Evaluating genetic traceability methods for captive-bred marine fish and their applications in fisheries management and wildlife forensics

Growing demands for marine fish products is leading to increased pressure on already depleted wild populations and a rise in aquaculture production. Consequently, more captive-bred fish are released into the wild through accidental escape or deliberate releases. The increased mixing of captive-bred and wild fish may affect the ecological and/or genetic integrity of wild fish populations. Unambiguous identification tools for captive-bred fish will be highly valuable to manage risks (fisheries management) and tracing of escapees and seafood products (wildlife forensics). Using single nucleotide polymorphism (SNP) data from captive-bred and wild populations of Atlantic cod Gadus morhua L. and sole Solea solea L., we explored the efficiency of population and parentage assignment techniques for the identification and tracing of captive-bred fish. Simulated and empirical data were used to correct for stochastic genetic effects. Overall, parentage assignment performed well when a large effective population size characterized the broodstock and escapees originated from early generations of captive breeding. Consequently, parentage assignments are particularly useful from a fisheries management perspective to monitor the effects of deliberate releases of captive-bred fish on wild populations. Population assignment proved to be more efficient after several generations of captive breeding, which makes it a useful method in forensic applications for well-established aquaculture species. We suggest the implementation of a case-by-case strategy when choosing the best method.

Carbon and nitrogen stable isotope ratio analysis of freshwater, brackish and marine fish from Belgian archaeological sites (1st and 2nd millennium AD)

Carbon and nitrogen stable isotope ratios were measured in 157 fish bone collagen samples from 15 different archaeological sites in Belgium which ranged in ages from the 3rd to the 18th c. AD. Due to diagenetic contamination of the burial environment, only 63 specimens produced results with suitable C:N ratios (2.9–3.6). The selected bones encompass a wide spectrum of freshwater, brackish, and marine taxa (N = 18), and this is reflected in the δ13C results (−28.2‰ to −12.9%). The freshwater fish have δ13C values that range from −28.2‰ to −20.2‰, while the marine fish cluster between −15.4‰ and −13.0‰. Eel, a catadromous species (mostly living in freshwater but migrating into the sea to spawn), plots between −24.1‰ and −17.7‰, and the anadromous fish (living in marine environments but migrating into freshwater to spawn) show a mix of freshwater and marine isotopic signatures. The δ15N results also have a large range (7.2‰ to 16.7‰) indicating that these fish were feeding at many different trophic levels in these diverse aquatic environments. The aim of this research is the isotopic characterization of archaeological fish species (ecology, trophic level, migration patterns) and to determine intra-species variation within and between fish populations differing in time and location. Due to the previous lack of archaeological fish isotope data from Northern Europe and Belgium in particular, these results serve as an important ecological backdrop for the future isotopic reconstruction of the diet of human populations dating from the historical period (1st and 2nd millennium AD), where there is zooarchaeological and historical evidence for an increased consumption of marine fish.

Fish use of flooded margins of an intermittently open estuary

Fish communities in the shallow flooded margins of an intermittently open estuary were examined over an 18 month period. A distinct shift in the fish assemblage occurred when the mouth of the estuary closed and was associated with changes in the hydro-period, food availability and physico-chemical changes in the main channel.

Aggressiveness Overcomes Body-Size Effects in Fights Staged between Invasive and Native Fish Species with Overlapping Niches

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Fish assemblages in stream stretches occupied by cattail (Typhaceae, Angiospermae) stands in Southeast Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Fish-assemblage structure of the Corumbatai river basin, São Paulo State, Brazil: characterization and anthropogenic disturbances

O rio Corumbataí é um dos principais tributários da margem direita do rio Piracicaba que é um tributário do rio Tietê. O rio Corumbataí integra a bacia do rio Paraná e é regionalmente importante não só por possuir águas de boa qualidade, mas também por possuir elementos raros na paisagem local. Este estudo visou caracterizar as assembléias de peixes do rio Corumbataí e fornecer dados que contribuam para uma avaliação da sua qualidade ambiental. Na bacia do rio Corumbataí, foram amostrados 4 rios principais, cada um com 3 pontos de coleta. Vinte e quatro amostras foram coletadas durante os meses de março a julho e de setembro a dezembro de 2001. Dados bióticos foram avaliados por medidas de diversidade. Um modelo linear ANCOVA foi utilizado para testar a hipótese de variação espaço-temporal nas assembléias de peixes, com a riqueza de espécies como variável resposta, ordem do rio como fator e temperatura e logaritmo natural do número de indivíduos como covariáveis. Esta análise mostrou uma variação espaço-temporal que é corroborada por conceitos exaustivamente discutidos na literatura, tais como relação espécie-área e o conceito de rio contínuo. Dados provenientes do rio Ribeirão Claro mostraram um padrão diferente quando comparados com os outros rios. Esta diferença foi provavelmente devido à interferência humana e atesta o processo de fragmentação de hábitats aquáticos que podem ter levado a um isolamento das populações locais de peixes.

Aggressiveness Overcomes Body-Size Effects in Fights Staged between Invasive and Native Fish Species with Overlapping Niches

Approximately 50 years ago, Nile tilapia were accidentally introduced to Brazil, and the decline of pearl cichlid populations, which has been intensified by habitat degradation, in some locations has been associated with the presence of Nile tilapia. There is, however, little strong empirical evidence for the negative interaction of non-native fish populations with native fish populations; such evidence would indicate a potential behavioural mechanism that could cause the population of the native fish to decline. In this study, we show that in fights staged between pairs of Nile tilapia and pearl cichlids of differing body size, the Nile tilapia were more aggressive than the pearl cichlid. Because this effect prevailed over body-size effects, the pearl cichlids were at a disadvantage. The niche overlap between the Nile tilapia and the pearl cichlid in nature, and the competitive advantage shown by the Nile tilapia in this study potentially represent one of several possible results of the negative interactions imposed by an invasive species. These negative effects may reduce population viability of the native species and cause competitive exclusion.

Novel tools for conservation genetics in marine fish: population structure and evolution of the European hake (Merluccius merluccius) inferred by SNP variation and applications to traceability

The research presented in my PhD thesis is part of a wider European project, FishPopTrace, focused on traceability of fish populations and products. My work was aimed at developing and analyzing novel genetic tools for a widely distributed marine fish species, the European hake (Merluccius merluccius), in order to investigate population genetic structure and explore potential applications to traceability scenarios. A total of 395 SNPs (Single Nucleotide Polymorphisms) were discovered from a massive collection of Expressed Sequence Tags, obtained by high-throughput sequencing, and validated on 19 geographic samples from Atlantic and Mediterranean. Genome-scan approaches were applied to identify polymorphisms on genes potentially under divergent selection (outlier SNPs), showing higher genetic differentiation among populations respect to the average observed across loci. Comparative analysis on population structure were carried out on putative neutral and outlier loci at wide (Atlantic and Mediterranean samples) and regional (samples within each basin) spatial scales, to disentangle the effects of demographic and adaptive evolutionary forces on European hake populations genetic structure. Results demonstrated the potential of outlier loci to unveil fine scale genetic structure, possibly identifying locally adapted populations, despite the weak signal showed from putative neutral SNPs. The application of outlier SNPs within the framework of fishery resources management was also explored. A minimum panel of SNP markers showing maximum discriminatory power was selected and applied to a traceability scenario aiming at identifying the basin (and hence the stock) of origin, Atlantic or Mediterranean, of individual fish. This case study illustrates how molecular analytical technologies have operational potential in real-world contexts, and more specifically, potential to support fisheries control and enforcement and fish and fish product traceability.

Communication in troubled waters: responses of fish communication systems to changing environments

Fish populations are increasingly being subjected to anthropogenic changes to their sensory environments. The impact of these changes on inter- and intra-specific communication, and its evolutionary consequences, has only recently started to receive research attention. A disruption of the sensory environment is likely to impact communication, especially with respect to reproductive interactions that help to maintain species boundaries. Aquatic ecosystems around the world are being threatened by a variety of environmental stressors, causing dramatic losses of biodiversity and bringing urgency to the need to understand how fish respond to rapid environmental changes. Here, we discuss current research on different communication systems (visual, chemical, acoustic, electric) and explore the state of our knowledge of how complex systems respond to environmental stressors using fish as a model. By far the bulk of our understanding comes from research on visual communication in the context of mate selection and competition for mates, while work on other communication systems is accumulating. In particular, it is increasingly acknowledged that environmental effects on one mode of communication may trigger compensation through other modalities. The strength and direction of selection on communication traits may vary if such compensation occurs. However, we find a dearth of studies that have taken a multimodal approach to investigating the evolutionary impact of environmental change on communication in fish. Future research should focus on the interaction between different modes of communication, especially under changing environmental conditions. Further, we see an urgent need for a better understanding of the evolutionary consequences of changes in communication systems on fish diversity.

Remote Monitoring of Fish in Small Streams: A Unified Approach Using Pit Tags

Accurate assessments of fish populations are often limited by re-observation or recapture events. Since the early 1990s, passive integrated transponders (PIT tags) have been used to understand the biology of many fish species. Until recently, PIT applications in small streams have been limited to physical recapture events. To maximize recapture probability, we constructed PIT antenna arrays in small streams to remotely detect individual fish. Experiences from two different laboratories (three case studies) allowed us to develop a unified approach to applying PIT technology for enhancing data assessments. Information on equipment, its installation, tag considerations, and array construction is provided. Theoretical and practical definitions are introduced to standardize metrics for assessing detection efficiency. We demonstrate how certain conditions (stream discharge, vibration, and ambient radio frequency noise) affect the detection efficiency and suggest that by monitoring these conditions, expectations of efficiency can be modified. We emphasize the importance of consistently estimating detection efficiency for fisheries applications.

Variations in coastal fish species composition captured by traps in Romsdalsfjord, Western Norway

Fish traps are widely used in Norwegian fjords, especially those designed for monitoring salmonid populations in the marine environment, although many other marine fish species are also captured. The composition and spatio-temporal variations of fish species captured by fish traps were monitored in five different coastal locations throughout the Romsdalsfjord region, Western Norway, from May to August during the three consecutive years (2011–2013). Twenty-three fish species were captured by traps in coastal waters, both resident and migratory fishes. The most common fish and with greater catchability were saithe (Pollachis virens) and sea trout (Salmo trutta), followed by cod (Gadus morhua), pollack (P. pollachius), herring (Clupea harengus) and mackerels (Trachurus trachurus and Scomber scombrus). However, the captured assemblage presented great spatial and seasonal variations, in terms of mean daily catch, probably associated with hydrographical conditions and migrational patterns. Information obtained in this study will help us to better understand the compositions and dynamic of coastal fish populations inhabiting Norwegian coastal waters. In addition, traps are highly recommended as a management tool for fish research (e.g. fish-tagging experiments, mark and recapture) and conservation purposes (coastal use and fisheries studies).

Habitat structure and fish communities of warmwater streams /

Mode of access: Internet.

Estimate of abundance, harvest, and exploitation of the fish population of Escanaba Lake, Wisconsin, 1946-69 /

Caption title.

Subtroprical wetland fish assemblages and changing salinity regimes: Implications for everglades restoration

During the 1960s, water management practices resulted in the conversion of the wetlands that fringe northeastern Florida Bay (USA) from freshwater/oligohaline herbaceous marshes to dwarf red mangrove forests. Coincident with this conversion were several ecological changes to Florida Bay’s fauna, including reductions in the abundances of top trophic-level consumers: piscivorous fishes, alligators, crocodiles, and wading birds. Because these taxa rely on a common forage base of small demersal fishes, food stress has been implicated as playing a role in their respective declines. In the present study, we monitored the demersal fishes seasonally at six sites over an 8-year time period. During monitoring, extremely high rainfall conditions occurred over a 3.5-year period leading to salinity regimes that can be viewed as “windows” to the area’s natural past and future restored states. In this paper, we: (1) examine the changes in fish communities over the 8-year study period and relate them to measured changes in salinity; (2) make comparisons among marine, brackish and freshwater demersal fish communities in terms of species composition, density, and biomass; and (3) discuss several implications of our findings in light of the intended and unintended water management changes that are planned or underway as part of Everglades restoration. Results suggest the reduction in freshwater flow to Florida Bay over the last several decades has reduced demersal fish populations, and thus prey availability for apex consumers in the coastal wetlands compared to the pre-drainage inferred standard. Furthermore, greater discharge of freshwater toward Florida Bay may result in the re-establishment of pre-1960s fauna, including a more robust demersal-fish community that should prompt increases in populations of several important predatory species.