STOREFISH 2.0: a database on the reproductive strategies of teleost fishes.

Teleost fishes show the most outstanding reproductive diversity of all vertebrates. Yet to date, no one has been able to decisively explain this striking variability nor to perform large-scale phylogenetic analyses of reproductive modes. Here, we describe STrategies Of REproduction in FISH (STOREFISH) 2.0, an online database easing the sharing of an original data set on reproduction published in 2007, enriched with automated data extraction and presentation to display the knowledge acquired on temperate freshwater fish species. STOREFISH 2.0 contains the information for 80 freshwater fish species and 50 traits from the analysis of 1219 references. It is anticipated that this new database could be useful for freshwater biodiversity research, conservation, assessment and management. Database URL: www.storefish.org.

Hierarchical analysis of ontogenetic time to describe heterochrony and taxonomy of developmental stages.

Even though an accurate description of early life stages is available for some teleostean species in form of embryonic and post-embryonic developmental tables, there is poor overlap between species-specific staging vocabularies beyond the taxonomic family level. What is called "embryonic period", "larval period", "metamorphosis", or "juvenile" is anatomically different across teleostean families. This problem, already pointed out 50 years ago, challenges the consistency of developmental biology, embryology, systematics, and hampers an efficient aquaculture diversification. We propose a general solution by producing a proof-of-concept hierarchical analysis of ontogenetic time using a set of four freshwater species displaying strongly divergent reproductive traits. With a parsimony analysis of a matrix where "operational taxonomic units" are species at a given ontogenetic time segment and characters are organs or structures which are coded present or absent at this time, we show that the hierarchies obtained have both very high consistency and retention index, indicating that the ontogenetic time is correctly grasped through a hierarchical graph. This allows to formally detect developmental heterochronies and might provide a baseline to name early life stages for any set of species. The present method performs a phylogenetic segmentation of ontogenetic time, which can be correctly seen as depicting ontophylogenesis.

The onset of piscivory in a freshwater fish species: analysis of behavioural and physiological traits.

The onset of piscivory in fish, resulting in a shift from zooplankton or invertebrate to fish prey, was studied on pikeperch (Sander lucioperca) larvae displaying and not displaying piscivorous behaviour at different ages (23, 30, 37, 44 and 52 days post-hatching) using behavioural (attack, capture and swimming activity), morphological (allometry) and digestive enzymatic (trypsin, α-amylase and pepsin) analyses. The shift from zooplanktonic food items (Artemia nauplii) to a piscivorous diet did not occur at the same time for all individuals within the same cohort. Predation tests, conducted under controlled conditions (20°C; ad libitum feeding), showed that some larvae attacked fish prey as early as the age of 3 weeks [11.0 ± 1.3 mm total length (TL)], whereas others did not start until the age of 6 weeks (16.6 ± 1.9 mm TL). Piscivorous individuals were bigger, with larger heads, longer tails, higher acid protease and lower alkaline protease activities, than non-piscivorous conspecifics. In conclusion, high interindividual variability in morphological and digestive system developments linked to the development of predatory abilities could induce cannibalism in fish.

Constant long photoperiod inhibits the onset of the reproductive cycle in roach females and males.

Photoperiod and temperature are commonly accepted as the determinant factors for the control of the reproductive cycle in freshwater fishes. However, this determining effect is dependent on fish species. While applying a constant long photoperiod has an inhibitory effect in some species, the same photoperiodic manipulation has a stimulating effect in others. In cyprinids, a decrease in temperature or photoperiod can induce the gonad recrudescence. However, in roach Rutilus rutilus an early spring spawner cyprinid, there is little knowledge about the cueing role of each environmental factor. The aim of this work was to study the effect of a constant long photoperiod on the gametogenesis in roach. Fish were kept under either naturally simulated photoperiod or artificial constant long photoperiod and sampled at three times: at the beginning of photoperiod decrease, at the beginning of temperature decrease, and at the end of temperature decrease. Morphological parameters (gonado-somatic, hepato-somatic, and viscera-somatic indexes), plasma sexual steroids, and proportion of gametogenesis stages were estimated at each sampling time. The results showed that a constant, long photoperiod exerted inhibitory effects on gametogenesis advancement in both females and males that could stem from decrease of sex steroid production. Roach displayed a similar response to photoperiodic manipulations to other early spring spawners like percids, such as European perch, yellow perch and pikeperch. These results clearly showed the cueing role of the photoperiod in the induction of the reproductive cycle in roach.

Temperature modifies activity, inter-individual relationships and group structure in a fish.

A host of abiotic factors modify fish social behavior. However, few studies have characterized the effects of temperature on behavior. In this study, brown trout Salmo trutta fry were reared at 5 different temperatures (4°C, 6°C, 8°C, 10°C, and 12°C). In order to characterize group structure, 3 behavioral parameters were investigated: group social structure (based on inter-individual distances), inter-individual relationships (based on physical contacts), and individual activity. These behavioral parameters were studied at the emergence stage, which corresponds to a switch from a social gregarious life in the gravel to a solitary one in the water column. Data analysis showed that the inter-individual distances increased with increasing temperature, particularly the nearest neighbor distance. The mean number of physical contacts between fry increased at both low and high temperatures. At high temperatures, most fry moved apart from each other after a physical contact. Swimming activity decreased at both the lower and upper temperatures (18% of activity at 4°C, 38% at 8°C, and 12% at 12°C). This study showed that temperature modifies brown trout fry activity, inter-individual relationships, and social behavior, which all affect group cohesion before emergence and can influence their survival and dispersal.

Strong Effects of Temperature on the Early Life Stages of a Cold Stenothermal Fish Species, Brown Trout (Salmo trutta L.).

Temperature is the main abiotic factor that influences the life cycle of poikilotherms. The present study investigated the thermal tolerance and phenotypic plasticity of several parameters (development time, morphometric measures, bioenergetics) for both embryos and fry of a cold stenothermal fish species, brown trout (Salmo trutta L.) in order to allow for a holistic evaluation of the potential effects of temperature. Five temperatures (4°C, 6°C, 8°C, 10°C, and 12°C) were tested, and the effects of temperature were analyzed at three stages: hatching, emergence, and first food intake. A mean of 5,440 (S.E. ± 573) eggs, coming from seven females and seven males (seven families) captured close to Linkebeek (Belgium), were used for each temperature. Maximum survival of well-formed fry at first food intake and better use of energy budget were found at 6°C and 8°C, temperatures at which the possible contribution to the next generation should therefore be greatest. At 12°C, the experimental population fell dramatically (0.9% survival rate for well-formed fry at first food intake), and fry had almost no yolk sac at first food intake. The present results on survival at 12°C are in accordance with predictions of a sharp decrease in brown trout numbers in France over the coming decades according to climate change projections (1°C to 5°C temperature rise by 2100 for France). At 10°C, there was also a lower survival rate (55.4% at first food intake). At 4°C, the survival rate was high (76.4% at first food intake), but the deformity rate was much higher (22% at first food intake) than at 6°C, 8°C, and 10°C. The energetic budget showed that at the two extreme temperatures (4°C and 12°C) there was less energy left in the yolk sac at first food intake, suggesting a limited ability to survive starvation.

The effect of hatching time on the bioenergetics of northern pike (Esox lucius) larvae from a single egg batch during the endogenous feeding period.

Size, caloric value and chemical composition were measured separately in the progeny of two northern pike (Esox lucius) females at 3-day intervals during the endogenous feeding period from hatching to final yolk resorption. Tissue, yolk and entire larvae were analysed separately in three groups of larvae that hatched at different times (between 88 and 106 degree-days post-fertilization). An integrated approach with the Gompertz model was used to compute the yolk conversion efficiency and time to maximum tissue size in early, mid and late hatched larvae. At hatching, unresorbed yolk of early hatched larvae contained more energy (39.20 J) and more protein (0.99 mg) compared to the yolk of larvae that hatched later (38.13 J and 0.92 mg protein for late hatched larvae, p < 0.05). In contrast, a significant reduction in tissue weight (-0.7 mg DW) and protein content (-0.5 mg) was found in early hatched larvae compared to those which hatched later (p < 0.05). Between days 9 and 12 post-hatching (108 and 144 degree-days post-hatching), close to the final yolk resorption, late hatched larvae stopped growing and their tissue began to be resorbed. This tissue resorption time was delayed in early hatched larvae which presented at the end of the experiment a greater tissue weight than late hatched ones. Yolk conversion efficiency in term of energy from hatching to complete yolk resorption stage was significantly higher for early and mid hatched larvae (51%) compared to late hatched ones (44%) (p = 0.004). Furthermore, the time to maximum tissue size was found to be negatively related to hatching time which implies that early hatched larvae take longer time to switch from one developmental stage to the next. The maximum tissue dry weight and energy content were found to be reached at approximately the same age post-fertilization for both early hatched and late hatched larvae, suggesting that the principal steps in a fish's lifespan are better correlated with time of fertilization than hatching time.

After 7 years and 1000 citations: comparative assessment of the DNA barcoding and the DNA taxonomy proposals for taxonomists and non-taxonomists.

In 2003, two different approaches-DNA taxonomy and DNA barcoding-were simultaneously proposed to overcome some of the perceived intrinsic weaknesses of the traditional morphology-based taxonomical system, and to help non-taxonomists to resolve their crucial need for accurate and rapid species identification tools. After 7 years, it seems unlikely that a completely new taxonomical system based on molecular characters only (DNA taxonomy) will develop in the future. It is more likely that both morphological and molecular data will be simultaneously analyzed, developing what has been coined as "integrative taxonomy". Concerning DNA barcoding, it is now clear that it does not focus on building a tree-of-life nor to perform DNA taxonomy, but rather to produce a universal molecular identification key based on strong taxonomic knowledge that is collated in the barcode reference library. The indisputable success of the DNA barcoding project is chiefly due to the fact that DNA barcoding standards considerably enhance current practices in the molecular identification field, and standardization offers virtually endless applications for various users.

Phylogeny of the Gadidae (sensu Svetovidov, 1948) based on their morphology and two mitochondrial genes.

Although Codfishes are probably one of the most studied groups of all teleost fishes worldwide owing to their great importance to fisheries, their phylogeny and classification are still far from being firmly established. In this study, we present phylogenetic relationships of 19 out of 22 genera traditionally included in the Gadidae based on the analysis of entire cytochrome b and partial cytochrome oxidase I genes (1530 bp). Maximum Parsimony, Maximum Likelihood, and Bayesian analyses all recovered five main clades that correspond to traditionally recognized groupings within Gadoids. The same clades were recovered with MP analysis based on 30 morphological characters (collected from the literature). Given these findings, we propose a revised provisional classification of Gadoids: one suborder Gadoidei containing two families, the Merlucciidae (1 genus) and the Gadidae (21 genera) distributed into four subfamilies: the Gadinae (12 genera), the Lotinae (3 genera), the Gaidropsarinae (3 genera), and the Phycinae (3 genera). Lastly, nuclear inserts of mitochondrial DNA (Numts) were identified in two species, i.e., Gadiculus argenteus and Melanogrammus aeglefinus.

Food and forensic molecular identification: update and challenges.

The need for accurate and reliable methods for animal species identification has steadily increased during past decades, particularly with the recent food scares and the overall crisis of biodiversity primarily resulting from the huge ongoing illegal traffic of endangered species. A relatively new biotechnological field, known as species molecular identification, based on the amplification and analysis of DNA, offers promising solutions. Indeed, despite the fact that retrieval and analysis of DNA in processed products is a real challenge, numerous technically consistent methods are now available and allow the detection of animal species in almost any organic substrate. However, this field is currently facing a turning point and should rely more on knowledge primarily from three fundamental fields--paleogenetics, molecular evolution and systematics.