Accurate Classification of Juvenile Weakfish Cynoscion regalis to Estuarine Nursery Areas Based on Chemical Signatures in Otoliths

We investigated the ability of trace element and isotopic signatures in otoliths to record the nursery areas of juvenile (young-of-the-year) weakfish Cynoscion regalis from the east coast of the USA. Juvenile C. regalis were captured with otter trawls at multiple sites in Doboy Sound (Georgia), Pamlico Sound (North Carolina), Chesapeake Bay (Virginia), Delaware Bay (Delaware) and Peconic Bay (New York), from July to September 1996. One sagittal otolith from each specimen was assayed for Mg/Ca, Mn/Ca, Sr/Ca and Ba/Ca ratios using inductively coupled plasma mass spectrometry (ICP-MS), while delta 13 C and delta 18 O values from the other sagittal otolith in the pair were determined using isotope ratio mass spectrometry (IR-MS). A multivariate analysis of variance determined that there were significant differences in trace element signatures among locations. Bootstrapped 95% confidence ellipses on canonical variates indicated that all 5 locations were significantly isolated in discriminant space. On the basis of these differences, linear discriminant function analysis (LDFA) and artificial neural network (ANN) models were used to classify individual fish to their natal estuary with an overall error rate of 37% for LDFA and 29.6% for ANN. Addition of delta 13C and delta 18O values to the LDFA and ANN models derived from the trace element data resulted in overall error around 10%. We will, therefore, be able to use chemical signatures from the juvenile portion of adult C. regalis otoliths to accurately classify these fish to their natal estuary

Composition and temporal patterns of larval fish communities in Chesapeake and Delaware Bays, USA

Comparing larval fish assemblages in different estuaries provides insights about the coastal distribution of larval populations, larval transport, and adult spawning locations. We simultaneously compared the larval fish assemblages entering 2 Middle Atlantic Bight (MAB) estuaries(Delaware Bay and Chesapeake Bay, USA) through weekly sampling from 2007 to 2009. In total,43 taxa (32 families) and 36 taxa (24 families) were collected in Delaware and Chesapeake Bays,respectively. Mean taxonomic diversity, mean richness, and evenness were generally lower in Delaware Bay. Communities of both bays were dominated by Anchoaspp., Gobiosomaspp.,Micropogonias undulatus, and Brevoortia tyrannus; Paralichthys spp. was more abundant in Delaware Bay and Microgobius thalassinus was more abundant in Chesapeake Bay. Inter-annual variation in the larval fish communities was low at both sites, with a relatively consistent composition across years, but strong seasonal (intra-annual) variation in species composition occurred in both bays. Two groups were identified in Chesapeake Bay: a ‘winter’ group dominated by shelf-spawned species and a ‘summer’ group comprising obligate estuarine species and coastal species.In Delaware Bay, 4 groups were identified: a ‘summer’ group of mainly obligate estuarine fishes being replaced by a ‘fall’ group; ‘winter’ and ‘spring’ groups were dominated by shelf-spawned and obligate estuarine species, respectively. This study demonstrates that inexpensive and simultaneous sampling in different estuaries provides important insights into the variability in community structure of fish assemblages at large spatial scales

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Decline in growth rate of juvenile European plaice (Pleuronectes platessa) during summer at nursery beaches along the west coast of Scotland

This study concludes that declines in growth rates of young-of-the-year European plaice (Pleuronectes platessa) (YOY plaice) during summer vary spatially and between years and that these dynamics are not driven by temperature, body size, or competition. RNA-predicted growth rates of YOY plaice on the west coast of Scotland declined linearly between mid-July and mid-September, with faster declines at beaches and in years where growth rates were initially high. Absolute growth estimates rarely approached ad libitum laboratory rates, and relative declines in growth rates were unrelated to temperature or body size allometry, indicating that maximum growth was rare. However, the absence of inverse relationships between spatial or temporal growth variation and YOY plaice or brown shrimp (Crangon crangon) densities suggests that competition did not limit growth. There were no consistent trends in morphometric condition factor, biochemical composition, or energy content during summer, indicating that apparent growth declines did not result from energy storage and did not result in depletion of energy stores. Influences of extrinsic factors (such as prey conditions, physical disturbance, and predator densities) on the diet, mediated by behavioral decisions to optimize growth with other ecological constraints, require further investigation as causes of growth variation in YOY plaice

Spatial variation in growth rate of early juvenile European plaice Pleuronectes platessa

Patterns and causes of spatial variation in RNA-predicted growth rates in mid-August were examined in young-of-the-year European plaice Pleuronectes platessa (‘YOY plaice’) at 22 beaches along a 300 km stretch of coastline in west Scotland in 3 consecutive years. According to restricted maximum likelihood models, growth rates varied among beaches (25 km scale), but these spatial patterns were not consistent across years. We found no evidence for spatial variation in growth at the scale of subregions (50 km) or regions (100 km). Growth rate was positively correlated with total length, both within and among beaches and years. In general, YOY plaice in mid-August grew more slowly than estimated ad libitum laboratory rates. Average growth rates by beach and year were inversely related to intraspecific competitor densities, but not interspecific competitor densities (brown shrimp Crangon crangon) or 2 environmental productivity metrics (nearshore chlorophyll a concentration and lugworm Arenicola marina cast density). Physical beach characteristics also explained a significant source of spatial growth variation, with fish growing faster at beaches with larger tidal range and wave fetch. Therefore, the hypothesis of sub-maximum growth due to intraspecific competition (density-dependent growth) was supported, but additional, previously unexplored processes related to physical beach characteristics appear to have important influences on the spatial growth dynamics of YOY plaice

Growth of the estuarine fish Fundulus heteroclitus in response to diel-cycling hypoxia and acidification: interaction with temperature

Growth rate of Fundulus heteroclitus was examined at 25 and 30 °C in nine treatments of diel-cycling dissolved oxygen (DO) and pH. Extreme diel-cycling DO (1-11 mg O2 L-1) negatively impacted growth during 10 days at 30 °C, but not at 25 °C. Moderate DO cycles (3-9 mg O2 L-1) had no direct growth impact at either temperature. Fish did not appear to acclimate, during days 10-30, to the initial growth-limiting effects of extreme diel DO cycles at 30 °C. Diel-cycling DO interacts synergistically with temperature to impact growth. There was no evidence of an independent growth effect of either moderate pH cycles (7.2-7.8) or extreme pH cycles (6.8-8.1) at either temperature. Mean low pCO2 levels in extreme cycles were ~32 000 and ~47 000 µatm, at 25 and 30 °C, respectively. It is noteworthy that these high mean nightly pCO2 levels are more than an order of magnitude higher than the chronic mean oceanic pCO2 of ~1000 μatm projected by the year 2100.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Growth dynamics of European plaice Pleuronectes platessa L. in nursery areas: a review

Young-of-the-year European plaice Pleuronectes platessa L. (hereafter: ‘YOY plaice’) in shallow, sandy areas is a long- and intensively-studied species and an ideal model for understanding growth dynamics in fish nurseries. In order to provide an overview of and access point to this rich literature and to guide future research on juvenile fish growth dynamics, we review patterns of growth variation in YOY plaice following settlement and evaluate evidence for underlying causes, including maximum growth, temperature, prey conditions and competition. A decline in growth rate during late summer and autumn was the clearest and most widespread pattern, but was not clearly related to any of the potential causes previously considered. Interannual growth variation was substantial and despite evidence that intraspecific competition was responsible, other possible causes were also supported and others were only rarely assessed. Growth also varied considerably at a range of spatial scales (100s of m–100s of km). Causes of small-scale (< 10 km) and regional (> 200 km) growth variation remain poorly understood and while intermediate-scale growth variation has been related to prey conditions and intraspecific competition, the role of interspecific competition requires further investigation. Therefore, despite clear evidence for growth heterogeneity at numerous spatiotemporal scales, underlying causes remain elusive. We highlight some principal challenges to measuring and understanding the complex and scale-dependent causes of growth variation. To overcome these challenges, and therefore resolve important nursery processes for juvenile fish, we recommend more detailed and spatiotemporally explicit investigations of growth, metabolic processes and physiological energetics in situ; a focus on possible proximate and ultimate factors driving these dynamics; and development of new hypotheses to explain growth variation starting with general physical features that define nursery environments

Small-scale spatial and temporal heterogeneity in growth and condition of juvenile fish on sandy beaches

To characterize fine-grained heterogeneity in the functional role of sandy beaches as fish nurseries, we measured RNA concentration, DNA concentration and RNA-predicted growth rate in young-of-the-year European plaice Pleuronectes platessa L. (‘YOY plaice’) at beaches on the western side of the British Isles at small alongshore (100–500 m), temporal (days to weeks), depth (0.5–2 m below waterline) and inter-individual scales. We compared variations in these nucleic-acid-based metrics of condition and growth with a null metric (total length) considered to be less responsive to short-term changes in environmental conditions. All four metrics varied at small spatial and temporal scales, particularly RNA-based metrics of short-term condition and growth. A decline in condition and growth during summer was the most important source of temporal variation. Condition and growth also increased with depth below waterline. Alongshore variations within a beach were relatively small, but variance among stations on the same beach (500 m scale) was similar in magnitude to variance among beaches separated by 100 km. High variance in nucleic acid concentrations among samples resulted not only from technical error but also from inter-individual variation. Our application of high-resolution biochemical indices therefore demonstrates that functional roles of sandy beaches can be structured at remarkably small spatial (500 m) and temporal (days) scales, within a single beach

Size variation of 0-group plaice: Are earlier influences on growth potential a contributing factor?

Over a decade of sampling has shown that there are consistent differences in the sizes of 0-group plaice by late summer comparing 21 nursery sites on the Scottish west coast. However, when young fish were collected from two sites which produce particularly small and large fish and reared using a common garden design, growth rates between fish from the two sites were indistinguishable. Either there is little selection for fast or slow growth up to a few weeks post-settlement, or such effects do not persist sufficiently strongly to influence later growth. There were also no significant correlations between the time-series of fish size comparing sites, although within some sites there was evidence of inter-annual density-dependent effects. Any influences of offshore regional scale factors, such as sea temperature or pelagic primary productivity on growth thus appear to be heavily modified by local conditions on the nursery grounds. The field observations combined with the experimental results lead us to conclude that the size 0-group plaice attain in late summer is mainly controlled by post-settlement habitat quality