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Professeur des universités - Université de Franche-Comté

Contact : Patrick.Giraudoux at

From a train station...

Téléphone :
+33 (0)

Site: La Bouloie (office -112M) 25030 Besançon cedex

This page has English and French versions.

Research interests

My research focuses on wildlife ecology and ecosystem health. It aims in particular at understanding how and on which spatial and temporal scales, the spatial structure of ecological systems determines the population dynamics of small mammals and their predators and pathogens.

It explores the consequences of land use changes: agricultural and pastoral practices, deforestation and reforestation. Questions are based on the conceptual framework of landscape ecology and on the multi-scale analysis of the disturbances of regional ecosystems, with implications in agriculture, health and conservation. They take place at the interface between several disciplines: ecology and health sciences, ecology and agronomy, ecology and ecotoxicology, ecology and conservation biology, etc..

My research is grounded on empirical field studies and mobilises networks of professionals in agriculture, conservation and health. It integrates methods of epidemiology and of population ecology, in a systems approach, in order to understand population interactions, wildlife - humans conflicts, and the processes by which pathogen organisms and chemical toxicants are transmitted/transferred at various spatial and temporal scales. It focuses on long term monitoring of wildlife and pathogen population dynamics at regional scale (e.g. > 10000 km2). Advanced methods of statistical and spatial modelling are combined with remote sensing, GIS and molecular genetics in order to characterize host and pathogen populations.

My study fields are mostly in mountainous areas of Europe (Jura, Alps), of Central Asia (Tibetan plateau, Tien Shan, loess plateaus, Pamir, etc.) and of south-western China (Three parallel rivers, Yunnan), and also in tropical areas such as Sumatra (Indonesia). I have also collaborative works on the high plateaus of northern Mexico and in Africa.

Professional curriculum

Professor of ecology at the University of Franche-Comté since 1998 (Cl.Ex1. CNU since 2010, Cl.Ex2 since 2015), associate-professor at the University of Burgundy from 1992 to 1998, biology-geology teacher in high schools and educational colleges in France (1980-1991) and Niger (1977-1979).

logo IUF Senior member of the Institut Universitaire de France since october 2012

Distinguished professor of the Yunnan University of Finance and Economics, China; co-founder and foreign director of the department of Wildlife management and ecosystem health and foreign director of the laboratory of wildlife management and ecosystem health since 2012


Founder and coordinator of the CNRS-INEE International Research Network (GDRI) "Ecosystem health and environmental disease ecology", since 2013; Co-founder and coordinator of the Long term ecological research (LTER) site "Jurassian Arc" (Zone atelier Arc jurassien) 2013-2016 ; Co-founder and vice-head of the research department Chrono-environment (UMR UFC/CNRS 6249) 2008-2011 ; Head of the Department of Environmental Biology EA3184 usc INRA 2004-2007; Vice-head 2000-2003 ; Co-founder and coordinator of the Master of Science "Ecosystems, contaminants, health" (ECoS) 2004-2014; Co-founder and vice-coordinator of the Master of Science "Environment, health and society", 2000-2003; Member of the board of the WHO Collaborating center for the Prevention and treatment of human echinococoses since 1995 (year of first designation).

Course design, lectures and practical training in population biology, community ecology, landscape ecology, eco-epidemiology, data mining and analysis, bio and geo-statistics and modelling based on modern statistics with R, GRASS-QGIS, etc. at undergraduate and postgraduate levels.

Research funding:
Principal Investigator or co-PI: from the European Union in 1998-2001, 1998, 1997, 1996-98, 1998-2001, 2001-2003; from the French-Chinese Programme of Advanced Research (Agency of the Ministry of Foreign Affairs) in 1995, 1997; from the Research agency of the Ministry of Environment in 1996-98, 1993-97; from the Regional Council of Franche-Comté and the Ministry of Environment (1992-1996, 1997-98, 2000-2006), from the US National Institutes of Health – Fogarty Institute (2001-2005, 2005-2008); from the French-Algerian programme TASSILI (2004-2007); from the Ministry of Agriculture and Fisheries since 2008. Partner of research programmes of the French Environment and Energy Management Agency (ADEME), the French National Research Agency (ANR) 2009-2013, the Japanese society for the promotion of science 2009-2013; 2011-2014 Co-App: Welcome Trust grant "Multi-species transmission of Echinococcus in Central Asia and on the Tibetan Plateau"; 2014-2019 from a consortium including the FREDON/Ministry of Agriculture and the Region of Franche-Comté "Determinants of the decline phase of cyclic Arvicola terrestris populations". 2016, Yunnan Province supported programme about wild elephant - human conflicts.

International consultancy:
in Algeria (ecology: Badji Mokhtar University, Annaba), 1989-1993 & 2003-2010;Japan (eco-epidemiology in Sichuan, China and in Bali, Indonesia: Asahikawa Medical College) and Indonesia (landscape ecology: CIRAD - SMART Research Institute) since 2007; in Mexico (landscape ecology: University of Guadalajara & Centro de Investigación Científica y de Educación Superior de Ensenada) since 2008 (see also last mission here); member of the Echinococcus expert group of the DISCONTOOLS project, FP7 EU, since 2011; 2011-2015 project CHOLTIC: "Cholera outbreaks at lake Tanganyika induced by climate change?", Royal Museum of Central Africa, Belgium; in Ningxia, China 2011-2013, "Does environmental changes drive the spatiotemporal transmission dynamics of Echinococcus spp.?" (grant APP1009539 of the Australian National Health and Medical Research Council). University of Kinshasa, Master ECOM-ALGER since 2013.

Referee for Alauda, Acta Oecologica, Acta Theriologica, Acta tropica, Agriculture ecosystems & environment, Annals of Tropical Medecine and Parasitology, Biological letters, Biological Reviews, BMC Public Health, Chemosphere, Conservation Biology, Emerging infectious diseases, European Journal of Wildlife Research, Folia Zoologica, Helminthologia, Integrative Zoology, International Journal for Parasitology, Journal of Mammalogy, Landscape Ecology, Mammalia, Parasite, Parasite & vectors, Parasitology, Pathogens and Global Health, Pest Management Science, PLoS NTD, PLOS Pathogens, Population Ecology, Transactions of the Royal Society for Tropical Medicine and Hygien, Trends in Parasitology, Revue d’écologie - Terre et Vie, Vector-Borne and Zoonotic Diseases, Zoonoses and Public Health, etc.; Editorial board of Parasite.


For a full list, see “Bibliographie / Publications”, at the top right of the page for accessing HAL via research box, or follow one of the links below:

Patrick Giraudoux

Article selection of the last two years


Comte S, Umhang G, Raton V, Raoul F, Giraudoux P; Combes B; Boué F 2017. Echinococcus multilocularis management by fox culling: an inappropriate paradigm. Preventive Veterinary Medicine. In Press.

Villette P, Afonso E, Couval G, Levret A, Galan G, Tatard C, Cosson JF, Giraudoux P 2017 Consequences of organ choice in describing bacterial assemblages in a rodent population. Epidemiology and Infection. In press.

Bessou, C., Verwilghen, A., Beaudoin-Ollivier, L., Marichal, R., Ollivier, J., Baron, V., Bonneau, X., Carron, M.-P., Snoeck, D., Naim, M., Ketuk Aryawan, A.A., Raoul, F., Giraudoux, P., Surya, E., Sihombing, E., Caliman, J.-P., 2017. Agroecological practices in oil palm plantations: examples from the field. OCL Epub available here.

Li WW, Clauzel C, Dai YC, Wu GS, Giraudoux P, Li L 2017 Improving landscape connectivity for the Yunnan snub-nosed monkey through cropland reforestation using graph theory. Journal for Nature Conservation. 38, 46–55. Available here.

Wu, C., Zhang, W., Ran, B., Fan, H., Wang, H., Guo, B., Zhou, C., Shao, Y., Zhang, W., Giraudoux, P., Knapp, J., Wen, H., Kuang, L., Li, J., 2017. Genetic variation of mitochondrial genes among Echinococcus multilocularis isolates collected in western China. Parasites & Vectors 10, 265. Available here.

Giraudoux P, Couval G, Levret A, Mougin D, Delavelle A 2017 Suivi à long terme d’une zone de pullulation cyclique de campagnols terrestres : le contrôle raisonné des populations est possible ! Fourrages, 230: 169-176.

Giraudoux P. Couval G, Coeurdassier M, Villette P 2017 Agriculture et campagnols : quels impacts sur les écosystèmes franguignons ? Bourgogne-Nature, 25: 253-261.

Shenbrot G, Bannikova A, Giraudoux P, Quéré JP, Raoul F, Lebedev V. 2017 A new recent genus and species of three-toed jerboas (Rodentia: Dipodinae) from China: Alive fossil? Journal of Zoological Systematics and Evolutionary Research. In press.

Romig T, Deplazes P, Jenkins D, Giraudoux P, Massolo A, Craig PS, Wassermann M, Takahashi K, de la Rue M 2017 Ecology and Life Cycle Patterns of Echinococcus Species, Advances in Parasitology. Academic Press. Available on line.

Afonso E, Goydadin AC, Giraudoux P, Farny G 2017 Investigating hybridization between the two sibling bat species Myotis myotis and M. blythii from guano in a natural mixed maternity colony. PLOS One. 2017 Feb 15;12(2):e0170534. Available here.

Prat-Mairet Y, Fourel I, Barrat J, Sage M, Giraudoux P, Coeurdassier M 2017. Non-invasive monitoring of Red fox exposure to rodenticides from scats. Ecological Indicators, 72: 777–783. Available here


Frossard, V., Verneaux, V., Giraudoux, P., 2016. Quantitative assessment of the reliability of chironomid remains in paleoecology: effects of count density and sample size. Journal of Paleolimnology, 1-8. Epub, ahead of print.

Umhang G, Comte S, Hormaz V, Boucher JM, Raton V, Favier S, Raoul F, Giraudoux P, Combes B, Boué F 2016 Retrospective analyses of fox feces by real-time PCR to identify new endemic areas of Echinococcus multilocularis in France. Parasitology Research, 115,(11): 4437-4441.

Swastika K, Dharmawan NS, Suardita IK, Kepeng IN, Wandra T, Sako Y, Okamoto M, Yanagida T, Sasaki M, Giraudoux P, Nakao M. Yoshida T, Eka Diarthini LP, Sudarmaja IM, Purba IE, Budke CM, Ito A, 2016. Swine cysticercosis in the Karangasem district of Bali, Indonesia: an evaluation of serological screening methods. Acta Tropica, 163: 46–53

Afonso E, Tournant P, Foltete JC, Giraudoux P, Baurand PM, Roue S, Canella V, Vey D, Scheifler R 2016 Is the lesser horseshoe bat (Rhinolophus hipposideros) exposed to causes that may have contributed to its decline? A non-invasive approach. Global Ecology and Conservation. 8: 123–137. Available here.

Foltête JC, Couval G, Fontanier M, Vuidel G, Giraudoux P 2016 A graph-based approach to support agro-ecological systems against water vole outbreaks. Ecological Indicators, 71: 87–98. Available here.

Wang, Q., Yu, W.-J., Zhong, B., Shang, J.-Y., Huang, L., Mastin, A., Renqingpengcuo, Huang, Y., Zhang, G.-J., He, W., Giraudoux, P., Wu, W.-P., Craig, P.S., 2016. Seasonal pattern of Echinococcus re-infection in owned dogs in Tibetan communities of Sichuan, China and its implications for control. Infectious Diseases of Poverty 5, 1-8.
Available here

Baudrot V, Perasso A, Fritsch C, Giraudoux P, Raoul F 2016 The adaptation of generalist predators’ diet in a multi-prey context: insights from new functional responses. Ecology, 97: 1832–1841. Available here

Marston C.G., Giraudoux P., Danson F.M., Armitage R.P., Reynolds S.C., Wang Q. Qiu J., Craig P.S. 2016 Vegetation phenology and habitat discrimination: impacts for E.multilocularis transmission host modelling. Remote Sensing of Environment. 176 (2016) 320–327. Available here.

Cadavid Restrepo A.M., Yang Y.R., McManus D.P., Gray D.J., Giraudoux P., Barnes T.S., Williams G.M., Soares Magalhães R.J., Hamm N.A.S., Clements A.C.A. 2016 The Landscape Epidemiology of Echinococcoses. Infectious disease of powerty. 5 (1), pp.13. Available here

Mellink E, Riojas-Lopez M, Giraudoux P 2016 A Neglected Opportunity for Bird Conservation: the Value of a Perennial, Semiarid Agroecosystem in the Llanos de Ojuelos, Central Mexico. Journal of Arid Environments, 124: 1-9. Available here.


Galanaud P, Galanaud A, Giraudoux P 2015 Historical Epidemics Cartography Generated by Spatial Analysis: Mapping the Heterogeneity of Three Medieval "Plagues" in Dijon. PLoS one. 10 (12), pp.e0143866. Available here.

Clauzel C, Deng X, Wu G, Giraudoux P, Li L 2015 Assessing the impact of road developments on connectivity across multiple scales: application to Yunnan snub-nosed monkey conservation. Biological Conservation. 192 (2015) 207–217. Available here

Li, L., Y.D. Xue, G.S. Wu, D.Q. Li and P. Giraudoux. 2015. Potential habitat corridors and restoration areas for the black-and-white snub-nosed monkey Rhinopithecus bieti in Yunnan, China. Oryx 49: 719-726. Available here

Raoul F, Hegglin D, Giraudoux P. 2015 Trophic ecology, behaviour and host population dynamics in Echinococcus multilocularis transmission. Veterinary Parasitology. 213(3–4): 162–171 Available here

Halliez G, Renault F, Vannard E, Farny G, Lavorel S, Giraudoux P 2015 Historical agricultural changes and the expansion of a water vole population in an Alpine valley. Agriculture, ecosystems and environment, 212: 198–206. Available here.

Han J, Bao GS, Jing T, Zhang DQ, Wu TJ, Gao PC, Craig PS, Giraudoux P, Zhang Y, Chen X, He LL 2015. A Newly Discovered Epidemic Area of Echinococcus multilocularis in West Gansu Province in China. PLOS One, on line Available here.

Afonso E, Knapp J , Tête N, Umhang G, Rieffel D, van Kesteren F, Ziadinov I, Craig PS, Torgerson P, Giraudoux P 2015 Echinococcus multilocularis in Kyrgyzstan: similarity in the Asian EmsB genotypic profiles from village populations of Eastern mole voles (Ellobius tancrei) and dogs in the Alay valley. Journal of Helminthology. , 89: 664-670.Available here.

Liccioli S, Giraudoux P, Deplazes P, Massolo A 2015 Wilderness in the ’city’ revisited: different urbes shape transmission of Echinococcus
multilocularis by altering predator and prey communities. Trends in Parasitology. 31 (7) 297–305 available here.

Verwilghen A, Rabillard MA, Chaval Y, Rieffel D, Sinaga MH, Naim M, Caliman JP, Giraudoux P, Raoul F 2015 Relative age determination of Rattus tiomanicus using allometric measurements. Mammalia, 79(1): 81–90 available on line.

Michelat D, Vionnet G, Giraudoux P 2015 Impact des pratiques agricoles sur les communautés d’oiseaux: l’exemple des prairies du Haut-Doubs. Nos Oiseaux, 62 : 67-90. Available here

Sustainable control of grassland small mammals

Candidatures à un stage professionnel de formation par la recherche

Les candidatures à partir de la licence, seront évaluées sur les critères suivants, à justifier dans la demande de stage :

Savoirs, savoir-faire :
- Connaissances spécifiques prouvées en écologie scientifique: notes de l’année en cours, notes et mentions des années antérieures, engagements personnels hors université (ex.: associatif, jobs, etc.), connaissance particulière d’une groupe taxonomique, d’un écosystème,...
- qualité du projet professionnel justifiant la demande de formation
- compétences et motivations en écologie numérique (R) et SIG (QGIS) proportionnée au niveau d’études acquis ou en cours d’acquisition (unité de biostats de L3 en L3, unités d’analyse des données en M1, etc…) et au sujet de stage
- maitrise de l’anglais lu et écrit (maîtrise de l’anglais oral appréciée)
- capacité rédactionnelle et à réaliser une bibliographie internationale

- motivation, dynamisme, enthousiasme et force de proposition
- rigueur, persévérance, autonomie
- anticipation, rigueur dans la gestion du temps
- ouverture d’esprit, qualités relationnelles
- aptitude pour le travail en équipe et sur le terrain, ponctualité, respect des autres et de leur temps
- curiosité scientifique et technique, capacité à évoluer et se former