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Accueil > Recherche > Axe 2 : Origine et Evolution de la Biodiversité > EQ 2.3 : Évolution, Génome, Environnement (EGE) > « EGE » Team

« EGE » Team

Members

Researchers :

Bernard BARASCUD MCF
Rémi CHAPPAZ PR
Jean-Pierre CORNEC MCF (retired)
Caroline COSTEDOAT MCF
Corinne CUOC MCF
Vincent DUBUT IGR
André GILLES MCF
Rémi Grenier AI
Emese MEGLECZ MCF
Gabriel NEVE MCF
Georges OLIVARI MCF (associated)
Nicolas PECH MCF
Yvan PEREZ MCF
Jeannine RAMPAL MCF (retired)

Visiting researchers
Chantal ASPE MCF (LPED, UMR 151 AMU-IRD)

PhD students and post-docs
Emmanuel CORSE Post-doc
Ivan PAZ Post-doc
Arnaud UNGARO PhD student

Research themes

Theme 1 : Systematics

This theme aims at examining understudied biological groups and understanding the evolution of their biodiversity. Our work focuses on evaluating or reevaluating their geographic distribution, their morpho-anatomic features, reproductive behavior, genetic diversity or phylogenetic relationships.
With this goal in mind, we develop new molecular markers from NGS-based microsatellite libraries from various taxonomic groups (e.g. fish and butterflies). We also put effort on acquiring transcriptomes (chaetognaths, acanthocephalans, and fish). Several biological models are studied in the team among which, for continental environment : freshwater fish (Cyprinidae, Cichlidae, Percidae) and their parasites (acanthocephalans) ; butterflies (Papilionidae,Nymphalidae) ; cockroaches (Oxyhaloinae) and for marine environment : copepods, thecosoms and chaetognats.
Our main objective is to eventually integrate those various sources of data to get a better understanding of the evolution of biodiversity in these groups. Applying this research in environment management and species conservation (species that may present a high patrimonial value) is insured through interactions with other teams from IMBE hence leading to solutions in environmental management strategies.

Theme 2 : Eco-genomics

The aim in this theme is to understand the associations between genomes and life history traits in a range of biological systems as well as their evolution in varying environments.
We have been working on hybrid zones of freshwater fish as an integrative model in Mediterranean environment (chondrostoma) for 15 years. We study the evolution of morphological modifications between species and their ontogenetic trajectories, as well as the plasticity of the diet using in-house diet barcoding tools (Eucaryota/18S – methodology that can be generalized to other ecosystems). We also acquire genomic information with nuclear (microsatellites) and mitochondrial sequence markers. The development and analysis of a large number of sequences from 454 pyrosequencing resulted in more than a hundred microsatellite markers, wich allowed estimating genomes diversity both for individual species and hybrid systems. We can now refine the studies focusing on the impact of the environment on different genome regions. This study will be jointly undertaken on a second freshwater fish model, Barbus (collaboration with university of Montpellier, ISEM). Finally the environmental barcoding will be generalized (collaboration with Montpellier SupAgro, CBGP).

Transversal theme for Axis 2 and Axis 6 : Contaminants and genes expression

Contamination of the aquatic environment induced by diverse human activities generates higher concentration and diversity of molecules with a high polluting potential. Moreover, effects related to the global climate change also increase, and directly impact on the quality and quantity of usable water resources, which itself brings consequences on ecosystems functioning.
This eco-genomics theme articulates around the study of ecosystems dynamics (in particular in the Durance basin) and the characterization of the impact of contaminants. This integrative approach combines both chemistry of pollutants (collaboration with LCP laboratory, Aix-Marseille University ; JL Boudenne) and genomics through the development genes expression methods (Illumina) used to establish the relationships between expression levels linked to heterogeneous environment, and persistence of populations. This study aims at answering the current stakes corresponding to an increased societal demand regarding the quality of aquatic ecosystems, the evaluation of risks (ecotoxicology in collaboration with axis 6 at IMBE) and the patrimonial management of biological natural resources.

Publications

Recent publications

2016

  • Sreng L., Temime-Roussel B., Wortham H. and Mourre C. 2016 Chemical Identification of « Maternal Signature Odors » in Rat.Chem. Senses, doi : 10.1093/chemse/bjw124 IF=2.5
  • Gettová L., Gilles A. and Šimková A. 2016 Metazoan parasite communities : support for the biological invasion of Barbus barbus and its hybridization with the endemic Barbus meridionalis. Parasites & Vectors, 9:588 IF=3.23
  • Aspe C., Gilles A. and Jacqué M. 2016. Irrigation canals as tools for climate change adaptation and fish biodiversity management in Southern France. Regional Environmental Change, 16:1975-1984 IF=2.26
  • Fourtune, L., Paz-Vinas, I., Loot, G., Prunier, J.G., Blanchet, S. 2016. Lessons from the fish : a multi-species analysis reveals common processes underlying similar species-genetic diversity correlations. Freshwater biology 61:1830-1845 IF=2.933
  • Harzsch, S., Perez, Y. and Müller, C.H.G. 2016. Chaetognatha. In Structure and Evolution of Invertebrate Nervous Systems, Schmidt-Rhaesa, A. Harzsch, S. and Purschke, G. (eds.) Oxford University Press. Chapter 50, pp.652-664.

2015

  • Nève, G. 2015. Milesia crabroniformis (F., 1775) et deux autres Syrphes nouveaux pour le département de l’Indre-et-Loire (France) (Diptera Syrphidae). L’Entomologiste 71:283-285.
  • Zarzoso-Lacoste, D., Bonnaud, E., Corse, E., Gilles, A., Meglécz, E., Costedoat, C., Gouni, A., Vidal, E. 2015. Improving morphological diet studies with molecular ecology : An application for invasive mammal predation on island birds. Biological Conservation 193:134-142 IF=3.762
  • Nève, G. , Barthélémy, E. 2015. Pigeon ramier. Dans Atlas des Oiseaux nicheurs de Marseille, E. Barthélémy (Coord.), Delachaux et Niestlé, Paris, pp 76-77
  • Nève, G. , Barthélémy, E. 2015. Tourterelle turque. Dans Atlas des Oiseaux nicheurs de Marseille, E. Barthélémy (Coord.), Delachaux et Niestlé, Paris, pp 78-79
  • Nève, G. , Barthélémy, E. 2015. Rougequeue noir. Dans Atlas des Oiseaux nicheurs de Marseille, E. Barthélémy (Coord.), Delachaux et Niestlé, Paris, pp 134-135
  • Nève, G. , Barthélémy, E. 2015. Moineau domestique. Dans Atlas des Oiseaux nicheurs de Marseille, E. Barthélémy (Coord.), Delachaux et Niestlé, Paris, pp 194-195
  • Junker M., Zimmermann M., Ramos A.A., Gros P., Konvicka M., Nève G., Rákosy L., Tammaru T., Castilho R. and Schmitt T. 2015. Three in one – multiple faunal elements within an endangered European butterfly species. PLoS ONE 10(11) : e0142282 IF=3,234
  • Rey O., Fourtune L., Paz-Vinas I., Loot G., Veyssière C., Roche B. and Blanchet S. 2015. Elucidating the spatio-temporal dynamics of an emerging wildlife pathogen using approximate Bayesian computation. Molecular Ecology 24:5348-5363 IF=6,494
  • Paz-Vinas I., Loot G, Stevens VM and Blanchet S. 2015. Evolutionary processes driving spatial patterns of intraspecific genetic diversity in river ecosystems. Molecular Ecology 24:4586-4604. IF=6,494
  • Paz-Vinas I., and Blanchet S. 2015. Dendritic connectivity shapes spatial patterns of genetic diversity : a simulation-based study. Journal of Evolutionary Biology DOI : 10.1111/jeb.12626 IF=3,483
  • Harzsch S., Perez Y. and Müller CHG. 2015. Chaetognatha. In Structure and evolution of invertebrate nervous systems. Schmidt-Rhaesa A., Harzsch S. and Purschke G. (eds.) Oxford University Press (in press).
  • Harzsch S., Müller CHG. and Perez Y. 2015. Chaetognatha. In Evolutionary Developmental Biology of Invertebrates Wanniger A. (ed.), Springer Springer Vienna., ISBN : 978-3-7091-1861-0. pp 215-240.

2014

  • Nève, G. 2014. Papillons de jour, Zygènes et Syrphides d’un pré humide de Crau. Etudes Vauclusiennes, 82:79-84.
  • Gasmi S., Nève G., Pech N., Tekaya S., Gilles A. and Perez Y. 2014. Evolutionary history of Chaetognatha inferred from molecular and morphological data : a case study for body plan simplification. Frontiers in Zoology 11:84 IF=2.30
  • Aspe C., Gilles A. and Jacqué M. 2014. The role of traditional irrigation canals in a long term environmental perspective — A case study in Southern France : The Durance Basin. Journal of Agricultural Science and Technology A, 4:1-12
  • Fridlender A., Pustahija F., Solic M.A, Abadzic S., Bourge M., Pech N., Siljak-Yakovlev S. and Brown S.C. 2014. Is it possible to identify Colchicum neapolitanum s.l. and C. autumnale s.l. in vegetative stage ? Biometry and flow cytometry approaches Botanica Serbica 38(1):43-56
  • Bossu A., Bertaudière-Montès V., Dubut V. and Manel S. 2014 Microsatellite primers in Parietaria judaica (Urticaceae) to assess genetic diversity and structure in urban landscapes. Applications in Plant Sciences 2(9):1400036. doi:10.3732/apps.1400036
  • Chen L., Deltheil T., Turle-Lorenzo N., Liberge M., Rosier C., Watabe I., Sreng L., Amalric M. and Mourre C. 2014. SK channel blockade reverses cognitive and motor deficits induced by nigrostriatal dopamine lesions in rats. International Journal of Neuropsychopharmacology 17(8):1295-1306 doi:10.1017/S1461145714000236 IF:5,641
  • Meglécz E., Pech N., Gilles A., Dubut V., Hingamp P., Trilles A., Grenier R. and Martin, JF. 2014. QDD version 3.1 : A user friendly computer program for microsatellite selection and primer design revisited : experimental validation of variables determining genotyping success rate. Molecular Ecology Resources 14:1302–1313 doi:10.1111/1755-0998.12271 IF:7,432
  • Aspe C., Jacqué M. and Gilles A. 2014. Analyse socio-environnementale des canaux d’irrigation agricole. Des outils d’ajustement aux effets climatiques des variations de la ressource en eau. Revue d’Études en Agriculture et Environnement 95(2):151-176
  • Müller CHG., Rieger V., Perez Y. and Harzsch S. 2014. Immunohistochemical and ultrastructural studies on ciliary sense organs of arrow worms (Chaetognatha). Zoomorphology 133(2):167-189 doi : 10.1007/s00435-013-0211-6 IF:1.133
  • Elliott CP., Enright NJ., Allcock RJN., Gardner MG., Meglécz E., Anthony J. and Krauss SL. 2014. Microsatellite markers from the Ion Torrent : a multi-species contrast to 454 shotgun sequencing. Molecular Ecology Resources, 14(3):554-568 doi : 10.1111/1755-0998.12192 IF:7,432
  • Fouquet A., Santana Cassini C., Baptista Haddad CF., Pech N. and Trefaut Rodrigues M. 2014. Species delimitation, patterns of diversification and historical biogeography of the Neotropical frog genus Adenomera (Anura, Leptodactylidae). Journal of Biogeography 41:855-870 doi : 10.1111/jbi.12250 IF=4,863
  • Perez Y., Müller C., Harzsch S. The Chaetognatha : an anarchistic taxon between Protostomia and Deuterostomia. In : Wägele JW, Bartholomaeus TW, Misof B (eds.). Deep metazoan phylogeny. The backbone of the tree of life : New insights from analyses of molecules, morphology, and theory of data analysis. Berlin : Walter de Gruyter, ISBN:978-3-11-027752-4

2013

  • Aspe C., Jacqué, M. 2013. French environmental sociology facing interdisciplinary research across social and natural sciences, European Scientific Journal, ISSN:1857-7881 IF:1,289
  • Charre G.M., Zavala-Hurtado J.A., Nève G., Ponce-Mendoza A., Corcuera P. 2013. Relationship between habitat traits and bird diversity and composition in selected urban greenareas of Mexico City. Ornitologia Neotropical 24 : 275-293
  • Corse E., Rampal J., Cuoc C., Pech N., Perez Y., and Gilles A. 2013. Phylogenetic analysis of thecosomata blainville, 1824 (holoplanktonic opisthobranchia) using morphological and molecular data. PLoS One, 12 ;8(4):e59439 IF:4,411
  • Gettová L., Gilles A., Berrebi P. and Šimková A. 2013. The 454 GS-FLX isolation and characterisation of microsatellites in Barbus meridionalis and cross-species amplification in three European tetraploid Barbus species : a tool for studying population genetics in hybrid zones. Molecular Ecology Resources, 13:966-968 IF:7,432
  • Grenier R., Costedoat C., Chappaz R., Dubut V. 2013. Two multiplexed sets of 21 and 18 microsatellites for Phoxinus phoxinus (L.) and Gobio gobio (L.) developed by cross-species amplification. Eur J Wildl Res, 59:291-297 IF:1,306
  • Michel F., Meglécz E., Martin JF. and Descimon, H. 2013. Erebia serotina Descimon & de Lesse 1953 (Lepidoptera : Nymphalidae), a recurrent hybrid between two distantly related species. Annales de la Société Entomologique de France, 49:100-116 IF:0,537
  • Paz-Vinas I., Comte L., Chevalier M., Dubut V., Veyssière C., Grenouillet G., Loot G., and Blanchet S. 2013. Combining genetic and demographic data for prioritizing conservation actions : insights from a threatened fish species. Ecology and Evolution, 3 : 2696-2710 IF=1,182
  • Perez Y., Rieger V., Martin E., Müller CH., and Harzsch S. 2013. Neurogenesis in an early protostome relative : progenitor cells in the ventral nerve center of chaetognath hatchlings are arranged in a highly organized geometrical pattern. J Exp Zool B Mol Dev Evol. 320:179-93
  • Sinama M., Gilles A., Costedoat C., Corse E., Olivier J-M., Chappaz R. and Pech N. 2013. Non-homogeneous combination of two porous genomes induces complex body shape trajectories in cyprinid hybrids. Frontiers in Zoology 10:22 IF:4,460
  • Šimková A., Civáňová K., Gettová L. and Gilles A. 2013. Genomic porosity between invasive Chondrostoma nasus and endangered endemic Parachondrostoma toxostoma (Cyprinidae) : the evolution of MHC IIB genes. Plos One, 8(6):e65883 IF:4,411
  • Winkelmann C., Gasmi S., Gretschel G., Müller C. and Perez Y. 2012. Description of Spadella valsalinae sp. nov., a neoendemic benthic chaetognath from Northern Adriatic Sea (Croatia) with remarks on its morphology, phylogeny and biogeography. Organisms Diversity & Evolution13(2):189-202, IF :1,648
  • Zarzoso-Lacoste D., Corse E. and Vidal E. 2013. Improving PCR detection of prey in molecular diet studies : importance of group-specific primer set selection and extraction protocol performances. Molecular Ecology Resources, 13:117-27 IF:7,432

2012

  • Bitja Nyom A.R., Gilles A., Pariselle A., Snoeks J. and Bilong Bilong C.F. 2012. Divergences morphologiques allopatriques et sympatriques de Tilapia kottae (Perciformes, Cichlidae) endémique des lacs Barombi Kotto et Mboandong et affinités avec des Tilapias de la Ligne Volcanique du Cameroun. Cybium, 6:335-348. IF :0,411
  • Corse E., Nève G., Sinama M., Pech N., Costedoat C., Chappaz R., Gilles A. 2012. Plasticity of Ontogenetic Trajectories in Cyprinids : a Source of Evolutionary Novelties. Biol. J. Linn. Soc., 106:342-355. IF :2,166
  • Coudereau J.P., Sreng L., Palme R., Touma C. and Pratte M. 2012. Do social statuses affect the startle reflex in male mice ? Behavioural Brain Research, 234:117-120. IF :3,417
  • Dubut V., Fouquet A., Voisin A., Chappaz R., Costedoat C., and Gilles A. 2012. From Late Miocene to Holocene : Processes of differentiation within Telestes genus, Actinopterygii : Cyprinidae. Plos One, 7(3):e34423. IF :4,411
  • Fouquet A., Noonan B.P., Rodrigues M.T., Pech N., Gilles A., and Gemmell N.J. 2012. Multiple Quaternary Refugia in the Eastern Guiana Shield Revealed by Comparative Phylogeography of 12 Frog Species. Systematic biology, 61(3):461-89 IF :9,532
  • Fouquet A., Ledoux J.B., Dubut V., Noonan B.P. and Scotti I. 2012. The interplay of dispersal limitation, rivers, and historical events shapes the genetic structure of an Amazonian frog. Biol. J. Linn. Soc., 106:356-373. IF :2,166
  • Meglécz E., Pech N., Gilles A., Martin J-F. and Gardner M.G. 2012. A shot in the genome : how accurately do shotgun 454 sequences represent a genome ? BMC Res. Notes., 5:259. Estimated IF :1,654
  • Meglécz E., Nève G., Biffin E. and Gardner M.G. 2012. Breakdown of Phylogenetic Signal : A Survey of Microsatellite Densities in 454 Shotgun Sequences from 154 Non Model Eukaryote Species. PLoS ONE, 7(7):e40861. IF :4,411
  • Nève, G. 2012. Methods for collecting, preserving and studying insects and other terrestrial arthropods. Australian Journal of Entomology 51 : 303-304 IF :0 ,967
  • Simkova A., Navratilova P., Davidova M., Ondrackova M., Sinama M., Chappaz R., Gilles A. and Costedoat C. 2012. Does invasive Chondrostoma nasus shift the parasite community structure of endemic Parachondrostoma toxostoma in sympatric zones ? Parasites & Vectors,5:200 IF :2,940
  • Truchet B., Manrique C., Sreng L., Chaillan F.A., Roman F.S., and Mourre C. 2012. Kv4 potassium channels modulate hippocampal EPSP-spike potentiation and spatial memory in rats. Learning & Memory, 19:282-293 IF :4,219

2011

  • Cuoc C. and Defaye D., 2011. Female genitalia in Cyclopidae (Cyclopoida) : How to reinterpret the internal structures ? Crustacean Monograph, numéro spécial Hommage à B.H. Dussart, 119-148
  • Drees C., Hüfner S., Matern A., Nève G. and Assmann T. 2011. Repeated sampling detects gene flow in a flightless ground beetle in a fragmented landscape. Hereditas, 148(1):36-45 DOI : 10.1111/j.1601-5223.2011.02212.x IF :0,788
  • Gilles A.*, Meglécz E.*, Pech N.*, Ferreira S., Malausa T. and Martin J-F. 2011. Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics, 12:245 IF :4,073
  • Habel J.C., Rödder D., Schmitt T. and Nève G. 2011. Global warming will affect the genetic diversity and uniqueness of Lycaena helle populations. Global Change Biology, 17:194-205. IF :6,862
  • Habel J.C., Finger A., Schmitt T. and Nève G. 2011. Survival of the endangered butterfly Lycaena helle in a fragmented environment : Genetic analyses over 15 years. Journal of Zoological Systematics and Evolutionary Research, 49(1):25-31 ; DOI : 10.1111/j.1439-0469.2010.00575. IF :1,950
  • Karsenti E, Acinas SG, Bork P et al (Tara Oceans Consortium, Gasmi S, Perez Y, Rampal J) 2011. PLoS Biology 9:e1001177 IF :11,452
  • Malausa T., Gilles A., Meglécz E., Blanquart H., Duthoy S., Costedoat C., Dubut V., Pech N., Castagnone-Sereno P., Délye C., Feau N., Frey P., Gauthier P., Guillemaud T., Hazard L., Le Corre V., Lung-Escarmant B., Malé P.J.G., Ferreira S. and Martin J-F. 2011. High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Mol. Ecol. Res., 11:638-644 ( DOI : 10.1111/j.1755-0998.2011.02992.x) IF :3,062
  • Meglécz E., Piry S., Desmarais E., Galan M., Gilles A., Guivier E., Pech N. and Martin J-F. 2011. SESAME (SEquence Sorter & AMplicon Explorer) : Genotyping based on high-throughput multiplex amplicon sequencing. Bioinformatics, 27:277-278 doi : 10.1093/bioinformatics/btq641. IF :5,468
  • Rieger V., Perez Y., Müller C.H., Lacalli T., Hansson B.S., Harzsch S. 2011. Development of the nervous system in hatchlings of Spadella cephaloptera (Chaetognatha), and implications for nervous system evolution in Bilateria. Dev Growth Differ. 53:740-59 IF :2,210
  • Sinama M., Dubut V., Costedoat C., Gilles A., Junker M., Malausa T., Martin J-F., Nève G., Pech N., Schmitt T., Zimmermann M. and Meglécz E. 2011. Challenge for microsatellite development in Lepidoptera : Euphydryas aurinia (Nymphalidae) as a case study. European Journal of Entomology, 108:261-266. IF :1,061

2010

  • Corse E., Costedoat C., Chappaz R., Pech N., Martin J-F. and Gilles A., 2010. PCR-based method for diet analysis in freshwater organisms using 18S rDNA barcoding on faeces. Molecular Ecology Resources, 10:96-108.
  • Dubut V. Grenier R., Meglécz E., Chappaz R., Costedoat C., Danancher D., Descloux S., Malausa T., Martin J-F., Pech N., and Gilles A. 2010. Development of 55 novel polymorphic microsatellite loci for the critically endangered Zingel asper L. (Actinopterygii : Perciformes : Percidae) and cross-species amplification in five other Percids. Eur. J. Wildl. Res., 56:931-938 doi 10.1007/s10344-010-0421-x
  • Dubut V.*, Sinama M.*, Martin J-F., Meglécz E., Fernandez J., Chappaz R., Gilles A., and Costedoat C. 2010. Cross-species amplification of 41 microsatellites in European cyprinids : A tool for evolutionary, population genetics and hybridization studies, BMC Res. Notes., 3:135.
  • Durbec M., Nguyen Thé Fontez B., Grey J., Harrod C., Stolzenberg N., Chappaz R. and Cavalli L. 2010. Biological influences on inter and intraspecific isotopic variability among paired chondrostomes fishes. C.R. Biologies. 333:613–621. Doi 10.1016/j.crvi
  • Fouquet A., Ficetola G.F., Haigh A., and Gemmell N. 2010 Using ecological niche modelling to infer past, present and future environmental suitability for Leiopelma hochstetteri, an endangered New Zealand native frog. Biological Conservation, 143:1375-1384
  • Fouquet A., Green D.M., Waldman B., Bowsher J.H., McBride K.P. and Gemmell N.J. 2010. Phylogeography of Leiopelma hochstetteri reveals strong genetic structure and suggests new conservation priorities. Conservation Genetics, 11:907-919.
  • Gilles A., Costedoat C., Barascud B., Voisin A., Banarescu P., Bianco P.G., Economidis P.S., Marić D., and Chappaz R. 2010. Speciation pattern of Telestes souffia complex (Teleostei, Cyprinidae) in Europe using morphological and molecular markers. Zoologica Scripta, 39:225-242.
  • Martin J-F., Pech N., Meglécz E., Ferreira S., Costedoat C., Dubut V., Malausa T and Gilles A. 2010. Representativeness of microsatellites distribution in genomes as revealed by 454 GS-FLX Titanium pyrosequencing, BMC Genomics, 11:560.
  • Meglécz E., Costedoat C., Dubut V., Gilles A., Malausa T., Pech N. and Martin JF. 2010. QDD : a user friendly program to choose microsatellite markers and design primers from large sequencing projects. Bioinformatics, 26:403-404.
  • Rieger V., Perez Y., Müller C.H.G., Lipke E., Sombke A., Shinn G.L., Hansson B.S. and Harzsch S. 2010. Immunohistochemical analysis and 3D-reconstruction of the cephalic nervous system of Chaetognatha : insights into the evolution of an early bilaterian brain ? Invertebrate Biology, 129:77-104.

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