The forgotten feeding ground: patterns in seasonal and depth-specific food intake of adult cod Gadus morhua in the western Baltic Sea.

This study presents the diet composition of western Baltic cod Gadus morhua based on 3150 stomachs sampled year-round between 2016 and 2017 using angling, gillnetting and bottom trawling, which enhanced the spatio-temporal coverage of cod habitats. Cod diet composition in shallow areas (<20 m depth) was dominated by benthic invertebrate species, mainly the common shore crab Carcinus maneas. Compared to historic diet data from the 1960s and 1980s (limited to depth >20 m), the contribution of herring Clupea harengus decreased and round goby Neogobius melanostomus occurred as a new prey species. Statistical modelling revealed significant relationships between diet composition, catch depth, fish length and season. Generalized additive modelling identified a negative relationship between catch depth and stomach content weight, suggesting reduced food intake in winter when cod use deeper areas for spawning and during peak summer when cod tend to avoid high water temperatures. The results of this study highlight the importance of shallow coastal areas as major feeding habitats of adult cod in the western Baltic Sea, which were previously unknown because samples were restricted to deeper trawlable areas. The results strongly suggest that historic stomach analyses overestimated the role of forage fish and underestimated the role of invertebrate prey. Eventually, this study shows the importance of a comprehensive habitat coverage for unbiased stomach sampling programmes to provide a more reliable estimation of top predator diet, a key information for food web analyses and multispecies models.

Effects of freezing on length and mass measurements of Atlantic cod Gadus morhua in the Baltic Sea.

An aggregated sample of 925 Atlantic cod Gadus morhua collected by four countries in different regions of the Baltic Sea during different seasons were measured (total length, LT = 161-890 mm and weighed (mass, M = 45-6900 g) both before freezing and after defrosting. The cod were found to decrease significantly in both LT and M following death and frozen storage. There was an average (±SD) change in LT of -2.91% (±0.05%) following freezing, independent of starting LT . Total M changed by -2.65% (±0.14%), independent of starting mass. Shrinkage of LT and M did not differ significantly between 1 and 4 months frozen storage, though LT shrinkage was significantly greater after 1 or 4 months in the freezer compared with after 5 days. There was significant variation in LT and M shrinkage between regions of capture. A significant negative relationship between condition of cod and LT or M change was also observed. Equations to back-calculate fresh LT and M from thawed LT , M and standard length (LS ), gutted LT , gutted LS and gutted M are provided.

Tidal-diel patterns in feeding and abundance of armed snook Centropomus armatus from macrotidal mangrove creeks of the tropical eastern Pacific Ocean.

We investigated the influence of temporal and spatial factors on the feeding habits of the armed snook Centropomus armatus (Centropomidae), the most abundant snook species in eastern Pacific mangrove ecosystems. The influence of the combination of semi-diurnal tides and diel cycles and salinity on the intertidal abundance, stomach fullness, diet composition and daily consumption of this species was investigated over 1 year in the macrotidal Colombian Pacific coast (Bahía Málaga). The abundance of juvenile C. armatus (5.6-23.6 cm total length) in the intertidal creeks was highest during neap tide-night conditions and lowest during spring-tide day conditions. Centropomus armatus fed predominantly on crustaceans (Alpheidae and Palaemonidae) and fishes. Stomach fullness index (ISF ), a proxy of feeding activity, was not influenced by salinity, but by tidal-diel conditions. Stomach fullness index was highest during neap tide nocturnal inundations, but lowest during diurnal neap tides. Nevertheless, the total daily consumption was higher at spring tide than at neap tides. Higher water temperatures in creeks during neap tides at night could explain not only high C. armatus abundance, but also greater accessibility to active prey. Comparison with the feeding patterns of fishes from other macrotidal mangrove ecosystems suggest that the habitat use and feeding patterns of intertidal fishes in mangroves are strongly influenced by the combination of spring-neap tide and diel cycles. However, the interaction between mangrove geomorphology and flooding regime of the specific mangrove forest might also play a role and deserves further investigation.

Trophic lengthening triggered by filamentous, N2-fixing cyanobacteria disrupts pelagic but not benthic food webs in a large estuarine ecosystem.

Eutrophication, increased temperatures and stratification can lead to massive, filamentous, N2-fixing cyanobacterial (FNC) blooms in coastal ecosystems with largely unresolved consequences for the mass and energy supply in food webs. Mesozooplankton adapt to not top-down controlled FNC blooms by switching diets from phytoplankton to microzooplankton, resulting in a directly quantifiable increase in its trophic position (TP) from 2.0 to as high as 3.0. If this process in mesozooplankton, we call trophic lengthening, was transferred to higher trophic levels of a food web, a loss of energy could result in massive declines of fish biomass. We used compound-specific nitrogen stable isotope data of amino acids (CSIA) to estimate and compare the nitrogen (N) sources and TPs of cod and flounder from FNC bloom influence areas (central Baltic Sea) and areas without it (western Baltic Sea). We tested if FNC-triggered trophic lengthening in mesozooplankton is carried over to fish. The TP of cod from the western Baltic (4.1 ± 0.5), feeding mainly on decapods, was equal to reference values. Only cod from the central Baltic, mainly feeding on zooplanktivorous pelagics, had a significantly higher TP (4.6 ± 0.4), indicating a strong carry-over effect trophic lengthening from mesozooplankton. In contrast, the TP of molluscivorous flounder, associated with the benthic food web, was unaffected by trophic lengthening and quite similar reference values of 3.2 ± 0.2 in both areas. This suggests that FNC blooms lead to a large loss of energy in zooplanktivorous but not in molluscivorous mesopredators. If FNC blooms continue to trigger the detour of energy at the base of the pelagic food web due to a massive heterotrophic microbial system, the TP of cod will not return to lower TP values and the fish stock not recover. Monitoring the TP of key species can identify fundamental changes in ecosystems and provide information for resource management.

New insights into the recent collapse of Eastern Baltic cod from historical data on stock health.

The Eastern Baltic cod (Gadus morhua) stock is currently in a very poor state, with low biomass and adverse trends in several life history and demographic parameters. This raises concern over whether and to what level recovery is possible. Here, we look for new insights from a historical perspective, extending the time series of various stock health indicators back to the 1940s, i.e. to the beginning of intensive exploitation of the Eastern Baltic cod. The historical data confirm that the stock deterioration in recent years is unprecedented, as all indicators are presently in their worst states on record. Cod body condition and energy reserves were equally low in the 1940s-1950s, accompanied by high parasitic liver worm infection, comparable to that measured in recent years. However, other stock parameters (size structure, size at maturity, stock distribution) are currently in their worst states over the past 80 years. In contrast, the state of cod in the 1970s to early 1990s that is often perceived as a desirable target, was exceptional, with the most favorable indicator levels in the time series. Long-term observation data reveal concurrent or asynchronous trends in different indicators of stock health and to what extent these have coincided with changes in possible external drivers. In this way, the extended time series contribute to ongoing research on understanding the collapse of the cod and its recovery potential.

Tracing growth patterns in cod (Gadus morhua L.) using bioenergetic modelling.

Understanding individual growth in commercially exploited fish populations is key to successful stock assessment and informed ecosystem-based fisheries management. Traditionally, growth rates in marine fish are estimated using otolith age-readings in combination with age-length relationships from field samples, or tag-recapture field experiments. However, for some species, otolith-based approaches have been proven unreliable and tag-recapture experiments suffer from high working effort and costs as well as low recapture rates. An important alternative approach for estimating fish growth is represented by bioenergetic modelling which in addition to pure growth estimation can provide valuable insights into the processes leading to temporal growth changes resulting from environmental and related behavioural changes. We here developed an individual-based bioenergetic model for Western Baltic cod (Gadus morhua), traditionally a commercially important fish species that however collapsed recently and likely suffers from climate change effects. Western Baltic cod is an ideal case study for bioenergetic modelling because of recently gained in-situ process knowledge on spatial distribution and feeding behaviour based on highly resolved data on stomachs and fish distribution. Additionally, physiological processes such as gastric evacuation, consumption, net-conversion efficiency and metabolic rates have been well studied for cod in laboratory experiments. Our model reliably reproduced seasonal growth patterns observed in the field. Importantly, our bioenergetic modelling approach implementing depth-use patterns and food intake allowed us to explain the potentially detrimental effect summer heat periods have on the growth of Western Baltic cod that likely will increasingly occur in the future. Hence, our model simulations highlighted a potential mechanism on how warming due to climate change affects the growth of a key species that may apply for similar environments elsewhere.

Evidence of hybridization between genetically distinct Baltic cod stocks during peak population abundance(s).

Range expansions can lead to increased contact of divergent populations, thus increasing the potential of hybridization events. Whether viable hybrids are produced will most likely depend on the level of genomic divergence and associated genomic incompatibilities between the different entities as well as environmental conditions. By taking advantage of historical Baltic cod (Gadus morhua) otolith samples combined with genotyping and whole genome sequencing, we here investigate the genetic impact of the increased spawning stock biomass of the eastern Baltic cod stock in the mid 1980s. The eastern Baltic cod is genetically highly differentiated from the adjacent western Baltic cod and locally adapted to the brackish environmental conditions in the deeper Eastern basins of the Baltic Sea unsuitable for its marine counterparts. Our genotyping results show an increased proportion of eastern Baltic cod in western Baltic areas (Mecklenburg Bay and Arkona Basin)-indicative of a range expansion westwards-during the peak population abundance in the 1980s. Additionally, we detect high frequencies of potential hybrids (including F1, F2 and backcrosses), verified by whole genome sequencing data for a subset of individuals. Analysis of mitochondrial genomes further indicates directional gene flow from eastern Baltic cod males to western Baltic cod females. Our findings unravel that increased overlap in distribution can promote hybridization between highly divergent populations and that the hybrids can be viable and survive under specific and favourable environmental conditions. However, the observed hybridization had seemingly no long-lasting impact on the continuous separation and genetic differentiation between the unique Baltic cod stocks.

Living apart together: Long-term coexistence of Baltic cod stocks associated with depth-specific habitat use.

Coexistence of fish populations (= stocks) of the same species is a common phenomenon. In the Baltic Sea, two genetically divergent stocks of Atlantic cod (Gadus morhua), Western Baltic cod (WBC) and Eastern Baltic cod (EBC), coexist in the Arkona Sea. Although the relative proportions of WBC and EBC in this area are considered in the current stock assessments, the mixing dynamics and ecological mechanisms underlying coexistence are not well understood. In this study, a genetically validated otolith shape analysis was used to develop the most comprehensive time series of annual stock mixing data (1977-2019) for WBC and EBC. Spatio-temporal mixing analysis confirmed that the two stocks coexist in the Arkona Sea, albeit with fluctuating mixing proportions over the 43-year observation period. Depth-stratified analysis revealed a strong correlation between capture depth and stock mixing patterns, with high proportions of WBC in shallower waters (48-61% in <20m) and increasing proportions of EBC in deeper waters (50-86% in 40-70m). Consistent depth-specific mixing patterns indicate stable differences in depth distribution and habitat use of WBC and EBC that may thus underlie the long-term coexistence of the two stocks in the Arkona Sea. These differences were also reflected in significantly different proportions of WBC and EBC in fisheries applying passive gears in shallower waters (more WBC) and active gears in deeper waters (more EBC). This highlights the potential for fishing gear-specific exploitation of different stocks, and calls for stronger consideration of capture depth and gear type in stock assessments. This novel evidence provides the basis for improved approaches to research, monitoring and management of Baltic cod stocks.

In vitro forestomach digestion experiments give less-biased estimates of food composition in odontocetes.

Diet composition of odontocetes is usually inferred from stomach content analyses and accounts for digestion rates derived from in vitro digestion experiments based on seal physiology. However, pinnipeds, being carnivores, have only one stomach compartment, while odontocetes, being cetartiodactyla, have up to four. Inappropriate extrapolation from digestion processes in simulated seal stomachs may result in biased estimates of odontocete diets. We simulated a forestomach accounting for muscle contractions and a pH=4 using in vitro experiments with three fish species. Whiting (Merlangius merlangus), black goby (Gobius niger) and sprat (Sprattus sprattus) showed highly variable exponential, sigmoid or linear digestion functions, and high digestion rates, taking between 50 and 230 min for completed digestion. Previous pinniped models (pH=2, lacking simulated muscular digestion) showed much slower and more similar digestion process. Our results suggest that present biomass intake estimates of odontocetes are biased towards bigger and fattier fish and need to be revised in general.

The role of genomic signatures of directional selection and demographic history in the population structure of a marine teleost with high gene flow.

Recent studies have uncovered patterns of genomic divergence in marine teleosts where panmixia due to high gene flow has been the general paradigm. These signatures of divergent selection are often impacted by structural variants, acting as "supergenes" facilitating local adaptation. The highly dispersing European plaice (Pleuronectes platessa)-in which putative structural variants (i.e., inversions) have been identified-has successfully colonized the brackish water ecosystem of the Baltic Sea. Thus, the species represents an ideal opportunity to investigate how the interplay of gene flow, structural variants, natural selection, past demographic history, and gene flow impacts on population (sub)structuring in marine systems. Here, we report on the generation of an annotated draft plaice genome assembly in combination with population sequencing data-following the salinity gradient from the Baltic Sea into the North Sea together with samples from Icelandic waters-to illuminate genome-wide patterns of divergence. Neutral markers pointed at large-scale panmixia across the European continental shelf associated with high gene flow and a common postglacial colonization history of shelf populations. However, based on genome-wide outlier loci, we uncovered signatures of population substructuring among the European continental shelf populations, i.e., suggesting signs of ongoing selection. Genome-wide selection analyses (xp-EHH) and the identification of genes within genomic regions of recent selective sweeps-overlapping with the outlier loci-suggest that these represent the signs of divergent selection. Our findings provide support for genomic divergence driven by local adaptation in the face of high gene flow and elucidate the relative importance of demographic history versus adaptive divergence in shaping the contemporary population genetic structure of a marine teleost. The role of the putative inversion(s) in the substructuring-and potentially ongoing adaptation-was seemingly not substantial.

Pond aquaculture effluents feed an anthropogenic nitrogen loop in a SE Asian estuary.

Coastal aquaculture expansion resulted in mangrove area loss and ecosystem degradation in the past decades, mainly in tropical Asia. Despite increasing environmental concerns regarding nutrient and organic matter-rich effluents, little is known on the effects on adjacent estuarine and coastal food webs. To assess the impact and fate of anthropogenic nitrogen released from aquaculture facilities, we studied water quality and nitrogen (N) flow across an estuarine food web in an estuary in Hainan, China, using nitrogen stable isotopes (δ15N). We found higher δ15N values of ammonium, nitrate and suspended matter in the pond-covered inner estuary than further upstream, suggesting a strong influence of untreated pond effluents, which had a high δ15N (ammonium: ~16‰, nitrate: ~7‰, suspended matter: ~8‰). Fish and benthic invertebrates of the inner estuary had a higher δ15N than consumers further upstream and in similar aquaculture-free estuaries elsewhere, most likely due to direct or indirect uptake of 15N-enriched aquaculture effluents by phytoplankton and benthic algae. A major part of the artisanal catches from the estuary consists of small-size fish which is used as feed in the local aquaculture. Thus, estuarine fish incorporating aquaculture-effluent based food web signals are harvested and recycled as feed in aquaculture facilities, whose effluents sustain this local food web. The δ15N being at the high end of the global range on all trophic levels indicates an anthropogenic nitrogen loop in which some portion of the reactive nitrogen initially introduced into aquaculture ponds is continuously recycled and affects the estuarine food web. This recycling also indicates a shortcut in the otherwise inefficient nitrogen sink function of estuaries. Therefore, in areas with large-scale coastal aquaculture like in China and SE Asia the effect of reactive nitrogen from aquaculture sources on the performance of coastal ecosystems may be larger than previously thought.

Assessing SNP-markers to study population mixing and ecological adaptation in Baltic cod.

Atlantic cod (Gadus morhua) is a species of great ecological and economical importance in the Baltic Sea. Here, two genetically differentiated stocks, the western and the eastern Baltic cod, display substantial mechanical mixing, hampering our understanding of cod ecology and impeding stock assessments and management. Based on whole-genome re-sequencing data from reference samples obtained from the study area, we designed two different panels of Single Nucleotide Polymorphisms markers (SNPs), which take into account the exceptional genome architecture of cod. A minimum panel of 20 diagnostic SNPs and an extended panel (20 diagnostic and 18 biologically informative SNPs, 38 in total) were developed and validated to distinguish unambiguously between the western and the eastern Baltic cod stocks and to enable studies of local adaptation to the specific environment in the Baltic Sea, respectively. We tested both panels on cod sampled from the southern Baltic Sea (n = 603) caught in 2015 and 2016. Genotyping results showed that catches from the mixing zone in the Arkona Sea, were composed of similar proportions of individuals of the western and the eastern stock. Catches from adjacent areas to the east, the Bornholm Basin and Gdansk Deep, were exclusively composed of eastern Baltic cod, whereas catches from adjacent western areas (Belt Sea and Öresund) were composed of western Baltic cod. Interestingly, the two Baltic cod stocks showed strong genetic differences at loci associated with life-history trait candidate genes, highlighting the species' potential for ecological adaptation even at small geographical scales. The minimum and the extended panel of SNP markers presented in this study provide powerful tools for future applications in research and fisheries management to further illuminate the mixing dynamics of cod in the Baltic Sea and to better understand Baltic cod ecology.

Genetic analyses reveal complex dynamics within a marine fish management area.

Genetic data have great potential for improving fisheries management by identifying the fundamental management units-that is, the biological populations-and their mixing. However, so far, the number of practical cases of marine fisheries management using genetics has been limited. Here, we used Atlantic cod in the Baltic Sea to demonstrate the applicability of genetics to a complex management scenario involving mixing of two genetically divergent populations. Specifically, we addressed several assumptions used in the current assessment of the two populations. Through analysis of 483 single nucleotide polymorphisms (SNPs) distributed across the Atlantic cod genome, we confirmed that a model of mechanical mixing, rather than hybridization and introgression, best explained the pattern of genetic differentiation. Thus, the fishery is best monitored as a mixed-stock fishery. Next, we developed a targeted panel of 39 SNPs with high statistical power for identifying population of origin and analyzed more than 2,000 tissue samples collected between 2011 and 2015 as well as 260 otoliths collected in 2003/2004. These data provided high spatial resolution and allowed us to investigate geographical trends in mixing, to compare patterns for different life stages and to investigate temporal trends in mixing. We found similar geographical trends for the two time points represented by tissue and otolith samples and that a recently implemented geographical management separation of the two populations provided a relatively close match to their distributions. In contrast to the current assumption, we found that patterns of mixing differed between juveniles and adults, a signal likely linked to the different reproductive dynamics of the two populations. Collectively, our data confirm that genetics is an operational tool for complex fisheries management applications. We recommend focussing on developing population assessment models and fisheries management frameworks to capitalize fully on the additional information offered by genetically assisted fisheries monitoring.

Tide- and rainfall-induced variations of physical and chemical parameters in a mangrove-depleted estuary of East Hainan (South China Sea).

The estuarine dynamics favoring the coexistence of mangroves, seagrass and corals at small river mouths are often poorly understood. We characterize the tidal, day/night and rainfall-induced short-term dynamics in salinity, pH, dissolved oxygen (DO), chlorophyll a (chl a), total suspended matter (TSM), water transparency, surface currents and dissolved nutrients (NO(x)(-), NH(4)(+), PO(4)(3)(-), Si(OH)(4)) of the Wenchang/Wenjiao Estuary (East Hainan, tropical China). Samples were taken at three fixed sites along the estuary during 24 h spring tide cycles in different seasons. Salinity, DO, water transparency and pH generally increased seawards while nutrients decreased. All parameters varied with the tidal cycle, partially in interaction with the diel cycle. Nutrients, chl a and TSM usually fluctuated inversely with water level. Stratification was strong. Inflowing bottom water was of higher salinity, DO and pH and lower temperature and nutrient concentrations than the surface water. Tidal mixing provided regular ventilation of the estuary and limited eutrophication effects of nutrients from aquaculture, agriculture and urban effluents. Under dry weather conditions, the brackish-water lagoon functioned as a sink of nutrients due to efficient uptake by phytoplankton. Presently, the runoff from common intense rains in the watershed affects the estuary with little time delay due to terrestrial deforestation, channelization and loss of mangrove area. The frequency, strength and duration of intermittent estuarization of the back-reef areas have likely increased in the past and deteriorate present seagrass and coral health.

Temporal patterns in the occurrence of selected tropical fishes in mangrove creeks: implications for the fisheries management in north Brazil

To examine the temporal patterns in the occurrence of a tropical ichthyofauna, fisheries-independent samples were collected between September 2003 and July 2004 from intertidal mangrove creeks in the Curuçá estuary, Pará, north Brazil. Juveniles occurred year-round with the most intense occurrence during the wet/dry transition season (Anchovia clupeoides, Cetengraulis edentulus, Rhinosardinia amazonica, Mugil sp.). The occurrence of Colomesus psittacus and Anchoa hepsetus was continuous. Sciades herzbergii displayed two peaks (wet and dry season) while Cathorops sp. peaked only in the wet season. The continuous presence of juveniles in the tropical mangroves suggested that the fisheries management should be based on large no-take areas rather than closed seasons.

Com o objetivo de examinar padrões temporais em recrutamento de uma ictiofauna tropical, pescarias experimentais foram realizadas entre setembro 2003 e Julio 2004 em canais de maré com vegetação de mangue no estuário do rio Curuçá, Pará, Norte do Brasil. Juvenis ocorreram durante todo o ano, entretanto com maior intensidade no período de recrutamento, durante a transição da estação chuvosa para a seca (Anchovia clupeoides, Cetengraulis edentulus, Rhinosardinia amazonica, Mugil sp.). O recrutamento foi continuo para Colomesus psittacus e Anchoa hepsetus. Sciades herzbergii apresentou dois picos de recrutamento (estação chuvosa e seca), entretanto Cathorops sp. teve somente um (estação chuvosa). A presença contínua de juvenis nos manguezais sugere que o manejo da pesca em regiões tropicais com vegetação de mangue deveria se direcionar em definir grandes áreas de proteção ao lugar de épocas de defeso.