Daily age, growth rate, and pelagic larval duration of commercially important snapper species in Abrolhos National Marine Park.

The age and daily growth of fish are registered through the deposition of increments in their otoliths, which are concretions formed by the precipitation of substances present in the endolymphatic fluid, mainly calcium carbonate (CaCO3). Faced with the need to fill some of the gaps in the knowledge on the occurrence and duration of the initial stages of snapper species' life cycles in the Abrolhos Bank, this study aimed to describe the growth rates, age, and period of pelagic larval duration (PLD) of three snapper species during the larval pre-settlement phase, in the Abrolhos Bank region. The post-larvae were captured using light traps. Otoliths were removed from 117 samples of snapper species; however, only 69 were viable for age estimation, of which 15 were Lutjanus analis, 25 were Lutjanus jocu, and 29 were Lutjanus synagris. Together, the samples presented individuals with total lengths ranging from 16.14 to 24.76 mm and ages from 21 to 39 days. Settlement marks were found for all three species, and the average PLD was ~25 days. The somatic growth of the snapper species was positively correlated with otolith growth. L. jocu presented the greatest daily growth compared to the other species. The three species use the Abrolhos Bank as a larval settlement site, demonstrating plasticity by using different habitats throughout their lives.

Otolith sectioning reveals higher maximum age in greater weever (Trachinus draco).

Growth and maximum age are two key parameters that inform resilience of fish populations to exploitation. Existing information on those for greater weever inhabiting the eastern North Sea is based on the analysis of whole otoliths. Here, we present a reanalysis using sectioned otoliths. The results reveal a different growth pattern and a higher maximum age than that previously reported. The higher maximum age makes greater weever populations more vulnerable to exploitation. Such information can serve as a basis for the estimation of the growth curve that can be used for future assessment of the species.

Pilot study to investigate the effect of long-term exposure to high pCO2 on adult cod (Gadus morhua) otolith morphology and calcium carbonate deposition.

To date the study of ocean acidification on fish otolith formation has been mainly focused on larval and juvenile stages. In the present pilot study, wild-captured adult Atlantic cod (Gadus morhua) were exposed to two different levels of pCO2, 422µatm (ambient, low pCO2) or 1091µatm (high pCO2), for a period of 30 weeks (from mid-October to early April 2014-2015) in order to study the effects on otolith size, shape and CaCO3 crystallization amongst other biological parameters. We found that otoliths from cod exposed to high pCO2 were slightly smaller (- 3.4% in length; - 3.3% in perimeter), rounder (- 2.9% circularity and + 4% roundness) but heavier (+ 5%) than the low pCO2 group. Interestingly, there were different effects in males and females; for instance, male cods exposed to high pCO2 exhibited significant changes in circularity (- 3%) and roundness (+ 4%) compared to the low pCO2 males, but without significant changes on otolith dimensions, while females exposed to high pCO2 had smaller otoliths as shown for length (- 5.6%), width (- 2%), perimeter (- 3.5%) and area (- 4.8%). Furthermore, while the majority of the otoliths analysed showed normal aragonite deposition, 10% of fish exposed to 1091µatm of pCO2 had an abnormal accretion of calcite, suggesting a shift on calcium carbonate polymorph crystallization in some individuals under high pCO2 conditions. Our preliminary results indicate that high levels of pCO2 in adult Atlantic cod might affect otolith growth in a gender-specific way. Our findings reveal that otoliths from adult cod are affected by ocean acidification, and we believe that the present study will prompt further research into this currently under-explored area.

The life history characteristics of Neosebastes pandus and the relationship between sexually dimorphic growth and reproductive strategy among Scorpaeniformes.

Scorpaeniformes are an important component of commercial and recreational fisheries world-wide. The Neosebastes species, found in the western Pacific and south-east Indian Ocean, have received little attention from a research perspective. Samples of the bighead gurnard perch, Neosebastes pandus, collected from the lower west and south coasts of Western Australia, were used to undertake the first comprehensive investigation of the biological characteristics of a Neosebastes species. Opaque zones in sectioned sagittal otoliths were validated as forming annually. Female N. pandus grow to a significantly larger size, on average, than males and dominate the largest size classes, while males, growing to a smaller size, accumulate in the intermediate size classes. Although males were far less numerous than females in those age classes in which both sexes were found, males and females attain similar maximum ages >25 years. Neosebastes pandus spawns over a brief period between May (austral late autumn) and July (austral mid-autumn) when water temperature and day length are declining. The mean monthly gonadosomatic indices (GSI, IGS ) values of females during the spawning period are 37-50 times higher than those of males, which mature at an earlier age and smaller length compared to females. Histological examination of the ovaries of females indicate that their structure is consistent with "general" teleost ovarian anatomy and thus differs from Scorpaena, Helicolenus and Sebastes species whose ovaries are adapted for specialized reproductive modes. The reproductive strategy of N. pandus of maximizing the reproductive output of females, by this sex attaining a larger size than males and pair spawning (i.e., large disparity in IGS values) demonstrates the close lineage between the Neosebastes and other Scorpaeniformes, such as the Scorpaena, Helicolenus and Sebastes.

The growth and age structure of Chilean jack mackerel (Trachurus murphyi) following its influx to New Zealand waters.

The Chilean jack mackerel (Trachurus murphyi) is a predominantly Southeast Pacific Ocean species. It is relatively difficult to determine its age, and multiple studies of its growth off South America have produced markedly different sets of von Bertalanffy parameters. T. murphyi was first identified from New Zealand waters in the mid-1980s and has comprised part of the commercial landings of Trachurus species (along with Trachurus declivis and Trachurus novaezelandiae) since then. Results from 13 years of age determination of New Zealand samples using sectioned otoliths indicate that a partially validated age determination method has been developed, with a precision level (average percentage error) of 4.6%. The best available von Bertalanffy growth parameters for the New Zealand population (sexes combined) are as follows: L∞ , 51.9 cm fork length; K, 0.223 per year; t0 , -0.5 year. Analyses by sex showed that males have a significantly larger L∞ than females. Estimated annual catch-at-length and catch-at-age distributions from the fishery are presented for 2007-2019. There have been at least two episodes of immigration of T. murphyi from international waters, but little evidence of spawning success to maintain the New Zealand population.

Century-long cod otolith biochronology reveals individual growth plasticity in response to temperature.

Otolith biochronologies combine growth records from individual fish to produce long-term growth sequences, which can help to disentangle individual from population-level responses to environmental variability. This study assessed individual thermal plasticity of Atlantic cod (Gadus morhua) growth in Icelandic waters based on measurements of otolith increments. We applied linear mixed-effects models and developed a century-long growth biochronology (1908-2014). We demonstrated interannual and cohort-specific changes in the growth of Icelandic cod over the last century which were mainly driven by temperature variation. Temperature had contrasting relationships with growth-positive for the fish during the youngest ages and negative during the oldest ages. We decomposed the effects of temperature on growth observed at the population level into within-individual effects and among-individual effects and detected significant individual variation in the thermal plasticity of growth. Variance in the individual plasticity differed across cohorts and may be related to the mean environmental conditions experienced by the group. Our results underscore the complexity of the relationships between climatic conditions and the growth of fish at both the population and individual level, and highlight the need to distinguish between average population responses and growth plasticity of the individuals for accurate growth predictions.

Individual back-calculated size-at-age based on otoliths from Pacific coral reef fish species.

Somatic growth is a critical biological trait for organismal, population, and ecosystem-level processes. Due to its direct link with energetic demands, growth also represents an important parameter to estimate energy and nutrient fluxes. For marine fishes, growth rate information is most frequently derived from sagittal otoliths, and most of the available data stems from studies on temperate species that are targeted by commercial fisheries. Although the analysis of otoliths is a powerful tool to estimate individual growth, the time-consuming nature of otolith processing is one barrier for collection of comprehensive datasets across multiple species. This is especially true for coral reef fishes, which are extremely diverse. Here, we provide back-calculated size-at-age estimates (including measures of uncertainty) based on sagittal otoliths from 710 individuals belonging to 45 coral reef fish species from French Polynesia. In addition, we provide Von Bertalanffy growth parameters which are useful to predict community level biomass production.

Explaining decisions of deep neural networks used for fish age prediction.

Age-reading of fish otoliths (ear stones) is important for the sustainable management of fish resources. However, the procedure is challenging and requires experienced readers to carefully examine annual growth zones. In a recent study, convolutional neural networks (CNNs) have been demonstrated to perform reasonably well on automatically predicting fish age from otolith images. In the present study, we carefully investigate the prediction rule learned by such neural networks to provide insight into the features that identify certain fish age ranges. For this purpose, a recent technique for visualizing and analyzing the predictions of the neural networks was applied to different versions of the otolith images. The results indicate that supplementary knowledge about the internal structure improves the results for the youngest age groups, compared to using only the contour shape attribute of the otolith. However, the contour shape and size attributes are, in general, sufficient for older age groups. In addition, within specific age ranges we find that the network tends to focus on particular areas of the otoliths and that the most discriminating factors seem to be related to the central part and the outer edge of the otolith. Explaining age predictions from otolith images as done in this study will hopefully help build confidence in the potential of deep learning algorithms for automatic age prediction, as well as improve the quality of the age estimation.

Age and growth of Brauer's lanternfish Gymnoscopelus braueri and rhombic lanternfish Krefftichthys anderssoni (Family Myctophidae) in the Scotia Sea, Southern Ocean.

This study examines age and growth of Brauer's lanternfish Gymnoscopelus braueri and rhombic lanternfish Krefftichthys anderssoni from the Scotia Sea in the Southern Ocean, through the analysis of annual growth increments deposited on sagittal otoliths. Otolith pairs from 177 G. braueri and 118 K. anderssoni were collected in different seasons from the region between 2004 and 2009. Otolith-edge analysis suggested a seasonal change in opaque and hyaline depositions, indicative of an annual growth pattern, although variation within the populations of both species was apparent. Age estimates varied from 1 to 6 years for G. braueri (40 to 139 mm standard length; LS ) and from 0 to 2 years for K. anderssoni (26 to 70 mm LS ). Length-at-age data were broadly consistent with population cohort parameters identified in concurrent length-frequency data from the region for both species. The estimated values of von Bertalanffy growth curves for G. braueri were L∞ = 133.22 mm, k = 0.29 year-1 and t0 = -0.21 year and the values for K. anderssoni were L∞ = 68.60 mm, k = 0.71 year-1 and t0 = -0.49 year. There were no significant (P > 0.05) differences in growth between sexes for either species, suggesting that males and females have similar growth and development trajectories in the Scotia Sea. A positive allometric relationship between LS and wet mass was found for each species, as well as a significant (P < 0.0001) linear relationship between otolith size and LS . Growth performance (Ф') was similar between the two species and congruent with other myctophid species across the Southern Ocean. This study provides important parameters for future Southern Ocean ecosystem studies in a resource management context.

An hypoxia-tolerant flatfish: consequences of sustained stress on the slender sole Lyopsetta exilis (Pleuronectidae) in the context of a changing ocean.

Slender sole Lyopsetta exilis is an abundant groundfish on the continental shelf and inner waters of British Columbia, Canada, where it reaches a maximum standard length of 44 cm. Benthic image surveys coupled with oxygen measurements in Saanich Inlet document a dense population in bottom conditions near anoxia (0.03 ml l-1 oxygen) where diel migrating zooplankton intersect the bottom; we confirm this species is a planktivore, which limits its depth range to the base of the migration layer. In a comparison with slender sole from a nearby well-oxygenated habitat, several probable effects of living in severe hypoxia emerge: both sexes are significantly smaller in Saanich and the sex ratio is male-skewed. Otoliths from the Saanich fish were difficult to read due to many checks, but both sexes were smaller at age with the largest female (20 cm) from the hypoxia zone registering 17 years. Hypoxia appears to have a direct consequence on growth despite good food supply in this productive basin. Hyperventilation, a low metabolic rate and a very low critical oxygen tension help this fish regulate oxygen uptake in severely hypoxic conditions; it will be particularly resilient as the incidence of hypoxia increases on the continental shelf. Data from small-mesh bottom-trawl surveys over four decades reveal an increase in mean annual catch per unit effort in southern regions of the province, including the outer shelf and the Strait of Georgia. The California Cooperative Oceanic Fisheries Investigations (CalCOFI) ichthyoplankton database records a general decline in fish larvae on the Oregon-California shelf since 1990, but slender sole larvae are increasing there, as they are in the Strait of Georgia. We project that the slender sole will gain relative benefits in the future warming, deoxygenated northeast Pacific Ocean.

Facultative amphidromy involving estuaries in an annual amphidromous fish from a subtropical marginal range.

Variation in the life cycle of diadromous fishes can be explained by differential food availability between marine and freshwater habitats, since migration is often interpreted as a mechanism for exploiting food resources. Theoretically, a migration pattern of mainly remaining in freshwater occurs in tropical and subtropical habitats where fluvial productivity possibly exceeds marine productivity. However, in Yakugachi River, Amami-Oshima Island, southern Japan, low nutrient concentrations in the river suggest that food availability is limited for the subtropical Ryukyu-ayu Plecoglossus altivelis ryukyuensis. Since Ryukyu-ayu is an amphidromous fish that mainly grows in rivers after spending 2 months in the sea, limited food availability in rivers would force this species to migrate to other habitats with better food availability. Otolith increment and Sr:Ca analyses of 48 adult Ryukyu-ayu collected from the Yakugachi River revealed that all individuals visited estuaries more than three times after moving upstream. Although the specific growth rates of this species in the river had no correlation with the salinity profile in the fluvial period, this movement may be an adaptive choice because the salinity profile significantly affected the body size at maturity. Our results highlighted individual-based variations in amphidromous migration for utilizing estuaries, which could be explained by relatively higher productivity in estuarine than in freshwater and marine habitats.

Age-based life history of humpback red snapper, Lutjanus gibbus, in New Caledonia.

This paper examines the life history of humpback red snapper Lutjanus gibbus, an important fishery species for coastal communities across the Indo-Pacific, in southern New Caledonia, where the species is lightly exploited. A total of 243 L. gibbus were sampled between January 2013 and December 2016 from occasional harvests of commercial fishers. Examination of sectioned otoliths revealed that opaque increment formation occurred annually between November and March, coinciding with the species' spawning season. Estimates of maximum age were similar between sexes, with observed ages of 38 and 36 years for females and males, respectively, extending the reported longevity of this species by at least 11 years. Growth differed significantly between sexes, with males reaching greater length at age and greater asymptotic length than females (38.88 v. 31.46 cm fork length (LF ). Total mortality for all samples was estimated as 0.13 and was slightly higher for males (0.16) than females (0.11). Estimates of natural and fishing mortality were low and slightly higher for males than females. Male L. gibbus were found to mature at slightly greater lengths and younger ages than females, with the length and age at which 50% of individuals attained maturity estimated to be 25.8 cm LF and 3.9 years of age for females and 26.8 cm LF and 3.4 years of age for males. The results provide key baseline information from which to assess the effect of fishing on the species for populations in New Caledonia and adjacent locations and, when viewed with those of other studies, highlight the importance of understanding spatial patterns in demography of harvested fish species across gradients of exploitation and environmental influences.

Life History Parameters of Genypterus brasiliensis (Teleostei: Ophidiidae), an Endemic Fisheries Resource of the Southwestern Atlantic.

Genypterus brasiliensis, a demersal fish of large size (1.3 m of total length), occurs in the southwest Atlantic (23 to 38oS) and well appreciated due to the quality of its flesh. It was analyzed through longline and trawl fisheries, and the average length and weight of 724 specimens were significantly different between them, with the biggest and heaviest specimens caught by the former. The weight-length relationships were significantly different based upon sex: females Wt=4x10-7Lt3.3799; r2=0.97; n=262; p<0.001, and males: Wt=4x10-7Lt3.3886; r2=0.95; n=190; p<0.001. Using the otoliths readings for 153 specimens (APE of 2% and CV of 4.2%), the growth parameters estimates reveal statistical differences between sexes (p=0.05; r2=0.889). The fisheries were composed of individuals aged 1 to 13 (females) and 1 to 14 years old (males), with ring formation in late spring. The back calculated parameters (VBGF) were: Loo=1,452.38 mm, K=0.0996, t0=-0.2757 yr-1 (females) and Loo=983.07 mm, K=0.155, t0=-0.236 yr-1 (males), and longevity as 29.8 and 19.1 years old, respectively. The low biological production allied to the slow growth and a late complete maturation and its endemism, allow classify G. brasiliensis as a vulnerable resource, jeopardizing a sustainable fishery. Until reliable quantitative biological data are available, precautionary management must be considered.

Exposure to cadmium causes inhibition of otolith development and behavioral impairment in zebrafish larvae.

Otolith consisting largely of calcium carbonate, fibrous and proteins, is vital for maintaining body balance and/or hearing of fish. The formation of otolith involves Ca2+ transport and deposition. In the present study, we investigated the effects of Cd2+ on otoliths development by using zebrafish embryos as model. The results showed that exposure to Cd2+ inhibited the utricular and saccular otoliths growth, indicated by reduced lateral areas. Swimming speeds were reduced and a losing balance control was observed in Cd2+ exposed larvae. The genes related to Ca2+ transport (e.g. plasma membrane Ca2+-ATPase isoform 2, pmca2; Ca2+-ATPase isoform 2, atp2b1a) and regulation (e.g. parathyroid hormone ligand type-1, pth1; stanniocalcin isoform 1, stc1) were significantly downregulated. However, the adverse effects of Cd2+ on otoliths growth and swimming activity can be protected by supplementation of Ca2+ in exposure medium. Body burden of Cd2+ in larvae was reduced upon the supplement with Ca2+. The overall results suggest that exposure to Cd2+ can inhibit influx of Ca2+, leading to less deposition of CaCO3 for otolith growth, and finally result in impaired balance control and swimming activity in zebrafish larvae.

Daily growth increments in otoliths of wild-caught honmoroko Gnathopogon caerulescens.

Otolith growth increments in wild-caught alizarin complex one (ALC)-marked honmoroko Gnathopogon caerulescens were examined to verify the veracity of the age determination method in cyprinids. ALC-marked G. caerulescens recaptured from their natural environment had lapilli increment counts outside the ALC ring mark that had formed on a daily basis during the juvenile stage. This apparently being the first direct evidence of daily periodicity of otolith increment formation in wild-caught cyprinids.

Otolith shape analysis and daily increment validation during ontogeny of larval and juvenile European chub Squalius cephalus.

This assesses features of otoliths from laboratory-reared embryos, larvae and juvenile European chub Squalius cephalus from hatching to 180 days post-hatching (dph). We observed the development of the three pairs of otoliths (lapilli, sagittae and asterisci) and more precisely shape changes, as well as timing and deposition rate of increments of the lapilli. The lapilli and the sagittae were present at hatching, whereas the asterisci formed between 20 and 30 dph. The lapillus and sagitta shapes were round until 20 dph. From 60 dph the anterior and the posterior rostra of the sagittae were well developed, but very thin, making this otolith too fragile to manipulate for further studies of shape and validation of otolith increment deposition rate. The lapilli provided reliable age estimates for free embryos, larvae and juveniles up to 120 dph. However, caution should be taken when ageing fish older than 150 dph as an underestimation was noticeable. The regression of the number of otolith increments on age showed a slope and an intercept not significantly different from 1 and 0, respectively, which indicated that otolith growth increments were deposited on a daily basis, with the first microincrement occurring at hatching. Increment counts were consistent between three interpreters, indicating a consistent and reliable age estimate. This study validates that the otolith increment deposition rate can be used to assess hatching dates and daily growth of wild S. cephalus under 150 dph and in environments similar to the conditions used in this study.

In vivo and in vitro analysis of starmaker activity in zebrafish otolith biomineralization.

Otoliths are one of the biominerals whose formation is highly controlled by proteins. The first protein discovered to be involved in otolith biomineralization in zebrafish was starmaker (Stm). Previously, Stm was shown to be responsible for the preferential formation of aragonite, a polymorph of calcium carbonate, in otoliths. In this work, proteomic analysis of adult zebrafish otoliths was performed. Stm is the only highly phosphorylated protein found in our studies. Besides previously studied otolith proteins, we discovered several dozens of unknown proteins that reveal the likely mechanism of biomineralization. A comparison of aragonite and vaterite otoliths showed similarities in protein composition. We observed the presence of Stm in both types of otoliths. In vitro studies of 2 characteristic Stm fragments indicated that the DS-rich region has a special biomineralization activity, especially after phosphorylation.-Kalka, M., Markiewicz, N., Ptak, M., Sone, E. D., Ozyhar, A., Dobryszycki, P., Wojtas, M. In vivo and in vitro analysis of starmaker activity in zebrafish otolith biomineralization.

Regulatory mechanisms of miR-96 and miR-184 abnormal expressions on otic vesicle development of zebrafish following exposure to ß-diketone antibiotics.

Chronic ototoxicity of ß-diketone antibiotics (DKAs) to zebrafish (Danio rerio) was explored in detail by following abnormal expressions of two hearing-related miRNAs. Dose-dependent down-regulation of miR-96 and miR-184 was observed in otoliths during embryonic-larval development. Continuous DKA exposure to 120-hpf larva decreased sensitivity to acoustic stimulation. Development of otolith was delayed in treatment groups, showing unclear boundaries and vacuolization at 72-hpf, and utricular enlargement as well as decreased saccular volume in 96-hpf or latter larval otoliths. If one miRNA was knocked-down and another over-expressed, only a slight influence on morphological development of the otic vesicle occurred, but knocked-down or over-expressed miRNA both significantly affected zebrafish normal development. Injection of miR-96, miR-184 or both micRNA mimics to yolk sac resulted in marked improvement of otic vesicle phenotype. However, hair cell staining showed that only the injected miR-96 mimic restored hair cell numbers after DKA exposure, demonstrating that miR-96 played an important role in otic vesicle development and formation of hearing, while miR-184 was only involved in otic vesicle construction during embryonic development. These observations advance our understanding of hearing loss owing to acute antibiotic exposure and provide theoretical guidance for early intervention and gene therapy for drug-induced diseases.

Morphology and Ontogeny of Statoliths in the Grooved Carpet Shell, Ruditapes decussatus.

Statoliths are nonskeletal calcified structures included in most invertebrates' gravireceptors. They have been identified and characterized in several gastropod and cephalopod molluscs and have proved to be very useful for age estimation, growth studies, and connectivity analysis, among other applications. Beyond the scarce available records on their occurrence in Class Bivalvia, statoliths are yet to be documented in the grooved carpet shell, Ruditapes decussatus, a species of high ecological and commercial value. An easy method for the extraction and processing of R. decussatus statoliths is described herein. The statolith growth was followed from the initial shell length (SL) of 2.5-3.5 mm (seed commercial size T1.5) for a period of 6 months in a nursery facility located in the Ria de Aveiro (an estuarine system in NW Portugal). The relationship between statolith diameter (StD) and SL follows the function StD=14.305 SL0.254 (N=173; r=0.855, p<0.001). All statoliths observed showed similar morphostructure and general chemistry: hard, translucent spheres of crystalline calcium oxalate (whewellite), with a central nucleus delimited by a growth check of 6.7±1.0 µm in diameter, possibly as a result of growth arrest during metamorphosis, a metamorphic ring, as described for their gastropod counterparts. Subsequent studies should validate this and will involve a search for the occurrence of additional checks that may potentially be present in older specimens and if they are, would open a new range of most promising applications for bivalve statoliths.

IsoFishR: An application for reproducible data reduction and analysis of strontium isotope ratios (87Sr/86Sr) obtained via laser-ablation MC-ICP-MS.

The IsoFishR application is a data reduction and analysis tool for laser-ablation strontium isotope data, following common best practices and providing reliable and reproducible results. Strontium isotope ratios (87Sr/86Sr) are a powerful geochemical tracer commonly applied in a wide range of scientific fields and laser-ablation inductively coupled mass spectrometry is considered the method of choice to obtain spatially resolved 87Sr/86Sr isotope ratios from a variety of sample materials. However, data reduction and analyses methods are variable between different research groups and research communities limiting reproducibility between studies. IsoFishR provides a platform to standardize these methods and can be used for both spot and time-resolved line transects. Furthermore, it provides advanced data analysis tools and filters for outlier removal, noise reduction, and visualization of time resolved data. The application can be downloaded from GitHub (https://github.com/MalteWillmes/IsoFishR) and the source code is available, encouraging future development and evolution of this software.