Lounès Chikhi (561D-E394-2580)

Curriculum Vitae

Lounès Chikhi

Lounas Chikhi completed his PhD in Population Genetics from Université de Paris VI (Pierre et Marie Curie) in 1995. He is Principal Investigator (PI) of the Population and Conservation Genetics group, at Instituto Gulbenkian de Ciência (IGC, Portugal), since 2005 and Directeur de Recherche (1st class) at the Evolution & Diversité Biologique lab (CNRS and Université de Toulouse 3, France) since 2002. L. Chikhi has published over 100 articles in international peer-reviewed journals and 19 book chapters, and is Editor for the Journal Heredity since 2016. He has organised, attended, and delivered presentations at several national and international conferences, workshops, and courses. He has supervised 40 students, one of which is a current PhD candidate at IGC. His current research interests include the population-level genetic consequences of events such as population collapses, expansions, and admixture, as well as changes in population structure and connectivity. L. Chikhi performs thus both theoretical work and applied research, for instance on populations of lemurs inhabiting increasingly fragmented forest mosaics in Madagascar.

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Identification

Personal identification

Full name: Lounès Chikhi

Citation names

CHIKHI, Lounès

Author identifiers

Ciência ID: 561D-E394-2580

Websites

http://www.igc.gulbenkian.pt/lchikhi (Professional)

Languages

Language	Speaking	Reading	Writing	Listening	Peer-review
French (Mother tongue)
English	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)
Portuguese	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)
Italian	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)

Education

	Degree	Classification
1991 - 1995 Concluded	Population Genetics (Docteur) Universite de Paris VI (Pierre et Marie Curie), France "Genetic differentiation in Sardinella aurita and S. maderensis, allozymes and mitochondrial DNA" (THESIS/DISSERTATION)
1990 - 1991 Concluded	Population Biology and Eco-ethology (DEA) Université de Tours, France
1988 - 1991 Concluded	Diplôme d'Ingénieur de l'Institut National Agronomique Paris-Gignon (Diplôme d´études supérieures) AgroParisTech, France

Affiliation

Science

	Category Host institution	Employer
2005 - Current	Principal Investigator (Research)	Instituto Gulbenkian de Ciência, Portugal

2002 - Current	Coordinating Researcher (Research)	Centre National de la Recherche Scientifique, France

2001 - 2002	Postdoc (Research)	University College London Division of Biosciences, United Kingdom
	University College London Division of Biosciences, United Kingdom
2001/01 - 2001/03	Researcher (Research)	Cardiff University, United Kingdom
	Cardiff University, United Kingdom
1999 - 2000	Postdoc (Research)	Queen Mary University of London, United Kingdom
	Queen Mary University of London, United Kingdom
1997 - 1999	Postdoc (Research)	Institute of Zoology of the Zoological Society of London, United Kingdom
	Institute of Zoology of the Zoological Society of London, United Kingdom
1996 - 1997	Researcher (Research)	Università degli Studi di Padova, Italy
	Università degli Studi di Padova, Italy

Projects

Grant

	Designation	Funders
2018/10/01 - Current	Demographic Inference in Structured Populations - DISPO PTDC-BIAEVL/30815/2017 Principal investigator Instituto Gulbenkian de Ciência, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2017/01/01 - 2020/05/31	INFRAGECO (Inference, Fragmentation, Genomics and Conservation) - ERA-NET Biodiversa2005 0000 Principal investigator Instituto Gulbenkian de Ciência, Portugal Stiftung Tierärztliche Hochschule Hannover, Germany Evolution et Diversité Biologique, France Institut de Mathématiques de Toulouse, France	Ongoing
2013/05/01 - 2016/02/29	Perda e fragmentação de habitat ao longo do tempo e do espaço do ponto de vista de vertebrados em Madagáscar PTDC/BIA-BIC/4476/2012 Principal investigator	Concluded
2010/03/01 - 2013/05/31	Efeitos genéticos da perda e fragmentação do habitat: análise comparativa de várias espécies de lémures em duas regiões adjacentes de Madgáscar. PTDC/BIA-BEC/100176/2008 Principal investigator	Concluded
2008/01/02 - 2011/12/31	Respostas demográficas e genéticas à fragmentação e perda de habitat em dois grandes mamíferos florestais PTDC/BIA-BDE/71299/2006 Principal investigator	Concluded
2008/01/01 - 2010/12/31	conservation, phylogéographie et génétique de lémuriens des habitats fragmentés de madagascar et de l'archiipel des comores CD-AOOI07003 Principal investigator Evolution et Diversité Biologique, France	Agence Française pour la Biodiversité Concluded

Contract

	Designation	Funders
2023/03/01 - 2026/02/28	The variation of Iberian sheep under domestication: an archaeogenetics study 2022.04843.PTDC 10.54499/2022.04843.PTDC Universidade de Lisboa Centro de Investigação Interdisciplinar em Sanidade Animal, Portugal Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, Portugal Universidade de Lisboa Centro de Arqueologia, Portugal Instituto Nacional de Investigação Agrária e Veterinária, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2023/03/01 - 2026/02/28	The variation of Iberian sheep under domestication: an archaeogenetics study 2022.04843.PTDC 10.54499/2022.04843.PTDC Universidade de Lisboa Centro de Investigação Interdisciplinar em Sanidade Animal, Portugal Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, Portugal Universidade de Lisboa Centro de Arqueologia, Portugal Instituto Nacional de Investigação Agrária e Veterinária, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2023/03/01 - 2026/02/28	The variation of Iberian sheep under domestication: an archaeogenetics study 2022.04843.PTDC 10.54499/2022.04843.PTDC Universidade de Lisboa Centro de Investigação Interdisciplinar em Sanidade Animal, Portugal Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, Portugal Universidade de Lisboa Centro de Arqueologia, Portugal Instituto Nacional de Investigação Agrária e Veterinária, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2021/01/01 - 2025/12/31	Life Sciences for a Healthy and Sustainable Future LA/P/0087/2020 10.54499/LA/P/0087/2020 Universidade Nova de Lisboa, Portugal Universidade Nova de Lisboa Microbiologia Molecular Estrutural e Celular, Portugal Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Instituto de Biologia Experimental e Tecnológica, Portugal Instituto Gulbenkian de Ciência, Portugal Instituto Português de Oncologia de Lisboa Francisco Gentil EPE, Portugal Universidade de Lisboa Centro de Estudos Comparatistas, Portugal BioResources 4 Sustainability, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2021/01/01 - 2025/12/31	Life Sciences for a Healthy and Sustainable Future LA/P/0087/2020 10.54499/LA/P/0087/2020 Universidade Nova de Lisboa, Portugal Universidade Nova de Lisboa Microbiologia Molecular Estrutural e Celular, Portugal Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Instituto de Biologia Experimental e Tecnológica, Portugal Instituto Gulbenkian de Ciência, Portugal Instituto Português de Oncologia de Lisboa Francisco Gentil EPE, Portugal Universidade de Lisboa Centro de Estudos Comparatistas, Portugal BioResources 4 Sustainability, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2021/01/01 - 2025/12/31	Life Sciences for a Healthy and Sustainable Future LA/P/0087/2020 10.54499/LA/P/0087/2020 Universidade Nova de Lisboa, Portugal Universidade Nova de Lisboa Microbiologia Molecular Estrutural e Celular, Portugal Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Instituto de Biologia Experimental e Tecnológica, Portugal Instituto Gulbenkian de Ciência, Portugal Instituto Português de Oncologia de Lisboa Francisco Gentil EPE, Portugal Universidade de Lisboa Centro de Estudos Comparatistas, Portugal BioResources 4 Sustainability, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2018/10/01 - 2022/06/30	Demographic Inference in Structured Populations PTDC/BIA-EVL/30815/2017 Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2018/10/01 - 2022/06/30	Demographic Inference in Structured Populations PTDC/BIA-EVL/30815/2017 Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2018/10/01 - 2022/06/30	Demographic Inference in Structured Populations PTDC/BIA-EVL/30815/2017 Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2017/01/01 - 2020/11/30	Inference, fragmentation, genomics and conservation BIODIVERSA/0003/2015 Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Instituto Gulbenkian de Ciência, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2017/01/01 - 2020/11/30	Inference, fragmentation, genomics and conservation BIODIVERSA/0003/2015 Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Instituto Gulbenkian de Ciência, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2017/01/01 - 2020/11/30	Inference, fragmentation, genomics and conservation BIODIVERSA/0003/2015 Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Instituto Gulbenkian de Ciência, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2019/01/01 - 2019/12/31	Instituto Gulbenkian de Ciência UID/Multi/04555/2019 Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Instituto Gulbenkian de Ciência, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2019/01/01 - 2019/12/31	Instituto Gulbenkian de Ciência UID/Multi/04555/2019 Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Instituto Gulbenkian de Ciência, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2019/01/01 - 2019/12/31	Instituto Gulbenkian de Ciência UID/Multi/04555/2019 Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Instituto Gulbenkian de Ciência, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2016/06/01 - 2019/11/30	Comparative landscape evolutionary genomics of West-African primates: a contribution of the anthropological biology to their conservation plan PTDC/IVC-ANT/3058/2014 Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Instituto Gulbenkian de Ciência, Portugal Universidade de Lisboa Instituto Superior de Ciências Sociais e Políticas, Portugal Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2016/06/01 - 2019/11/30	Comparative landscape evolutionary genomics of West-African primates: a contribution of the anthropological biology to their conservation plan PTDC/IVC-ANT/3058/2014 Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Instituto Gulbenkian de Ciência, Portugal Universidade de Lisboa Instituto Superior de Ciências Sociais e Políticas, Portugal Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2016/06/01 - 2019/11/30	Comparative landscape evolutionary genomics of West-African primates: a contribution of the anthropological biology to their conservation plan PTDC/IVC-ANT/3058/2014 Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Instituto Gulbenkian de Ciência, Portugal Universidade de Lisboa Instituto Superior de Ciências Sociais e Políticas, Portugal Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2013/05/01 - 2016/02/29	A vertebrate's eye view on habitat loss and fragmentation across time and space in Madagascar PTDC/BIA-BIC/4476/2012 Fundação Calouste Gulbenkian, Portugal Evolution et diversité biologique, France Instituto Gulbenkian de Ciência, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2013/05/01 - 2016/02/29	A vertebrate's eye view on habitat loss and fragmentation across time and space in Madagascar PTDC/BIA-BIC/4476/2012 Fundação Calouste Gulbenkian, Portugal Evolution et diversité biologique, France Instituto Gulbenkian de Ciência, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2013/05/01 - 2016/02/29	A vertebrate's eye view on habitat loss and fragmentation across time and space in Madagascar PTDC/BIA-BIC/4476/2012 Fundação Calouste Gulbenkian, Portugal Evolution et diversité biologique, France Instituto Gulbenkian de Ciência, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2010/02/01 - 2013/07/31	Tracing back animal domestication in Iberia: Clues from zooarchaeology and DNA analysis PTDC/HIS-ARQ/100225/2008 Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal Uppsala Universitet, Sweden University of California Davis, United States Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Instituto Gestao do Patrimonio Arquitectonico e Aqueologico, Portugal Max-Planck-Institut fur Dynamik komplexer technischer Systeme, Germany Instituto Nacional de Investigação Agrária e Veterinária, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2010/02/01 - 2013/07/31	Tracing back animal domestication in Iberia: Clues from zooarchaeology and DNA analysis PTDC/HIS-ARQ/100225/2008 Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal Uppsala Universitet, Sweden University of California Davis, United States Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Instituto Gestao do Patrimonio Arquitectonico e Aqueologico, Portugal Max-Planck-Institut fur Dynamik komplexer technischer Systeme, Germany Instituto Nacional de Investigação Agrária e Veterinária, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2010/02/01 - 2013/07/31	Tracing back animal domestication in Iberia: Clues from zooarchaeology and DNA analysis PTDC/HIS-ARQ/100225/2008 Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal Uppsala Universitet, Sweden University of California Davis, United States Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Instituto Gestao do Patrimonio Arquitectonico e Aqueologico, Portugal Max-Planck-Institut fur Dynamik komplexer technischer Systeme, Germany Instituto Nacional de Investigação Agrária e Veterinária, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2010/03/01 - 2013/05/31	Genetic effects of habitat loss and fragmentation: comparative analysis of several lemur species in two neighbouring regions of Madagascar. PTDC/BIA-BEC/100176/2008 Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Evolution et diversité biologique, France Instituto Gulbenkian de Ciência, Portugal University of Reading, United Kingdom	Fundação para a Ciência e a Tecnologia Concluded
2010/03/01 - 2013/05/31	Genetic effects of habitat loss and fragmentation: comparative analysis of several lemur species in two neighbouring regions of Madagascar. PTDC/BIA-BEC/100176/2008 Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Evolution et diversité biologique, France Instituto Gulbenkian de Ciência, Portugal University of Reading, United Kingdom	Fundação para a Ciência e a Tecnologia Concluded
2010/03/01 - 2013/05/31	Genetic effects of habitat loss and fragmentation: comparative analysis of several lemur species in two neighbouring regions of Madagascar. PTDC/BIA-BEC/100176/2008 Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal Evolution et diversité biologique, France Instituto Gulbenkian de Ciência, Portugal University of Reading, United Kingdom	Fundação para a Ciência e a Tecnologia Concluded
2010/02/01 - 2013/01/31	Exploring pathogen diversity in disease epidemiology and vaccine research PTDC/BIA-BEC/103484/2008 Fundação Calouste Gulbenkian, Portugal Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal Fundação Oswaldo Cruz, Brazil Instituto Gulbenkian de Ciência, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2010/02/01 - 2013/01/31	Exploring pathogen diversity in disease epidemiology and vaccine research PTDC/BIA-BEC/103484/2008 Fundação Calouste Gulbenkian, Portugal Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal Fundação Oswaldo Cruz, Brazil Instituto Gulbenkian de Ciência, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2010/02/01 - 2013/01/31	Exploring pathogen diversity in disease epidemiology and vaccine research PTDC/BIA-BEC/103484/2008 Fundação Calouste Gulbenkian, Portugal Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal Fundação Oswaldo Cruz, Brazil Instituto Gulbenkian de Ciência, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2008/01/02 - 2011/12/31	Demographic and genetic responses to habitat fragmentation and habitat loss in large forest mammals PTDC/BIA-BDE/71299/2006 Fundação Calouste Gulbenkian, Portugal Instituto Gulbenkian de Ciência, Portugal Evolution et diversité biologique, France	Fundação para a Ciência e a Tecnologia Concluded
2008/01/02 - 2011/12/31	Demographic and genetic responses to habitat fragmentation and habitat loss in large forest mammals PTDC/BIA-BDE/71299/2006 Fundação Calouste Gulbenkian, Portugal Instituto Gulbenkian de Ciência, Portugal Evolution et diversité biologique, France	Fundação para a Ciência e a Tecnologia Concluded
2008/01/02 - 2011/12/31	Demographic and genetic responses to habitat fragmentation and habitat loss in large forest mammals PTDC/BIA-BDE/71299/2006 Fundação Calouste Gulbenkian, Portugal Instituto Gulbenkian de Ciência, Portugal Evolution et diversité biologique, France	Fundação para a Ciência e a Tecnologia Concluded

Outputs

Publications

Book chapter	Salgado-Lynn, Milena; Jalil, Mohammad Fairus B.; CHIKHI, Lounès ; Ancrenaz, Marc; Ambu, Laurentius N.; Bruford, Michael W.; Goossens, Benoît. "Landscape Genetics Applied to the Conservation of Primates in Flooded Forests: A Case Study of Orangutans in the Lower Kinabatangan Wildlife Sanctuary". In Primates in Flooded Habitats, edited by Nowak, K.; Barnett; Matsuda, I., 297-303. Cambridge, United Kingdom: Cambridge University Press, 2019. 10.1017/9781316466780.039 Banks, M.A.; Patel, E.R.; CHIKHI, Lounès ; Salmona, J.. "Perrier’s Sifaka Propithecus perrieri Lavauden, 1931: Madagascar (2000, 2002, 2004, 2014, 2016)". In Primates in peril : the world's 25 most endangered primates, 2016-2018, edited by Schwitzer, C.; Mittermeier, R.A.; Rylands, A.B.; Chiozza, F.; Williamson, E.A.; Macfie, E.J.; Wallis, J.; Cotton, A.. IUCN SSC Primate Specialist Group (PSG), International Primatological Society (IPS), Conservation International (CI), Bristol Zoological Society (BZS), 2017. Published Lynn, Milena Salgado; Sechi, Pierfrancesco; CHIKHI, Lounès ; Goossens, Benoit. "Primate conservation genetics at the dawn of conservation genomics". In An Introduction to Primate Conservation, 53-78. Oxford University Press, 2016. 10.1093/acprof:oso/9780198703389.003.0005 Banks, M.A.; Patel, E.R.; CHIKHI, Lounès ; Salmona, Jordi. "Perrier’s Sifaka Propithecus perrieri Lavauden, 1931: Madagascar (2000, 2002, 2004, 2014, 2016)". In Primates in peril : the world's 25 most endangered primates, 2014-2016, edited by Schwitzer, C.; Mittermeier, R.A.; Rylands, A.B.; Chiozza, F.; Williamson, E.A.; Wallis, J.; Cotton, A., 38-41. UCN SSC Primate Specialist Group (PSG), International Primatological Society (IPS), Conservation International (CI), Bristol Zoological Society (BZS), 2015. Published Arenas, M.; Mona, S.; Trochet, A.; Hanulova, A.S.; Ray, N.; CHIKHI, Lounès ; Rasteiro, R.; Schmeller, D.S.; Excoffier, L.. "The scaling of genetic diversity in a changing and fragmented world". In Scaling in Ecology and Biodiversity Conservation, edited by Henle, K.; Potts, S.; Kunin, W.; Matsinos, Y.G.; Simila, J.; Pantis, J.; Grobelnik,; Penev, L.; Settele, J.. 2014. Published Thomas, M.G.; Kivisild, T.; CHIKHI, Lounès ; Burger, J.. "Europe and Western Asia: genetics and population history". In The Encyclopedia of Global Human Migration, edited by Ness, I.; Bellwood, P., 146-156. Wiley-Blackwell, 2013. Published Rakotoarisoa, G.; Radespiel, U.; CHIKHI, Lounès. "Anjiamangirana and Marosely". In Lemurs of Madagascar: A Strategy for their Conservation 2013-2016, edited by Schwitzer, C.; Mittermeier, R.A.; Davies, N.; Johnson, S.; Ratsimbazafy, J.; Razfindramanana, J.; Louis Jr., E.E.; Rajaobelina, S.. IUCN SSC Primate Specialist Group; Bristol Conservation and Science Foundation; Conservation International, 2013. Published CHIKHI, Lounès; Goossens, B.; Jalil, M. F.; James, S. S.; Lackman-Ancrenaz, I.; Bruford, M.W.; Chikhi, L.; et al. "Taxonomy, geographic variation and population genetics of the Bornean and Sumatran orangutans". In Orangutans: geographic variation in behavioural ecology and conservation, 1-14. Reino Unido, United Kingdom: Oxford University Press, 2009. Published • 10.1093/acprof:oso/9780199213276.003.0001 CHIKHI, Lounès; Barbujani, G.; Chikhi, L.. "Human genetic diversity and its history". In Handbook of Statistical Genetics, 0-0. Reino Unido, United Kingdom: Wiley, 2007. Published • 10.1002/9780470061619.ch31 Wheeler, J.C.; CHIKHI, Lounès ; Bruford, M.W.. "Genetic analysis of the origins of domestic South American camelids". In Documenting domestication: new genetic and archaeological paradigms, edited by Zeder, M.A.; Bradley, D.; Emshwiller, E.; Smith, B.D., 329-334. University California Press, 2006. Published Garnier-Géré, P.; CHIKHI, Lounès. "Genetics of large populations and association studies". In Encyclopedia of the Human Genome. 2006. Published CHIKHI, Lounès; Wheeler, J.; Bruford, M.W.. "Case study in genetics of animal domestication: South American camelids". In Documenting Domestication: New Genetic and Archaeological Paradigms, 329-334. Califórnia, United States: University of California Press, 2005. Published CHIKHI, Lounès; Bruford, M.W.; Chikhi, L.; Bruford, M. W.; Bruford, M.. "Mammalian population genetics and genomics". In Mammalian population genetics and genomics, 539-583. Reino Unido, United Kingdom: CABI Publishers, 2005. Published CHIKHI, Lounès; Beaumont, M.A.. "Modelling Human Genetic History". In Encyclopaedia of Genetics, Genomics, Proteomics & Bioinformatics, 0-0. Reino Unido, United Kingdom: Wiley, 2005. Published CHIKHI, Lounès; Cierco-Ayrolles, C.; Abdallah, J.; Boitard, S.; Tsitrone, A.; Veyrieras, J.-B.; Mangin, B.; de Rochambeau, H.. "On linkage disequilibrium measures: methods and aplications studies". In Research Signpost. Recent Research Developments in Genetics and Breeding, 151-180. xxxx, United Kingdom: xxxx, 2004. Published CHIKHI, Lounès; Garnier-Géré, P.. "Genetics of large populations and association studies". In Encyclopedia of the Human Genome. Londres, United Kingdom: Nature Publishing Group, 2003. Published • 10.1002/9780470015902.a0005446.pub2 CHIKHI, Lounès; Barbujani, G.. "Estimating the contribution of Palaeolithic and Neolithic groups to the European gene pool.". In Genes, Fossils and behaviour: an integrated approach to human evolution, 189-204. United Kingdom, United Kingdom: IOS Press, 2001. Published CHIKHI, Lounès; Barbujani, G.. "Genetic population structure of Europeans, inferred from nuclear and mitochondrial AND polymorphism.". In Genetic population structure of Europeans, inferred from nuclear and mitochondrial DNA polymorphisms, 119-129. Londres, United Kingdom: Oxford, 2000. Published CHIKHI, Lounès; Bonhomme, F.; Agnese, J. F.. "The search for genetic differentiation of two sardine species (Sardinella aurita and S. maderensis)". In Dynamics and use of sardinella resources from upwelling off Ghana and Ivory Coast, 152-168. França, France: l`ORSTOM, 1994. Published
Conference paper	CHIKHI, Lounès. "Admixture in Europe Y chromosome data support the Demic Diffusion model". 2002. Published
Journal article	Balboa, Renzo F.; Bertola, Laura D.; Brüniche-Olsen, A.; Rasmussen, Malthe Sebro; Liu, Xiaodong; Besnard, Guillaume; Salmona, Jordi; et al. "African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival". Nature Communications 15 1 (2024): https://doi.org/10.1038/s41467-023-44105-1. Open access • Published • 10.1038/s41467-023-44105-1 Sgarlata, Gabriele Maria; Rasolondraibe, Emmanuel; Salmona, Jordi; Le Pors, Barbara; Ralantoharijaona, Tantely; Rakotonanahary, Ando; Jan, Fabien; et al. "The genomic diversity of the Eliurus genus in northern Madagascar with a putative new species". Molecular Phylogenetics and Evolution 193 (2023): https://doi.org/10.1016/j.ympev.2023.107997. Open access • Published • 10.1016/j.ympev.2023.107997 Ramsay, M.S.; Sgarlata, G.M.; Barratt, C.D.; Salmona, J.; Andriatsitohaina, B.; Kiene, F.; Manzi, S.; et al. "Effects of Forest Fragmentation on Connectivity and Genetic Diversity in an Endemic and an Invasive Rodent in Northwestern Madagascar". Genes 14 7 (2023): https://doi.org/10.3390/genes14071451. Published • 10.3390/genes14071451 Minhós, T; Borges, F; Parreira, B; Oliveira, R; Aleixo-Pais, I; Calvignac, S; Leendertz, F; et al. "The importance of well protected forests for the conservation genetics of West African colobine monkeys". American Journal of Primatology 85 1 (2023): Open access • Published • 10.1002/ajp.23453 Tiley, G. P.; van Elst, T.; Teixeira, H.; Schüßler, D.; Salmona, J.; Blanco, M.B.; Ralison, J.M.; et al. "Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests". Molecular Ecology 31 19 (2022): 4901-4918. https://doi.org/10.1111/mec.16632. Published • 10.1111/mec.16632 Armando Arredondo; Beatriz Mourato; Khoa Nguyen; Simon Boitard; Willy Rodríguez; Olivier Mazet; Lounès Chikhi. "Correction: Inferring number of populations and changes in connectivity under the n-island model". Heredity (2022): https://doi.org/10.1038/s41437-022-00511-7. 10.1038/s41437-022-00511-7 Boitard, Simon; Arredondo, Armando; Chikhi, Lounès; Mazet, Olivier. "Heterogeneity in effective size across the genome: effects on the inverse instantaneous coalescence rate (IICR) and implications for demographic inference under linked selection". Genetics 220 3 (2022): http://dx.doi.org/10.1093/genetics/iyac008. 10.1093/genetics/iyac008 Teixeira, Helena; Salmona, Jordi; Arredondo, Armando; Mourato, Beatriz; Manzi, Sophie; Rakotondravony, Romule; Mazet, Olivier; et al. "Impact of model assumptions on demographic inferences: the case study of two sympatric mouse lemurs in northwestern Madagascar". BMC Ecology and Evolution 21 1 (2021): http://dx.doi.org/10.1186/s12862-021-01929-z. 10.1186/s12862-021-01929-z CHIKHI, Lounès ; Barbujani, Guido. "Luca Cavalli-Sforza, 100 years after his birth". Human Population Genetics and Genomics 1 1 (2021): 1-4. https://doi.org/10.47248/hpgg2101010001. Open access • Published • 10.47248/hpgg2101010001 Teixeira, Helena; Montade, Vincent; Salmona, Jordi; Metzger, Julia; Bremond, Laurent; Kasper, Thomas; Daut, Gerhard; et al. "Past environmental changes affected lemur population dynamics prior to human impact in Madagascar". Communications Biology 4 1 (2021): http://dx.doi.org/10.1038/s42003-021-02620-1. 10.1038/s42003-021-02620-1 Schlebusch, Carina M.; Loog, Liisa; Groucutt, Huw S.; King, Turi; Rutherford, Adam; Barbieri, Chiara; Barbujani, Guido; et al. "Human origins in Southern African palaeo-wetlands? Strong claims from weak evidence". Journal of Archaeological Science 130 (2021): 105374. http://dx.doi.org/10.1016/j.jas.2021.105374. 10.1016/j.jas.2021.105374 Armando Arredondo; Beatriz Mourato; Khoa Nguyen; Simon Boitard; Willy Rodríguez; Olivier Mazet; Lounès Chikhi. "Inferring number of populations and changes in connectivity under the n-island model". Heredity 126 6 (2021): 896-912. https://doi.org/10.1038/s41437-021-00426-9. 10.1038/s41437-021-00426-9 Rasmus Heller; Casia Nursyifa; Genís Garcia-Erill; Jordi Salmona; Lounes Chikhi; Jonas Meisner; Thorfinn Sand Korneliussen; Anders Albrechtsen. "A reference-free approach to analyse RADseq data using standard next generation sequencing toolkits". Molecular Ecology Resources (2021): https://doi.org/10.1111/1755-0998.13324. 10.1111/1755-0998.13324 Parreira, Bárbara; Quéméré, Erwan; Vanpé, Cécile; Carvalho, Inês; Chikhi, Lounès. "Genetic consequences of social structure in the golden-crowned sifaka". Heredity 125 5 (2020): 328-339. http://dx.doi.org/10.1038/s41437-020-0345-5. Published • 10.1038/s41437-020-0345-5 Schüßler, Dominik; Blanco, Marina B.; Salmona, Jordi; Poelstra, Jelmer; Andriambeloson, Jean B.; Miller, Alex; Randrianambinina, Blanchard; et al. "Ecology and morphology of mouse lemurs ( Microcebus spp.) in a hotspot of microendemism in northeastern Madagascar, with the description of a new species". American Journal of Primatology 82 9 (2020): http://dx.doi.org/10.1002/ajp.23180. Published • 10.1002/ajp.23180 Poelstra, Jelmer W; Salmona, Jordi; Tiley, George P; Schüßler, Dominik; Blanco, Marina B; Andriambeloson, Jean B; Bouchez, Olivier; et al. "Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent". Systematic Biology (2020): http://dx.doi.org/10.1093/sysbio/syaa053. Published • 10.1093/sysbio/syaa053 Hending, Daniel; Sgarlata, Gabriele M; Le Pors, Barbara; Rasolondraibe, Emmanuel; Jan, Fabien; Rakotonanahary, Ando N; Ralantoharijaona, Tantely N; et al. "Distribution and conservation status of the endangered Montagne d’Ambre fork-marked lemur (Phaner electromontis)". Journal of Mammalogy 101 4 (2020): 1049-1060. http://dx.doi.org/10.1093/jmammal/gyaa065. Published • 10.1093/jmammal/gyaa065 Le Pors, Barbara; Sgarlata, Gabriele Maria; Salmona, Jordi; Rasolondraibe, Emmanuel; Ralantoharijaona, Tantely; Randriamaroson, Jacquis; Rasoloharijaona, Solofonirina; Andriaholinirina, Nicole Volasoa; CHIKHI, Lounès. "Lemur inventory of the Analabe forest, SAVA region, and observation of an albino Eulemur". Lemur News 22 (2020): 56-63. Published Sgarlata, Gabriele Maria; Salmona, Jordi; Le Pors, Barbara; Rasolondraibe, Emmanuel; Jan, Fabien; Ralantoharijaona, Tantely; Rakotonanahary, Ando; et al. "Genetic and morphological diversity of mouse lemurs ( Microcebus spp.) in northern Madagascar: The discovery of a putative new species?". American Journal of Primatology 81 12 (2019): http://dx.doi.org/10.1002/ajp.23070. Published • 10.1002/ajp.23070 Scerri, Eleanor M. L.; Chikhi, Lounès; Thomas, Mark G.. "Beyond multiregional and simple out-of-Africa models of human evolution". Nature Ecology & Evolution 3 10 (2019): 1370-1372. http://dx.doi.org/10.1038/s41559-019-0992-1. 10.1038/s41559-019-0992-1 da Fonseca, Rute R.; Ureña, Irene; Afonso, Sandra; Pires, Ana Elisabete; Jørsboe, Emil; Chikhi, Lounès; Ginja, Catarina. "Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle". BMC Genomics 20 1 (2019): http://dx.doi.org/10.1186/s12864-019-5685-2. 10.1186/s12864-019-5685-2 Pires, Ana Elisabete; Detry, Cleia; CHIKHI, Lounès ; Rasteiro, Rita; Amorim, Isabel R.; Simões, Fernanda; Matos, José; et al. "The curious case of the Mesolithic Iberian dogs: An archaeogenetic study". Journal of Archaeological Science 105 (2019): 116-129. Published Aleixo-Pais, Isa; Salmona, Jordi; Sgarlata, Gabriele Maria; Rakotonanahary, Ando; Sousa, Ana Priscilla; Parreira, Bárbara; Kun-Rodrigues, Célia; et al. "The genetic structure of a mouse lemur living in a fragmented habitat in Northern Madagascar". Conservation Genetics 20 2 (2018): 229-243. http://dx.doi.org/10.1007/s10592-018-1126-z. 10.1007/s10592-018-1126-z Scerri, Eleanor M.L.; Thomas, Mark G.; Manica, Andrea; Gunz, Philipp; Stock, Jay T.; Stringer, Chris; Grove, Matt; et al. "Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter?". Trends in Ecology & Evolution 33 8 (2018): 582-594. http://dx.doi.org/10.1016/j.tree.2018.05.005. 10.1016/j.tree.2018.05.005 Miller, Alex; Mills, Harriet; Ralantoharijaona, Tantely; Volasoa, Nicole Andriaholinirina; Misandeau, Chantal; Chikhi, Lounès; Bencini, Roberta; Salmona, Jordi. "Forest Type Influences Population Densities of Nocturnal Lemurs in Manompana, Northeastern Madagascar". International Journal of Primatology 39 4 (2018): 646-669. http://dx.doi.org/10.1007/s10764-018-0055-5. 10.1007/s10764-018-0055-5 Grusea, Simona; Rodríguez, Willy; Pinchon, Didier; Chikhi, Lounès; Boitard, Simon; Mazet, Olivier. "Coalescence times for three genes provide sufficient information to distinguish population structure from population size changes". Journal of Mathematical Biology 78 1-2 (2018): 189-224. http://dx.doi.org/10.1007/s00285-018-1272-4. 10.1007/s00285-018-1272-4 Anania, Alessio; Salmona, Jordi; Rasolondraibe, Emmanuel; Jan, Fabien; Chikhi, Lounès; Fichtel, Claudia; Kappeler, Peter M.; Rasoloarison, Rodin. "Taboo adherence and presence of Perrier’s sifaka (Propithecus perrieri) in Andrafiamena forest". Madagascar Conservation & Development 13 1 (2018): 6. http://dx.doi.org/10.4314/mcd.v13i1.1. 10.4314/mcd.v13i1.1 Sgarlata, Gabriele Maria; Salmona, Jordi; Aleixo-Pais, Isa; Rakotonanahary, Ando; Sousa, Ana Priscila; Kun-Rodrigues, Célia; Ralantoharijaona, Tantely; et al. "Genetic Differentiation and Demographic History of the Northern Rufous Mouse Lemur (Microcebus tavaratra) Across a Fragmented Landscape in Northern Madagascar". International Journal of Primatology 39 1 (2018): 65-89. http://dx.doi.org/10.1007/s10764-018-0015-0. 10.1007/s10764-018-0015-0 Pedersen, Casper-Emil T.; Albrechtsen, Anders; Etter, Paul D.; Johnson, Eric A.; Orlando, Ludovic; Chikhi, Lounes; Siegismund, Hans R.; Heller, Rasmus. "A southern African origin and cryptic structure in the highly mobile plains zebra". Nature Ecology & Evolution 2 3 (2018): 491-498. http://dx.doi.org/10.1038/s41559-017-0453-7. 10.1038/s41559-017-0453-7 Sharma, Reeta; Goossens, Benoit; Heller, Rasmus; Rasteiro, Rita; Othman, Nurzhafarina; Bruford, Michael W.; Chikhi, Lounès. "Genetic analyses favour an ancient and natural origin of elephants on Borneo". Scientific Reports 8 1 (2018): http://dx.doi.org/10.1038/s41598-017-17042-5. 10.1038/s41598-017-17042-5 Chikhi, L.; Rodríguez, W.; Grusea, S.; Santos, P.; Boitard, S.; Mazet, O.. "The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: Insights into demographic inference and model choice". Heredity 120 1 (2018): 13-24. http://www.scopus.com/inward/record.url?eid=2-s2.0-85037727450&partnerID=MN8TOARS. 10.1038/s41437-017-0005-6 Knoop, Simon Benjamin; CHIKHI, Lounès ; Salmona, Jordi. "Mouse lemurs’ use of degraded habitat: a review of the literature". Lemur news 21 (2018): http://static1.1.sqspcdn.com/static/f/1200343/27923521/1528375088833/LN21.pdf?token=TiwILptZcE2X6JhGbHkekHQJi1k%3D. Open access • Published Salmona, Jordi; Rasolondraibe, Emmanuel; Jan, Fabien; Rakotonanahary, Ando; Ralantoharijaona, Tantely; Le Pors, Barbara; Ousseni, Dhurham Said Ali; et al. "The unique and isolated Phaner population of Analafiana (Vohémar, SAVA)". Lemur news 21 (2018): http://static1.1.sqspcdn.com/static/f/1200343/27923521/1528375088833/LN21.pdf?token=ULSsco7NUMYieHOxrXbNYa%2FBOVQ%3D. Published Salmona, J.; Rasolondraibe, E.; Jan, F.; Rakotonanahary, A.N.; Ralantoharijaona, T.; Le Pors, B.; Ousseni, D.S.; et al. "Re-discovering the forgotten Phaner population of the small and isolated Analafiana forest (Vohémar, SAVA)". Lemur News 21 (2018): 31-36. Published Salmona, J.; Heller, R.; Quéméré, E.; Chikhi, L.. "Climate change and human colonization triggered habitat loss and fragmentation in Madagascar". Molecular Ecology 26 19 (2017): 5203-5222. http://www.scopus.com/inward/record.url?eid=2-s2.0-85021444039&partnerID=MN8TOARS. 10.1111/mec.14173 López, S.; Thomas, M.G.; van Dorp, L.; Ansari-Pour, N.; Stewart, S.; Jones, A.L.; Jelinek, E.; et al. "The Genetic Legacy of Zoroastrianism in Iran and India: Insights into Population Structure, Gene Flow, and Selection". American Journal of Human Genetics 101 3 (2017): 353-368. http://www.scopus.com/inward/record.url?eid=2-s2.0-85028026843&partnerID=MN8TOARS. 10.1016/j.ajhg.2017.07.013 Prunier, J.G.; Dubut, V.; Chikhi, L.; Blanchet, S.. "Contribution of spatial heterogeneity in effective population sizes to the variance in pairwise measures of genetic differentiation". Methods in Ecology and Evolution 8 12 (2017): 1866-1877. http://www.scopus.com/inward/record.url?eid=2-s2.0-85022335273&partnerID=MN8TOARS. 10.1111/2041-210X.12820 Minhós, T.; Chikhi, L.; Sousa, C.; Vicente, L.M.; Ferreira da Silva, M.; Heller, R.; Casanova, C.; Bruford, M.W.. "Genetic consequences of human forest exploitation in two colobus monkeys in Guinea Bissau". Biological Conservation 194 (2016): 194-208. http://www.scopus.com/inward/record.url?eid=2-s2.0-84960928793&partnerID=MN8TOARS. 10.1016/j.biocon.2015.12.019 Ottoni, C.; Rasteiro, R.; Willet, R.; Claeys, J.; Talloen, P.; Van de Vijver, K.; Chikhi, L.; Poblome, J.; Decorte, R.. "Comparing maternal genetic variation across two millennia reveals the demographic history of an ancient human population in southwest Turkey". Royal Society Open Science 3 2 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84959422332&partnerID=MN8TOARS. 10.1098/rsos.150250 Mazet, O.; Rodríguez, W.; Grusea, S.; Boitard, S.; Chikhi, L.. "On the importance of being structured: Instantaneous coalescence rates and human evolution-lessons for ancestral population size inference?". Heredity 116 4 (2016): 362-371. http://www.scopus.com/inward/record.url?eid=2-s2.0-84960388143&partnerID=MN8TOARS. 10.1038/hdy.2015.104 Goossens, B.; Sharma, R.; Othman, N.; Kun-Rodrigues, C.; Sakong, R.; Ancrenaz, M.; Ambu, L.N.; et al. "Habitat fragmentation and genetic diversity in natural populations of the Bornean elephant: Implications for conservation". Biological Conservation 196 (2016): 80-92. http://www.scopus.com/inward/record.url?eid=2-s2.0-84958811362&partnerID=MN8TOARS. 10.1016/j.biocon.2016.02.008 Sgarlata, G.M.; Salmona, J.; Razanaparany, T.P.; Rabarivola, C.J.; Jan, F.; Rasolondraibe, E.; Andriaholinirina, N.V.; et al. "Mitochondrial genetic diversity in the crowned sifaka (Propithecus coronatus) in a fragmented landscape". Primate Conservation 30 1 (2016): 39-57. http://www.scopus.com/inward/record.url?eid=2-s2.0-85031747480&partnerID=MN8TOARS. J Salmona; M Banks; TN Ralantoharijaona; E Rasolondraibe; R Zaranaina; A Rakotonanahary; S Wohlhauser; BJ Sewall; L Chikhi. "The value of the spineless monkey orange tree (Strychnos madagascariensis) for conservation of northern sportive lemurs (Lepilemur milanoii and L. ankaranensis)". Madagascar Conservation & Development 10 2 (2015): 53-53. https://doi.org/10.4314%2Fmcd.v10i2.3. 10.4314/mcd.v10i2.3 Salmona, J.; Teixeira, H.; Rasolondraibe, E.; Aleixo-Pais, I.; Kun-Rodrigues, C.; Rakotonanahary, A.N.; Jan, F.; et al. "Genetic Diversity, Population Size, and Conservation of the Critically Endangered Perrier’s Sifaka (Propithecus perrieri)". International Journal of Primatology 36 6 (2015): 1132-1153. http://www.scopus.com/inward/record.url?eid=2-s2.0-84953636884&partnerID=MN8TOARS. 10.1007/s10764-015-9881-x Parreira, B.R.; Chikhi, L.. "On some genetic consequences of social structure, mating systems, dispersal, and sampling". Proceedings of the National Academy of Sciences of the United States of America 112 26 (2015): E3318-E3326. http://www.scopus.com/inward/record.url?eid=2-s2.0-84937832635&partnerID=MN8TOARS. 10.1073/pnas.1414463112 Mazet, O.; Rodríguez, W.; Chikhi, L.. "Demographic inference using genetic data from a single individual: Separating population size variation from population structure". Theoretical Population Biology 104 (2015): 46-58. http://www.scopus.com/inward/record.url?eid=2-s2.0-84938719094&partnerID=MN8TOARS. 10.1016/j.tpb.2015.06.003 Amir, N.; Sahnoune, M.; Chikhi, L.; Atmani, D.. "STR-based genetic structure of the Berber population of Bejaia (Northern Algeria) and its relationships to various ethnic groups". Gene 574 1 (2015): 140-148. http://www.scopus.com/inward/record.url?eid=2-s2.0-84943581825&partnerID=MN8TOARS. 10.1016/j.gene.2015.08.002 Alves, J.M.; Lima, A.C.; Pais, I.A.; Amir, N.; Celestino, R.; Piras, G.; Monne, M.; et al. "Reassessing the evolutionary history of the 17q21 inversion polymorphism". Genome Biology and Evolution 7 12 (2015): 3239-3248. http://www.scopus.com/inward/record.url?eid=2-s2.0-84982128086&partnerID=MN8TOARS. 10.1093/gbe/evv214 Miller, A.; Ralantoharijaona, T.; Misandeau, C.; Andriaholinirina, Nicole Volasoa; Mills, H.; Bencini, R; CHIKHI, Lounès ; Salmona, J.. "A biological survey of Antsahanadraitry forest (Alan'Antanetivy corridor, Manompana) reveals the presence of the hairy-eared dwarf lemur (Allocebus trichotis)". Lemur news 19 (2015): Published J. M. Alves; L. Chikhi; A. Amorim; A. M. Lopes. "The 8p23 Inversion Polymorphism Determines Local Recombination Heterogeneity across Human Populations". Genome Biology and Evolution 6 4 (2014): 921-930. http://dx.doi.org/10.1093/gbe/evu064. 10.1093/gbe/evu064 Razafindramanana, J.; King, T.; Chikhi, L.; Schwitzer, C.; Ratsimbazafy, J.. "Special section on the crowned sifaka propithecus coronatus: Introduction". Primate Conservation 28 1 (2014): 39-42. http://www.scopus.com/inward/record.url?eid=2-s2.0-84926489885&partnerID=MN8TOARS. 10.1896/052.028.0115 Salmona, J.; Rasolondraibe, E.; Jan, F.; Besolo, A.; Rakotoarisoa, H.; Meyler, S.V.; Wohlhauser, S.; Rabarivola, C.; Chikhi, L.. "Conservation status and abundance of the crowned sifaka (Propithecus coronatus)". Primate Conservation 28 1 (2014): 73-83. http://www.scopus.com/inward/record.url?eid=2-s2.0-84926453641&partnerID=MN8TOARS. 10.1896/052.028.0122 Maja P Greminger; Kai N Stölting; Alexander Nater; Benoit Goossens; Natasha Arora; Rémy Bruggmann; Andrea Patrignani; et al. "Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms". BMC Genomics 15 1 (2014): 16-16. http://dx.doi.org/10.1186/1471-2164-15-16. 10.1186/1471-2164-15-16 Kun-Rodrigues, C.; Salmona, J.; Besolo, A.; Rasolondraibe, E.; Rabarivola, C.; Marques, T.A.; Chikhi, L.. "New density estimates of a threatened sifaka species (propithecus coquereli) in ankarafantsika national park". American Journal of Primatology 76 6 (2014): 515-528. http://www.scopus.com/inward/record.url?eid=2-s2.0-84899976653&partnerID=MN8TOARS. 10.1002/ajp.22243 Schwitzer, C.; Mittermeier, R.A.; Johnson, S.E.; Donati, G.; Irwin, M.; Peacock, H.; Ratsimbazafy, J.; et al. "Averting lemur extinctions amid Madagascar's political crisis". Science 343 6173 (2014): 842-843. http://www.scopus.com/inward/record.url?eid=2-s2.0-84894278452&partnerID=MN8TOARS. 10.1126/science.1245783 Besnard, G.; Dupuy, J.; Larter, M.; Cuneo, P.; Cooke, D.; Chikhi, L.. "History of the invasive African olive tree in Australia and Hawaii: Evidence for sequential bottlenecks and hybridization with the Mediterranean olive". Evolutionary Applications 7 2 (2014): 195-211. http://www.scopus.com/inward/record.url?eid=2-s2.0-84892978146&partnerID=MN8TOARS. 10.1111/eva.12110 Schwitzer, C.; Chikhi, L.; Donati, G.; Irwin, M.; Johnson, S.E.; Mittermeier, R.A.; Peacock, H.; et al. "Protecting lemurs: Response". Science 344 6182 (2014): 358-360. http://www.scopus.com/inward/record.url?eid=2-s2.0-84899516361&partnerID=MN8TOARS. 10.1126/science.344.6182.358-c Salmona, J.; Jan, F.; Rasolondraibe, E.; Besolo, A.; Ousseni, D.S.; Beck, A.; Zaranaina, R.; et al. "Extensive survey of the endangered coquerel's sifaka Propithecus coquereli". Endangered Species Research 25 2 (2014): 175-183. http://www.scopus.com/inward/record.url?eid=2-s2.0-84940376832&partnerID=MN8TOARS. 10.3354/esr00622 Salmona, J.; Rakotonanahary, A.N.; Thani, I.M.; Zaranaina, R.; Ralantoharijaona, T.; Jan, F.; Rasolondraibe, E.; et al. "Estimation des densités et tailles de population du Microcèbe Roux du Nord de (Microcebus tavaratra) dans la région Loky-Manambato (Daraina)". Lemur news 18 (2014): Salmona, J.; Ralantoharijaona, T.; Thani, I.M.; Rakotonanahary, A.N.; Zaranaina, R.; Jan, F.; Rasolondraibe, E.; et al. "Daraina sportive lemur (Lepilemur milanoii) density and population size estimates in most of its distribution range: the Loky-Manambato region". Lemur news 18 (2014): Sharma, R.; Goossens, B.; Kun-Rodrigues, C.; Teixeira, T.; Othman, N.; Boone, J.Q.; Jue, N.K.; et al. "Erratum: Two different high throughput sequencing approaches identify thousands of de novo genomic markers for the genetically depleted bornean elephant". PLoS ONE 8 7 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84898745951&partnerID=MN8TOARS. 10.1371/annotation/8aaa2a9c-9c15-4214-808d-db8b0bd8ab88 Vanpé, C.; Salmona, J.; Pais, I.; Kun-Rodrigues, C.; Pichon, C.; Meyler, S.V.; Rabarivola, C.; et al. "Noninvasive molecular sexing: An evaluation and validation of the SRY- and amelogenin-based method in three new lemur species". American Journal of Physical Anthropology 150 3 (2013): 492-503. http://www.scopus.com/inward/record.url?eid=2-s2.0-84874420680&partnerID=MN8TOARS. 10.1002/ajpa.22222 Quéméré, E.; Hibert, F.; Miquel, C.; Lhuillier, E.; Rasolondraibe, E.; Champeau, J.; Rabarivola, C.; et al. "A DNA Metabarcoding Study of a Primate Dietary Diversity and Plasticity across Its Entire Fragmented Range". PLoS ONE 8 3 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84875104888&partnerID=MN8TOARS. 10.1371/journal.pone.0058971 Rasteiro, R.; Chikhi, L.. "Female and Male Perspectives on the Neolithic Transition in Europe: Clues from Ancient and Modern Genetic Data". PLoS ONE 8 4 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84876262517&partnerID=MN8TOARS. 10.1371/journal.pone.0060944 Heller, R.; Chikhi, L.; Siegismund, H.R.. "The Confounding Effect of Population Structure on Bayesian Skyline Plot Inferences of Demographic History". PLoS ONE 8 5 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84877134593&partnerID=MN8TOARS. 10.1371/journal.pone.0062992 Paz-Vinas, I.; Quéméré, E.; Chikhi, L.; Loot, G.; Blanchet, S.. "The demographic history of populations experiencing asymmetric gene flow: Combining simulated and empirical data". Molecular Ecology 22 12 (2013): 3279-3291. http://www.scopus.com/inward/record.url?eid=2-s2.0-84879016166&partnerID=MN8TOARS. 10.1111/mec.12321 Salmona, J.; Jan, F.; Rasolondraibe, E.; Zaranaina, R.; Ousseni, D.S.; Mohamed-Thani, I.; Rakotonanahary, A.N.; et al. "Survey of the Critically Endangered Perrier's sifaka (Propithecus perrieri) across most of its distribution range". Lemur news 17 (2013): 9-12. Sabin, E.; Delarue, C.; Misandeau, C.; Besse, P.; Salmona, J.; CHIKHI, Lounès. "Taille de la population d'Avahi laniger dans la réserve d'Ambodiriana-Manompana, Nord-est de Madagascar". Lemur news 17 (2013): 70-72. Published Garnier-Géré, P.; CHIKHI, Lounès. "Population Subdivision, Hardy–Weinberg Equilibrium and the Wahlund Effect". eLS (2013): https://onlinelibrary.wiley.com/doi/full/10.1002/9780470015902.a0005446.pub3. Published Gamba, C.; FernÚndez, E.; Tirado, M.; Deguilloux, M.F.; Pemonge, M.H.; Utrilla, P.; Edo, M.; et al. "Ancient DNA from an Early Neolithic Iberian population supports a pioneer colonization by first farmers". Molecular Ecology 21 1 (2012): 45-56. http://www.scopus.com/inward/record.url?eid=2-s2.0-84155160700&partnerID=MN8TOARS. 10.1111/j.1365-294X.2011.05361.x Sousa, V.C.; Beaumont, M.A.; Fernandes, P.; Coelho, M.M.; Chikhi, L.. "Population divergence with or without admixture: Selecting models using an ABC approach". Heredity 108 5 (2012): 521-530. http://www.scopus.com/inward/record.url?eid=2-s2.0-84859974526&partnerID=MN8TOARS. 10.1038/hdy.2011.116 Meyler, S.V.; Salmona, J.; Ibouroi, M.T.; Besolo, A.; Rasolondraibe, E.; Radespiel, U.; Rabarivola, C.; Chikhi, L.. "Density Estimates of Two Endangered Nocturnal Lemur Species From Northern Madagascar: New Results and a Comparison of Commonly Used Methods". American Journal of Primatology 74 5 (2012): 414-422. http://www.scopus.com/inward/record.url?eid=2-s2.0-84859898614&partnerID=MN8TOARS. 10.1002/ajp.21997 Rasteiro, R.; Bouttier, P.A.; Sousa, V.C.; Chikhi, L.. "Investigating sex-biased migration during the Neolithic transition in Europe, using an explicit spatial simulation framework.". Proceedings. Biological sciences / The Royal Society 279 1737 (2012): 2409-2416. http://www.scopus.com/inward/record.url?eid=2-s2.0-84862232165&partnerID=MN8TOARS. 10.1098/rspb.2011.2323 Quéméré, E.; Amelot, X.; Pierson, J.; Crouau-Roy, B.; Chikhi, L.. "Genetic data suggest a natural prehuman origin of open habitats in northern Madagascar and question the deforestation narrative in this region". Proceedings of the National Academy of Sciences of the United States of America 109 32 (2012): 13028-13033. http://www.scopus.com/inward/record.url?eid=2-s2.0-84864703849&partnerID=MN8TOARS. 10.1073/pnas.1200153109 Salmona, J.; Salamolard, M.; Fouillot, D.; Ghestemme, T.; Larose, J.; Centon, J.-F.; Sousa, V.; et al. "Signature of a pre-human population decline in the critically endangered reunion island endemic forest bird coracina newtoni". PLoS ONE 7 8 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84865173885&partnerID=MN8TOARS. 10.1371/journal.pone.0043524 Sharma, R.; Arora, N.; Goossens, B.; Nater, A.; Morf, N.; Salmona, J.; Bruford, M.W.; et al. "Effective Population Size Dynamics and the Demographic Collapse of Bornean Orang-Utans". PLoS ONE 7 11 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84869234346&partnerID=MN8TOARS. 10.1371/journal.pone.0049429 Sharma, R.; Goossens, B.; Kun-Rodrigues, C.; Teixeira, T.; Othman, N.; Boone, J.Q.; Jue, N.K.; et al. "Two Different High Throughput Sequencing Approaches Identify Thousands of De Novo Genomic Markers for the Genetically Depleted Bornean Elephant". PLoS ONE 7 11 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84869784350&partnerID=MN8TOARS. 10.1371/journal.pone.0049533 Alves, J.M.; Lopes, A.M.; Chikhi, L.; Amorim, A.. "On the structural plasticity of the human genome: Chromosomal inversions revisited". Current Genomics 13 8 (2012): 623-632. http://www.scopus.com/inward/record.url?eid=2-s2.0-84870196858&partnerID=MN8TOARS. 10.2174/138920212803759703 Sousa, V.; Penha, F.; Pala, I.; CHIKHI, Lounès ; Coelho, M. M.; Sousa, V. C.; Chikhi, L.. "Conservation genetics of a critically endangered Iberian minnow: evidence of population decline and extirpations". Animal Conservation 13 2 (2010): 162-171. http://dx.doi.org/10.1111/j.1469-1795.2009.00317.x. Published • 10.1111/j.1469-1795.2009.00317.x Beaumont, M. A.; Nielsen, R.; Robert, C.; Hey, J.; Gaggiotti, O.; Knowles, L.; Estoup, A.; et al. "In defence of model-based inference in phylogeography REPLY". Molecular Ecology 19 3 (2010): 436-446. Published • 10.1111/j.1365-294X.2009.04515.x Bray, T. C.; Sousa, V. C.; Parreira, B.; Bruford, M. W.; Chikhi, L.. "2BAD: an application to estimate the parental contributions during two independent admixture events". Molecular Ecology Resources 10 3 (2010): 538-541. Published • 10.1111/j.1755-0998.2009.02766.x Quemere, E.; Champeau, J.; Besolo, A.; Rasolondraibe, E.; Rabarivola, C.; Crouau-Roy, B.; Chikhi, L.. "Spatial Variation in Density and Total Size Estimates in Fragmented Primate Populations: The Golden-Crowned Sifaka (Propithecus tattersalli)". American Journal of Primatology 72 1 (2010): 72-80. Published • 10.1002/ajp.20754 Quemere, E.; Crouau-Roy, B.; Rabarivola, C.; Louis, E. E.; Chikhi, L.. "Landscape genetics of an endangered lemur (Propithecus tattersalli) within its entire fragmented range". Molecular Ecology 19 8 (2010): 1606-1621. Published • 10.1111/j.1365-294X.2010.04581.x Bruford, M.W.; Ancrenaz, M.; Chikhi, L.; Lackman-Ancrenaz, I.; Andau, M.; Ambu, L.; Goossens, B.. "Projecting genetic diversity and population viability for the fragmented orang-utan population in the Kinabatangan floodplain, Sabah, Malaysia". Endangered Species Research 12 3 (2010): 249-261. http://www.scopus.com/inward/record.url?eid=2-s2.0-78449287751&partnerID=MN8TOARS. 10.3354/esr00295 Schneider, N.; Chikhi, L.; Currat, M.; Radespiel, U.. "Signals of recent spatial expansions in the grey mouse lemur (Microcebus murinus)". BMC Evolutionary Biology 10 1 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77951028543&partnerID=MN8TOARS. 10.1186/1471-2148-10-105 Salmona, J.; Dawson, D.A.; Fouillot, D.; Ghestemme, T.; Thebaud, C.; Chikhi, L.; Salamolard, M.. "The utility of existing passerine microsatellite markers for genetic studies in endangered species: As demonstrated for a critically endangered forest bird endemic to réunion island, the réunion cuckooshrike (Coracina newtoni)". Conservation Genetics Resources 2 SUPPL.1 (2010): 361-364. http://www.scopus.com/inward/record.url?eid=2-s2.0-84859938085&partnerID=MN8TOARS. 10.1007/s12686-010-9254-x Chikhi, L.; Sousa, V.C.; Luisi, P.; Goossens, B.; Beaumont, M.A.. "The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes". Genetics 186 3 (2010): 983-995. http://www.scopus.com/inward/record.url?eid=2-s2.0-78951476873&partnerID=MN8TOARS. 10.1534/genetics.110.118661 Quéméré, Erwan; Louis, Edward E.; Ribéron, Alexandre; CHIKHI, Lounès ; Crouau-Roy, Brigitte; Quéméré, E.; Louis Jr., E.E.; et al. "Non-invasive conservation genetics of the critically endangered golden-crowned sifaka (Propithecus tattersalli): high diversity and significant genetic differentiation over a small range". Conservation Genetics 11 3 (2009): 675-687. http://dx.doi.org/10.1007/s10592-009-9837-9. 10.1007/s10592-009-9837-9 Bray, T. C.; Chikhi, L.; Sheppy, A. J.; Bruford, M. W.. "The population genetic effects of ancestry and admixture in a subdivided cattle breed". Animal Genetics 40 4 (2009): 393-400. Published • 10.1111/j.1365-2052.2009.01850.x Craul, M.; Chikhi, L.; Sousa, V. C.; Olivieri, G. L.; Rabesandratana, A.; Zimmermann, E.; Radespiel, U.. "Influence of forest fragmentation on an endangered large-bodied lemur in northwestern Madagascar". Biological Conservation 142 12 (2009): 2862-2871. Published • 10.1016/j.biocon.2009.05.026 Giovannini, A.; Zanghirati, G.; Beaumont, M. A.; Chikhi, L.; Barbujani, G.. "A novel parallel approach to the likelihood-based estimation of admixture in population genetics". Bioinformatics 25 11 (2009): 1440-1441. Published • 10.1093/bioinformatics/btp136 Parreira, B.; Trussart, M.; Sousa, V. C.; Hudson, R.; Chikhi, L.. "SPAms: A user-friendly software to simulate population genetics data under complex demographic models". Molecular Ecology Resources 9 3 (2009): 749-753. Published • 10.1111/j.1755-0998.2009.02533.x Rasteiro, R.; Chikhi, L.. "Revisiting the peopling of Japan: an admixture perspective". Journal of Human Genetics 54 6 (2009): 349-354. Published • 10.1038/jhg.2009.39 Sousa, V. C.; Fritz, M.; Beaumont, M. A.; Chikhi, L.. "Approximate Bayesian Computation Without Summary Statistics: The Case of Admixture". Genetics 181 4 (2009): 1507-1519. Published • 10.1534/genetics.108.098129 Chikhi, L.; Destro-Bisol, G.; Pascali, V.; Baravelli, V.; Dobosz, M.; Barbujani, G.; CHIKHI, Lounès. "Clinal variation in the nuclear DNA of Europeans". Human Biology 81 5-6 (2009): 625-638. http://www.scopus.com/inward/record.url?eid=2-s2.0-77952948124&partnerID=MN8TOARS. 10.3378/027.081.0611 Chikhi, L.. "Update to Chikhi et al.'s "clinal variation in the nuclear DNA of Europeans" (1998): Genetic data and storytelling - From archaeogenetics to astrologenetics?". Human Biology 81 5-6 (2009): 639-643. http://www.scopus.com/inward/record.url?eid=2-s2.0-77952910924&partnerID=MN8TOARS. 10.3378/027.081.0612 Bonhomme, M.; Blancher, A.; Cuartero, S.; Chikhi, L.; Crouau-Roy, B.. "Origin and number of founders in an introduced insular primate: estimation from nuclear genetic data". Molecular Ecology 17 4 (2008): 1009-1019. Published • 10.1111/j.1365-294X.2007.03645.x Chikhi, L.. "Genetic markers: How accurate can genetic data be?". Heredity 101 6 (2008): 471-472. Published • 10.1038/hdy.2008.106 Olivieri, G. L.; Sousa, V. C.; Chikhi, L.; Radespiel, U.; Olivieri, Gillian L.; Sousa, Vitor; Chikhi, Lounès; Radespiel, Ute. "From genetic diversity and structure to conservation: Genetic signature of recent population declines in three mouse lemur species (Microcebus spp.)". Biological Conservation 141 5 (2008): 1257-1271. http://dx.doi.org/10.1016/j.biocon.2008.02.025. Published • 10.1016/j.biocon.2008.02.025 Radespiel, U.; Rakotondravony, R.; Chikhi, L.. "Natural and anthropogenic determinants of genetic structure in the largest remaining population of the endangered golden-brown mouse lemur, Microcebus ravelobensis". American Journal of Primatology 70 9 (2008): 860-870. Published • 10.1002/ajp.20574 Sousa, V. C.; Penha, F.; Collares-Pereira, M. J.; Chikhi, L.; Coelho, M. M.. "Genetic structure and signature of population decrease in the critically endangered freshwater cyprinid Chondrostoma lusitanicum". Conservation Genetics 9 4 (2008): 791-805. Published • 10.1007/s10592-007-9399-7 Amaral, A. J.; Silva, A. B.; Grosso, A. R.; Chikhi, L.; Bastos-Silveira, C.; Dias, D.; Amaral, A.J.; Silva, A.B.; Grosso, A.R.. "Detection of hybridization and species identification in domesticated and wild quails using genetic markers". Folia Zoologica 56 56 (2007): 285-300. http://www.scopus.com/inward/record.url?eid=2-s2.0-36048956045&partnerID=MN8TOARS. Published Adepo-Gourène, B.; Chikhi, L.; Agnèse, J.-F.; Gourène, G.; Hervé, A.. "A preliminary study of allozyme differences amongst Carcharhinus sharks from the continental slope near Abidjan, Côte d'Ivoire". African Journal of Aquatic Science 32 3 (2007): 305-310. http://www.scopus.com/inward/record.url?eid=2-s2.0-37149035996&partnerID=MN8TOARS. 10.2989/AJAS.2007.32.3.11.310 Goossens, B.; Chikhi, L.; Ancrenaz, M.; Lackman-Ancrenaz, I.; Andau, P.; Bruford, M. W.. "Genetic signature of anthropogenic population collapse in orang-utans". Plos Biology 4 e25 (2006): 285-291. Published • 10.1371/journal.pbio.0040025 Goossens, B.; Setchell, J. M.; James, S. S.; Funk, S. M.; Chikhi, L.; Abulani, A.; Ancrenaz, M.; Lackman-Ancrenaz, I.; Bruford, M. W.. "Philopatry and reproductive success in Bornean orang-utans (Pongo pygmaeus)". Molecular Ecology 15 9 (2006): 2577-2588. Published • 10.1111/j.1365-294X.2006.02952.x Barbujani, G.; Chikhi, L.. "Population genetics: DNAs from the European Neolithic". Heredity 97 2 (2006): 84-85. http://www.scopus.com/inward/record.url?eid=2-s2.0-33748419800&partnerID=MN8TOARS. 10.1038/sj.hdy.6800852 Altunok, V.; Koban, E.; Chikhi, L.; Schaffer, A.; Pedersen, N. C.; Nizamlioglu, M.; Togan, I.; Pedersen, N.C.. "Genetic evidence for the distinctness of Kangal dogs". Bulletin of the Veterinary Institute in Pulawy 49 2 (2005): 249-254. http://www.scopus.com/inward/record.url?eid=2-s2.0-23644450394&partnerID=MN8TOARS. Published Goossens, B.; Chikhi, L.; Jalil, M. F.; Ancrenaz, M.; Lackman-Ancrenaz, I.; Mohamed, M.; Andau, P.; et al. "Patterns of genetic diversity and migration in increasingly fragmented and declining orang-utan (Pongo pygmaeus) populations from Sabah, Malaysia". Molecular Ecology 14 2 (2005): 441-456. http://www.scopus.com/inward/record.url?eid=2-s2.0-13444283975&partnerID=MN8TOARS. Published • 10.1111/j.1365-294X.02421.x Bortolini, M. C.; Thomas, M. G.; Chikhi, L.; Aguilar, J. A.; Castro-De-Guerra, D.; Salzano, F. M.; Ruiz-Linares, A.; et al. "Ribeiro's typology, genomes, and Spanish colonialism, as viewed from Gran Canaria and Colombia". Genetics and Molecular Biology 27 1 (2004): 1-8. http://www.scopus.com/inward/record.url?eid=2-s2.0-2342622132&partnerID=MN8TOARS. Published Chikhi, L.; Goossens, B.; Treanor, A.; Bruford, M. W.. "Population genetic structure of and inbreeding in an insular cattle breed, the Jersey, and its implications for genetic resource management". Heredity 92 5 (2004): 396-401. Published • 10.1038/sj.hdy.6800433 Dupanloup, I.; Bertorelle, G.; Chikhi, L.; Barbujani, G.. "Estimating the impact of prehistoric admixture on the genome of Europeans". Molecular Biology and Evolution 21 7 (2004): 1361-1372. Published • 10.1093/molbev/msh135 Laitung, B.; Chauvet, E.; Feau, N.; Feve, K.; Chikhi, L.; Gardes, M.; Beryl Laitung; et al. "Genetic diversity in Tetrachaetum elegans, a mitosporic aquatic fungus". Molecular Ecology 13 6 (2004): 1679-1692. http://dx.doi.org/10.1111/j.1365-294x.2004.02135.x. Published • 10.1111/j.1365-294X.2004.02135.x Bentley, R. A.; Chikhi, L.; Price, T. D.; Bentley, R.A.; Price, T.D.. "The Neolithic transition in Europe: Comparing broad scale genetic and local scale isotopic evidence". Antiquity 77 295 (2003): 63-66. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037367518&partnerID=MN8TOARS. Published Chikhi, Lounès. "Postdocs face hardship across mainland Europe". Nature 415 6869 (2002): 259-259. http://dx.doi.org/10.1038/415259a. 10.1038/415259a Chikhi, L.; Nichols, R. A.; Barbujani, G.; Beaumont, M. A.. "Y genetic data support the Neolithic demic diffusion model". Proceedings of the National Academy of Sciences of the United States of America 99 17 (2002): 11008-11013. Published • 10.1073/pnas.162158799 Goldstein, D. B.; Chikhi, L.. "Human migrations and population structure: What we know and why it matters". Annual Review of Genomics and Human Genetics 3 0 (2002): 129-152. Published • 10.1146/annurev.genom.3.022502.103200 Chikhi, L.. "Postdocs face hardship across mainland europe: Those who follow the funding and work abroad may not find a job when they go home [1] [multiple letters]". Nature 415 6869 (2002): http://www.scopus.com/inward/record.url?eid=2-s2.0-0037122802&partnerID=MN8TOARS. Langella, O.; Chikhi, L.; Beaumont, M. A.; Beaumont, M.A.. "LEA (likelihood-based estimation of admixture): a program to estimate simultaneously admixture and time since the admixture event". Molecular Ecology Notes 1 4 (2001): 357-358. http://www.scopus.com/inward/record.url?eid=2-s2.0-0346906674&partnerID=MN8TOARS. Published • 10.1046/j.1471-8278 Chikhi, L.; Bruford, M.W.; Beaumont, M.A.; Bruford, M. W.; Beaumont, M. A.. "Estimation of admixture proportions: A likelihood-based approach using Markov Chain Monte Carlo". Genetics 158 3 (2001): 1347-1362. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034918729&partnerID=MN8TOARS. Published Goossens, B.; Chikhi, L.; Taberlet, P.; Waits, L.P.; Allainé, D.; Waits, L. P.; Allaine, D.. "Microsatellite analysis of genetic variation among and within Alpine marmot populations in the French Alps". Molecular Ecology 10 1 (2001): 41-52. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035143965&partnerID=MN8TOARS. Published • 10.1046/j.1365-294X.2001.01192.x Goossens, B.; Chikhi, L.; Utami, S.S.; De Ruiter, J.; Bruford, M.W.. "A multi-samples, multi-extracts approach for microsatellite analysis of faecal samples in an arboreal ape". Conservation Genetics 1 2 (2000): 157-162. http://www.scopus.com/inward/record.url?eid=2-s2.0-0000762468&partnerID=MN8TOARS. Bickham, J.W.; Sandhu, S.; Hebert, P.D.N.; Chikhi, L.; Athwal, R.; Bickham, J. W.; Hebert, P. D. N.. "Effects of chemical contaminants on genetic diversity in natural populations: Implications for biomonitoring and ecotoxicology". Mutation Research - Reviews in Mutation Research 463 1 (2000): 33-51. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034214289&partnerID=MN8TOARS. Published • 10.1016/S1383-5742(00)00004-1 Chikhi, L.; Bonhomme, F.; Agnese, J. F.; Agnèse, J.-F.. "Low genetic variability in a widely distributed and abundant clupeid species, Sardinella aurita. New empirical results and interpretations". Journal of Fish Biology 52 5 (1998): 861-878. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032078703&partnerID=MN8TOARS. Published • 10.1006/jfbi.1997.0637 Chikhi, L.; Destro-Bisol, G.; Bertorelle, G.; Pascali, V.; Barbujani, G.. "Clines of nuclear DNA markers suggest a largely Neolithic ancestry of the European gene pool". Proceedings of the National Academy of Sciences of the United States of America 95 15 (1998): 9053-9058. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032555227&partnerID=MN8TOARS. Published • 10.1073/pnas.95.15.9053 Barbujani, G.; Bertorelle, G.; Chikhi, L.; Richards, M.; Sykes, B.; Mackey, D.; Oostra, R.-J.; et al. "Evidence for Paleolithic and Neolithic gene flow in Europe [2] (multiple letters)". American Journal of Human Genetics 62 2 (1998): 488-491. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031889484&partnerID=MN8TOARS. 10.1086/301719 Lounès Chikhi; Jean-François Agnèse; François Bonhomme. "Fortes différences des ADN mitochonclriaux de populations de Sardinella aurita de la mer Méditerranée et de l'Atlantique Est". Comptes Rendus de l'Académie des Sciences - Series III - Sciences de la Vie 320 4 (1997): 289-297. http://dx.doi.org/10.1016/s0764-4469(97)82770-9. 10.1016/s0764-4469(97)82770-9 De García León, F.J.; Chikhi, L.; Bonhomme, F.; DeLeon, F. J. G.. "Microsatellite polymorphism and population subdivision in natural populations of European sea bass Dicentrarchus labrax (Linnaeus, 1758)". Molecular Ecology 6 1 (1997): 51-62. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031051940&partnerID=MN8TOARS. Published Chikhi, L.; Agnèse, J.-F.; Bonhomme, F.; Agnese, J. F.. "Marked mitochondrial DNA differences between Mediterranean and Eastern Atlantic populations of the round sardinella, Sardinella aurita \| Fortes differences des ADN mitochondriaux de populations de Sardinella aurita de la mer Mediterranee et de l'Atlantique Est". Comptes Rendus de l'Academie des Sciences - Serie III 320 4 (1997): 289-297. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031112487&partnerID=MN8TOARS. Published • 10.1016/S0764-4469(97)82770-9 Borsa, P.; Naciri, M.; Bahri, L.; Chikhi, L.; Garcia de Leon, F.J.; Kotoulas, G.; Bonhomme, F.. "Infraspecific zoogeography of the Mediterranean: population genetic analysis on sixteen Atlanto-Mediterranean species (fishes and invertebrates) \| Zoogeographie infra-specifique de la Mer Mediterranee: analyse des donnees genetiques populationnelles sur seize especes atlanto-mediterraneennes (poissons et invertebres)". Vie et Milieu 47 4 (1997): 295-305. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031403021&partnerID=MN8TOARS. Borsa, P.; Naciri, M.; CHIKHI, Lounès ; Garcia de Leon, F.J.; Kotoulas, G.; Bonhomme, F.. "Zoogéographie infraspécifique de la mer Méditerranée". Vie et Milieu 47 4 (1997): 295-305. Published Richard-Yris, Marie-Annick; CHIKHI, Lounès. "Maternal behaviour in domestic hens (Gallus gallus domesticus): cues from chicks and maintenance of maternal responsiveness". International Journal of Comparative Psychology 4 4 (1991): 275-286. https://escholarship.org/uc/item/0623f4f0. Open access • Published
Magazine article	"Un berceau à l’échelle du continent africain", La Recherche, 2020 CHIKHI, Lounès ; d'Errico, F.. "Vers une origine graduelle et composite de l’humanité et des cultures modernes", La Recherche, 2020 d'Errico, F.; CHIKHI, Lounès. "La nascita delle culture umane", Le Scienze, 2019 d'Errico, F.; CHIKHI, Lounès. "Ni d’Eve ni d’Adam : les origines Homo sapiens", Archéologia, 2018 Besolo, C.J.; Rasolondraibe, E.; Quéméré, E.; Rabarivola, C.; Crouau-Roy, B.; CHIKHI, Lounès. "Le propithèque de Tattersall conservation dune espèce de lémurien menacée", CEPA (Conservation des Espèces et des Populations Animales) Magazine, 2009 CHIKHI, Lounès. "Nos ancêtres dans nos gènes", La Recherche, 2008 CHIKHI, Lounès ; Quéméré, E.; Crouau-Roy, B.. "L'Or de Daraina", CEPA (Conservation des Espèces et des Populations Animales) Magazine, 2006
Newspaper article	CHIKHI, Lounès. "Diversité génétique et évolution humaine", Journal de l Université Paul Sabatier, 2009 Dionísio, F.; Gordo, I.; CHIKHI, Lounès ; Bettencourt Dias, M.; Martinho, R.; Magalhães, S.. "Será que existem raças humanas?", Público, 2007, https://www.publico.pt/2007/11/03/jornal/sera-que-existem-racas-humanas-236150. Goossens, B.; CHIKHI, Lounès ; Bruford, M.W.. "Jersey cattle what the genes tell us", The Journal of the Royal Jersey Agricultural Horticultural Society, 2001 CHIKHI, Lounès ; Goossens, B.; Bruford, M.W.. "A study of the genes of Jersey cattle", The Journal of the Royal Jersey Agricultural Horticultural Society, 1999
Preprint	Rémi Tournebize; Lounès Chikhi. "Questioning Neanderthal admixture: on models, robustness and consensus in human evolution". 2023. https://doi.org/10.1101/2023.04.05.535686. 10.1101/2023.04.05.535686 Gabriele Maria Sgarlata; Tiago Maié; Tiago de Zoeten; Rita Rasteiro; Lounès Chikhi. "The effect of habitat loss and fragmentation on isolation-by-distance and time". 2022. https://doi.org/10.1101/2022.10.26.513874. 10.1101/2022.10.26.513874 Gabriele Maria Sgarlata; Tiago Maié; Tiago de Zoeten; Rita Rasteiro; Lounès Chikhi. "On the genetic consequences of habitat contraction: edge effects and habitat loss". 2022. https://doi.org/10.1101/2022.10.25.513679. 10.1101/2022.10.25.513679
Report	Andriaholinirina, N.V.; Baden, A.; Blanco, M.; CHIKHI, Lounès ; Cooke, A.; Davies, N.; Dolch, R.; et al. 2014. Eulemur macaco. The IUCN Red List of Threatened Species 2014.

Other

Other output

Heterogeneity in effective size across the genome: effects on the Inverse Instantaneous Coalescence Rate (IICR) and implications for demographic inference under linked selection. 2021. Simon Boitard; Armando Arredondo; Camille Noûs; Lounès Chikhi; Olivier Mazet. https://doi.org/10.1101/2021.06.11.448122.
10.1101/2021.06.11.448122
Inferring number of populations and changes in connectivity under the n-island model. 2020. Armando Arredondo; Beatriz Mourato; Khoa Nguyen; Simon Boitard; Willy Rodríguez; Camille Noûs; Olivier Mazet; Lounès Chikhi. https://doi.org/10.1101/2020.09.03.282251.
10.1101/2020.09.03.282251
Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle. 2018. Rute R. da Fonseca; Irene Ureña; Sandra Afonso; Ana Elisabete Pires; Emil Jørsboe; Lounes Chikhi; Catarina Ginja. https://doi.org/10.1101/466821.
10.1101/466821
The IICR and the non-stationary structured coalescent: demographic inference with arbitrary changes in population structure. 2018. Willy Rodríguez; Olivier Mazet; Simona Grusea; Simon Boitard; Lounès Chikhi. https://doi.org/10.1101/341750.
10.1101/341750
18 Europe and western Asia: genetics and population history. 2013. Mark G. Thomas; Toomas Kivisild; Lounes Chikhi; Joachim Burger.
10.1002/9781444351071.wbeghm818
Software SPAms (A user-friendly software to simulate population genetics data under complex demographic models). Described in the paper Parreira et al. (2009, Molecular Ecology Resources). 2009. Parreira, B.; Trussart, M.; Sousa, V.; Hudson, R.; CHIKHI, Lounès.
Software 2BAD (an application to estimate the parental contributions during two independent admixture events). Described in Bray et al. (2009, Molecular Ecology Resources).. 2009. Bray, T. C.; Sousa, V.; Parreira, B.; Bruford, Michael W.; CHIKHI, Lounès.
Software parLEA (a novel parallel approach to the likelihood-based estimation of admixture in population genetics). Described in Giovannini et al. (2009, Bioinformatics).. 2009. Giovannini, A.; Zanghirati, G.; Beaumont, M. A.; CHIKHI, Lounès ; Barbujani, G..
Population Subdivision, Hardy-Weinberg Equilibrium and the Wahlund Effect. 2001. Pauline Garnier-Géré; Lounès Chikhi.
10.1002/9780470015902.a0005446.pub3
Software LEA (Likelihood-based estimation of admixture). Software based on the admixture method developed in the paper Chikhi et al. (2001, Genetics). Site http://www.cnrs gif.fr/pge/bioinfo/lea/index.php?lang=en. 2001. Langella, O.; CHIKHI, Lounès ; Beaumont, M.A..
Software GENETIX 3.0. Logiciel d'analyse de données de génétique des populations.. 1999. Belkhir, K.; Borsa, P.; Goudet, J.; CHIKHI, Lounès ; Bonhomme, F..

Activities

Oral presentation

	Presentation title	Event name Host (Event location)
2019/11/28	Dados genéticos, espécies ameaçadas e evolução humana	Dia Aberto do Instituto Gulbenkian de Ciência Instituto Gulbenkian de Ciência (Oeiras, Portugal)
2019/07/29	Genomics, population structure and fragmentation: importance for mouse lemurs and other endangered species	Mouse Lemur Workshop University of Antananarivo (Madagascar)
2019/07/10	Genetic data to reconstruct the recent evolutionary past of species	FCT Ciência 2019 (Lisboa, Portugal)
2019/07/03	Genética e historia evolutiva humana (based on a true story)	Laboratório de Arqueociências (Lisboa, Portugal)
2019/06/11	On the importance of inferring structure and on the recent evolutionary history of species	Institute For Advanced Study in Toulouse (Toulouse, France)
2019/05/02	Genética de Populações e da Conservação	Escola Secundária Fernando Namora (Lisboa, Portugal)
2019/04/30	Population structure, the IICR and the recent evolutionary history of species	Evolution Club Instituto Gulbenkian de Ciência (Oeiras, Portugal)
2019/03/27	Genética de Populações e da Conservação	Escola Secundária de Miraflores (Lisboa, Portugal)
2019/03/20	Population structure, the IICR and the recent evolutionary history of species	INFRAGECO meeting (Hanover, Germany)
2019/02/26	On the importance of inferring structure and on the recent evolutionary history of species	Instituto Gulbenkian de Ciência (Oeiras, Portugal)
2019/02/08	The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice	McGill University (Montréal, Canada)
2019/02/07	Des génomes à remonter le temps	Coeur des Sciences, Université du Québec à Montréal (Montréal, Canada)
2019/02/07	Génétique des populations et histoire démographique	Collège international Marie de France (Montréal, Canada)
2000/05	European human population genetics	Human Evolution Meeting University of Ferrara (Italy)
1997/09	Effects of chemical contaminants on genetic diversity in natural populations	VIIème International Conference on Environmental Mutagens (France)

Supervision

	Thesis Title Role	Degree Subject (Type) Institution / Organization
2016 - Current	Habitat loss and fragmentation: effects on genetic diversity and differentiation Supervisor	Instituto Gulbenkian de Ciência, Portugal
2019 - 2020	Estimation de la présence/absence, de la densité et la distribution de Lepilemur spp dans les fragments de forêts de la partie Nord-est de Madagascar Co-supervisor	Université de Mahajanga, Madagascar
2018 - 2019	Morphologie, Distribution et Densité de Microcebus arnholdi (Louis et al. 2008) dans les trois sites Andravory, Maladialina et Ambalasoa, dans le Corridor forestier Marojejy-Anjanaharibe-Sud-Tsaratanana (COMATSA), au Nord-Est de Madagascar Co-supervisor	Université de Mahajanga, Madagascar
2018 - 2019	Estimation de la densité et variabilité morphologique de Microcebus spp dans le corridor forestier de COMATSA et les fragments forestiers voisins Co-supervisor	Université de Mahajanga, Madagascar
2016 - 2017	Distribution et Abondance des Populations de Microcebus spp dans les Forêts d'Ampiho, d'Orangia et de Montagne d'Ambre, Nord Madagascar Co-supervisor	Université de Mahajanga, Madagascar
2008 - 2016	Patterns of genetic diversity in socially structured populations: an individual-based approach Supervisor	Instituto Gulbenkian de Ciência, Portugal
2010/11 - 2015/12	Comparative conservation genetics of several threatened lemur species living in fragmented environments. A glimpse through natural history of northern Madagascar lemurs Supervisor	Instituto Gulbenkian de Ciência, Portugal
2014 - 2015	Estimation de la densité, diversité morphologique et identification du dortoir chez Lepilemur ankaranensis (Rumpler et Albignac 1975) dans le PN Ankarana, RS Analamerana et au fragment forestier d’Ankarongana au Nord de Madagascar Co-supervisor	Université de Mahajanga, Madagascar
2013 - 2014	Présence, répartition, estimation de densité et diversité morphologique des populations du genre Lepilemur dans des fragments forestiers des régions du Nord de Madagascar (Ankarana, Andrafiamena et Andavakoera) Co-supervisor	Université de Mahajanga, Madagascar
2012 - 2013	Etude de la diversité morphologique et estimation de la densité chez Microcebus tavaratra (Rasoloarison et al., 2000) dans la région Loky-Manambato Co-supervisor
2012 - 2013	Contribution à l'Etude sur l’estimation de la Densité et les Niveaux des Strates Utilisées chez Propithecus coronatus (Edwards, 1871) dans la Partie Ouest de Madagascar Co-supervisor	Université de Mahajanga, Madagascar
2011 - 2012	Application des différent méthodes d’estimation de densité, diversité morphologique et caractéristiques du dortoir de populations chez Lepilemur milanoii (Louis et al., 2006) dans les fragments agments forestiers de la Loky-Manambato Loky au Nord de Madagascar Co-supervisor	Université de Mahajanga, Madagascar
2011 - 2012	Impacts des différents facteurs (naturels et anthropiques) sur la diversité morphologique et estimation de la densité des populations de Microcebus sp. (E. Geoffroy, 1828) et Lepilemur sp. (E. Geoffroy, 1851) du Nord de Madagascar Co-supervisor	Université de Mahajanga, Madagascar
2006/01 - 2010/04	Inference of admixture and population size changes in structured populations with applications to conservation genetics Supervisor
2009 - 2010	Distribution spatiale des ressources alimentaires chez Propithecus tattersalli (SIMONS, 1988) , P. coquereli (GRANDIDIER, 1867) et P. coronatus (MILNE – EDWARDS, 1871) ainsi que certains aspects de sa distribution Co-supervisor	Université de Mahajanga, Madagascar
2009 - 2010	Estimation de la densité de Propithecus Tattersalli (Simons, 1988) au Nord-Est, de Propithecus Coquereli (Grandidier, 1867) et Propithecus Coronatus (Edwards, 1871) au Nord-Ouest de Madagascar Co-supervisor	Université de Mahajanga, Madagascar

Event organisation

	Event name Type of event (Role)	Institution / Organization
2006 - Current	Workshop on the Coalescent Theory (2006) Workshop (Co-organisor)	Instituto Gulbenkian de Ciência, Portugal
2019/07/29 - 2019/08/03	Symposium in conference - The challenges of connectivity in a fragmented world: insights from Malagasy forests (ATBC2019, Antananarivo, Madagascar) (2019/07/29 - 2019/08/03) Symposium (Co-organisor)
2019/06/20 - 2019/06/21	Open conference - On models and modelling in biology: from ecology and evolution to epidemiology and gene networks (2019/06/20 - 2019/06/21) Conference	INSA Toulouse, France
2003 - 2019	5-day course in Population Genetics and Demographic History (The Gulbenkian Training Programme in Bioinformatics) (2003 - 2019) Workshop (Co-organisor)	Instituto Gulbenkian de Ciência, Portugal

Association member

	Society Organization name	Role
2012 - Current	Associação Portuguesa de Biologia Evolutiva (APBE)

Course / Discipline taught

	Academic session	Degree Subject (Type)	Institution / Organization
2019/05/20 - 2019/05/24	Demography and Approximate Bayesian Simulation		Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
2005 - 2017	Population Genetics	(Doutoramento)	Instituto Gulbenkian de Ciência, Portugal
2003 - 2017	Population and Conservation Genetics	(Master)	Université Toulouse III Paul Sabatier, France

Evaluation committee

	Activity description Role	Institution / Organization	Funding entity
2005 - 2005	Member of the VolkswagenStifung Jury 2005	VolkswagenStiftung, Germany

Journal scientific committee

	Journal title (ISSN)	Publisher
2016 - Current	Heredity (0018-067X)	Springer Science and Business Media LLC
2000 - 2010	Molecular Ecology (1365-294X)	Wiley (Blackwell Publishing)
1998 - 1998	Italian Journal of Zoology (1748-5851)	Informa UK (Taylor & Francis)

Distinctions

Award

2006	"One of the promising French scientists" by the Journal Marianne Journal Marianne, France
1998	Gabriel Lasker Prize for the best article published in "Human Biology"
1996	Marie Currie Fellow 1996-1997
1994	Christiane Doré Prize for "the best scientific contribution of an ORSTOM student"

Other distinction

2009	"Special Issue of Human Biology" on Gabriel Lasker Prize Holders