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Tag-recapture data contain valuable information about individual fish growth, which can enhance the estimation of growth parameters. Tag-recapture data are especially useful when age-determination uncertainties throw age-based growth estimates and stock assessments into question, as is the present situation with several important gadoid stocks. Length-based (GROTAG method) and age-based (LEP method) growth functions were fit to a large data set of tagged and recaptured cod (Gadus morhua) from an artificial reef in the western Baltic Sea to calculate improved growth parameter estimates. The LEP method allowed integration of different data formats, including tag-recapture, length frequency, and length-at-age, to estimate a more robust and comprehensive growth function (von Bertalanffy growth parameters: [L.sub.[infinity]] = 154.56 cm, k = 0.11, [t.sub.0] = -0.13). Two heavily exploited cod stocks inhabit the Baltic Sea, subsisting at the upper thermal and lower salinity limits of the species. Otolith shape analyses indicated that, unexpectedly, individuals from both populations were resident at the reef. Compared with cod populations elsewhere, cod in the western Baltic Sea grow relatively slowly and with weak seasonal fluctuations in growth rates, potentially due to adverse conditions for growth. Les donnees de marquage-recapture contiennent de l'information utile sur la croissance individuelle des poissons qui peut ameliorer l'estimation des parametres de croissance. Ces donnees sont particulierement utiles quand les incertitudes associees a la determination de l'age jettent un doute sur les estimations de la croissance et les evaluations de stock basees sur l'age, comme c'est actuellement le cas pour plusieurs stocks importants de gadides. Des fonctions de croissance basees sur la longueur (methode GROTAG) et sur l'age (methode LEP) ont ete calees sur un grand ensemble de donnees de morues (Gadus morhua) marquees et recapturees d'un recif artificiel dans l'ouest de la mer Baltique afin d'obtenir de meilleures estimations des parametres de croissance. La methode LEP a permis l'integration de differents formats de donnees, dont des donnees de marquage-recapture, de frequence de longueurs et de longueur selon l'age, pour estimer une fonction de croissance plus robuste et complete (parametres de croissance de von Bertalanffy : [L.sub.[infinity]] = 154,56 cm, k = 0,11, [t.sub.0] = -0,13). Deux stocks de morues faisant l'objet d'une exploitation intensive sont presents dans la mer Baltique, ou ils subsistent a la limite de temperature superieure et a la limite de salinite inferieure de l'espece. Des analyses de la forme d'otolites indiquent que, contrairement aux attentes, des specimens des deux populations sont des residents du recif. Comparativement aux populations de morues en d'autres endroits, la morue de l'ouest de la mer Baltique a une croissance relativement lente caracterisee par de faibles fluctuations saisonnieres, possiblement a cause de conditions non propices a la croissance. [Traduit par la Redaction], Introduction Estimating individual growth of fish has been a central theme in fisheries science for decades, as an intrinsic characteristic of a fish population and an essential component of stock [...]

Despite increased deployment of archival tags on exploited fish species, analytical methods for including archival tag data in fishery assessment models are lacking. We present a method for integrating archival tag data into a spatial tag-recapture model for estimating natural mortality, fishing mortality, abundance, and movement. Archival tags provide important information on fish movement not available from conventional tags that facilitates separation of movement from mortality estimates. Using simulations, we evaluate the benefit of including archival tag data in the model using two model formulations: one with a general spatial structure and one with movement and fishery dynamics based on juvenile southern bluefin tuna (SBT; Thunnus maccoyii). If fish are not tagged in all regions and time periods, then including archival tag data can substantially improve the precision of the fishing mortality and movement estimates. For example, with the general spatial structure and specific scenario presented, standard errors of the fishing mortality estimates decreased by an average of 34% (21%) when 25 archival tags were released in addition to 500 (2500) conventional tags in each region and period of tagging, respectively. Furthermore, with the SBT spatial structure, archival tag data were necessary for all parameters to be estimable. Malgre le deploiement croissant d'etiquettes enregistreuses chez les especes de poissons exploitees, les methodes analytiques permettant d'inclure les donnees fournies par ces instruments dans les modeles devaluation des ressources halieutiques font defaut. Une methode est presentee pour l'integration des donnees d'etiquettes enregistreuses dans un modele spatial de marquage-recapture pour l'estimation de la mortalite naturelle, de la mortalite par peche, de l'abondance et des deplacements. Les etiquettes enregistreuses fournissent d'importants renseignements sur les deplacements des poissons que ne permettent pas d'obtenir les etiquettes ordinaires. Ces donnees facilitent l'exclusion des deplacements des estimations de la mortalite. Des simulations sont utilisees pour evaluer l'avantage d'inclure des donnees d'etiquettes enregistreuses dans le modele en utilisant deux formulations de ce dernier : l'un pour une structure spatiale generale et l'autre reposant sur les deplacements et la dynamique des peches du thon rouge du Sud (SBT; Thunnus maccoyii) juvenile. Si des poissons ne sont pas marques dans toutes les regions et pour toutes les periodes, l'inclusion de donnees d'etiquettes enregistreuses peut accroitre de maniere sensiblement la precision des estimations de la mortalite par peche et des deplacements. A titre d'exemple, pour les scenarios de structure spatiale generale et specifique susmentionnes, l'ecart-type moyen des estimations de mortalite a diminue de 34 % (21 %) quand 25 etiquettes enregistreuses etaient relachees, en plus de 500 (2500) etiquettes ordinaires, dans chaque region et pour chaque periode de marquage, respectivement. En outre, l'utilisation de donnees d'etiquettes enregistreuses s'est averee necessaire pour l'estimation de tous les parametres de la structure spatiale associee au SBT. [Traduit par la Redaction], Introduction The deployment of archival (data-logging) tags on commercially exploited fish species has become increasingly common over the past decade, with particular focus on the wide-ranging and valuable tuna species. [...]

Abstract--Tagging experiments are a useful tool in fisheries for estimating mortality rates and abundance of fish. Unfortunately, nonreporting of recovered tags is a common problem in commercial fisheries which, if [...]

Abstract: The underlying sources of growth variability in a population cannot generally be known, so when modelling growth it is important to understand the consequences of assuming an incorrect error [...]

Abstract: A comprehensive framework for modelling data from multiyear tagging experiments in a fishery context is presented that incorporates catch data into the traditional Brownie tag-recapture model. Incorporation of catch [...]

Abstract Background Poorly preserved biological tissues have become an important source of DNA for a wide range of zoological studies. Measuring the quality of DNA obtained from these samples is often desired; however, there are no widely used techniques available for quantifying damage in highly degraded DNA samples. We present a general method that can be used to determine the frequency of polymerase blocking DNA damage in specific gene-regions in such samples. The approach uses quantitative PCR to measure the amount of DNA present at several fragment sizes within a sample. According to a model of random degradation the amount of available template will decline exponentially with increasing fragment size in damaged samples, and the frequency of DNA damage (λ) can be estimated by determining the rate of decline. Results The method is illustrated through the analysis of DNA extracted from sea lion faecal samples. Faeces contain a complex mixture of DNA from several sources and different components are expected to be differentially degraded. We estimated the frequency of DNA damage in both predator and prey DNA within individual faecal samples. The distribution of fragment lengths for each target fit well with the assumption of a random degradation process and, in keeping with our expectations, the estimated frequency of damage was always less in predator DNA than in prey DNA within the same sample (mean λpredator = 0.0106 per nucleotide; mean λprey = 0.0176 per nucleotide). This study is the first to explicitly define the amount of template damage in any DNA extracted from faeces and the first to quantify the amount of predator and prey DNA present within individual faecal samples. Conclusion We present an approach for characterizing mixed, highly degraded PCR templates such as those often encountered in ecological studies using non-invasive samples as a source of DNA, wildlife forensics investigations and ancient DNA research. This method will allow researchers to measure template quality in order to evaluate alternate sources of DNA, different methods of sample preservation and different DNA extraction protocols. The technique could also be applied to study the process of DNA decay.

Advances in DNA sequencing technology have revolutionized the field of molecular analysis of trophic interactions, and it is now possible to recover counts of food DNA sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer's diet should we work strictly with data sets summarizing frequency of occurrence of different food taxa, or is it possible to use relative number of sequences? Both approaches are applied to obtain semi‐quantitative diet summaries, but occurrence data are often promoted as a more conservative and reliable option due to taxa‐specific biases in recovery of sequences. We explore representative dietary metabarcoding data sets and point out that diet summaries based on occurrence data often overestimate the importance of food consumed in small quantities (potentially including low‐level contaminants) and are sensitive to the count threshold used to define an occurrence. Our simulations indicate that using relative read abundance (RRA) information often provides a more accurate view of population‐level diet even with moderate recovery biases incorporated; however, RRA summaries are sensitive to recovery biases impacting common diet taxa. Both approaches are more accurate when the mean number of food taxa in samples is small. The ideas presented here highlight the need to consider all sources of bias and to justify the methods used to interpret count data in dietary metabarcoding studies. We encourage researchers to continue addressing methodological challenges and acknowledge unanswered questions to help spur future investigations in this rapidly developing area of research. [ABSTRACT FROM AUTHOR]

DNA metabarcoding is a powerful new tool allowing characterization of species assemblages using high-throughput amplicon sequencing. The utility of DNA metabarcoding for quantifying relative species abundances is currently limited by both biological and technical biases which influence sequence read counts. We tested the idea of sequencing 50/50 mixtures of target species and a control species in order to generate relative correction factors ( RCFs) that account for multiple sources of bias and are applicable to field studies. RCFs will be most effective if they are not affected by input mass ratio or co-occurring species. In a model experiment involving three target fish species and a fixed control, we found RCFs did vary with input ratio but in a consistent fashion, and that 50/50 RCFs applied to DNA sequence counts from various mixtures of the target species still greatly improved relative abundance estimates (e.g. average per species error of 19 ± 8% for uncorrected vs. 3 ± 1% for corrected estimates). To demonstrate the use of correction factors in a field setting, we calculated 50/50 RCFs for 18 harbour seal ( Phoca vitulina) prey species ( RCFs ranging from 0.68 to 3.68). Applying these corrections to field-collected seal scats affected species percentages from individual samples (Δ 6.7 ± 6.6%) more than population-level species estimates (Δ 1.7 ± 1.2%). Our results indicate that the 50/50 RCF approach is an effective tool for evaluating and correcting biases in DNA metabarcoding studies. The decision to apply correction factors will be influenced by the feasibility of creating tissue mixtures for the target species, and the level of accuracy needed to meet research objectives. [ABSTRACT FROM AUTHOR]

Ref.: Can. J. Fish. Aquat. Sci. 63: 534-548 (2006). Two of the equations in Appendix A contain typographical errors. First, there is a missing [GAMMA] in the denominator of the [...]

The demographics of the southern bluefin tuna (SBT) Thunnus maccoyii spawning stock were examined through a large-scale monitoring program of the Indonesian longline catch on the spawning ground between 1995 and 2012. The size and age structure of the spawning population has undergone significant changes since monitoring began. There has been a reduction in the relative abundance of larger/older SBT in the catch since the early 2000s, and a corresponding decrease in mean length and age, but there was no evidence of a significant truncation of the age distribution. Pulses of young SBT appear in the catches in the early- and mid-2000s and may be the first evidence of increased recruitment into the spawning stock since 1995. Fish in these two recruitment pulses were spawned around 1991 and 1997. Size-related variations in sex ratio were also observed with female bias for fish less than 170 cm FL and male bias for fish greater than 170 cm FL. This trend of increasing proportion of males with size above 170 cm FL is likely to be related to sexual dimorphism in growth rates as male length-at-age is greater than that for females after age 10 years. Mean length-at-age of fish aged 8–10 years was greater for both males and females on the spawning ground than off the spawning ground, suggesting that size may be the dominant factor determining timing of maturation in SBT. In addition to these direct results, the data and samples from this program have been central to the assessment and management of this internationally harvested stock. [ABSTRACT FROM AUTHOR]

Length and age at maturity are important life history parameters for estimating spawning stock biomass and reproductive potential of fish stocks. Bias in estimates of size and age at maturity can arise when disparate distributions of mature and immature fish within a population are not accounted for in the analysis. Here we investigate the spatial and temporal variability in observed size and age at maturity of female albacore tuna, Thunnus alalunga, using samples collected across the South Pacific. Maturity status was identified using consistent histological criteria that were precise enough to allow for mature but regenerating females to be distinguished from immature females during the non-spawning season, permitting year-round sampling for maturity estimation in albacore. Using generalised linear mixed models, we found that the proportion of mature females at length varied significantly with latitude and time of year. Specifically, females at northern latitudes (∼10–20°S, where spawning occurs) were mature at significantly smaller lengths and ages than females at southern latitudes (∼20–40°S), particularly during the spawning season (October–March). This variation was due to different geographic distributions of mature and immature fish during the year. We present a method for estimating an unbiased maturity ogive that takes into account the latitudinal variation in proportion mature at length during a given season (spawning or non-spawning). Applying this method to albacore samples from the western region of the South Pacific gave a predicted length at 50% mature of ∼87 cm fork length (4.5 years). [ABSTRACT FROM AUTHOR]

Presents a letter to the editor about a general method of fitting growth curves to capture-recapture data derived from several western rock lobsters.

A correction to the article "Integrating catch-at-age and multiyear tagging data: a combined Brownie and Petersen estimation approach in a fishery context," by Tom Polacheck, J. Paige Eveson, Geoff M. Laslett, Kenneth H. Pollock, and William S. Hearn is presented.