Crustaceans and fish abundances and species at and around artificially introduced tetrapod fields in the southern North Sea, 2010-2011

In the coming decades, artificial defence structures will increase in importance worldwide for the protection of coasts against the impacts of global warming. However, the ecological effects of such structures on the natural surroundings remain unclear. We investigated the impact of experimentally introduced tetrapod fields on the demersal fish community in a hard-bottom area in the southern North Sea. The results indicated a significant decrease in fish abundance in the surrounding area caused by migration effects towards the artificial structures. Diversity (HB) and evenness (E) values exhibited greater variation after the introduction of the tetrapods. Additionally, a distinct increase in young-of-the-year (YOY) fish was observed near the structures within the second year after introduction. We suggest that the availability of adequate refuges in combination with additional food resources provided by the artificial structures has a highly species-specific attraction effect. However, these findings also demonstrate that our knowledge regarding the impact of artificial structures on temperate fish communities is still too limited to truly understand the ecological processes that are initiated by the introduction of artificial structures. Long-term investigations and additional experimental in situ work worldwide will be indispensable for a full understanding of the mechanisms by which coastal defence structures interact with the coastal environment.

Seawater carbonate chemistry and length, weight, survival rate, metabolic rate of coral reef fish Amphiprion melanopus in a laboratory experiment

Carbon dioxide concentrations in the surface ocean are increasing owing to rising CO2 concentrations in the atmosphere. Higher CO2 levels are predicted to affect essential physiological processes of many aquatic organisms, leading to widespread impacts on marine diversity and ecosystem function, especially when combined with the effects of global warming. Yet the ability for marine species to adjust to increasing CO2 levels over many generations is an unresolved issue. Here we show that ocean conditions projected for the end of the century (approximately 1,000 µatm CO2 and a temperature rise of 1.5-3.0 °C) cause an increase in metabolic rate and decreases in length, weight, condition and survival of juvenile fish. However, these effects are absent or reversed when parents also experience high CO2 concentrations. Our results show that non-genetic parental effects can dramatically alter the response of marine organisms to increasing CO2 and demonstrate that some species have more capacity to acclimate to ocean acidification than previously thought.

Physicochemical properties and fish occurrence in 35 Icelandic lakes housing Arctic charr (Salvelinus alpinus)

The common occurrence of parallel phenotypic patterns suggests that a strong relationship exists between ecological dynamics and micro-evolution. Comparative studies from a large number of populations under varying sets of ecological drivers could contribute to a better understanding of this relationship. We used data on morphology of arctic charr (Salvelinus alpinus) and ecological factors from 35 Icelandic lakes to test the hypothesis that morphological patterns among monomorphic charr populations from different lakes are related to interlake variation in ecological characteristics. There is extensive phenotypic diversity among populations of Icelandic charr, and populations are easily distinguished based on overall body morphology. The results obtained in the present study showed that the morphological diversity of charr was related to large-scale diversity in lake ecology. Variation in charr morphology was related to water origin (e.g. spring fed versus run-off), bedrock age, and fish community structure. The present study shows how various ecological factors can shape the biological diversity that we observe.

Unexpected beta2-microglobulin sequence diversity in individual rainbow trout.

For mammals beta2-microglobulin (beta2m), the light chain of major histocompatibility complex (MHC) class I molecules, is invariant (or highly conserved) and is encoded by a single gene unlinked to the MHC. We find that beta2m of a salmonid fish, the rainbow trout (Oncorhynchus mykiss), does not conform to the mammalian paradigm. Ten of 12 randomly selected beta2m cDNA clones from an individual fish have different nucleotide sequences. A complex restriction fragment length polymorphism pattern is observed with rainbow trout, suggesting multiple beta2m genes in the genome, in excess of the two genes expected from the ancestral salmonid tetraploidy. Additional duplication and diversification of the beta2m genes might have occurred subsequently. Variation in the beta2m cDNA sequences is mainly at sites that do not perturb the structure of the mature beta2m protein, showing that the observed diversity of the trout beta2m genes is not primarily a result of pathogen selection.

Origin and diversity of the Sox transcription factor gene family: genome-wide analysis in Fugu rubripes

The SOX family of transcription factors are found throughout the animal kingdom and are important in a variety of developmental contexts. Genome analysis has identified 20 Sox genes in human and mouse, which can be subdivided into 8 groups, based on sequence comparison and intron-exon structure. Most of the SOX groups identified in mammals are represented by a single SOX sequence in invertebrate model organisms, suggesting a duplication and divergence mechanism has operated during vertebrate evolution. We have now analysed the Sox gene complement in the pufferfish, Fugu rubripes, in order to shed further light on the diversity and origins of the Sox gene family. Major differences were found between the Sox family in Fugu and those in humans and mice. In particular, Fugu does not have orthologues of Sry, Sox,15 and Sox30, which appear to be specific to mammals, while Sox19, found in Fugu and zebrafish but absent in mammals, seems to be specific to fishes. Six mammalian Sox genes are represented by two copies each in Fugu, indicating a large-scale gene duplication in the fish lineage. These findings point to recent Sox gene loss, duplication and divergence occurring during the evolution of tetrapod and teleost lineages, and provide further evidence for large-scale segmental or a whole-genome duplication occurring early in the radiation of teleosts. (C) 2004 Elsevier B.V. All rights reserved.

Endoparasite communities of five fish species (Labridae : Cheilininae) from Lizard Island: how important is the ecology and phylogeny of the hosts?

The parasite community of animals is generally influenced by host physiology, ecology, and phylogeny. Therefore, sympatric and phylogenetically related hosts with similar ecologies should have similar parasite communities. To test this hypothesis we surveyed the endoparasites of 5 closely related cheilinine fishes (Labridae) from the Great Barrier Reef. They were Cheilinus chlorounts, C. trilobatus, C. fasciatils, Epibulus insidiator and OxYcheilinus diagrainnia. VVe examined the relationship between parasitological variables (richness, abundance and diversity) and host characteristics (bodv weight, diet and phuylogeny). The 5 fishes had 31 parasite species with 9-18 parasite species per fish species. Cestode larvae (mostly Tetraphyllidea) were the most abundant and prevalent parasites followed by nematodes and digeneans. Parasites, body size and diet of hosts differed between fish species. In general, body weight, diet and host phylogeny each explained some of the variation in richness and composition of parasites among the fishes. The 2 most closely related species, Cheilinus chlorourus and C. trilobatus, had broadly similar parasites but the Other fish species differed significantly in all variables. However, there was no all -encompassing pattern. This may, be because different lineages of parasites may react differently to ecological variables. We also argue that adult parasites may respond principally to host diet. In contrast, larval parasite composition may respond both to host diet and predator-prey interactions because this is the path by which many, parasites complete their life-cycles. Finally, variation in parasite phylogeny and parasite life-cycles among hosts likely increase the complexity of the system making it difficult to find all-encompassing patterns between host characteristics and parasites, particularly when all the species in rich parasite communities are considered.

Evaluation of the use and management of fish resources in the pachitea river basin, Peruvian Amazon

The purpose of this study was to analyze the interrelations between the needs of local people and their usage and management of natural fisheries. Between June and August 2001, 177 households in the basin were interviewed regarding their fishing customs. The results were analyzed with parametric and nonparametric statistics considering a cultural and a geographic comparison. Results confirm that indigenous households rely more on fisheries as a resource than colonists. Fishing takes place throughout the year but is more common in the dry season. Fishing is commonly practiced using hooks and cast nets. More destructive techniques such as dynamite and "barbasco" (poisonous plant) were also used. Indigenous people use a greater array of techniques and they fish at a greater diversity of sites. Respondents also reported that fishing yields have decreased recently. Some of the most common fish genera captured are Pimelodus and Leporinus.

Application of microarrays (phylochips) for analysis of community diversity by species identification

Abstract Molecular probe-based methods (Fluorescent in-situ hybridisation or FISH, Next Generation Sequencing or NGS) have proved successful in improving both the efficiency and accuracy of the identification of microorganisms, especially those that lack distinct morphological features, such as picoplankton. However, FISH methods have the major drawback that they can only identify one or just a few species at a time because of the reduced number of available fluorochromes that can be added to the probe. Although the length of sequence that can be obtained is continually improving, NGS still requires a great deal of handling time, its analysis time is still months and with a PCR step it will always be sensitive to natural enzyme inhibitors. With the use of DNA microarrays, it is possible to identify large numbers of taxa on a single-glass slide, the so-called phylochip, which can be semi-quantitative. This review details the major steps in probe design, design and production of a phylochip and validation of the array. Finally, major microarray studies in the phytoplankton community are reviewed to demonstrate the scope of the method.

Application of microarrays (phylochips) for analysis of community diversity by species identification

Abstract Molecular probe-based methods (Fluorescent in-situ hybridisation or FISH, Next Generation Sequencing or NGS) have proved successful in improving both the efficiency and accuracy of the identification of microorganisms, especially those that lack distinct morphological features, such as picoplankton. However, FISH methods have the major drawback that they can only identify one or just a few species at a time because of the reduced number of available fluorochromes that can be added to the probe. Although the length of sequence that can be obtained is continually improving, NGS still requires a great deal of handling time, its analysis time is still months and with a PCR step it will always be sensitive to natural enzyme inhibitors. With the use of DNA microarrays, it is possible to identify large numbers of taxa on a single-glass slide, the so-called phylochip, which can be semi-quantitative. This review details the major steps in probe design, design and production of a phylochip and validation of the array. Finally, major microarray studies in the phytoplankton community are reviewed to demonstrate the scope of the method.

DNA from historical and trophy samples provides insights into white shark population origins and genetic diversity

Characterizing genetic variation by retrospective genotyping of trophy or historical artifacts from endangered species is an important conservation tool. Loss of genetic diversity in top predators such as the white shark Carcharodon carcharias remains an issue, exacerbated in this species by declining, sometimes isolated philopatric populations. We successfully sequenced mitochondrial DNA (mtDNA) D-loop from osteodentine of contemporary South African white shark teeth (from 3 jaws), and from 34 to 129 yr old dried cartilage and skin samples from 1 Pacific Ocean and 5 Mediterranean sharks. Osteodentine-derived sequences from South African fish matched those derived from an individual’s finclips, but were generally of poorer quality than those from skin and cartilage of historical samples. Three haplotypes were identified from historical Mediterranean samples (n = 5); 2 individuals had unique sequences and 3 shared the contemporary Mediterranean haplotype. Placement of previously undescribed mtDNA haplotypes from historical material within both the Mediterranean and Pacific clades fits with the accepted intra-specific phylogeny derived from contemporary material, verifying our approaches. The utility of our methodology is in its provision of additional genetic resources from osteodentine (for species lacking tooth pulp) and cartilage of rare and endangered species held in often uncurated, contemporary and historical dry collections. Such material can usefully supplement estimates of connectivity, population history, and stock viability. We confirm the depauperate haplotype diversity of historical Mediterranean sharks, consistent with founding by a small number of Pacific colonizers. The consequent lack of diversity suggests serious challenges for the maintenance of this top predator and the Mediterranean ecosystem.

DNA from historical and trophy samples provides insights into white shark population origins and genetic diversity

Characterizing genetic variation by retrospective genotyping of trophy or historical artifacts from endangered species is an important conservation tool. Loss of genetic diversity in top predators such as the white shark Carcharodon carcharias remains an issue, exacerbated in this species by declining, sometimes isolated philopatric populations. We successfully sequenced mitochondrial DNA (mtDNA) D-loop from osteodentine of contemporary South African white shark teeth (from 3 jaws), and from 34 to 129 yr old dried cartilage and skin samples from 1 Pacific Ocean and 5 Mediterranean sharks. Osteodentine-derived sequences from South African fish matched those derived from an individual’s finclips, but were generally of poorer quality than those from skin and cartilage of historical samples. Three haplotypes were identified from historical Mediterranean samples (n = 5); 2 individuals had unique sequences and 3 shared the contemporary Mediterranean haplotype. Placement of previously undescribed mtDNA haplotypes from historical material within both the Mediterranean and Pacific clades fits with the accepted intra-specific phylogeny derived from contemporary material, verifying our approaches. The utility of our methodology is in its provision of additional genetic resources from osteodentine (for species lacking tooth pulp) and cartilage of rare and endangered species held in often uncurated, contemporary and historical dry collections. Such material can usefully supplement estimates of connectivity, population history, and stock viability. We confirm the depauperate haplotype diversity of historical Mediterranean sharks, consistent with founding by a small number of Pacific colonizers. The consequent lack of diversity suggests serious challenges for the maintenance of this top predator and the Mediterranean ecosystem.

Like a fish in water? Experiences of Muslim families in the British education system

This article summarises the explorations of two Initial Teacher Education (ITE) lecturers looking particularly at Muslim families’ sense of belonging as they encounter the British education system. The study draws on Garcia’s (2009, Alstad, 2013) view of monoglossic and heteroglossic settings, and on Cremin’s (2015) proposition of the super-diversity of inner-city experiences. Case studies of individual families are used to create a picture that reflects the complexity and shifting nature of cultures, languages and identities in present-day Britain. Video and tape interviews are used and data coded and analysed to identify prevailing themes. The families and schools taking part are active participants in the research process, giving informed and ongoing consent, and having control of the resulting findings. Parents’ and children’s perceptions and experience have evolved in complex ways across the generations, and in ways that challenge the stereotypes that dominate media portrayals. Early findings suggest that existing paradigms for discussing identity fail to capture the increasingly complex and super-diverse realities. In a world where xenophobia currently fuels rigid and stereotypical views of cultures in general and Muslim cultures in particular, it is important that the complexity of families’ identities and relationships to the existing systems is seen, heard and appreciated.

Studies on Mahshahr Creeks macrobenthos with emphasis on their importance in fish feeding

To study the macrobenthic community at Mahshahr creek four Creeks namely Bihad, Doragh, Ghazaleh and Ghanam were chosen. Sampling was conducted on bimonthly basis and carried out from August 1996 to June 1997, 216 sediment samples were collected from 12 stations using 0.1 m^2 Van Veen Grab, The stations were located at the mouth, middle and the end of each Creek. In situ measurements of temperature pH, DO and salinity were done using different sensors. The samples for the measurements of TOM, grain size were collected and analysed in vitro. The results indicate spatial and temporal heterogeneity in the structure of macro faunal assemblages of the creeks. A total of 12 macrofaunal groups were identified within the study area. Amphipods were the most dominant group (43%) followed by polychaetes (42%), copepods (3.5%), tanaids (3.1%) and other groups (8.4%). The range for the numerical abundance of macrobenthos was between 12583 to 3648 individual per m2 and the variation was done to different bottom texture the variable environment conditions governing the different parts of each creek as well as within creeks. Application of diversity indices (Shannon H and Simpson indices) on the dominant macrobenthic assemblages (crustaceans & polychaetes) was varied between 1 to 2.5 being higher in Bihad and Ghanarn and much reduced Shannon H index or a higher Simpson in Ghazaleh. Probably brought about activities in this creek. Gut content analysis of four species of fish showed that the main food items consist of Crab, Shrimps and other crustacean species, The secondary production of macrobenthic fauna and hence a fish production were assessed. To do this first the production of most dominant species Apseudes sp. was computed through Cohort analysis. The total macrobenthic production was estimated and from this fish production was computed. The macrobenthic and fish secondary productions were 24300 tons/year) and 24300 (tons/year) respectively. These values were lower than those with similar areas in the Indian Ocean.