A simulation-based option to assess data-limited fisheries off West African waters
Ontology highlight
ABSTRACT:
SUBMITTER: Kindong R
PROVIDER: S-EPMC10504299 | biostudies-literature | 2023 Jan
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Current variant calling (VC) approaches have been designed to leverage populations of long-range haplotypes and were benchmarked using populations of European descent, whereas most genetic diversity is found in non-European such as Africa populations. Working with these genetically diverse populations, VC tools may produce false positive and false negative results, which may produce misleading conclusions in prioritization of mutations, clinical relevancy and actionability of genes. The most prominent question is which tool or pipeline has a high rate of sensitivity and precision when analysing African data with either low or high sequence coverage, given the high genetic diversity and heterogeneity of this data. Here, a total of 100 synthetic Whole Genome Sequencing (WGS) samples, mimicking the genetics profile of African and European subjects for different specific coverage levels (high/low), have been generated to assess the performance of nine different VC tools on these contrasting datasets. The performances of these tools were assessed in false positive and false negative call rates by comparing the simulated golden variants to the variants identified by each VC tool. Combining our results on sensitivity and positive predictive value (PPV), VarDict [PPV = 0.999 and Matthews correlation coefficient (MCC) = 0.832] and BCFtools (PPV = 0.999 and MCC = 0.813) perform best when using African population data on high and low coverage data. Overall, current VC tools produce high false positive and false negative rates when analysing African compared with European data. This highlights the need for development of VC approaches with high sensitivity and precision tailored for populations characterized by high genetic variations and low linkage disequilibrium.
| S-EPMC8294538 | biostudies-literature
Project description:Small-scale fisheries (SSF) account for much of the global fish catch, but data to assess them often do not exist, impeding assessments of their historical dynamics and status. Here, we propose an approach to assess 'data-less' SSF using local knowledge to produce data, life history theory to describe their historical multispecies dynamics, and length-based reference points to evaluate stock status. We demonstrate use of this approach in three data-less SSFs of the Congo Basin. Fishers' recalls of past fishing events indicated fish catch declined by 65-80% over the last half-century. Declines in and depletion of many historically important species reduced the diversity of exploited species, making the species composition of the catch more homogenous in recent years. Length-at-catch of 11 of the 12 most important species were below their respective lengths-at-maturity and optimal lengths (obtained from Fishbase) in recent years, indicating overfishing. The most overfished species were large-bodied and found in the Congo mainstem. These results show the approach can suitably assess data-less SSF. Fishers' knowledge produced data at a fraction of the cost and effort of collecting fisheries landings data. Historical and current data on fish catch, length-at-catch, and species diversity can inform management and restoration efforts to curb shifting baselines of these fisheries. Classification of stock status allows prioritizing management efforts. The approach is easy to apply and generates intuitive results, having potential to complement the toolkits of researchers and managers working in SSF and engage stakeholders in decision-making processes.Supplementary informationThe online version contains supplementary material available at 10.1007/s11160-023-09770-x.
| S-EPMC10030197 | biostudies-literature
Project description:As the amount of data generated by biomolecular simulations dramatically increases, new tools need to be developed to help manage this data at the individual investigator or small research group level. In this paper, we introduce iBIOMES Lite, a lightweight tool for biomolecular simulation data indexing and summarization. The main goal of iBIOMES Lite is to provide a simple interface to summarize computational experiments in a setting where the user might have limited privileges and limited access to IT resources. A command-line interface allows the user to summarize, publish, and search local simulation data sets. Published data sets are accessible via static hypertext markup language (HTML) pages that summarize the simulation protocols and also display data analysis graphically. The publication process is customized via extensible markup language (XML) descriptors while the HTML summary template is customized through extensible stylesheet language (XSL). iBIOMES Lite was tested on different platforms and at several national computing centers using various data sets generated through classical and quantum molecular dynamics, quantum chemistry, and QM/MM. The associated parsers currently support AMBER, GROMACS, Gaussian, and NWChem data set publication. The code is available at https://github.com/jcvthibault/ibiomes .
| S-EPMC4076027 | biostudies-literature
Project description:Mislabelling of fish and fish products has attracted much attention over the last decades, following public awareness of the practice of substituting high-value with low-value fish in markets, restaurants, and processed seafood. In some cases, mislabelling includes illegal, unreported, and unregulated (IUU) fishing, contributing to overexploit substitute species that are undetectable when sold under wrong names. This is the first study of DNA barcoding to assess the level of mislabelling in fish marketed in Ghana, focusing on endangered shark species. Genetic identification was obtained from 650 base pair sequences within the cytochrome c oxidase I (COI) gene. All except one of 17 shark fillets analysed were wrongly labelled as compared with none of 28 samples of small commercial pelagic fish and 14 commercial shark samples purchased in Europe. Several substitute shark species in Ghana are endangered (Carcharhinussignatus and Isurusoxyrinchus) and critically endangered (Squatina aculeata). Shark products commercialized in Europe (n = 14) did not reveal mislabelling, thus specific shark mislabelling cannot be generalized. Although based on a limited number of samples and fish markets, the results that reveal trade of endangered sharks in Ghana markets encourage Ghanaian authorities to improve controls to enforce conservation measures.
| S-EPMC8305889 | biostudies-literature
Project description:Fisheries bycatch has been identified as the greatest threat to marine mammals worldwide. Characterizing the impacts of bycatch on marine mammals is challenging because it is difficult to both observe and quantify, particularly in small-scale fisheries where data on fishing effort and marine mammal abundance and distribution are often limited. The lack of risk frameworks that can integrate and visualize existing data have hindered the ability to describe and quantify bycatch risk. Here, we describe the design of a new geographic information systems tool built specifically for the analysis of bycatch in small-scale fisheries, called Bycatch Risk Assessment (ByRA). Using marine mammals in Malaysia and Vietnam as a test case, we applied ByRA to assess the risks posed to Irrawaddy dolphins (Orcaella brevirostris) and dugongs (Dugong dugon) by five small-scale fishing gear types (hook and line, nets, longlines, pots and traps, and trawls). ByRA leverages existing data on animal distributions, fisheries effort, and estimates of interaction rates by combining expert knowledge and spatial analyses of existing data to visualize and characterize bycatch risk. By identifying areas of bycatch concern while accounting for uncertainty using graphics, maps and summary tables, we demonstrate the importance of integrating available geospatial data in an accessible format that taps into local knowledge and can be corroborated by and communicated to stakeholders of data-limited fisheries. Our methodological approach aims to meet a critical need of fisheries managers: to identify emergent interaction patterns between fishing gears and marine mammals and support the development of management actions that can lead to sustainable fisheries and mitigate bycatch risk for species of conservation concern.
| S-EPMC7446845 | biostudies-literature
Project description:The loggerhead sea turtle (Caretta caretta, Linnaeus, 1758) is the most abundant sea turtle species in the Mediterranean Sea, where commercial fishing appears to be the main driver of mortality. So far, information on sea turtle bycatch in Italy is limited both in space and time due to logistical problems in data collected through onboard observations and on a limited number of vessels involved. In the present study, sea turtle bycatch in Italian waters was examined by collecting fishermen's information on turtle bycatch through an interview-based approach. Their replies enabled the identification of bycatch hotspots in relation to area, season and to the main gear types. The most harmful fishing gears resulted to be trawl nets, showing the highest probabilities of turtle bycatch with a hotspot in the Adriatic Sea, followed by longlines in the Ionian Sea and in the Sicily Channel. Estimates obtained by the present results showed that more than 52,000 capture events and 10,000 deaths occurred in Italian waters in 2014, highlighting a more alarming scenario than earlier studies. The work shows that in case of poor data from other sources, direct questioning of fishermen and stakeholders could represent a useful and cost-effective approach capable of providing sufficient data to estimate annual bycatch rates and identify high-risk gear/location/season combinations.
| S-EPMC5408728 | biostudies-literature
Project description:The data described in this article are sets of daily rainfall values derived from observed station records. The data was recorded by 72 in-situ rain gauges spread over the West African Sahel. The daily rainfall time series from synoptic, climate, agro-meteorological, and rainfall stations are assessed for quality and consistency before extreme values are extracted based on 90th, 95th, and 99th percentile thresholds. This data is free for use as part of the study "Scales for rating heavy rainfall events in West African Sahel" [1] (Salack et al., 2018). Complementary and up to date time series can be taken from WASCAL data infrastructure (WADI) geoportal https://wascal-dataportal.org/wascal_searchportal2/. This is a derived product (DP), made public in line with WASCAL׳s "3rd party data sharing policy" signed by the WASCAL member countries.
| S-EPMC6143746 | biostudies-literature
Project description:Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa
| PRJEB42452 | ENA
Project description:Our understanding of the role of fire and effect of ant species composition, beyond their diversity and abundance, on the effectiveness of mutualism defence is limited. Most of our knowledge of ant-plant defence in tropical Africa is biased towards East African savannas which have richer soil, higher primary productivity and a more diverse arthropods and mammal community than West African savannas. We assessed the diversity of ant species associated with Acacia species in the Pendjari Biosphere Reserve in the Dahomey Gap, and their impacts on elephant damage. Elephant damage, ant diversity and abundance were measured in stands of five Acacia species. Eleven ant species were identified in the Acacia stands. The composition of these ant communities varied across Acacia species. Pair of ant species co-occurred in only 2 % of sampled trees, suggesting a strong competitive exclusion. Within this annually burnt environment, ants were rare on small trees. The intensity of elephant-caused branch breaking did not vary between trees with ants and trees without ants, suggesting limited Acacia-ant mutualism. Such limited biotic defence may mask strong physical and chemical defence mechanisms of Acacia trees against elephant damage. Ant assemblages in West Africa, unlike those in the more productive East Africa, are particularly species-poor. However, there is a convergence between these two regions in low rate of ant co-occurrence which might indicate strong competitive exclusion. Our study suggests that such low ant species richness while limiting the efficacy of mutualism in controlling mega-herbivore damage may mask a strong defence syndrome.
| S-EPMC8255073 | biostudies-literature
Project description: Not available
| S-EPMC4121246 | biostudies-literature