Browsing by Author "Bonhomme, F."
Now showing 1 - 4 of 4
Results Per Page
Sort Options
- Ecological genetics in the North Atlantic: environmental gradients and adaptation at specific lociPublication . Schmidt, P. S.; Serrão, Ester; Pearson, G. A.; Riginos, C.; Rawson, P. D.; Hilbish, Thomas J.; Brawley, S. H.; Trussell, G. C.; Carrington, E.; Wethey, D. S.; Grahame, J. W.; Bonhomme, F.; Rand, D. M.The North Atlantic intertidal community provides a rich set of organismal and environmental material for the study of ecological genetics. Clearly defined environmental gradients exist at multiple spatial scales: there are broad latitudinal trends in temperature, meso-scale changes in salinity along estuaries, and smaller scale gradients in desiccation and temperature spanning the intertidal range. The geology and geography of the American and European coasts provide natural replication of these gradients, allowing for population genetic analyses of parallel adaptation to environmental stress and heterogeneity. Statistical methods have been developed that provide genomic neutrality tests of population differentiation and aid in the process of candidate gene identification. In this paper, we review studies of marine organisms that illustrate associations between an environmental gradient and specific genetic markers. Such highly differentiated markers become candidate genes for adaptation to the environmental factors in question, but the functional significance of genetic variants must be comprehensively evaluated. We present a set of predictions about locus-specific selection across latitudinal, estuarine, and intertidal gradients that are likely to exist in the North Atlantic. We further present new data and analyses that support and contradict these simple selection models. Some taxa show pronounced clinal variation at certain loci against a background of mild clinal variation at many loci. These cases illustrate the procedures necessary for distinguishing selection driven by internal genomic vs. external environmental factors. We suggest that the North Atlantic intertidal community provides a model system for identifying genes that matter in ecology due to the clarity of the environmental stresses and an extensive experimental literature on ecological function. While these organisms are typically poor genetic and genomic models, advances in comparative genomics have provided access to molecular tools that can now be applied to taxa with well-defined ecologies. As many of the organisms we discuss have tight physiological limits driven by climatic factors, this synthesis of molecular population genetics with marine ecology could provide a sensitive means of assessing evolutionary responses to climate change.
- Genomic resources for the aquaculture of European sea bassPublication . Volckaert, F.; Batargias, C.; Bonhomme, F.; Canario, Adelino V. M.; Chistiakov, D.; Choudhuri, J. V.; Galibert, F.; Georgoudis, A.; Haley, Chris; Hellemans, Bart; Kuhl, H.; Kotoulas, Georgios; Law, A.; Libertini, A.; Magoulas, A.; McAndrew, B. J.; Reinhardt, Richard; Senger, Fabrice; Souche, E.; Tsigenopoulos, C.; Whitaker, H. A.The BASSMAP consortium, funded by the European Union, has been set up to improve the understanding of the genome of European sea bass (Dicentrarchus labrax). The specific aim is to locate genes of known function on the physical map and to compare specific regions among perciforms. We have produced an F1 cross of outbred sea bass as mapping panel and a Bacterial Artificial Chromosome library (7× redundancy and 165 kb average insert size). End sequencing of the BAC library is in progress and a radiation hybrid panel is under construction.
- Has time come for the genetic management of sea bass?Publication . Volckaert, F.; Alvarez, M. C.; Argenton, F.; Bonhomme, F.; Chatain, B.; Colombo, L.; Castilho, Rita; Chevassus, B.; Gorshkova, G.; Kohler, M.; Magoulas, A.; Martinez, G.; McAndrew, B. J.; Piferrer, F.; Vandeputte, M.; Zanuy, S.Since 1980 the industrial production of European sea bass has risen considerably up to at least 18,000 MT in 1996 ( see also Josupeit, Aquaculture Europe 20(2):-12, 1995). This growth is remarkable since few were able to culture the species in the seventies. Several "classical" stages of development can be observed; they are typical of a rapidly expanding bioindustry.
- Increasing genomic information in bivalves through new EST collections in four species: Development of new genetic markers for environmental studies and genome evolutionPublication . Tanguy, A.; Bierne, N.; Saavedra, Carlos; Pina, B.; Bachere, E.; Kube, M.; Bazin, E.; Bonhomme, F.; Boudry, P.; Boulo, V.; Boutet, I.; Cancela, Leonor; Dossat, C.; Favrel, P.; Huvet, A.; Jarque, S.; Jollivet, D.; Klages, Sven; Lapegue, S.; Leite, Ricardo; Moal, J.; Moraga, D.; Reinhardt, Richard; Samain, J. F.; Zouros, E.; Canario, Adelino V. M.The generation of EST information is an essential step in the genomic characterisation of species. In the context of the European Network Marine Genomics, a common goal was to significantly increase the amount of ESTs in commercial marine mollusk species and more specifically in the less studied but ecologically and commercially important groups, such as mussel and clam genera. Normalized cDNA libraries were constructed for four different relevant bivalves species (Crassostrea gigas, Mytilus edulis, Ruditapes decussatus and Bathymodiolus azoricus), using numerous tissues and physiological conditions. In this paper, we present the analysis of the 13,013 expressed sequence tags (ESTs) generated. Each EST library was independently assembled and 1300–3000 unique sequences were identified in each species. For the different species, functional categories could be assigned to only about 16 to 27% of ESTs using the GO annotation tool. All sequences have been incorporated into a publicly available database and form the basis for subsequent microarray design, SNP detection and polymorphism analysis, and the placement of novel markers on genetic linkage maps.