Center Regional Agrhymet
Center Regional Agrhymet
Rey O.,Montpellier SupAgro |
Loiseau A.,Montpellier SupAgro |
Facon B.,Montpellier SupAgro |
Foucaud J.,Montpellier SupAgro |
And 11 more authors.
Molecular Biology and Evolution | Year: 2011
The little fire ant, Wasmannia auropunctata, displays a peculiar breeding system polymorphism. Classical haplo-diploid sexual reproduction between reproductive individuals occurs in some populations, whereas, in others, queens and males reproduce clonally. Workers are produced sexually and are sterile in both clonal and sexual populations. The evolutionary fate of the clonal lineages depends strongly on the underlying mechanisms allowing reproductive individuals to transmit their genomes to subsequent generations. We used several queen-offspring data sets to estimate the rate of transition from heterozygosity to homozygosity associated with recombination events at 33 microsatellite loci in thelytokous parthenogenetic queen lineages and compared these rates with theoretical expectations under various parthenogenesis mechanisms. We then used sexually produced worker families to define linkage groups for these 33 loci and to compare meiotic recombination rates in sexual and parthenogenetic queens. Our results demonstrate that queens from clonal populations reproduce by automictic parthenogenesis with central fusion. These same parthenogenetic queens produce normally segregating meiotic oocytes for workers, which display much lower rates of recombination (by a factor of 45) than workers produced by sexual queens. These low recombination rates also concern the parthenogenetic production of queen offspring, as indicated by the very low rates of transition from heterozygosity to homozygosity observed (from 0% to 2.8%). We suggest that the combination of automixis with central fusion and a major decrease in recombination rates allows clonal queens to benefit from thelytoky while avoiding the potential inbreeding depression resulting from the loss of heterozygosity during automixis. In sterile workers, the strong decrease of recombination rates may also facilitate the conservation over time of some coadapted allelic interactions within chromosomes that might confer an adaptive advantage in habitats disturbed by human activity, where clonal populations of W. auropunctata are mostly found. © 2011 The Author.
Badenhorst D.,Stellenbosch University |
Dobigny G.,French National Institute for Agricultural Research |
Dobigny G.,Center Regional Agrhymet |
Adega F.,IBB Institute for Biotechnology And Bioengineering |
And 5 more authors.
Chromosome Research | Year: 2011
The Rattini (Muridae, Murinae) includes the biologically important model species Rattus norvegicus (RNO) and represents a group of rodents that are of clinical, agricultural and epidemiological importance. We present a comparative molecular cytogenetic investigation of ten Rattini species representative of the genera Maxomys, Leopoldamys, Niviventer, Berylmys, Bandicota and Rattus usingchromosome banding, cross-species painting (Zoofluorescent in situ hybridization or FISH) and BACFISH mapping. Our results show that these taxa are characterised by slow to moderate rates of chromosome evolution that contrasts with the extensive chromosome restructuring identified in most other murid rodents, particularly the mouse lineage. This extends to genomic features such as NOR location (for example, NORs on RNO 3 are present on the corresponding chromosomes in all species except Bandicota savilei and Niviventer fulvescens, and the NORs on RNO 10 are conserved in all Rattini with the exception of Rattus). The satellite I DNA family detected and characterised herein appears to be taxon (Rattus) specific, and of recent origin (consistent with a feedback model of satellite evolution). BACmapping using clones that span regions responsible for the morphological variability exhibited by RNO 1, 12 and 13 (acrocentric/submetacentric) and their orthologues in Rattus species, demonstrated that the differences are most likely due to pericentric inversions as exemplified by data on Rattus tanezumi. Chromosomal characters detected using R. norvegicus and Maxomys surifer whole chromosome painting probes were mapped to a consensus sequence-based phylogenetic tree thus allowing an objective assessment of ancestral states for the reconstruction of the putative Rattini ancestral karyotype. This is thought to have comprised 46 chromosomes that, with the exception of a single pair of metacentric autosomes, were acrocentric in morphology. © 2011 Springer Science+Business Media B.V.
Badenhorst D.,Stellenbosch University |
Dobigny G.,Center Regional Agrhymet |
Robinson T.J.,Stellenbosch University
Cytogenetic and Genome Research | Year: 2012
We report on the construction of a comparative chromosome map between the emblematic laboratory rat, Rattus norvegicus (RNO), and Delacour's Marmoset rat, Hapalomys delacouri (HDE), based on cross-species fluorescence in situ hybridization with R. norvegicus painting probes. Sixteen R. norvegicus chromosomes (RNO 3-6, 8, 10-15, 17-20, and X) were retained in their entirety (as a conserved block or as a single chromosome) in the H. delacouri genome. The remaining 5 R. norvegicus chromosomes (RNO 1, 2, 7, 9, and 16) produced 2 signals in the H. delacouri karyotype. Our analysis allowed the detection of an X-autosome translocation between RNO X and 11 that occurred convergently in an unrelated species, Bandicota savilei, and a single B chromosome that accounts for the 2n = 48 karyotype observed in this specimen. In total, the rat chromosome paints revealed 27 segments of conserved synteny in H. delacouri. The analysis showed 7 NOR bearing pairs in H. delacouri (HDE 1, 3, 6, 7, 8, 10, and 13) and the occurrence of an interstitial telomeric signal at the centromeric regions of 8 H. delacouri chromosomes (HDE 3, 10, 11, 12, 13, 16, 19, and 22). These data, together with published comparative maps, enabled a revision of the previously postulated murine ancestral condition suggesting that it probably comprised a wholly acrocentric karyotype with 2n = 46-50. Copyright © 2012 S. Karger AG.
Agency: European Commission | Branch: FP7 | Program: CP-FP-SICA | Phase: ENV.2011.4.1.4-1 | Award Amount: 4.12M | Year: 2011
AGRICAB aims to strengthen Earth Observation (EO) capacities in Africa by building on the open data sharing through GEONETCast, connecting the available satellite and other data with predictive models in order to facilitate integration in agriculture and forestry planning and management processes. Dedicated national applications in various African countries are designed to address particular policy issues related to livestock, crop systems and forest management. Through these applications, twinning partnerships are developed between a European and an African partner, to maximize knowledge transfer and integration. Experiences learned will form a good basis for regional trainings to the member states of the Observatoire du Sahara et du Sahel (OSS) in Tunisia, the Regional Centre for Mapping Resources for Development (RCMRD) in Kenya and the AGRHYMET regional centre in Niger, covering almost the entire African continent. These activities will be linked with Africa-wide management and research initiatives and programmes on Forest and Agriculture and builds on experiences from the GEONETCast for and by Developing Countries (DevCoCast) and Global Monitoring for Food Security (GMFS) projects.
Agency: European Commission | Branch: FP7 | Program: CSA-SA | Phase: ENV.2007.4.1.4.3. | Award Amount: 2.15M | Year: 2008
The DevCoCast project aims at involving Developing Countries in the GEONETCast initiative. Many Developing Countries are exposed to serious environmental risks and their need for adequate information is high. Unfortunately, reliable and continuous access to real time environmental information is often lacking. The GEONETCast concept overcomes existing telecommunication limitations and is able to provide reliable and fast access to environmental information. The DevCoCast project will 1. disseminate existing environmental added-value datasets (both in-situ and satellite based) from various sources in Africa, South- and Central America and Europe in (near) real time and at no cost via GEONETCast to a broad range of user communities in Developing Countries and 2. promote and support the use of these products. By utilizing the existing EUMETCast dissemination system, we can directly take benefit from the operational infrastructures and from a well developed user base in Africa and South-America. This enables us to focus our effort on the support of the use of the data and building up and maintaining the capacity in Developing Countries which includes training, workshops, networking and outreach. The project sets up a number of pilot cases in Africa, South- and Central America and Asia and is conceived to have a big impact with a limited budget, by building upon existing production (SPOT-VEGETATION a.o.) and dissemination infrastructures (EUMETCast, FengYunCast), existing research projects (GEOLAND, VGT4AFRICA, MERSEA, GOOS, YEOS a.o.) and servicing all relevant environmental end-user communities. The ultimate ambition is to introduce and embed the GEONETCast data in a systematic manner into reporting systems in support of planning and decision making processes. This effort will enable authorities in Developing Countries in fulfilling their increasing monitoring and reporting obligations and help them to better manage their natural resources.
Agency: European Commission | Branch: FP7 | Program: CP | Phase: ENV.2013.6.2-6 | Award Amount: 11.20M | Year: 2013
By 2050, global agricultural productivity will need to increase with at least 70%. In order to guarantee food production for future generations, agricultural production will need to be based on sustainable land management practises. At present, earth observation based (global) crop monitoring systems focus mostly on short-term agricultural forecasts, thereby neglecting longer term environmental effects. However, it is well known that unsustainable cultivation practises may lead to a degradation of the (broader) environment resulting in lower agricultural productivity. As such, agricultural monitoring systems need to be complemented with methods to also assess environmental impacts of change in crop land and shifting cultivation practises. It is thereby important that this is addressed at the global level. SIGMA presents a global partnership of expert institutes in agricultural monitoring, with a strong involvement in GEO and the Global Agricultural Geo-Monitoring (GEO-GLAM) initiative. SIGMA aims to develop innovative methods, based upon the integration of in-situ and earth observation data, to enable the prediction of the impact of crop production on ecosystems and natural resources. The proposed project will address methods to: i. enable sharing and integration of satellite and in situ observations according to GEOSS Data CORE principles; ii. assess the impact of cropland areas and crop land change on other ecosystems; iii. understand and assess shifts in cultivation practises and cropping systems to evaluate impacts on biodiversity and the environment. Furthermore, dedicated capacity building activities are planned to increase national and international capacity to enable sustainable management of agriculture. Lastly, a strong coordinating mechanism will be put in place, through the project partners, between SIGMA and the G20 Global Agricultural Geo-Monitoring Initiative (GEOGLAM), in order to assure transparency and alignment of the SIGMA activities.
Bryja J.,Academy of Sciences of the Czech Republic |
Granjon L.,IRD Montpellier |
Dobigny G.,IRD Montpellier |
Dobigny G.,Center Regional Agrhymet |
And 10 more authors.
Molecular Ecology | Year: 2010
Rodents of the Praomys daltoni complex are typical inhabitants of the Sudanian savanna ecosystem in western Africa and represent a suitable model for testing the effects of Quaternary climatic oscillations on extant genetic variation patterns. Phylogeographical analyses of mitochondrial DNA sequences (cytochrome b) across the distribution range of the complex revealed several well-defined clades that do not support the division of the clade into the two species currently recognized on the basis of morphology, i.e. P.daltoni (Thomas, 1892) and Praomys derooi (Van der Straeten & Verheyen 1978). The observed genetic structure fits the refuge hypothesis, suggesting that only a small number of populations repeatedly survived in distinct forest-savanna mosaic blocks during the arid phases of the Pleistocene, and then expanded again during moister periods. West African rivers may also have contributed to genetic differentiation, especially by forming barriers after secondary contact of expanding populations. The combination of three types of genetic markers (mtDNA sequences, microsatellite loci, cytogenetic data) provides evidence for the presence of up to three lineages, which most probably represent distinct biological species. Furthermore, incongruence between nuclear and mtDNA markers in some individuals unambiguously points towards a past introgression event. Our results highlight the importance of combining different molecular markers for an accurate interpretation of genetic data. © 2010 Blackwell Publishing Ltd.
Leroux L.,CIRAD - Agricultural Research for Development |
Jolivot A.,CIRAD - Agricultural Research for Development |
Begue A.,CIRAD - Agricultural Research for Development |
Lo Seen D.,CIRAD - Agricultural Research for Development |
Zoungrana B.,Center Regional Agrhymet
Remote Sensing | Year: 2014
Accurate cropland maps at the global and local scales are crucial for scientists, government and nongovernment agencies, farmers and other stakeholders, particularly in food-insecure regions, such as Sub-Saharan Africa. In this study, we aim to qualify the crop classes of the MODIS Land Cover Product (LCP) in Sub-Saharan Africa using FAO (Food and Agricultural Organisation) and AGRHYMET (AGRiculture, Hydrology and METeorology) statistical data of agriculture and a sample of 55 very-high-resolution images. In terms of cropland acreage and dynamics, we found that the correlation between the statistical data and MODIS LCP decreases when we localize the spatial scale (from R2 = 0.86 *** at the national scale to R2 = 0.26 *** at two levels below the national scale). In terms of the cropland spatial distribution, our findings indicate a strong relationship between the user accuracy and the fragmentation of the agricultural landscape, as measured by the MODIS LCP; the accuracy decreases as the crop fraction increases. In addition, thanks to the Pareto boundary method, we were able to isolate and quantify the part of the MODIS classification error that could be directly linked to the performance of the adopted classification algorithm. Finally, based on these results, (i) a regional map of the MODIS LCP user accuracy estimates for cropland classes was produced for the entire Sub-Saharan region; this map presents a better accuracy in the western part of the region (43%-70%) compared to the eastern part (17%-43%); (ii) Theoretical user and producer accuracies for a given set of spatial resolutions were provided; the simulated future Sentinel-2 system would provide theoretical 99% user and producer accuracies given the landscape pattern of the region. © 2014 by the authors.
Belem M.,Center Regional Agrhymet |
Muller J.P.,CIRAD - Agricultural Research for Development
Simulation Modelling Practice and Theory | Year: 2013
This paper presents Organization-Role-Entity-Aspect (OREA) model, an organizational model for multi-scale and multi-formalism description of complex systems. OREA is based on the assumption that one issue in complex system simulation is to integrate multi-scale and multi-formalism representation. To achieve this issue, we use an approach based on organization-centered multi-agents systems and Discrete Event System Specification (DEVS) formalism. While the organizational approach allows to deal with an explicit representation of global and local levels, DEVS formalism allows integration of models of different types to describe a system perceived at different scales. Integration of OREA formalism within DEVS allows multi-formalism specification of a model both at global and local levels. In addition, this allows specification of the social structure of a complex system following DEVS formalism. In OREA, the organizational structure is specified without any assumption on entities structure. The roles description in OREA concerns only the detailed description of interactions within organization. The way that individuals conceive their system and make decision is defined through the concepts of aspect. OREA is applied in implementation of a generic model for carbon dynamics simulation in West-African Savanna. Future works would concern the integration of organizational dynamics and holonic representation in OREA. © 2013 Elsevier B.V. All rights reserved.
Panthou G.,Joseph Fourier University |
Vischel T.,Joseph Fourier University |
Lebel T.,Joseph Fourier University |
Blanchet J.,Ecole Polytechnique Federale de Lausanne |
And 2 more authors.
Water Resources Research | Year: 2012
In a world of increasing exposure of populations to natural hazards, the mapping of extreme rainfall remains a key subject of study. Such maps are required for both flood risk management and civil engineering structure design, the challenge being to take into account the local information provided by point rainfall series as well as the necessity of some regional coherency. Two approaches based on the extreme value theory are compared here, with an application to extreme rainfall mapping in West Africa. The first approach is a local fit and interpolation (LFI) consisting of a spatial interpolation of the generalized extreme value (GEV) distribution parameters estimated independently at each station. The second approach is a spatial maximum likelihood estimation (SMLE); it directly estimates the GEV distribution over the entire region by a single maximum likelihood fit using jointly all measurements combined with spatial covariates. Five LFI and three SMLE methods are considered, using the information provided by 126 daily rainfall series covering the period 1950-1990. The methods are first evaluated in calibration. Then the predictive skills and the robustness are assessed through a cross validation and an independent network validation process. The SMLE approach, especially when using the mean annual rainfall as covariate, appears to perform better for most of the scores computed. Using the Niamey 104 year time series, it is also shown that the SMLE approach has the capacity to deal more efficiently with the effect of local outliers by using the spatial information provided by nearby stations.© 2012. American Geophysical Union. All Rights Reserved.