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Gautier Mathieu

Researcher (CR1), INRA, département SPE

© Mathieu Gautier
My research is mainly focused on the development of population genomics methods for demographic inference and for the identification of footprints of selection using Next-Generation Sequencing and Genotyping data.

Curriculum Vitae

Academic career

2010- Researcher, INRA, UMR CBGP, Montferrier sur Lez

2004-2010 Researcher, INRA, UMR GABI, Jouy-en-Josas

2003-2004 Post-doc UMB University, Norway (Supervisor: Pr. Theo Meuwissen)

1999-2003 PhD in Molecular and Quantitative Genetics, AgroParisTech

Publication List


[79] Manirakiza J, Hatungumukama G, Thévenon S, Gautier M, Besbes B, Flori L, Detilleux J (2017). Effect of genetic European taurine ancestry on milk yield of Ankole-Holstein crossbred dairy cattle in mixed smallholders system of Burundi highlands. Animal Genetics, in press.
[78]Gautier M, Klassmann A, Vitalis R (2017). rehh 2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure. Molecular Ecology Resources, 17 (1): 78-90.
[77] Bourgeois YXC, Delahaie B, Gautier M, Lhuillier E, Malé PJG, Bertrand JAM, Cornuault J, Wakamatsu K, Bouchez O, Mould C, Bruxaux J, Holota H, Milá B, Thébaud C (2017). A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird. Royal Society Open Science, 4 (2): 160805.
[76] Bennett EA, Champlot S, Peters J, Arbuckle BS, Guimaraes S, Pruvost M, Bar-David S, Davis SJM, Gautier M, Kaczensky P, Kuehn R, Mashkour M, Morales-Muñiz A, Pucher E, Tournepiche JF, Uerpmann HP, Bălăşescu A, Germonpré M, Gündem CY, Hemami MR, Moullé PE, Ötzan A, Uerpmann M, Walzer C, Grange T, Geigl EM (2017). Taming the late Quaternary phylogeography of the Eurasiatic wild ass through ancient and modern DNA. PloS One, 12 (4): e0174216.


[75] Gautier M., Moazami-Goudarzi K, Leveziel H, Parinello H, Grohs C, Rialle S, Kowalczyk R, Flori L (2016). Deciphering the wisent demographic and adaptive histories from individual whole-genome sequences. Molecular Biology and Evolution, 33 (11): 2801-2814.

[74] Burban C, Gautier M., Leblois R, Landes J, Santos H, Paiva MR, Branco M, Kerdelhue C (2016). Evidence for low-level hybridization between two allochronic populations of the pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae). Biological Journal of the Linnean Society. 119 (2): 311-328.

[73] Cruaud A, Gautier M., Rossi JP, Rasplus JY, Gouzy J (2016). RADIS: Analysis of RAD-seq data for InterSpecific phylogeny. Bioinformatics, 32 (19): 3027-3028.

[72] Estoup A, Ravigné V, Hufbauer RA, Vitalis R, Gautier M., Facon B (2016). Is there a genetic paradox of biological invasion? Annual Review of Ecology, Evolution and Systematics, 47: 51-72.

[71]Pudlo P, Marin JM, Estoup A, Cornuet JM, Gautier M, Robert CP (2016). Reliable ABC model choice via random forests.  Bioinformatics, 32(6):859-66.


[70]Gautier M. (2015). Genome-Wide Scan for Adaptive Differentiation and Association Analysis with population-specific covariates. Genetics, 201(4):1555-79.

[69]Sempéré G, Moazami-Goudarzi K, Eggen A, Laloë D, Gautier M, Flori L. (2015). WIDDE: a Web-Interfaced next generation Database for genetic Diversity Exploration, with a first application in cattle. BMC Genomics, 16(1):940

[68]Wangkumhang P, Wilantho A, Shaw PJ, Flori L, Moazami-Goudarzi K, Gautier M, Duangjinda M, Assawamakin A, Tongsima S (2015). Genetic analysis of Thai cattle reveals a Southeast Asian indicine ancestry. PeerJ, 3:e1318.

[67]Floriot S, Vesque C, Rodriguez S, Bourgain-Guglielmetti F, Karaiskou A, Gautier M, Duchesne A, Barbey S, Fritz S, Vasilescu A, Bertaud M, Moudjou M, Halliez S, Cormier-Daire V, El Hokayem J, Nigg EA, Manciaux L, Guatteo R, Cesbron N, Toutirais G, Schneider-Maunoury Z, Boichard D, Eggen A, Sobczak-Thépot J, Schibler L. (2015). Mutation of C-Nap1-encoding gene affects centriole cohesion and is associated with a Seckel-like syndrome in cattle. Nature Communications, 6:6894.


[66]Gautier M. (2014) Using genotyping data to assign markers to their chromosome type and to infer the sex of individuals: a Bayesian model-based classifier. Molecular Ecology Resources, 14:1141-1159.

[65]Cornuet J.M., Pudlo P., Veyssier J., Dehne-Garcia A., Gautier M., Leblois R., Marin J.M., Estoup A. (2014). DIYABC v2.0: a software to make Approximate Bayesian Computation inferences about population history using Single Nucleotide Polymorphism, DNA sequence and microsatellite data. Bioinformatics, 30:1187-1189.

[64]Flori L., Thevenon S., Dayo G.-K., Senou M., Sylla S., Berthier D., Moazami-Goudarzi K., Gautier M. (2014). Adaptive admixture in the West African bovine hybrid zone: insight from the Borgou population. Molecular Ecology. 23(13):3241-57

[63]Guillot G., Vitalis R., le Rouzic A. et Gautier M. (2014) Detecting correlation between allele frequencies and environmental variables as a signature of selection. A fast computational approach for genome-wide studies. Spatial Statistics, 8:145-155.

[62]Cruaud A., Gautier M., Galan M., Foucaud J., Sauné L., Genson G., Dubois E., Nidelet S., Deuve T., Rasplus J.Y. (2014) Empirical Assessment of RAD Sequencing for Interspecific Phylogeny. Molecular Biology and Evolution, 31(5):1272-4.

[61]Vitalis R, Gautier M., Dawson KJ et Beaumont MA (2014) Detecting and measuring selection from gene frequency data. Genetics, 196(3):799-817.


[60]Clément J.A.J., Toulza E., Gautier M, Parrinello H., Roquis D., Boissier J., Rognon A., Moné H., Mouahid G., Buard J., Mitta G. and Grunau C.  (2013).  Private Selective Sweeps Identified from Next-Generation Pool-Sequencing Reveal Convergent Pathways under Selection in Two Inbred Schistosoma mansoni Strains. Plos Neglected Tropical Disease. 7:e2591

[59]Druet T, Perez-Pardal L, Charlier C, Gautier M (2013). Identification of large selective sweeps associated with major genes in cattle. Animal Genetics. 44(6):758-62.

[58] Gautier M, Foucaud J, Gharbi K, Cezard T, Galan M, Loiseau A, Thomson M, Pudlo P, Kerdelhue C and Estoup A (2013). Estimation of population allele frequencies from next-generation sequencing data: pooled versus individual genotyping. Molecular Ecology. 22(14):3766-79.

[57] Ségurel L, Austerlitz F, Toupance B, Gautier M, Kelley JL, Pasquet P, Lonjou C, Georges M, Voisin S, Cruaud C, Couloux A, Hegay T, Aldashev A, Vitalis R, Heyer E (2013). Positive selection of protective variants for type 2 diabetes from the Neolithic onward: a case study in Central Asia. Eur. J. Hum. Genet. 21 : 1146-1151.

[56]Gautier M, Gharbi K., Cezard T., Foucaud J., Kerdelhue C., Pudlo P., Cornuet J.M., Estoup A. (2013). The effect of RAD allele dropout on the estimation of genetic variation within and between populations. Molecular Ecology.  22(11):3165-3178.

[55]Gautier M and Vitalis R. (2013). Inferring population histories using genome-wide allele frequency data. Molecular Biology and Evolution. 30(3):654–668.


[54] Flori L., Gonzatti M.I., Thevenon S., Chantal I., Pinto J., Berthier D., Aso P.M and Gautier M (2012). A quasi-exclusive European ancestry in the Senepol tropical cattle breed highlights the importance of the slick locus in tropical adaptation. PLoS One. 7(5):e36133.

[53] Smadja CM, Canbäck B, Vitalis R, Gautier M, Ferrari J, Zhou JJ and Butlin RK. (2012). Large-scale candidate gene scan reveals the role of chemoreceptor genes in host plant specialisation and speciation in the pea aphid. Evolution 66(9):2723-38.

[52] Gautier M. and Vitalis R. (2012). rehh : An R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics 28(8):1176-7.

[51] Leroy G, Danchin-Burge C, Palhiere I, Baumung R, Fritz S, Mériaux JC and Gautier M (2012). An ABC estimate of pedigree error rate: application in dog, sheep and cattle breeds. Animal Genetics, 43(3):309-314.

[50] Dayo GK, Gautier M, Berthier D, Poivey JP, Sidibe I, Bengaly Z, Eggen A,Boichard D, Thevenon S (2012). Association studies in QTL regions linked to bovine trypanotolerance in a West African crossbred population. Animal Genetics, 43(2):123-132.


[49]Gautier M and Naves M (2011). Footprints of selection in the ancestral admixture of a New World Creole cattle breed. Molecular Ecology. 20:3128-3143.

[48] Felius M., Koolmees P.A., Theunissen B., European Cattle Genetic Diversity Consortium (incl. Gautier M.) Lenstra J.A. (2011). On the Breeds of Cattle—Historic and Current Classifications. Diversity, 3(4): 660-692.

[47] Edwards CJ, Ginja C, Kantanen J, Pérez-Pardal L, Tresset A, Stock F, European Cattle Genetic Diversity Consortium (incl. Gautier M.), Gama LT, Penedo MC, Bradley DG, Lenstra JA, Nijman IJ (2011). Dual origins of dairy cattle farming--evidence from a comprehensive survey of European Y-chromosomal variation. Plos One. 6(1):e15922.


[46]Gautier M, Laloe D and Mozami-Goudarzi K (2010). Insights into the origin of French cattle from dense SNP data on 47 worldwide breeds. Plos One. 6(1):e13038

[45]Gautier M, Hocking TD and Foulley JL (2010). A Bayesian outlier criterion to identify SNPs under selection in large data sets. Plos One. 4(8):e11913 


 [44]Gautier M, Flori L, Riebler A, Jaffrézic F, Laloe D, Gut I, Mozami-Goudarzi K and Foulley JL (2009). A Whole Genome Bayesian Scan for Adaptive Genetic Divergence in West African Cattle. BMC Genomics.10:550

 [43] Flori L, Fritz S, Jaffrézic F, Boussaha M, Gut I, Heath S, Foulley JL and M Gautier (2009). The Genome Response to Artifical Selection: A case study in dairy cattle. Plos One. 4(8):e6595

 [42] Dayo GK, Thevenon S, Berthier D, Moazami-Goudarzi K, Denis C, Cuny G, Eggen A and M Gautier (2009). Detection of selection signatures within candidate regions underlying trypanotolerance in outbred cattle populations. Molecular Ecology. 18:1801-1813.

 [41] Capitan A, Grohs C, Gautier M, and A Eggen (2009). The scurs inheritance: New insights from the French Charolais breed. BMC Genetics. 10:33. 


[40] Ben Jemaa S, Druet T, Guillaume F, Fritz S, Eggen A and M Gautier (2008). Detection of QTL affecting Non Return Rate in French dairy cattle. J. Anim Breed. Genetics. 125:280-8.

[39] Druet T, Fritz S, Boussaha M, Ben-Jemaa S, Guillaume F, Derbala D, Zelenika D, Lechner D, Charon C, Boichard D, Gut I, Eggen A and M Gautier (2008). Fine-mapping of QTLs affecting female fertility in dairy cattle on BTA03 using a dense SNP map. Genetics. 178:2227-35.

[38] Duchesne A., L. Manciaux, Gautier M, S. Floriot, C. Grohs, S. Fritz, T. Druet, F. Schelcher, A. Ducos and A. Eggen (2008)A Generalized Caprine-like Hypoplasia Syndrome is localized within a 6-cM interval on bovine chromosome 13 in the Montbéliarde breed. Animal Genetics. 39: 112-120.

[37] Murmann A.E., A. Mincheva, M.O. Scheuermann, M. Gautier, F. Yang, J. Buitkamp, P.L. Strissel, R. Strick, J.D. Rowley, P. Lichter (2008). Comparative gene mapping in cattle, Indian muntjac, and Chinese muntjac by fluorescence in situ hybridization. Genetica. 134: 345-351. 


[36]Gautier M., T. Faraut, K. Moazami-Goudarzi, V. Navratil, M. Foglio, C. Grohs, A. Boland, J.G. Garnier, D. Boichard, G.M. Lathrop, I.G. Gut, A. Eggen (2007). Genetic and haplotypic structure in 14 European and African cattle breeds. Genetics. 177: 1059-1070.

[35] Snelling W.M., R. Chiu, J.E. Schein, M. Hobbs, C.A. Abbey, D.L. Adelson, G.L. Bennett, I.E. Bosdet, M. Boussaha, R. Brauning, A.R. Caetano, M.M. Costa, A.M. Crawford, B.P. Dalrymple, A. Eggen, A. Everts-van der Wind, S. Floriot, M. Gautier, C.A. Gill, R.D. Green, R. Holt, S.J.M. Jones, S.M. Kappes, J.W. Keele, P.J. de Jong, D.M. Larkin, H.A. Lewin, J.C. McEwan, S. McKay, S. McWilliam, M.A. Marra, C.A. Mathewson, L.K. Matukumalli, S.S. Moore, B. Murdoch, F. Nicholas, K. Osoegawa, A. Roy, H. Salih, L. Schibler, R. Schnabel, L. Silveri, L.C. Skow, T.P.L. Smith, T.S. Sonstegard, J. Taylor, R. Tellam, C.P. Van Tassell, J.L. Williams, J.E. Womack, N.H. Wye, G. Yang and S. Zhao (2007). A physical map of the bovine genome. Genome Biology. 2007;8(8):R165.

[34] Pierre A.,M. Gautier, I. Callebaut, M. Bontoux, E. Jeanpierre, P. Pontarotti and P. Monget (2007). Structural characterization, genomic organization and phylogenetic analysis of the eutherian Ndg1/Dppa5/Ecat1/Coep gene family. Characterization of an atypical KH domain and localization in instable regions in mammalian genomes. Genomics. 90(5):583-94.

[33]Gautier M, A. Capitan, S. Fritz, A. Eggen, D. Boichard, and T. Druet (2007). Characterization of the DGAT1 K232A and variable number of tandem repeat polymorphisms in French dairy cattle. Journal of Dairy Science. 90(6):2980-8.

[32] Thévenon S, G.K. Dayo, S. Sylla, I. Sidibe, D. Berthier, H. Legros, D. Boichard, A. Eggen and M. Gautier (2007). The extent of linkage disequilibrium in a large cattle population of western Africa and its consequences for association studies. Animal Genetics. 38(3):277-86.

[31] Guillaume F, M. Gautier, S. Ben Jemaa, S. Fritz, A. Eggen, D. Boichard and T.Druet (2007). Refinement of two female fertility QTL by using alternative measures in French Holstein dairy cattle. Animal Genetics. 38(1):72-4. 


[30] Duchesne A, M. Gautier, S. Chadi, C. Grohs, S. Floriot, Y. Gallard, G. Caste, A. Ducos and A. Eggen (2006).Identification of a doublet missense substitution in the bovine LRP4 gene as a candidate causal mutation for syndactyly in Holstein cattle. Genomics. 88(5) :610-21.

[29]Gautier M, RR Barcelona, S. Fritz, C. Grohs, T. Druet, D. Boichard, A. Eggen and T.H.E. Meuwissen (2006). Fine mapping and physical characterization of two linked quantitative trait loci affecting milk fat yield in dairy cattle on BTA26. Genetics. 172(1):425-36.

[28] Demars J, J. Riquet, K. Feve, M. Gautier, M. Morisson, O. Demeure, C. Renard, P. Chardon, D. Milan (2006). High resolution physical map of porcine chromosome 7 QTL region and comparative mapping of this region among vertebrate genomes. BMC Genomics. 24;7:13.  


[27] Murmann AE, J. Gao, M. Encinosa, M. Gautier, ME Peter, R. Eils, P. Lichter and JD Rowley (2005). Local gene density predicts the spatial position of genetic loci in the interphase nucleus. Exp Cell Res. 311(1):14-26.

[26] Roy R, P. Zaragoza, C. Rodellar, M. Gautier and A. Eggen (2005). Radiation hybrid and genetic linkage mapping of two genes related to fat metabolism in cattle: fatty acid synthase (FASN) and glycerol-3-phosphate acyltransferase mitochondrial (GPAM). Anim Biotechnol. 16(1):1-9.

[25] Olsen, H. G., S. Lien, M. Gautier, H. Nilsen, H. Roseth, et al. (2005). Mapping of a Milk Production QTL on BTA6 to a 420 kb Region on Bovine Chromosome 6. Genetics: 169(1):275-83.


[24] Bønsdorff, T., M. Gautier, K. Rønningen, F. Lingaas and I. Olsaker (2004). Mapping of the bovine genes of the de novo AMP synthesis pathway and their expression in testis, epididymis and corpus luteum. Animal Genetics 35(6):438-44.

[23] Schibler, L., A. Roig, M. F. Mahe, J. C. Save, M. Gautier, et al. (2004). A first generation bovine BAC-based physical map. Genet Sel Evol 36(1): 105-22. [22] Snelling, W. M., M. Gautier, J. W. Keele, T. P. L. Smith, R. T. Stone, et al. (2004). Integrating linkage and radiation hybrid mapping data for bovine chromosome 15. BMC Genomics5(1):77.


[21] Bonnet-Garnier, A., F. Claro, S. Thevenon, M. Gautier and H. Hayes (2003). Identification by R-banding and FISH of chromosome arms involved in Robertsonian translocations in several deer species. Chromosome Res11(7): 649-63.

[20] Bonsdorff, T., A. Eggen, M. Gautier, H. C. Asheim, K. Ronningen, et al. (2003). Identification and physical mapping of genes expressed in the corpus luteum in cattle. Animal Genetics  34(5): 325-33.

[19] Di Meo, G. P., A. Perucatti, M. Gautier, H. Hayes, D. Incarnato, et al. (2003). Chromosome localization of the 31 type I Texas bovine markers in sheep and goat chromosomes by comparative FISH-mapping and R-banding. Animal Genetics  34(4): 294-6.

[18]Gautier, M., H. Hayes, T. Bonsdorff and A. Eggen (2003). Development of a comprehensive comparative radiation hybrid map of bovine chromosome 7 (BTA7) versus human chromosomes 1 (HSA1), 5 (HSA5) and 19 (HSA19). Cytogenet Genome Res102(1-4): 25-31.

[17]Gautier, M., H. Hayes and A. Eggen (2003). A comprehensive radiation hybrid map of bovine Chromosome 26 (BTA26): comparative chromosomal organization between HSA10q and BTA26 and BTA28. Mamm Genome 14(10): 711-21.

[16] Hayes, H., C. Elduque, M. Gautier, L. Schibler, E. Cribiu, et al. (2003). Mapping of 195 genes in cattle and updated comparative map with man, mouse, rat and pig. Cytogenet Genome Res 102(1-4): 16-24.

[15] Roy, R., M. Gautier, H. Hayes, P. Zaragoza, A. Eggen, et al. (2003). Assignment of monoglyceride lipase (MGLL) gene to bovine chromosome 22q24 by in situ hybridization and confirmation by radiation hybrid mapping. Cytogenet Genome Res 101(1): 92A.


[14]Gautier, M., H. Hayes and A. Eggen (2002). An extensive and comprehensive radiation hybrid map of bovine Chromosome 15: comparison with human Chromosome 11. Mamm Genome 13(6): 316-9.

[13] Roy, R., M. Gautier, H. Hayes, P. Laurent, P. Zaragoza, et al. (2002). Assignment of maltase glucoamylase (MGAM) gene to bovine chromosome 4q34 by in situ hybridization and confirmation by radiation hybrid mapping. Cytogenet Genome Res 98(4): 311C.

[12] Roy, R., M. Gautier, H. Hayes, P. Laurent, P. Zaragoza, et al. (2002). Assignment of mitochondrial glycerol-3-phosphate acyltransferase (GPAM) gene to bovine chromosome 26 (26q22) by in situ hybridization and confirmation by somatic cell hybrid mapping. Cytogenet Genome Res 97(3-4): 276F.

[11] Williams, J. L., A. Eggen, L. Ferretti, C. J. Farr, M. Gautier, et al. (2002). A bovine whole-genome radiation hybrid panel and outline map. Mamm Genome 13(8): 469-74.


[10] Bernard, L., C. Leroux, H. Hayes, M. Gautier, Y. Chilliard, et al. (2001). Characterization of the caprine stearoyl-CoA desaturase gene and its mRNA showing an unusually long 3'-UTR sequence arising from a single exon. Gene 281(1-2): 53-61.

[9] Bonnet, A., S. Thevenon, F. Claro, M. Gautier and H. Hayes (2001). Cytogenetic comparison between Vietnamese sika deer and cattle: R-banded karyotypes and FISH mapping. Chromosome Res  9(8): 673-87.

[8] Eggen, A., M. Gautier, A. Billaut, E. Petit, H. Hayes, et al. (2001). Construction and characterization of a bovine BAC library with four genome-equivalent coverage. Genet Sel Evol   33(5): 543-8.

[7]Gautier, M., H. Hayes, S. Taourit, P. Laurent and A. Eggen (2001). Syntenic assignment of sixteen genes from the long arm of human chromosome 10 to bovine chromosomes 26 and 28: refinement of the comparative map. Chromosome Res 9(8): 617-21.

[6]Gautier, M., H. Hayes, S. Taourit, P. Laurent and A. Eggen (2001). Assignment of eight additional genes from human chromosome 11 to bovine chromosomes 15 and 29: refinement of the comparative map. Cytogenet Cell Genet  93(1-2): 60-4.

[5]Gautier, M., P. Laurent, H. Hayes and A. Eggen (2001). Development and assignment of bovine-specific PCR systems for the Texas nomenclature marker genes and isolation of homologous BAC probes. Genet Sel Evol 33(2): 191-200.

[4] Iannuzzi, L; Di Meo, GP; Hayes, H; Perucatti, A; Incarnato, D; Gautier, M; Eggen, A. 2001. FISH-mapping of 31 type I loci (Texas markers) to river buffalo chromosomes. Chromosome Res 9: 339-342.

[3] Roy, R., M. Gautier, H. Hayes, P. Laurent, R. Osta, et al. (2001). Assignment of the fatty acid synthase (FASN) gene to bovine chromosome 19 (19q22) by in situ hybridization and confirmation by somatic cell hybrid mapping. Cytogenet Cell Genet  93(1-2): 141-2.


[2]Gautier, M., P. Laurent and A. Eggen (2000). Syntenic assignment of the selectin P gene (SELP) to bovine chromosome 16. Animal Genetics  31(5): 343-4.

[1] Hayes, H., G. P. Di Meo, M. Gautier, P. Laurent, A. Eggen, et al. (2000). Localization by FISH of the 31 Texas nomenclature type I markers to both Q- and R-banded bovine chromosomes. Cytogenet Cell Genet  90(3-4): 315-20.