates of harvest rate. In addition, the joint model can assess whether marking animals with radio transmitters affects the individual's probability of being harvested, caused by hunter selectivity or changes in a marked animal's behavior.     

A finite-state continuous-time approach for inferring regional migration and mortality rates from archival tagging and conventional tag-recovery experiments

Spatially structured population dynamics models are important management tools for harvested, highly mobile species and although conventional tag recovery experiments remain useful for estimation of various demographic parameters of these models, archival tagging experiments are becoming an important data source for analyzing migratory behavior of mobile marine species. We provide a likelihood-based approach for estimating the regional migration and mortality rate parameters intrinsic to these models that may use information obtained from conventional tag recovery and archival tagging experiments. Specifically, we assume that the regional location and survival of animals through time is a finite-state continuous-time stochastic process. The stochastic process is the basis of probability models for observations provided by the different types of tags. Results from application to simulated tagging experiments for western Atlantic bluefin tuna show that maximum likelihood estimators based on archival tagging observations and corresponding confidence intervals perform similar to conventional tagging observations for a given number of tag releases and releasing tags in each region can improve the behavior of maximum likelihood estimators regardless of tag type. We provide an example application with Atlantic bluefin tuna released with conventional tags in 1990-1992.     

Tag retention and mortality of adult Atlantic salmon Salmo salar gastrically tagged with different sized telemetry transmitters

A batch of 1 sea winter pre‐spawning adult Salmo salar from the Bush river in Northern Ireland, U.K., were gastrically tagged with large (13 mm diameter) and small (9 mm diameter) dummy acoustic telemetry tags alongside untagged control fish. Survival differed between control and tagged fish and the estimated probability of survival by the end of the study for control fish with no tag was 0·94, small tags was 0·90 and large tags was 0·72. Tag loss through regurgitation was slightly higher for fish tagged with larger tags than for fish tagged with smaller tags and the estimated probability of tag loss for fish with a small tag was 0·10 and for large tags was 0·14.     

Goodness-of-fit tests in proportional hazards models with random effects

This paper deals with testing the functional form of the covariate effects in a Cox proportional hazards model with random effects. We assume that the responses are clustered and incomplete due to right censoring. The estimation of the model under the null (parametric covariate effect) and the alternative (nonparametric effect) is performed using the full marginal likelihood. Under the alternative, the nonparametric covariate effects are estimated using orthogonal expansions. The test statistic is the likelihood ratio statistic, and its distribution is approximated using a bootstrap method. The performance of the proposed testing procedure is studied through simulations. The method is also applied on two real data sets one from biomedical research and one from veterinary medicine.     

A Space-Time Process Model for the Evolution of DNA Sequences

We describe a model for the evolution of DNA sequences by nucleotide substitution, whereby nucleotide sites in the sequence evolve over time, whereas the rates of substitution are variable and correlated over sites. The temporal process used to describe substitutions between nucleotides is a continuous-time Markov process, with the four nucleotides as the states. The spatial process used to describe variation and dependence of substitution rates over sites is based on a serially correlated gamma distribution, i.e., an auto-gamma model assuming Markov-dependence of rates at adjacent sites. To achieve computational efficiency, we use several equal-probability categories to approximate the gamma distribution, and the result is an auto-discrete-gamma model for rates over sites. Correlation of rates at sites then is modeled by the Markov chain transition of rates at adjacent sites from one rate category to another, the states of the chain being the rate categories. Two versions of nonparametric models, which place no restrictions on the distributional forms of rates for sites, also are considered, assuming either independence or Markov dependence. The models are applied to data of a segment of mitochondrial genome from nine primate species. Model parameters are estimated by the maximum likelihood method, and models are compared by the likelihood ratio test. Tremendous variation of rates among sites in the sequence is revealed by the analyses, and when rate differences for different codon positions are appropriately accounted for in the models, substitution rates at adjacent sites are found to be strongly (positively) correlated. Robustness of the results to uncertainty of the phylogenetic tree linking the species is examined.     

The fate of dead fish tagged with biotelemetry transmitters in an urban stream

Mortality is a key factor in understanding the population dynamics of fish. For studies using biotelemetry, missing individuals pose a challenge since the ultimate fate of both the animal and the tag are unknown. In this study, we document three releases of carcasses in a simulated small-scale summer fish kill in a small urban stream using juvenile white sucker (Catostomus commersonii). Passive integrated transponder (PIT) and radio tags were affixed to carcasses that were tracked to determine the fate of both the dead fish and the tags. Mean daily dispersal distances ranged from 0.0 to 7.6 m day^?1 and included downstream and lateral dispersal. Of the 44 radio-tagged carcasses, 26 tags (and presumably carcasses) were consumed by scavengers; the majority were consumed by snapping turtles (Chelydra serpentina) with fewer carcasses scavenged by great blue heron (Ardea herodias), raccoon (Procyon lotor) and muskrat (Ondatra zibethicus). We also contrasted the decomposition rates of in-stream carcasses with those experimentally placed on the riverbank and found that while there was no significant difference in the time to carcass evisceration, the rate of decomposition was more rapid in-stream compared to on-shore. Radio tag loss during the decomposition study was moderate (one of three lost); PIT tag loss occurred when carcasses became eviscerated, typically by invertebrates. By examining the role of scavengers, dispersal and decomposition, it is possible to understand the fate of dead fish, the fate of tags and role of mortality in tagging experiments and the connections between stream and riparian habitats and organisms. This information will help inform the interpretation of potential mortalities in fish tracking studies and improve fish kill investigations.