Assessing the Impact of Bycatch on Dolphin Populations: The Case of the Common Dolphin in the Eastern North Atlantic

Fisheries interactions have been implicated in the decline of many marine vertebrates worldwide. In the eastern North Atlantic, at least 1000 common dolphins (Delphinus delphis) are bycaught each year, particularly in pelagic pair-trawls. We have assessed the resulting impact of bycatch on this population using a demographic modeling approach. We relied on a sample of females stranded along the French Atlantic and western Channel coasts. Strandings represent an extensive source of demographic information to monitor our study population. Necropsy analysis provided an estimate of individual age and reproductive state. Then we estimated effective survivorship (including natural and human-induced mortality), age at first reproduction and pregnancy rates. Reproductive parameters were consistent with literature, but effective survivorship was unexpectedly low. Demographic parameters were then used as inputs in two models. A constant parameter matrix proposed an effective growth rate of −5.5±0.5%, corresponding to the current situation (including bycatch mortality). Subsequently, deterministic projections suggested that the population would be reduced to 20% of its current size in 30 years and would be extinct in 100 years. The demographic invariant model suggested a maximum growth rate of +4.5±0.09%, corresponding to the optimal demographic situation. Then, a risk analysis incorporating Potential Biological Removal (PBR), based on two plausible scenarii for stock structure suggested that bycatch level was unsustainable for the neritic population of the Bay of Biscay under a two-stock scenario. In depth assessment of stock structure and improved observer programs to provide scientifically robust bycatch estimates are needed. Effective conservation measures would be reducing bycatch to less than 50% of the current level in the neritic stock to reach PBR. Our approach provided indicators of the status and trajectory of the common dolphin population in the eastern North Atlantic and therefore proved to be a valuable tool for management, applicable to other dolphin populations

Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny

<p>Abstract</p> <p>Background</p> <p>Folding and intermingling of chromosomes has the potential of bringing close to each other loci that are very distant genomically or even on different chromosomes. On the other hand, genomic rearrangements also play a major role in the reorganisation of loci proximities. Whether the same loci are involved in both mechanisms has been studied in the case of somatic rearrangements, but never from an evolutionary standpoint.</p> <p>Results</p> <p>In this paper, we analysed the correlation between two datasets: (i) whole-genome chromatin contact data obtained in human cells using the Hi-C protocol; and (ii) a set of breakpoint regions resulting from evolutionary rearrangements which occurred since the split of the human and mouse lineages. Surprisingly, we found that two loci distant in the human genome but adjacent in the mouse genome are significantly more often observed in close proximity in the human nucleus than expected. Importantly, we show that this result holds for loci located on the same chromosome regardless of the genomic distance separating them, and the signal is stronger in gene-rich and open-chromatin regions.</p> <p>Conclusions</p> <p>These findings strongly suggest that part of the 3D organisation of chromosomes may be conserved across very large evolutionary distances. To characterise this phenomenon, we propose to use the notion of spatial synteny which generalises the notion of genomic synteny to the 3D case.</p

Leishmania species identification by PCR-RFLP analysis and its applications in FrenchGuiana

International audienceLeishmania (Viannia) guyanensis was for many years the only species commonly identified in French Guiana, but precise species identifications were quite rare. We describe a new RFLP-PCR technique using a 615 bp fragment of the RNA polymerase II gene and two restriction enzymes, TspR1 and Hga1. Seven reference strains (L.(L)amazonensis, L.(V)lainsoni, L.(V)braziliensis, L.(V)guyanensis, L.(V)naiffi, L.(L)major / L.(L)infantum) and 112 clinical samples from positive lesions were used for the development of the technique. The rates of positive species identification were 85.7% for punch skin biopsy specimens, 93.1% for positive Giemsa-stained smears and 100% for positive culture supernatants. In the framework of cutaneous leismaniasis species surveillance for the 2006-2008 period, parasite identification was carried out for 199 samples from different patients. The prevalence of the various Leishmania species was 84.4% for L.(V)guyanensis, 8.0% for L.(V)braziliensis, 5.0% for L.(V)amazonensis and 2.6% for L.(V)lainsoni. L.(V)braziliensis seems to be locally an emerging pathogen

New insights into the nutritional regulation of gluconeogenesis in carnivorous rainbow trout (Oncorhynchus mykiss): a gene duplication trail.

The rainbow trout (Oncorhynchus mykiss) is considered to be a strictly carnivorous fish species that is metabolically adapted for high catabolism of proteins and low utilisation of dietary carbohydrates. This species consequently has a "glucose-intolerant" phenotype manifested by persistent hyperglycaemia when fed a high-carbohydrate diet. Gluconeogenesis in adult fish is also poorly, if ever, regulated by carbohydrates, suggesting that this metabolic pathway is involved in this specific phenotype. In this study, we hypothesised that the additional round of whole genome duplication occurring in trout (Ss4R) could represent a major evolutionary event leading to adaptive innovation via gene duplication and might provide new elements to enhance our understanding of gluconeogenesis and poor dietary carbohydrates use in this species. Our evolutionary analysis of gluconeogenic genes revealed that pck1, pck2, fbp1a and g6pca were retained as singletons after Ss4r while g6pcb1, g6pcb2 and fbp1b ohnologue pairs were maintained. For all genes, duplication may have led to sub- or neo-functionalisation. Expression profiles suggested that the gluconeogenesis pathway remained active in trout fed a no carbohydrate diet. When trout were fed a high-carbohydrate diet (30%), most of the gluconeogenic genes were non- or down-regulated, except for g6pbc2 ohnologues the RNA levels of which were surprisingly increased. This study demonstrated that Ss4R in trout involved adaptive innovation via gene duplication and via the outcome of the resulting ohnologues. Indeed, maintenance of ohnologuous g6pcb2 pair may contribute in a significant way to the "glucose-intolerant" phenotype of trout and may partially explain its poor use of dietary carbohydrates

Glucose Metabolism Ontogenesis in Rainbow Trout (Oncorhynchus Mykiss) in the Light of the Recently Sequenced Genome: New Tools for Intermediary Metabolism Programming

International audienc

Glucose Metabolism Ontogenesis in Rainbow Trout (Oncorhynchus Mykiss) in the Light of the Recently Sequenced Genome : New Tools for Nutritional Programming

International audienc

Long-Term Programming Effect of Embryonic Hypoxia Exposure and High-Carbohydrate Diet at First Feeding on Glucose Metabolism in Juvenile Rainbow Trout

International audienc

Comparison of glucose and lipid metabolic gene expressions between fat and lean lines of rainbow trout after a glucose load.

Two experimental rainbow trout lines developed through divergent selection for low (Lean 'L' line) or high (Fat 'F' line) muscle fat content were used as models to study the genetic determinism of fat depots. Previous nutritional studies suggested that the F line had a better capability to use glucose than the L line during feeding trials. Based on that, we put forward the hypothesis that F line has a greater metabolic ability to clear a glucose load effectively, compared to L line. In order to test this hypothesis, 250 mg/kg glucose was intraperitoneally injected to the two rainbow trout lines fasted for 48 h. Hyperglycemia was observed after glucose treatment in both lines without affecting the phosphorylation of AMPK (cellular energy sensor) and Akt-TOR (insulin signaling) components. Liver glucokinase and glucose-6-phosphate dehydrogenase expression levels were increased by glucose, whereas mRNA levels of β-oxidation enzymes (CPT1a, CPT1b, HOAD and ACO) were down-regulated in the white skeletal muscle of both lines. Regarding the genotype effect, concordant with normoglycemia at 12 h after glucose treatment, higher muscle glycogen was found in F line compared to L line which exhibited hyperglycemia. Moreover, mRNA levels of hepatic glycolytic enzymes (GK, 6PFK and PK), gluconeogenic enzyme PEPCK and muscle fatty acid oxidation enzymes (CPT1a, CPT1b and HOAD) were concurrently higher in the F line. Overall, these findings suggest that F line may have a better ability to maintain glucose homeostasis than L line