ALBERT

Description: (1). During 2003 a total of 3,852 Metric Tonnes (MT) of fish was landed on Mahe, Praslin and La Digue by 405 fishing boats. 80.5% of the total catch was landed on Mahe alone. The total artisanal catch decreased by 1063 (MT) compared to 2002, whilst the number of boats operating increased by 31 over the same period (excluding sport fishing vessels). (2). The most important species groups landed (greater than 5% of the total catch) were carangues (33.6%), job (15.8%), bourgeois (9.1%), cordonier (6.6%), capitaine (6.1%), becune (6.0%), and maquereau doux (5.4%). Compared to 2002, there were notable increases in the relative importance of cordonier and bourgeois to the overall catch. (3). Peak landings occurred in November (463.7 MT) and the lowest catch was recorded in September (137.3 MT). The average monthly catch in 2003 was 321 (MT). (4). Slight seasonal variation in total catch was observed in 2003. The mean monthly catch during the months of May — October, inclusive; was 290.5 MT, compared to a mean montly catch of 318.1 MT during the months of December — March, inclusive. In contrast to the patterns observed in 2001 and 2002, the highest catches for carangues occurred in November rather than April. Catches of cordonnier continued to increase (254.7 MT) over the previous two years, with peak monthly catches coinciding with the peak spawning months for those species, namely October to December. (5). The percentage of the total artisanal catch taken by the small boat fishery (pirogues and outboards) was 28.3%, similar to the estimate obtained in 2002. Fishermen on foot landed 0.6% of the total artisanal catch, with octopus catches from this fishery totaling 21.3 MT in 2003. 5.4 MT of maquereau were landed by pirogues using beach seines. Carangues (22.6%) replaced maquereau doux (19.2%) as the most important species landed by vessels with outboards in 2003, other important groups in this fishery including cordonier (22.3%) and other trap fish (11.9%). In 2003, landings by the small boats and foot fishermen were divided equally between pelagic and semi-pelagic species (48.2%) and demersal/ reef species (51.8%). (6). Typical of previous years, the whaler handline fishery dominated artisanal fisheries catches, accounting for 63.4% of total landings in 2003. An average of 96 whalers operated each month during 2003, an increase of 5 vessels compared to 2002. Carangues made up 42.1% of the total whaler handline catch. Other important species in the catch were, in order of importance, job gris (22.1%), becune (8.3%) bourgeois (8.3%) and bonite (3.7%). For the second consecutive year, catches of bourgeois by the whaler handline fishery increased, by 22.2% over 2002. (7). A maximum of 16 schooners were in operation during 2002 and these vessels accounted for 6.8% of total landings. Bourgeois was again the most important species caught (36.9%), followed by the 'others' category (18.6%) and job gris (8.5%). The spanner crab Ranina ranina accounted for 5.8% of schooner landings. (8). Fish purchases from the artisanal fisheries by Oceana Fisheries Co. Ltd. were equivalent to 10.4% total landings (400.7 MT). Major species groups purchased were red snappers and bourgeois (219 MT), job (57.4 MT), groupers (30,6 MT), capitaine (23.2 MT), octopus (21.9 MT) and carangue (17 MT). (9). Fish purchases from foreign longline and purse seine vessels by Oceana Fisheries Co. Ltd. were 245.9 MT during 2002. Species purchased were all pelagic, of which bonito bait was the most common (112.8 MT), followed by yellowfin (40.3 MT), dorade (37.3 MT) and skipjack (14.1 MT). (10). Fish exports by Oceana Fisheries Co. Ltd. amounted to 201.1 MT, a decrease of around 25 MT compared to 2002. These exports were valued at SR 5.6 million (C.I.F). Compared to the previous year, the markets shifted in order of importance in 2003, with Mauritius constituting the major importer of Seychelles fish products (69.9 MT), followed by Reunion (55.6 MT), England (50.1 MT) and France (14.6 MT). Pelagic fishes (33.8%), bourgeois (29.5%) and job (15.8%) were the most important fish groups exported. (11). A comparison of data collected between 1991 and 2003 follows, The proportion of catch by boat type and number of boats operating shown in the following table does not include the research vessel (RJV L'Amitie) of the Seychelles Fishing Authority, which landed 3.1 MT of fish in 2003, contributing 0.1% to the total artisanal catch.

Description: Published

Description: (1). During 2002 an estimated total of 4915 tonnes of fish was landed on Mahe, Praslin and La Digue by 374 fishing boats. 83.1% of the total catch was landed on Mahe alone. The total catch increased by 625 tonnes compared to 2001, and the number of boats operating decreased by 3 over the same period. (2). The most important species groups landed (greater than 5% of the total catch) were carangues (41.5%), job (12.4%), capitaine (6.8%), becune (6.1%), maquereau doux (5.7%) and bourgeois (5.7%). (3). Peak landings occurred in October (576.5 MT) and the lowest catch was recorded in January (222.51 MT). The average catch per month was 409.6 tonnes. (4). Seasonal variation in catches of demersal species was less marked compared to previous years. The mean monthly catch during the SE Trades (May — October, inclusive) was 420.5 MT, compared to a mean monthly catch of 359.4 MT during the NW monsoon (December — March, inclusive). High catches were probably maintained during the period of May to October in 2002 due to the comparatively weak strength of the SE Trades in that year, as determined by lower than average wind speeds for most months in that period (Meteorological Office, pers. comm.). Identical to the pattern observed in 2001, the highest catches for carangues occurred in April. Catches of cordonnier in 2002 (203.0 MT) were more than double those recorded in 2001 (90.5), and were lowest during the period of March to June, inclusive. (5). In total, the small boat fishery accounted for 26.4% of fish landings during 2002. Compared to the total artisanal catch, the percentage catch by boat type for the small boat fishery was as follows: fishermen on foot — 0.6%; pirogues — 0.6%; outboards -25.2% and whalers with traps — 2.2%. Fishermen on foot mostly landed octopus (87.0%), although cordonnier catches by this category were also recorded in 2002 (12.6%). Due to changes in fisheries fieldworker coverage in 2002, landings of maquereau by pirogue were not recorded, with cordonnier (57.6%) and other trap fish (23.2%) dominating landings instead. The predominant species groups landed by outboards were, in order of importance, maquereau doux (22.6%), carangues (21.7%), other trap fish (13.9%) and cordonnier (13.6%). Whalers with traps landed mainly capitaine (61.3%), other trap fish (20.1%) and cordonnier (12.3%). In 2002, landings by the small boat fleet were once again approximately divided equally between pelagic (51.3%) and demersal/ reef species (47.4%). (6). The whaler handline fishery accounted for 67.9% of total landings. An average of 91 whalers operated each month during 2002, indicating an increase of 1 vessel operating when compared to 2001. Carangues made up 52.5% of the total whaler handline catch. Other important species in the catch were, in order of importance, job gris (16.4%), becune (8.4%) bourgeois (5.0%), bordemar (2.6%) and vara vara (2.2%). Catches of Bourgeois decreased by 28.8% in 2002 compared to the catch of 2001. (7). Purchases from the artisanal fisheries by Oceana Fisheries were equivalent to 10.3% of total landings (504.2 MT). Oceana Fisheries purchased all fish from the Port Victoria site. Major species groups purchased were red snappers and bourgeois (57.5%), job (12.7%), groupers (5.2%) and capitaine (5.9 %). (8). Fish purchases from foreign longline vessels were in the order of 152.3 MT of frozen fish (gutted and ungutted) during 2002. Species purchased were all pelagic, of which bonito bait was the most common (98.0 MT), followed by yellowfin (18.9 MT), dorade (12.6 MT) and skipjack (12.6 MT). (9). Fish exports by Oceana Fisheries amounted to 226.6 MT, 85.9% of which was fresh and 14.1% frozen. These exports were valued at SR 7.1 million (CIF). Major destinations for the fish were England (34.5%), Reunion (30.3%) and Mauritius (17.0%). Pelagic fish (41.5%), bourgeois (23.4%), and Job (19.2%). formed the most important fish groups exported. (10). A comparison of data collected between 1990 and 2002 follows. The proportion of catch by boat type and number of boats operating shown in the following table do not include the research vessels of the Seychelles Fishing Authority which landed 11.7 tonnes of fish in 2002, contributing 0.2% of the total catch.

Description: Published

Description: Many coral reef fish form transient spawning aggregations at sites located a few to hundreds of kilometres from their normal residence areas. Reef fish spawning aggregations ("FSAs") are often heavily exploited, which make them targets for management with marine reserves. We used a per-recruit model to compare the long-term conservation (impacts on female spawning-stock biomass-per-recruit (SSBR) and female : male sex ratio, SR) and fisheries effects (impacts on yield-per-recruit, YPR) of spawning reserves vs. normal residence reserves for two data-poor populations from Seychelles with contrasting life history traits and sexual modes: the Siganus sutor population of the main granitic islands, which has a fast life history and is gonochoristic and the Epinephelus fuscoguttatus population of Farquhar Atoll, which has a slow life history and is protogynous. Overall, our results suggest that normal residence reserves are more effective at improving both the SSBR and YPR of S. sutor . In contrast, the protection of a substantial fraction of spawning sites is preferable for E. fuscoguttatus to ensure the reproductive output of this protogynous population through normalization of SR and maintenance of high SSBR. Neither spawning reserves nor normal residence reserves improved the YPR of E. fuscoguttatus . However, yields of E. fuscoguttatus may increase on the long term via recruitment subsidy if a substantial fraction of spawning sites is protected. This may occur only if the population was recruitment limited in the absence of reserves and increases in SSBR compensate for lost opportunities caused by the area closures. Sensitivity analyses revealed that the relative effects of spawning reserves and normal residence reserves relate more to the change in catchability occurring with FSA formation than to life history traits. Thus, normal residence reserves should be preferred over spawning reserves for S. sutor essentially because its catchability at spawning sites is low relative to many other aggregation-forming populations. S. sutor therefore suffers higher fishing mortality in normal residence areas than at FSA sites. Our study demonstrates that spawning reserves are not always the most effective tool for balancing conservation and exploitation objectives for FSA-forming populations, and that this measure should ideally be weighed against other management options.

Description: The Immuno Polymorphism Database (IPD) was developed to provide a centralized system for the study of polymorphism in genes of the immune system. Through the IPD project we have established a central platform for the curation and publication of locus-specific databases involved either directly or related to the function of the Major Histocompatibility Complex in a number of different species. We have collaborated with specialist groups or nomenclature committees that curate the individual sections before they are submitted to IPD for online publication. IPD consists of five core databases, with the IMGT/HLA Database as the primary database. Through the work of the various nomenclature committees, the HLA Informatics Group and in collaboration with the European Bioinformatics Institute we are able to provide public access to this data through the website http://www.ebi.ac.uk/ipd/ . The IPD project continues to develop with new tools being added to address scientific developments, such as Next Generation Sequencing, and to address user feedback and requests. Regular updates to the website ensure that new and confirmatory sequences are dispersed to the immunogenetics community, and the wider research and clinical communities.

Description: Motivation: Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing and other mechanisms, and that most alternative isoforms vary in expression between human tissues. As RNA-Seq datasets grow in size, it remains challenging to visualize isoform expression across multiple samples. Results: To help address this problem, we present Sashimi plots, a quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. Sashimi plots can be made using the Broad Integrated Genome Viewer or with a stand-alone command line program. Availability and implementation: Software code and documentation freely available here: http://miso.readthedocs.org/en/fastmiso/sashimi.html Contact: mesirov@broadinstitute.org , airoldi@fas.harvard.edu or cburge@mit.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : Although the 1000 Genomes haplotypes are the most commonly used reference panel for imputation, medical sequencing projects are generating large alternate sets of sequenced samples. Imputation in African Americans using 3384 haplotypes from the Exome Sequencing Project, compared with 2184 haplotypes from 1000 Genomes Project, increased effective sample size by 8.3–11.4% for coding variants with minor allele frequency 〈1%. No loss of imputation quality was observed using a panel built from phenotypic extremes. We recommend using haplotypes from Exome Sequencing Project alone or concatenation of the two panels over quality score-based post-imputation selection or IMPUTE2’s two-panel combination. Contact: yunli@med.unc.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: The study of genetic influences on drug response and efficacy (‘pharmacogenetics’) has existed for over 50 years. Yet, we still lack a complete picture of how genetic variation, both common and rare, affects each individual's responses to medications. Exome sequencing is a promising alternative method for pharmacogenetic discovery as it provides information on both common and rare variation in large numbers of individuals. Using exome data from 2203 AA and 4300 Caucasian individuals through the NHLBI Exome Sequencing Project, we conducted a survey of coding variation within 12 Cytochrome P450 ( CYP ) genes that are collectively responsible for catalyzing nearly 75% of all known Phase I drug oxidation reactions. In addition to identifying many polymorphisms with known pharmacogenetic effects, we discovered over 730 novel nonsynonymous alleles across the 12 CYP genes of interest. These alleles include many with diverse functional effects such as premature stop codons, aberrant splicesites and mutations at conserved active site residues. Our analysis considering both novel, predicted functional alleles as well as known, actionable CYP alleles reveals that rare, deleterious variation contributes markedly to the overall burden of pharmacogenetic alleles within the populations considered, and that the contribution of rare variation to this burden is over three times greater in AA individuals as compared with Caucasians. While most of these impactful alleles are individually rare, 7.6–11.7% of individuals interrogated in the study carry at least one newly described potentially deleterious alleles in a major drug-metabolizing CYP .

Description: Many coral reef fish species form predictable, transient spawning aggregations. Many aggregations are overfished, making them a target for spatial management. Here, we develop a per-recruit model to evaluate the performance of no-take marine reserves protecting transient spawning aggregations. The model consists of only 14 demographic and exploitation-related parameters. We applied the model to a protogynous grouper and a gonochoristic rabbitfish from Seychelles and tested six scenarios regarding the extent of protected areas, the level of fish spawning-site fidelity, and fishing effort redistribution post reserve implementation. Spawning aggregation reserves improve spawning-stock biomass-per-recruit and reduce the sex ratio bias in protogynous populations for all scenarios examined. However, these benefits are often small and vary among the different scenarios and as a function of sexual ontogeny. In all scenarios, increases in yield-per-recruit do not occur or are negligible. The long-term yield increases due to spawning aggregation reserves may still occur, but only if spawning-stock biomass recovery results in a recruitment subsidy. Given these limited benefits, the value of no-take reserves must be weighed against those of other management options, such as fishing effort reduction and seasonal fishery closures. The latter is particularly appropriate when spawning and non-spawning areas overlap in space.

Description: There is a global trend in the depletion of transient reef fish spawning aggregations ("FSAs"), making them a primary target for management with marine protected areas (MPAs). Here, we review the observed and likely effectiveness of FSA MPAs, discuss how future studies could fill knowledge gaps, and provide recommendations for MPA design based on species' life history and behaviour, enforcement potential, and management goals. Modelling studies indicate that FSA MPAs can increase spawning-stock biomass and normalize sex ratio in protogynous fish populations, unless fishing mortality remains high outside protected FSA sites and spawning times. In the field, observations of no change or continued decline in spawning biomass are more common than population recovery. When empirical studies suggest that FSA MPAs may not benefit fish productivity or recovery, extenuating factors such as insufficient time since MPA creation, poor or lack of enforcement, inadequate design, and poorly defined management objectives are generally blamed rather than failure of the MPA concept. Results from both the empirical and modelling literature indicate that FSA MPAs may not improve exploitable biomass and fisheries yields; however, investigations are currently too limited to draw conclusions on this point. To implement effective FSA MPAs, additional modelling work, long-term monitoring programmes at FSA sites, and collections of fisheries-dependent data are required, with greater attention paid to the design and enforcement of area closures. We recommend a harmonized, adaptive approach that combines FSA MPA design with additional management measures to achieve explicitly stated objectives. Conservation objectives and, therefore, an overall reduction in mortality rates should be targeted first. Fisheries objectives build on conservation objectives, in that they require an overall reduction in mortality rates while maintaining sufficient access to exploitable biomass. Communication among researchers, regulatory agencies, park authorities, and fishers will be paramount for effective action, along with significant funds for implementation and enforcement.

Description: Let $E$ be a normed linear space and suppose that ${\mathbb A}$ is the global attractor of either (i) a homeomorphism $F\colon E\rightarrow E$ or (ii) a semigroup $S(\cdot )$ on $E$ that is injective on ${\mathbb A}$ . In both cases, ${\mathbb A}$ has trivial shape, and the dynamics on ${\mathbb A}$ can be described by a homeomorphism $F\colon {\mathbb A}\rightarrow {\mathbb A}$ (in the second case we set $F=S(t)$ for some $t 〉 0$ ). If the topological dimension of ${\mathbb A}$ is finite, then we show that for any $\epsilon 〉 0$ there is an embedding $e\colon {\mathbb A}\rightarrow {\mathbb R}^k$ , with $k\sim {\rm dim}({\mathbb A})$ , and a (dynamical) homeomorphism $f\colon {\mathbb R}^k\rightarrow {\mathbb R}^k$ such that $F$ is conjugate to $f$ on ${\mathbb A}$ (that is, $F|_{\mathbb A}=e^{-1}\circ f\circ e$ ) and $f$ has a global attractor $A_f$ with $e({\mathbb A})\subseteq A_f\subseteq N(e({\mathbb A}),\epsilon )$ . In other words, we show that the dynamics on ${\mathbb A}$ are essentially finite dimensional. We characterise subsets of ${\mathbb R}^n$ that can be the global attractors of homeomorphisms as cellular sets, give elementary proofs of various topological results connected to Borsuk's theory of shape and cellularity in Euclidean spaces, and prove a controlled homeomorphism extension theorem. We also show that we could achieve $e({\mathbb A})=A_f$ under the assumption of a stronger controlled homeomorphism extension theorem.