Population structure of the common sole (<Emphasis Type="Italic">Solea solea</Emphasis>) in the Northeastern Atlantic and the Mediterranean Sea: revisiting the divide with EPIC markers

Spatial and temporal population genetic structures of the common sole, Solea solea, were studied in Northeastern Atlantic and Mediterranean Sea populations, using three polymorphic exon-primed intron-crossing (EPIC) markers. Results demonstrated significant multilocus differentiation among Eastern Mediterranean and a group composed by Western Mediterranean and Atlantic populations (θ = 0.150, P < 0.001), but also suggested unrecorded genetic differentiation of the Adriatic Sea population. No pattern of isolation-by-distance was recorded across the range covered by sampling, from the Kattegat to the Aegean Sea. Conversely to genetically structured Mediterranean populations, Atlantic populations ranging from Denmark to Portugal could be considered as representative of the same panmictic unit (θ = 0.009, not significant). Results further demonstrated stability of multilocus genetic structure among temporarily replicated cohort samples [0+, 1+, subadults] from several coastal and estuarine locations from Bay of Biscay, excepted for the amylase locus Am2B3-2 at one location (Pertuis d’Antioche). Despite coherence of such observed patterns of multilocus differentiation with previous allozymic surveys in sole, and with patterns generally obtained for other marine fish species, single-locus results from EPICs indicated divergent coalescence schemes supporting a complex response to ecology and history of sole’s populations. Results stress the use of nuclear genes such as EPIC markers to investigate population structure, but also historical, demographic, and possibly selective processes in marine fishes.     

Population structure and life history of orange roughy (Hoplostethus atlanticus) in the SW Pacific: inferences from otolith chemistry

We examined site differences in the elemental composition of the primordium and ontogenetic variability of Sr in otoliths of fish from Australia and New Zealand and, as an out-group, the North Atlantic. Differences among sites in primordium composition are slight, but significant for all five elements assayed (Sr, Pb, Cu, Zn and Hg), but principally reflect differences between the North Atlantic and SW Pacific specimens, do not replicate for independent samples in the SW Pacific and constitute a poor “natural tag” in roughy, with <25% of fish successfully assigned to source location. However, mean Sr weight-fractions at the primordium showed similar latitudinal variation across sites in Australia, New Zealand and the Tasman Sea, indicating both spatially structured populations and a common structuring process across the region. Comparisons of ontogenetic variability of Sr in otoliths from juveniles and young adults within and between sites in the SW Pacific strongly support the hypothesis that variability in this element is site-specific and environmentally sensitive, although the environmental factors involved are not obvious. The otolith analysis confirms previous suggestions that juvenile and adult Hoplostethus atlanticus are relatively sedentary, but also indicates that the population sub-structuring by age within sites is more complex and there are likely to be more spawning areas in Australian waters than previously thought. More broadly, although single point analysis of otolith composition at the primordium resolves a population structure in roughy, alone it is not precise enough to test hypotheses about the processes causing this structure. Ontogenetic variability in Sr provides better resolution of spatial structure, even in a relatively homogenous marine environment like the deep ocean, and also provides insight into behavioural and ecological factors. Ontogenetic analyses of Sr in otoliths are expensive to obtain, require more effort in specimen preparation than single point analyses, and are difficult to compare statistically, but the increased information they yield warrants their broader consideration in marine species.     

Genetic structure and allozyme variation of sea bass (Dicentrarchus labrax and D. punctatus) in the Mediterranean Sea

This paper reports data on 28 allozyme loci in wild and artificially reared sea bass (Dicentrarchus labrax) samples, originating from either coastal lagoon or marine sites in the Mediterranean Sea. F _ST analysis (θ estimator) indicated strong genetic structuring among populations; around 34% of the overall genetic variation is due to interpopulation variation. Pairwise θ estimates showed that, on average, the degree of genetic structuring was much higher between marine populations than between samples from lagoons. Six polymorphic loci showed differences in allele frequencies between marine and lagoon samples. Multivariate analyses of individual allozymic profiles and of allele frequencies suggested that different arrays of genotypes prevail in lagoons compared to marine samples, particularly at those loci that, on the basis of previous acclimation experiments, had been implicated in adaptation to freshwater. On the other hand, variation at “neutral” allozyme loci reflects to a greater extent the geographic location of populations. Allozyme differentiation was also studied in a D. labrax population from the Portuguese coast. Average genetic distance between this population and the Mediterranean populations was quite high (Nei's D = 0.236) and calls into question the taxonomic status of the Portuguese population. Finally, genetic relationships between D. labrax and D. punctatus were evaluated. Average Nei's D was 0.648, revealing high genetic differentiation between the two species, even for two sympatric populations of these species in Egypt; thus gene flow was not indicated between species. Received: 24 October 1996 / Accepted: 27 November 1996     

In situ experiment of ontogenetic variability in the otolith chemistry of Stegastes partitus

Otolith chemistry can be used to assess pelagic larval fish connectivity by comparing spatially variable otolith edge chemistry (corresponding to the site of collection) to otolith core chemistry (corresponding to the site of hatching). However, because the otolith’s edge and core represent different life stages, the deposition of elements may differ, thus complicating direct comparisons of edge and core chemistry to investigate connectivity. Here we present data from a field experiment in which otoliths from embryos (3 days post-fertilization) and juveniles of Stegastes partitus were collected at the same site and time, and chemically analyzed to assess whether elemental concentrations of otoliths vary ontogenetically. Separate multivariate analyses, each investigating the spatial/temporal variability in the chemistry of either embryo otoliths or the edges of juvenile otoliths, revealed significant differences, suggesting an environmental influence to the chemical signals of otoliths. A nested multivariate analysis assessing whether otolith chemistry varied with life history stage (i.e., ontogenetic variability) indicated that elemental concentrations of embryo otoliths were significantly greater than that of juvenile otolith edges. Specifically, embryo elemental concentrations of Mn, Zn, Sn, Ba, Ce, and Pb were between 2 and 163 times greater than those of the corresponding juvenile otoliths, and thus the environment was not the primary determinant of embryo otolith chemistry. Consequently, caution is warranted when interpreting environmental patterns of otolith cores, particularly when using them as a proxy for natal signatures.     

Elevated manganese concentrations at the cores of clupeid otoliths: possible environmental,physiological, or structural origins

Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) was used to investigate the distribution of manganese (Mn) in Atlantic herring (Clupea harengus L.) otoliths. An unusual pattern of Mn concentration, which has not previously been reported in fish otoliths, was observed. Time-resolved plots (time roughly equivalent to ablation depth) of the Mn signal recorded in the ICP-MS detector during ablation of otoliths contained a distinct peak, suggesting that elevated Mn concentrations were specific to certain regions. Ablation inside and outside of the otolith core revealed that the region of high Mn concentration coincided with the ablation of the core. It was initially suggested that Mn from the gravel substrate on which herring eggs are incubated is incorporated into the otolith core, producing elevated Mn concentrations in this region. It was hypothesised that otoliths from fish whose eggs are not incubated in gravel will not contain high Mn concentrations at the core. To test this, otoliths of sprat (Sprattus sprattus), which have a pelagic embryological stage, and from reared herring, which were incubated on glass plates, were analysed using LA-ICP-MS. Peaks in the Mn signal were observed during the ablation of cores from some sprat and reared herring otoliths, indicating that incubation on a gravel substrate is not necessary for the accumulation of Mn at the otolith core and that otoliths from both pelagic and demersally spawning fish species can contain elevated Mn concentrations. The results suggest that Mn concentrations at the otolith core do not reflect the external environment of the developing embryo. Two other hypotheses are considered. A dramatic increase in Mn concentrations in the egg, associated with embryological development, may produce elevated Mn levels at the otolith core. Alternatively, the high levels of Mn observed at the otolith core may reflect spatial variation in the crystal structure of the calcium carbonate portion of the otolith. The possible influence of physiological or structural factors on the chemical composition of the otolith core may confound the environmental signal in this region of the otolith. This has important implications for the interpretation of otolith chemistry data.Communicated by J.P. Thorpe, Port Erin     

Exploring the potential of otolith microchemistry to enhance diet analysis in pinnipeds

Increasing the scope and accuracy of information about pinniped diets obtainable from non-invasive techniques is increasingly important, particularly in cases where pinniped species are threatened or endangered. This study is the first to explore the potential for using elemental analysis of the otoliths found in scat to enhance the information available for diet analyses. We investigated the effects of pinniped digestion on otolith microchemistry using laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS). We compared the elements contained in the edges (adult stage) and cores (larval/juvenile stage) of otoliths from Pacific herring (Clupea pallasii), Atka mackerel (Pleurogrammus monopterygius), and Walleye pollock (Theragra chalcogramma) recovered from the scat of captive Steller sea lions (Eumetopias jubatus) to elements in a sample of pristine (undigested) otoliths. We found that digestion had a significant effect on four of the six sampled combinations of species and otolith region (herring edges and cores, mackerel edges, and pollock cores), and that Rb most frequently showed significant differences in concentration after digestion. We could significantly discriminate among species of both pristine and digested otoliths using either otolith edges or cores with the elements Ba, Rb, Sr, Y, and Mg. When compared to previously identified digested otoliths, unknown samples of the three species of digested otoliths could be discriminated with 55–100% accuracy depending on species and otolith region. When compared to a library of previously identified pristine and digested otoliths, unknown samples of digested otoliths could be discriminated to species with 65–88% accuracy. When the group of unknown digested otoliths was compared to known pristine otoliths, discrimination ranged from 45 to 65%. These results indicate that elemental analysis could be used to supplement visual identification of otoliths from scat. However, further research is required to determine whether elemental analysis of digested otoliths could be useful for prey fish population studies.     

Climatic effects on the growth of a temperate reef fish from the Southern Hemisphere: a biochronological approach

Increments in the hard parts of marine organisms (otoliths, skeletons, shells) can provide long-term chronologies of growth analogous to tree rings. For the first time in the Southern Hemisphere, we use a dendrochronological (tree-ring analysis) approach to develop a multidecadal chronology of growth for a temperate reef fish, Girella tricuspidata, from the coast of northern New Zealand. Growth patterns in the otoliths of this species were strongly synchronous among individual fish over a period spanning 27 years (1980–2006). We then compared our otolith chronology to climatic records and found strong positive correlations of growth with sea surface temperature, and weak negative correlations with the multivariate El Nino Southern Oscillation (ENSO) index. Strongest correlations were found between summer sea surface temperature and otolith growth. This relationship was consistent across all years and explained 44 % of the variation (y = −2.0 + 0.1785 × temperature, r ² = 0.4367, P = 0.0002) in the G. tricuspidata growth chronology. Our study illustrates how otolith chronologies provide remarkable records of annual growth patterns over decadal time scales that will be useful for forecasting the likely effects of climate change on marine ecosystems.     

Existence of two widespread semi-isolated genetic entities within Mediterranean anchovies

We investigated genetic transitions in European anchovies (Engraulidae) by analysing one mitochondrial and six nuclear microsatellite loci in samples from 28 geographical locations, primarily in the Western Mediterranean with external samples from the Black Sea in the East, and the Gulf of Biscay in the West. Four samples were collected from lagoons or shallow waters in France, Morocco and Tunisia. Two strongly differentiated loci and nucleo-cytoplasmic disequilibrium allowed us unambiguously to confirm the existence of a coastal genetic entity that is distinct from the more offshore marine populations. By contrast, four microsatellites were undifferentiated within the entire set of samples, testifying to a variable permeability of the two interacting genomes. Our findings strengthen and extend previous reports of the existence of a coastal anchovy entity that is widespread in Mediterranean lagoons.     

Isolation of Atlantic cod (<Emphasis Type="Italic">Gadus morhua</Emphasis>) nursery areas

This study examines the degree of isolation among 0-group Atlantic cod in a region where a number of resident adult congregations have been found. The location of key nursery areas in Scottish coastal waters was identified from trawl surveys of settled 0-group cod around the Scottish coast. Segregation among four of these key areas; within the Clyde, Shetland Isles, Moray Firth and Buchan was investigated using otolith elemental composition. Isotope concentrations in the otoliths of cod were analysed by solution-based inductively coupled plasma mass spectrometry of the whole otolith. Discriminant analyses showed a clear separation between nursery areas based on the concentrations of three elements (manganese, barium and magnesium). The concentration of these elements was not affected by the age or size of individuals. Classification accuracy exceeded 90% for all four sites. Evidence of temporal persistence in the relative spatial differences in elemental concentrations between two sites for 2 year-classes was found. The results suggest limited exchange between sites during some period of the early life history. The significance of this limited exchange is discussed in relation to recent evidence for adult fidelity and the utility of closed areas for protecting nursery grounds.     

Effects of fish feeding by snorkellers on the density and size distribution of fishes in a Mediterranean marine protected area

Although there is a great deal of evidence to show that supplementary feeding by humans in terrestrial environments causes pronounced changes in the distribution and behaviour of wild animals, at present very little is known about the potential for such effects on marine fish. This study evaluated the consequences of feeding by snorkellers on fish assemblages in the no-take area of the Ustica Island marine protected area (MPA; western Mediterranean) by (1) determining if reef fish assemblage structure is affected in space and time by tourists feeding the fish; (2) assessing the effects of feeding on the abundance of the most common fish species; and (3) assessing the effects of feeding on the size structure of the two most numerically dominant ones. In particular, we hypothesised that both the abundance and the size structure of some fish species would increase at the study site following supplementary feeding, since the additional food provided by humans would make the site more appealing to them. Fish feeding influenced the fish assemblages within the Ustica MPA, and significant spatio-temporal changes occurred. While fish feeding appeared to have no effect on the ornate wrasse Thalassoma pavo, there was a noticeable increase in the number of Oblada melanura and Epinephelus marginatus in the impacted location after feeding. It is very likely that aggregations of fishes that evolve as a result of fish feeding by the public may have negative effects on local populations of fishes and invertebrates that make up their prey. Recreational use of coastal areas and MPAs is increasing elsewhere, making fish feeding a generalised human activity. Accurate information about its effect on the fish assemblage is essential to make responsible management decisions.Communicated by R. Cattaneo-Vietti, Genova     

鱼类耳石元素指纹研究进展

耳石是沉积在真骨鱼类内耳中的一种矿物结构,其主要成分是碳酸盐.在鱼类的生活过程中,水环境中的化学元素经过代谢稳定地沉积在耳石上,由于生活水域化学环境的差异,鱼类耳石的元素组成或含量存在一定的差异,而使耳石上的元素指纹成为一种天然标志,记录了鱼类所经历的生态环境及其变化.耳石元素指纹研究主要包括同位素成分分析、锶钙比率研究(Sr/Ca)以及一些痕量元素分析等,这些可以用于鱼类种群识别、生活史研究、生活环境重建,以及高龄鱼的年龄鉴定,在鱼类生态学和渔业资源学研究中具有广泛的应用前景.参57     

Spatial variation of otolith elemental signatures among juvenile gray snapper (<Emphasis Type="Italic">Lutjanus griseus</Emphasis>) inhabiting southern Florida waters

Juvenile gray snapper, Lutjanus griseus, are believed to use bays and estuaries in southern Florida as nurseries before moving out to the adjoining reef tract as adults. Using high-resolution sector field-inductively coupled plasma-mass spectrometry (SF-ICP-MS), the elemental chemistry of the otoliths of juveniles from five nursery regions was resolved by establishing elemental “signatures” for each region. In this study we simultaneously analyzed 32 elements including a suite of rare earth elements. A stepwise variable selection procedure retained a subset of eight elements that contributed substantially to separating otolith samples, including two rare earth elements; this is one of the first studies in which rare earth elements in otoliths have contributed to separation of fish stocks. The classification success rate in assigning fishes to the correct region of origin was 82%. Resolution of sites less than 10 km apart suggested high site fidelity in juvenile gray snapper and little mixing of water masses between sites. The juvenile nursery signatures will be used to determine the relative contribution of different nurseries to the adult population on an adjoining reef tract.     

Elemental composition of otolith growth marks in three geographically separated populations of European hake (Merluccius merluccius)

The composition of the opaque and translucent bands in the otoliths of European hake (Merluccius merluccius) from three different populations (Celtic Sea, Galicia shelf and Cretan Sea) was analysed with wavelength dispersive spectrometry (WDS) and differences in Ca, Sr and Na were compared. The translucent bands (annual marks and checks altogether) were significantly richer in Sr and Ca and significantly poorer in Na than opaque bands. Results support the idea of a more compact arrangement of crystals in translucent bands compared to opaque. Analyses did not help to discriminate between putative annual marks and checks. Clear differences in the range of Sr/Ca variation across the otolith as well as in the composition of the otolith core were observed among the three populations. As a result it was possible to discriminate the natal origin of each fish using the composition of the otolith core in Ca, Sr and Na. Nevertheless, the overall pattern across the otolith was similar among the three populations suggesting the existence of ontogenetic trends. Variation of Na/Ca ratios was largely uninformative. Based on these results, a conceptual model for hake is proposed which integrates the different sources of otolith Sr/Ca variation: ambient Sr/Ca, endogenous cues (ontogeny) and exogenous cues (environment).     

Atlantic-Mediterranean and within-Mediterranean molecular variation in <Emphasis Type="Italic">Coris julis</Emphasis> (L. 1758) (Teleostei,Labridae)

Sequence variation in the mitochondrial control region was studied in the Mediterranean rainbow wrasse (Coris julis), a species with pronounced pelagic larval phase inhabiting the Mediterranean Sea and the adjacent coastal eastern Atlantic Ocean. A total of 309 specimens from 19 sampling sites were analysed with the aim of elucidating patterns of molecular variation between the Atlantic and the Mediterranean as well as within the Mediterranean Sea. Phylogeographic analyses revealed a pronounced structuring into a Mediterranean and an Atlantic group. Samples from a site at the Moroccan Mediterranean coast in the Alboran Sea showed intermediate frequencies of “Mediterranean” and “Atlantic” haplotypes. We recognised a departure from molecular neutrality and a star-like genealogy for samples from the Mediterranean Sea, which we propose to have happened due to a recent demographic expansion. The results are discussed in the light of previous studies on molecular variation in fish species between the Atlantic and the Mediterranean and within the Mediterranean.     

Recruitment and ontogenetic habitat shifts of the yellow snapper (<Emphasis Type="Italic">Lutjanus argentiventris</Emphasis>) in the Gulf of California

We examined recruitment and ontogenetic habitat shifts of the yellow snapper Lutjanus argentiventris in the Gulf of California, by conducting surveys and collections in multiple mangrove sites and major marine coastal habitats from 1998 to 2007. Over 1,167 juvenile individuals were collected and 516 otoliths were aged to describe the temporal pattern of the settlement. L. argentiventris recruits in mangroves, where juveniles remain until they are approximately 100 mm in length or 300-days-old. Back-calculated settlement dates and underwater surveys indicated a major recruitment peak during September and October, around 8 days before and after the full moon. The majority of mangrove sites in the Gulf of California had a similar L. argentiventris average size at the beginning of the settlement season for the cohort of 2003; although there were significant differences in individual sizes at the end of the nursery stage. When sub-adults leave mangroves, they live in shallow rocky reefs and later become abundant in deeper rocky reefs. The density of migratory individuals (10–20 cm SL) decreased exponentially as the distance between a reef and a nearby mangrove site increased. This finding has important implications for local fishery regulations and coastal management plans.     

Variation in concentrations of trace elements in otoliths and eye lenses of a temperate reef fish, Parma microlepis, as a function of depth, spatial scale, and age

 Territorial Parma microlepis (Günther) (Pomacentridae) were collected at different depths, at three sites in each of four estuaries near Sydney, Australia. Element concentrations were measured by induc- tively-coupled–plasma mass spectrometry. Significant differences in concentrations of Mn and Ba were found in the otoliths of fish sampled in different depth strata, with concentrations generally greatest in fish found in water <4 m deep. Depth-related differences varied among estuaries (e.g. 0 to 1.2 μg Ba g⁻¹ otolith). In most estuaries there was a negative linear relationship between concentrations of Mn and Ba in otoliths and actual depth. Great variation was found within an estuary among sites separated by 0.5 to 3 km. In the eye lenses, concentrations of Rb differed according to depth of capture of fish. The age of fish (1+ to 34 yr) had no influence on the concentrations of elements in otoliths or lenses. Multivariate comparisons of elemental composition (= fingerprints) detected significant differences among depth strata. Fish collected from shallow water had the clearest multivariate classification according to depth. There was a close match between our shallow strata and the average depths reached by low-salinity/high-temperature estuarine plumes. The element composition of whole otoliths and lenses represents average concentrations experienced by the fish. The temporal resolution of differences in ambient conditions is likely to be coarse in the fish (i.e. months to years). Received: 9 April 1999 / Accepted: 29 February 2000     

Scales of variation in otolith elemental chemistry of juvenile staghorn sculpin (<Emphasis Type="Italic">Leptocottus armatus</Emphasis>) in three Pacific Northwest estuaries

Although distinct otolith elemental signatures are often observed in fish collected from different estuaries, significant differences are also observed among sites within estuaries. Variation at these smaller spatial scales is not well quantified and has the potential to lead to inappropriate interpretations of otolith elemental data. To quantify variation at multiple scales, the otolith elemental composition (Mg:Ca, Mn:Ca, Sr:Ca, Ba:Ca, and Pb:Ca) of juvenile staghorn sculpin (Leptocottus armatus Girard, 1854) collected from five sites within three estuaries, the Columbia River (two sites) and Coos Bay (one site), Oregon, and Humboldt Bay, California (two sites), was examined. Using laser ablation-inductively coupled plasma mass spectrometry, each otolith was sampled at three zones: (1) within the primordium, which represents the egg and early larval periods; (2) at the outer edge, which represents the juvenile period just prior to collection; and (3) midway between the primordial and edge samples, which represents the late larval and early juvenile period. There were significant differences in otolith metal-to-calcium ratios at all scales examined. Using multi-element otolith signatures, fish were classified to estuary and site within estuary with relatively high levels of accuracy (av = 70–90%). The largest differences in metal-to-calcium ratios were observed between sites within estuaries (<5 km apart) and the smallest differences were observed among otolith zones. Variation in otolith chemistry may be used to provide information on probable habitat use by estuarine fish but studies must be carefully designed. Electronic supplementary material  Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Genetic structure in lagoons: the effects of habitat discontinuity and low dispersal ability on populations of <Emphasis Type="Italic">Atherina boyeri</Emphasis>

Atherina boyeri is a common inhabitant of the Mediterranean brackish and coastal waters. Several recent studies proposed the recognition of three distinct forms/species (one lagoon/freshwater and two marine) within an A. boyeri complex. In this study, we used 10 newly available microsatellite loci to better define the genetic structure of the lagoon form. A total of 428 fishes from 11 lagoons along the Italian and Albanian coasts and three Italian lakes were analyzed. A pronounced genetic spatial structure was confirmed for all considered geographic scales (near, medium and broad). A restricted gene flow was detected, suggesting reduced population connectivity. The comparison of present data and previous studies, based on mtDNA and RAPD markers, allowed a preliminary identification of the roles of recent factors (gene flow, habitat discontinuity and water currents) and past events (e.g., Pleistocene glaciations) in shaping the pattern of genetic differentiation.     

Use of remote sensing for the characterization of the Mediterranean coastal environment—the case ofPosidonia oceanica

The beds ofPosidonia oceanica, a marine vascular plant species endemic to the Mediterranean, form a major Mediterranean marine ecosystem. These beds are well-developed along the sandy east coast of Corsica, where the continental shelf is wide and extends for ca. 100 km. The upper limit of this ecosystem has been mapped by means of a computer image processing technique using 1/20 000 colour photographs. One of the major problems for image processing in the marine environment is the impact of the water layer (of variable thickness and quality), which can result in variations of the spectral signature for a particular vegetation or bottom type. In an attempt to reduce the impact of this artefact, a processing technique that takes into account bathymetric factors has been tested. Cartographical data obtained for an area extending from Bastia to Solenzara are presented. In the vicinity of the mouths of coastal rivers, a systematic indentation of the upper limit of the seagrass beds has been revealed. On the basis of these results, local variations in the quality of the marine environment can be detected, in particular with regard to salinity, turbidity and/or the impact of sedimentation. The overall surface area of thePosidonia oceanica beds has also been calculated.