New genomic resources for three exploited Mediterranean fishes

Extensive fishing has led to fish stock declines throughout the last decades. While clear stock identification is required for designing management schemes, stock delineation is problematic due to generally low levels of genetic structure in marine species. The development of genomic resources can help to solve this issue. Here, we present the first mitochondrial and nuclear draft genome assemblies of three economically important Mediterranean fishes, the white seabream, the striped red mullet, and the comber. The assemblies are between 613 and 785 Mbp long and contain between 27,222 and 32,375 predicted genes. They were used as references to map Restriction-site Associated DNA markers, which were developed with a single-digest approach. This approach provided between 15,710 and 21,101 Single Nucleotide Polymorphism markers per species. These genomic resources will allow uncovering subtle genetic structure, identifying stocks, assigning catches to populations and assessing connectivity. Furthermore, the annotated genomes will help to characterize adaptive divergence.     

Intra- and interspecific changes in retinal morphology among mesopelagic and demersal teleosts from the slope waters of New Zealand

Synopsis Retinae from mesopelagic teleosts with adult ranges in the shallow, mid and deep mesopelagic zones, respectively, were examined by light microscopy. Retinal characteristics were described, and photoreceptor densities, outer segment dimensions, and convergence ratios measured from transverse sections. Juveniles of all species had lower photoreceptor densities, outer segment lengths and convergence ratios than adults. In species with multiple banks of photoreceptors, additional banks were added as the retina increased in size. A positive correlation was found between the degree of retinal specialisation for vision in dim light, and the depth of occurrence. The retina of each specimen was given a rank based on log unit changes in photoreceptor density and convergence ratio, the length of photoreceptor outer segments and the presence or absence of multiple banks of photoreceptors. Higher ranks (indicating greater retinal specialisation) were found among species occurring at greater depths. Among species showing a change in depth preference with growth, there was a corresponding increase in retinal rank. It is suggested that the proposed system of ranks has application in predicting the depth of occurrence of a species with a given pattern of retinal morphology.     

New records of deep-sea fishes from the waters around the Falkland Islands

The manefish Caristius groenlandicus , the spiny eel Notacanthus sexspinis , the cutthroat eel Diastobranchus capensis and the Giant Grenadier Albatrossia pectoralis are new records for the waters of the Falkland Islands, and the latter is a new record in the Atlantic Ocean.     

Viviparity and the reproductive ecology of clinid fishes (Clinidae) from temperate Australian waters

Synopsis Viviparity is reported in twelve species of the family Clinidae in Tasmanian waters, and superfoetation (the simultaneous development of multiple batches of eggs and/or embryos) in nine of the twelve (all in the subfamily Clinini). The reproductive anatomy and life history features are documented in two superfoetate, shallow-water species,Heteroclinus perspicillatus andHeteroclinus sp. nov. (Scott's Weedfish). Gestation of embryos is intrafollicular and their mode of nutrition shifts from lecithotrophy during early development to trophodermal matrotrophy and, eventually, intestinal nutrient transfer. The sizes of the newly born larvae differ between species, but in all cases maternal investment in individual offspring (as measured by the proportionate increase in embryo dry weight)—20125%, 5744% and 3140% forH. perspicillatus, Scott's Weedfish andH. heptaeolus, respectively — is among the highest recorded for teleosts. Relative fecundity, however, is comparable to those of temperate, demersal spawning blennioids, and this suggests that high levels of maternal investment and relatively advanced stages of larval development at parturition for the sub-family as a whole do not involve a cost in individual fecundity. Parturition, which occurs over several months in spring and summer, is asynchronous. After parturition, the larva spend from 3 to 7 weeks in the plankton, primarily in in-shore waters. Post-settlement growth is rapid and most of the reproductive populations consist of fishes in the 1 + year-class.     

Notes on the diet of seven grenadier fishes (Macrouridae) from the lower continental slope of Chatham Rise, New Zealand

Diets of 8 rarely sampled species of grenadiers were examined from the lower continental slope (1178 to 1837 m) on Chatham Rise, New Zealand and includes the first known records of the diet of Bathygadus cottoides, Coryphaenoides mcmillani, C. murrayi, and Idiolophorhynchus andriashevi. Most species fed benthopelagically on small crustaceans, e.g., calanoid copepods, amphipods and mysids and others.     

Genome size evolution in New Zealand triplefin fishes

The genome sizes of 18 species of New Zealand triplefin fishes (family Tripterygiidae) were determined by flow cytometry of erythrocytes. The evolutionary relationships of these species were examined with a molecular phylogeny derived from DNA sequence data based on 1771 base pairs from fragments of three mitochondrial loci (12S and 16S ribosomal RNA, and the control region) and one nuclear locus (ETS2). Haploid genome sizes ranged from .85 pg (1C) to 1.28 pg with a mean of 1.15 +/- .01pg. Genome size appeared to be highly plastic, with up to 20% variation occurring within genera and a 50% difference in size between the smallest and the largest genome. No evidence was found to indicate polyploidy as a mechanism for speciation in New Zealand triplefins. Factors suggested to influence genome sizes of other organisms, such as morphological complexity, neoteny, and longevity, do not appear to be associated with shifts in the genome sizes of New Zealand triplefins.     

Notes on the reproductive biology of brachiopods from southern New Zealand

Abstract

The gonads of Notosaria nigricans, Terebratella inconspicua, T. ronguinea, Liothyrella neozelanica. and Neothyris ienticuiaris from southern New Zealand are described and their breeding state is determined. Attempts to induce spawning were not successful even with individuals that appdatred ripe. Sinlce normal fertilisation did not take place even with stripped gametes, it is concluded that either the brachiopods examined were not fully ripe or some indeterminate factor was inhibiting normal development of the zygotes.     

Records of fishes from the West Norfolk Ridge,north-west of New Zealand

Abstract

A total of 89 species of elasmobranch and teleost fish was recorded from the West Norfolk Ridge in 1986. Between 50 and 60 of these have not previously been reported from the area. Fish species were caught in bottom trawls at depths between 100 m and 1100 m, principally on the Wanganella Bank. Depth distribution is discussed. Species composition is very similar to that of northern New Zealand.     

Seasonal habitat use of three predatory fishes in a freshwater ecosystem

Hydrobiologia - To understand the spatiotemporal overlap in the habitat use of sympatric predators, we studied longitudinal activity and reservoir section and depth use of pike (Esox lucius),...     

Comparative genetic stock structure in three species of commercially exploited Indo-Malay Carangidae (Teleosteii,Perciformes)

We examine genetic structuring in three commercially important species of the teleost family Carangidae from Malaysian waters: yellowtail scad Atule mate, bigeye scad Selar crumenophthalmus and yellowstripe scad Selaroides leptolepis, from the Indo-Malay Archipelago. In view of their distribution across contrasting habitats, we tested the hypothesis that pelagic species display less genetic divergence compared with demersal species, due to their potential to undertake long-distance migrations in oceanic waters. To evaluate population genetic structure, we sequenced two mitochondrial (mt)DNA [650 bp of cytochrome oxidase I (coI), 450 bp of control region (CR)] and one nuclear gene (910 bp of rag1) in each species. One hundred and eighty samples from four geographical regions within the Indo-Malay Archipelago including a population of yellowtail from Kuwait were examined. Findings revealed that the extent of genetic structuring among populations in the semi-pelagic and pelagic, yellowtail and bigeye were lower than demersal yellowstripe, consistent with the hypothesis that pelagic species display less genetic divergence compared with demersal species. The yellowtail phylogeny identified three distinct clades with bootstrap values of 86%–99% in mtDNA and 63%–67% in rag1. However, in bigeye, three clades were also observed from mtDNA data while only one clade was identified in rag1 dataset. In yellowstripe, the mtDNA tree was split into three closely related clades and two clades in rag1 tree with bootstraps value of 73%–99% and 56% respectively. However, no geographic structure appears in both mtDNA and rag1 datasets. Hierarchical molecular variance analysis (AMOVA), pair wise F_ST comparisons and the nearest-neighbour statistic (S_nn) showed significant genetic differences among Kuwait and Indo-Malay yellowtail. Within the Indo-Malay Archipelago itself, two distinct mitochondrial lineages were detected in yellowtail suggesting potential cryptic species. Findings suggests varying degrees of genetic structuring, key information relevant to management of exploited stocks, though more rapidly evolving genetic markers should be used in future to better delimit the nature and dynamics of putative stock boundaries.     

Seasonal variation in assemblages of mobile epifauna inhabiting three subtidal brown seaweeds in northeastern New Zealand

Seasonal variation in densities of mobile epifauna associated with three species of subtidal brown seaweeds (Phaeophyta) was investigated over 2–3 years in northeastern New Zealand. There was strong seasonal variation in the total number of individuals per plant wet weight for epifauna inhabiting two fucalean seaweeds of the genus Carpophyllum, with epifaunal densities roughly tracking solar irradiance. In contrast, epifaunal densities on the laminarian Ecklonia radiata peaked during autumn/winter in the first two years of sampling, and during spring in the third, showing no predictable seasonal pattern of abundance. Few individual epifaunal taxa showed clear seasonal abundance patterns, even on the Carpophyllum spp. The composition of the epifaunal assemblage on each seaweed species was fairly constant over time.     

Shrimps remove ectoparasites from fishes in temperate waters

We have found that two very common species of North Atlantic shallow water shrimp, Palaemon adspersus and Palaemon elegans, remove and feed on ectoparasites on plaice (Pleuronectes platessa L.). The relationship could be mutualistic, as we did not observe any attempts by the fishes to feed on the shrimps. The ectoparasites removed included monogenean worms (Gyrodactylus sp.) and sea lice (Lepeophtheirus pectoralis). An experiment showed that there were 65% more Gyrodactylus parasites on the fishes that had been apart from compared with those that had been together with shrimps for 48h. Shrimps on coral reefs are known for cleaning fishes, but that shrimps in temperate waters show parasite-cleaning behaviour is, to our knowledge, a new observation.     

Diet changes in vertical distributions of larval fishes in unstratified coastal waters off southeastern Australia

Larval fishes were sampled at four depth strata during the dayand night at two locations in unstratified (winter) inner continentalshelf waters off Sydney, Australia, in May and June 1993. Assemblagesat both locations and in both sampling periods were stronglydepth stratified during the day; however, this structure weakenedat night with most taxa being found throughout the entire watercolumn. Two daytime patterns of larval fish vertical distribution(surface and deep dwellers) were evident, and taxon-specificdaytime vertical distributions were strong and not dependenton thermal stratification of the water column. Most larvae caughtwere preflexion and there was little evidence of ontogeneticdifferences in vertical distributions. For most taxa, the patternsof diel change in vertical distribution were similar at bothlocations and in both sampling periods.     

The reproductive biology of the New Zealand flora

New Zealand's long isolation from other elements of Gondwanaland, oceanic climate, the unusual combination of ancient Gondwanic, tropical and more recently arrived elements in its flora, and its relatively depauperate pollinator and disperser fauna have set the stage for the evolution of a subtle, complex and distinctive reproductive biology. This contrasts markedly with the neighbouring continent of Australia where the fauna is diverse and the flowers vivid. Recent advances in understanding New Zealand's floral biology include evidence that the ancestor to the anthophytes was cosexual, with insect pollinators receiving stigmatic nectar rewards; the discovery of ground-level bat pollination in an obligate root parasite; the finding that the greater resource sensitivity of fruit set in males than in females may account for sex ratio variation in gynodioecious species; and, evidence for much more pronounced mast seeding at higher altitudes even in the absence of mammalian seed predators.     

Assessing multiple paternity in three commercially exploited shark species: Mustelus mustelus,Carcharhinus obscurus and Sphyrna lewini

In this study, multiple paternity (MP) was investigated in three commercially important shark species, common smoothhound Mustelus mustelus, dusky shark Carcharhinus obscurus and scalloped hammerhead Sphyrna lewini occurring in southern Africa. Reduced marker panels of between five and six microsatellite loci were constructed for each species and used to genotype and assess the presence of MP in a total of 60 M. mustelus individuals from six litters, 90 C. obscurus individuals from 14 litters and 54 S. lewini individuals from 13 litters. Analysis in GERUD and COLONY revealed the presence of MP in all three species. Multiple paternities were observed in 67, 35 and 46% of the litters of M. mustelus, C. obscurus and S. lewini, with corresponding average sire size of 1·6, 1·4 and 2·0, respectively. The variation in the rate of MP among the three species is in accordance with previous studies whilst the comparatively high frequency of MP observed for M. mustelus, matches what has previously been reported for shark species demonstrating aggregation behaviour.     

Effects of temperature on the food processing of three species of seaweed-eating fishes from European coastal waters

Food consumption, gut transit times and assimilation efficiencies of the temperate fishes Lipophrys pholis and Parablennius sanguinolentus (Blenniidae) and Gobius cobitis (Gobiidae. when fed the green alga Ulva lactuca were determined at four temperatures in the laboratory. Food consumption increased and gut transit times decreased with increase in temperature in all three species. Assimilation efficiencies for algal carbon and nitrogen did not vary with temperature in G. cobitis . Carbon but not nitrogen assimilation efficiency varied with temperature in P. sanguinolentus , and both carbon and nitrogen assimilation efficiencies changed broadly with temperature in L. pholis , the most omnivorous of the three fishes. Assimilation efficiencies of all three species were generally within the previously reported ranges for herbivorous marine fishes. These species are thus clearly capable of extracting energy from algal food sources.     

The impact of trout on galaxiid fishes in New Zealand

Compared with the effect of invaders on the native terrestrial fauna of New Zealand, interactions between native fishes and introduced trout (sports fish in the genera Salmo, Oncorhynchus and Salvelinus) are less well known and there have been fewer efforts to remedy their effects. Trout have caused widespread reductions in the distribution and abundance of native galaxiid fishes, a family dominated by threatened species. The effects have been most severe on non-diadromous species (those lacking a marine migratory stage), which are commonly eliminated from streams by trout. Galaxiid populations in lakes, and those with migratory ?whitebait? stages, have also been affected, but the extent of the impacts are less understood. The mechanisms controlling negative interactions between trout and native fish, and how the environment modifies those interactions, will be important for future management. Experiments and field comparisons indicate size-specific predation by trout is the main driver of negative interactions. Large trout (>150 mm long) do the greatest damage and small galaxiids (those with adult sizes <150 mm long) are the most at risk. The fry stage of non-diadromous galaxiids is particularly vulnerable. Despite galaxiid fry production in some trout-invaded reaches, often no fry survive making them population ?sinks? that must be sustained by adult dispersal. Trout are also associated with changes in galaxiid behaviour and alterations to stream benthic communities. However, effects on galaxiid growth and fecundity have been little studied. Recent work also indicates that habitat conditions, especially floods, low flows and natural acidity, can mediate trout?galaxiid interactions. We argue that managers should be more proactive in their response to the plight of galaxiids, and we identify avenues of research that will benefit native fish conservation activities in the future.     

First record of a notacanth leptocephalus; a benthopelagic capture in the slope waters off Ireland

A metamorphosing notacanth leptocephalus is reported from the Porcupine Sea-Bight, southwest of Ireland. It is described and compared with juvenile Notacanthus chemnitzi and N. bonapartei from the same area. The adult diagnostic features evident are shown to conform with N. chmnitzi. The posterior location of the anus in the leptocephalus relative to the post-metamorphic condition is noted. The ecological significance of the benthopelagic occurrence of this exceptional larva in slope waters is considered.