Publications
Preprints & forthcomings
[97]. Chenal, C., Marco, C., Sabot, F., Clarkson, C. S., Miles, A., Simard, F., Costantini, C., Fiston-Lavier, A.-S., & Fontaine, M. C. Pangenomic variations and differentiation between the two African malaria vector sister species Anopheles gambiae and Anopheles coluzzii. bioRrXiv.
[96]. Carrasco-Valenzuela, T., Marino, A., Storer, J., Bonnici, I., Mazzoni, C. J., Fontaine, M. C., Haudry, A., Boulesteix, M., & Fiston-Lavier, A.-S. Manual versus automatic annotation of transposable elements: case studies in Drosophila melanogaster and Aedes albopictus, balancing accuracy and biological relevance. biorXiv. doi:10.1101/2025.01.10.632341
[95]. McCann, R. S., Courneya, J.-P., Donnelly, M. J., Laufer, M. K., Mzilahowa, T., Stewart, K., Agossa, F., Tezzo, F. W. s., Miles, A., Takala-Harrison, S., O’Connor, T. D., & The Ag1000G Consortium. Variation in spatial population structure in the Anopheles gambiae species complex. bioRrXiv. https://doi.org/10.1101/2024.05.26.595955
[94]. Lefebvre, M. J. M., Degrugillier, F., Arnathau, C., González, C., Rondón, S., Chaves, A., Benavides, J., Scarpellini Campos, A., dos Santos, E., Huff, R., Dornelles da Silva, C. M., Vanderhoeven, E., De Thoisy, B., Fontaine, M. C.†, Prugnolle, F.†, & Rougeron, V.† Genomic insights into Plasmodium vivax and Plasmodium simium host shifts in Latin America. (†co-last authors) bioRrXiv. doi: 10.1101/2024.12.19.629455.
[93]. Daron, J., Bouafou, L., Tennessen, J., Rahola, N., Makanga, B., Ousman, A.-E., Ngangue, M.F., Longo Pendy, N.M., Paupy, C., Neafsey, D.E., Fontaine, M.C.†, Ayala, D.† Genomic signatures of microgeographic adaptation in Anopheles coluzzii along an anthropogenic gradient in Gabon. biorXiv. (†co-last authors). doi:10.1101/2024.05.16.594472.
[92]. Brinker, P., Falcao Salles, J.†, Beukeboom, L. W.†, & Fontaine, M. C.† (2025). Wolbachia: The architect of microbial assemblies in response to environmental changes. bioRrXiv. . (†co-last authors). doi:TBA
2025
[91]. Foote, A.D., Louis, M., Alexander, A., Carroll, E.L., and Fontaine, M.C. (2025). Genomic insights into demographic and evolutionary histories. In The Evolution of Cetacean Societies, A.D. Foote, D. Croft, E. Garland, and S. King, eds. (Chicago Press). In press. More information here
[90]. Corley, M., Cosme, L., Armbruster, P., Sharakhova, M., Torre, A.d., Caputo, B., Pichler, V., Bega, A., Urbanelli, S., Martins, A., et al. (2025). Population structure of the invasive Asian tiger mosquito, Aedes albopictus, in Europe. Ecology and Evolution, In press. Authorea preprints 10.22541/au.172683590.01925550/v1.
[89]. Lefebvre, M.J.M., Degrugillier, F., Arnathau, C., Fontecha, G.A., Noya, O., Houze, S., Severini, C., Pradines, B., Berry, A., Trape, J.F., Sàenz, F.E., Prugnolle, F.†, Fontaine, M.C.†, Rougeron, V.† (2025). Genomic exploration of the complex journey of Plasmodium vivax in Latin America.. († Co-last authors). PLoS Pathogens 21(1), e1012811. doi:https://doi.org/10.1371/journal.ppat.1012811
2024
[88]. Pierce, G.J., Petitguyot, M.A.C., Gutierrez-Muñoz, P., Fariñas-Bermejo, A., Fernández-Fernández, D., Dolman, S., Fontaine, M.C., Hernández-González, A., Gil, A., Read, F.L., et al. (2024). An endangered population of harbour porpoise Phocoena phocoena hidden in plain sight: biology, ecology and conservation of the Iberian porpoise. Oceanography and Marine Biology - An Annual Review. doi: 10.1201/9781003477518‐1 Open Access link.
[87]. Amaya Romero, J.E., Chenal, C., Ben Chehida, Y., Miles, A., Clarkson, C.S., Pedergnana, V., Wertheim, B., and Fontaine, M.C. (2024). Mitochondrial Variation in Anopheles gambiae and Anopheles coluzzii: Phylogeographic Legacy and Mitonuclear Associations With Metabolic Resistance to Pathogens and Insecticides. Genome Biology & Evolution 16. evae172. doi:10.1093/gbe/evae172.
[86]. Cosme, L.V., Corley, M., Johnson, T., Severson, D.W., Yan, G., Wang, X., Beebe, N., Maynard, A., Bonizzoni, M., Khorramnejad, A., et al. (2024). A genotyping array for the globally invasive vector mosquito, Aedes albopictus. Parasites & Vectors 17, 106. doi:10.1186/s13071-024-06158-z.
[85]. Conklin, J.R., Verkuil, Y.I., Lefebvre, M.J.M., Battley, P.F., Bom, R.A., Gill, R.E., Hassell, C.J., ten Horn, J., Ruthrauff, D.R., Tibbitts, T.L., Tomkovich, P.S., Warnock, N., Piersma, T., and Fontaine, M.C. (2024). Phylogeography of bar-tailed godwits: pre-LGM structure in Beringia and westward colonization of post-glacial Europe. Molecular Ecology. e17452. doi:10.1111/mec.17452
[84]. Crossman, C. A., Fontaine, M.C.†, & Frasier, T. R.† (2024). A comparison of genomic diversity and demographic history of the North Atlantic and Southwest Atlantic southern right whales. Moleculat Ecology, 33(20), e17099, doi:10.1111/mec.17099 (†Co-last author)
2023
[83]. Ben Chehida, Y., Stelwagen, T., Hoekendijk, J.P.A., Ferreira, M., Eira, C., Pereira, A.T., Nicolau, L., Thumloup, J., and Fontaine, M.C. (2023). Harbor porpoise losing its edges: genetic time series suggests a rapid population decline in Iberian waters over the last 30 years. Ecology & Evolution 13, e10819. doi:10.1002/ece3.10819
[82]. Kyriazis, C.C., Robinson, J.A., Nigenda-Morales, S.F., Beichman, A.C., Rojas-Bracho, L., Robertson, K.M., Fontaine, M.C., Wayne, R.K., Taylor, B.L., Lohmueller, K.E., and Morin, P.A. (2023). Models based on best-available information support a low inbreeding load and potential for recovery in the vaquita. Heredity 130, 183-187. doi:10.1038/s41437-023-00608-7
[81]. Lefebvre, M. J. M., Daron, J., Legrand, E., Fontaine, M. C.†, Rougeron, V.†, & Prugnolle, F.† (2023). Population genomic evidence of adaptive response during the invasion history of Plasmodium falciparum in the Americas. Molecular Biology & Evolution. 40, msad082. doi:10.1093/molbev/msad082 (†Co-last author)
[80]. Louis, M., Korlević, P., Nykänen, M., Archer, F., Berrow, S., Brownlow, A., Lorenzen, E. D., O’Brien, J., Post, K., Racimo, F., Rogan, E., Rosel, P. E., Sinding, M. H. S., van der Es, H., Wales, N., Fontaine, M. C.†, Gaggiotti, O.†, & Foote, A. D.† (2023). Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters. Nature Communcations 14, 4020. doi:10.1038/s41467-023-39532-z (†Co-last author)
[79]. Small, S. T., Costantini, C., Sagnon, N. F., Guelbeogo, M. W., Emrich, S. J., Kern, A. D., Fontaine, M. C., & Besansky, N. J. (2023). Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria vector. PNAS 120(11), e2219835120. doi:10.1073/pnas.2219835120
2022
[78]. Rougeron, V., Daron, J., Fontaine, M. C., & Prugnolle, F. (2022). Evolutionary history of Plasmodium vivax and Plasmodium simium in the Americas. Malaria Journal, 21(1), 141, doi: 10.1186/s12936-022-04132-7
[77]. Robinson, J. A., Kyriazis, C. C., Nigenda-Morales, S. F., Beichman, A. C., Rojas-Bracho, L., Robertson, K. M., Fontaine, M. C., Wayne, R. K., Lohmueller, K. E., Taylor, B. L., & Morin, P. A. (2022). The critically endangered vaquita is not doomed to extinction by inbreeding depression. Science, 376(6593), 635-639. doi:10.1126/science.abm1742
[76]. Fontaine, M. (2022). Reticulated evolution marks the rapid diversification of the Delphinoidae. PCI Evolutionary Biology. doi:10.24072/pci.evolbiol.100139
[75]. Conklin, J. R., Verkuil, Y. I., Battley, P. F., Hassell, C. J., Ten Horn, J., Johnson, J. A., Tomkovich, P. S., Baker, A. J., Piersma, T., & Fontaine, M. C. (2022). Global flyway evolution in red knots Calidris canutus and genetic evidence for a Nearctic refugium. Molecular Ecology, 31(7), 2124-2139. doi:10.1111/mec.16379
[74]. Brinker, P., Chen, F., Ben Chehida, Y., Beukeboom, L. W., Fontaine, M. C., & Falcao Salles, J. (2022). Microbiome composition is shaped by geography and population structure in the parasitic wasp Asobara japonica, but not in the presence of the endosymbiont Wolbachia. Molecular Ecolology. doi:10.1111/mec.16699
2021
[73]. Yanos, C. L., Haanstra, E. P., Colgan Carey, F., Passmore, S. A., Eklof, J. S., Bergstrom, U., Hansen, J. P., Fontaine, M. C., Maan, M. E., & Eriksson, B. K. (2021). Predator biomass and vegetation influence the coastal distribution of threespine stickleback morphotypes. Ecol Evol, 11(18), 12485-12496. https://doi.org/10.1002/ece3.7993
[72]. Xue, A. T., Schrider, D. R., Kern, A. D., & The Anopheles gambiae 1000 Genomes Consortium. (2021). Discovery of Ongoing Selective Sweeps within Anopheles Mosquito Populations Using Deep Learning. Molecular Biology and Evolution, 38(3), 1168-1183. https://doi.org/10.1093/molbev/msaa259
[71]. Wagah, M. G., Korlevic, P., Clarkson, C., Miles, A., The Anopheles gambiae 1000 Genomes Consortium, Lawniczak, M. K. N., & Makunin, A. (2021). Genetic variation at the Cyp6m2 putative insecticide resistance locus in Anopheles gambiae and Anopheles coluzzii. Malar J, 20(1), 234. https://doi.org/10.1186/s12936-021-03757-4
[70]. Nelson, J. T., Cornejo, O. E., & The Anopheles gambiae 1000 Genomes Consortium. (2021). Evolutionary implications of recombination differences across diverging populations of Anopheles. biorXiv. https://doi.org/10.1101/2021.02.04.429659
[69]. Müller, N. F., Ogilvie, H. A., Zhang, C., Fontaine, M. C., Amaya-Romero, J. E., Drummond, A. J., & Stadler, T. (2021). Joint inference of species histories and gene flow. biorXiv. https://doi.org/10.1101/348391
[68]. Morin, P. A., Forester, B. R., Forney, K. A., Crossman, C. A., Hancock-Hanser, B. L., Robertson, K. M., Barrett-Lennard, L. G., Baird, R. W., Calambokidis, J., Gearin, P., Hanson, M. B., Schumacher, C., Harkins, T., Fontaine, M. C., Taylor, B. L., & Parsons, K. M. (2021). Population structure in a continuously distributed coastal marine species, the harbor porpoise, based on microhaplotypes derived from poor-quality samples. Mol Ecol, 30(6), 1457-1476. https://doi.org/10.1111/mec.15827
[67]. Louis, M., Galimberti, M., Archer, F., Berrow, S., Brownlow, A., Fallon, R., Nykanen, M., O’Brien, J., Roberston, K. M., Rosel, P. E., Simon-Bouhet, B., Wegmann, D., Fontaine, M. C., Foote, A. D., & Gaggiotti, O. E. (2021). Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins. Sci Adv, 7(44), eabg1245. https://doi.org/10.1126/sciadv.abg1245
[66]. Grau-Bové, X., Lucas, E., Pipini, D., Rippon, E., van ‘t Hof, A. E., Constant, E., Dadzie, S., Egyir-Yawson, A., Essandoh, J., Chabi, J., Djogbénou, L., Harding, N. J., Miles, A., Kwiatkowski, D., Donnelly, M. J., Weetman, D., & The Anopheles gambiae 1000 Genomes Consortium. (2021). Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus. PLOS Genetics, 17(1). https://doi.org/10.1371/journal.pgen.1009253
[65]. Fontaine, M. C., Labbe, F., Dussert, Y., Deliere, L., Richart-Cervera, S., Giraud, T., & Delmotte, F. (2021). Europe as a bridgehead in the worldwide invasion history of grapevine downy mildew, Plasmopara viticola. Curr Biol, 31(10), 2155-2166 e2154. https://doi.org/10.1016/j.cub.2021.03.009
[64]. Eriksson, B. K., Yanos, C., Bourlat, S. J., Donadi, S., Fontaine, M. C., Hansen, J. P., Jakubavičiūtė, E., Kiragosyan, K., Maan, M. E., Merilä, J., Austin, Å. N., Olsson, J., Reiss, K., Sundblad, G., Bergström, U., & Eklöf, J. S. (2021). Habitat segregation of plate phenotypes in a rapidly expanding population of three‐spined stickleback. Ecosphere, 12(6), e03561. https://doi.org/10.1002/ecs2.3561
[63]. Daron, J., Boissiere, A., Boundenga, L., Ngoubangoye, B., Houze, S., Arnathau, C., Sidobre, C., Trape, J. F., Durand, P., Renaud, F., Fontaine, M. C., Prugnolle, F., & Rougeron, V. (2021). Population genomic evidence of Plasmodium vivax Southeast Asian origin. Sci Adv, 7(18), abc3713. https://doi.org/10.1126/sciadv.abc3713
[62]. Clarkson, C. S., Miles, A., Harding, N. J., O’Reilly, A. O., Weetman, D., Kwiatkowski, D., Donnelly, M. J., & The Anopheles gambiae 1000 Genomes Consortium. (2021). The genetic architecture of target‐site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii. Molecular Ecology, 30(21), 5303-5317. https://doi.org/10.1111/mec.15845
[61]. Ben Chehida, Y., Loughnane, R., Thumloup, J., Kaschner, K., Garilao, C., Rosel, P. E., & Fontaine, M. C. (2021). No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications. Evol Appl, 14(6), 1588-1611. https://doi.org/10.1111/eva.13227
2020
[60]. Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii. The Anopheles gambiae 1000 Genomes Consortium Genome Res 2020: 30(10), 1533-1546. DOI:https://doi.org/10.1101/gr.262790.120
[59]. Radiation with reticulation marks the origin of a major malaria vector Small, S. T., Labbe, F., Lobo, N. F., Koekemoer, L. L., Sikaala, C. H., Neafsey, D. E., Hahn, M. W., Fontaine, M.C., & Besansky, N. J. Proc Natl Acad Sci U S A 2020:117(50), 31583-31590. DOI: https://doi.org/10.1073/pnas.2018142117
[58]. Is Iberian harbour porpoise (Phocoena phocoena) threatened by interactions with fisheries? Pierce, G., J, Weir, C., Gutierrez, P., Verutes, G., Fontaine, M. C., Hernandez Gonzalez, A., Saavedra, C., Llavona, A., Martínez-Cedeira, J., Covelo, P., López, A., Read, F., L, & Dolman, S., J. IWC Scientific Committee Paper 2020:SC/68B/SM/04 Rev62. https://hal.archives-ouvertes.fr/hal-03420827
[57]. Building genomic infrastructure: Sequencing platinum -standard reference-quality genomes of all cetacean species. Morin PA, Alexander A, Blaxter M, Caballero S, Fedrigo O, Fontaine MC, Foote AD, Kuraku S, Maloney B, McCarthy ML, McGowen MR, Mountcastle J, Nery MF, Olsen MT, Rosel PE, Jarvis ED. Marine Mammal Sciences 2020, 6(4):1356-1366 DOI: 10.1111/mms.12721
[56]. Evolution of the Insecticide Target Rdl in African Anopheles Is Driven by Interspecific and Interkaryotypic Introgression. Grau-Bové, X., Tomlinson, S., O’Reilly, A. O., Harding, N. J., Miles, A., Kwiatkowski, D., Donnelly, M. J., Weetman, D., & The Anopheles gambiae 1000 Genomes Consortium [including Fontaine MC]. Molecular Biology and Evolution 2020, 37(10), 2900-2917. DOI: https://doi.org/10.1093/molbev/msaa128
[55]. Assessing connectivity despite high diversity in island populations of the malaria mosquito Anopheles gambiae Bergey CM, Lukindu M, Wiltshire RM, Fontaine MC, Kayondo J, Besansky NJ. Evolutionary Applications 2020, 13:417-431 Doi: https://doi.org/10.1111/eva.12878
[54]. Genetic homogeneity in face of morphological heterogeneity in the harbor porpoises from the Black Sea and adjacent waters Chehida YB, Thumloup J, Vishnyakova K, Gol’din P, Fontaine MC. Heredity 2020, 124:469-484. doi: https://doi.org/10.1038/s41437-019-0284-1
[53]. Evolutionary history of the porpoises (Phocoenidae) across the speciation continuum: a mitogenome phylogeographic perspective. (2020). Chehida YB, Aguilar A, Borrell A, Ferreira M, Taylor BL, Rojas-Bracho L, Roberston KM, Thumloup J, Schumacher C, Harkins T, Víkingsson GA, Weyna A, Romiguier J, Morin PA, Fontaine MC. doi: https://doi.org/10.1038/s41598-020-71603-9
2019
[52]. In Silico Karyotyping of Chromosomally Polymorphic Malaria Mosquitoes in the Anopheles gambiaeComplex. Love RR, Redmond SN, Pombi M, Caputo B, Petrarca V, della Torre A, The Anopheles gambiae 1000 Genomes Consortium (including Fontaine MC), Besansky NJ. G3: Genes, Genomes, Genetics. 2019;9(10):3249-3262. Doi:10.1534/g3.119.400445.
[51]. Report of Joint IMR/NAMMCO International Workshop on the Status of Harbour Porpoises in the North Atlantic. Tromsø, Norway. North Atlantic Marine Mammal Commission and the Norwegian Institute of Marine Research. (2019). (Link: https://nammco.no/wp-content/uploads/2020/03/final-report_hpws_2018_rev2020.pdf)
[50]. Whole-genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes. Lucas ER, Miles A, Harding NJ, Clarkson CS, Lawniczak MKN, Kwiatkowski DP, Weetman D, Donnelly MJ, The Anopheles gambiae 1000 Genomes Consortium (including Fontaine MC) Genome Research 2019, 29:1250–1261. Doi: https://doi.org/10.1101/gr.245795.118
[49]. Population genetics and connectivity in the apex predator Carcharhinus leucas. Pirog A, Ravigné V, Fontaine MC, Rieux A, Gilabert A, Cliff G, Clua E, Daly R, Heithaus MR, Kiszka JJ, Matich P, Nevill JEG, Smoothey AF, Temple AJ, Jequemet S, Magalon H. Ecology and Evolution 2019, 9: 12980-13000 Doi: https://doi.org/10.1002/ece3.5597.
[48]. Host, symbionts, and the microbiome: the missing tripartite interaction. Brinker P, Fontaine MC, Beukeboom LW, Falcao Salles J.
Trends in Microbiology 2019, 27: 480-88. Doi: https://doi.org/10.1016/j.tim.2019.02.002
2018
[47]. Resilience of harbour porpoises to anthropogenic disturbance: must they really feed continuously? Hoekendijk JPA, Spitz J, Read AJ, Leopold MF, Fontaine MC, 2018. Marine Mammal Science 34: 258-264. (https://doi.org/10.1111/mms.12446).
2017
[46]. Genetic Footprint of Population Fragmentation and Contemporaneous Decline in the Endangered Yangtze Finless Porpoise. Chen M.*, Fontaine M. C.*, Chehida Y. B.*, Zheng J., Mei Z., Hao Y., Wang K., Wu M., Zhao Q., Wang D. Scientific Reports 7: 14449. (https://doi.org/10.1038/s41598-017-14812-z). * These authors contributed equally and are considered co-first authors.
[45]. A genomic perspective is needed for the re-evaluation of species boundaries, evolutionary trajectories and conservation strategies for the Galapagos giant tortoises. Fontaine MC, 2017 PCI Evol Biol. 100031.(https://doi.org/10.24072/pci.evolbiol.100031).
[44]. Demographic history of Armillaria ostoyae population in a managed pine forest in southwestern France. Labbé F., Fontaine M. C., Robin C., Dutech C. Heredity, 119: 402–410. (https://doi.org/10.1038/hdy.2017.58).
[43]. Natural diversity of the malaria vector Anopheles gambiae. Miles A., Harding N. J., Botta G., Clarkson C., Antão T., Kozak K., Schrider D., Kern A., Redmond S., Sharakhov I., Pearson R., Bergey C., Fontaine M. C., Troco A., Diabaté A., Costantini C., Rohatgi K., Elissa N., Coulibaly B., Dinis J., Midega J., Mbogo C., Mawejje H., Stalker J., Rockett K., Drury E., Mead D., Jeffreys A., Hubbart C., Rowlands K., Isaacs A., Jyothi D., Malangone C., Vauterin P., Jeffrey B., Wright I., Hart L., Kluczynski K., Cornelius V., MacInnis B., Henrichs C., Giacomantonio R., Ayala D., Bejon P., Besansky N., Burt A., Caputo B., Torre della A., Godfray C., Hahn M., Neafsey D. E., O’Loughlin S., Pinto J., Riehle M., Vernick K., Weetman D., Wilding C., White B., Lawniczak M., Donnelly M., Kwiatkowski D. (Pre-print Biorxiv: 096289). Nature, 552: 96-100. (https://doi.org/10.1038/nature24995)
[42]. Genomic and proteomic identification of Late Holocene cetaceans: a Black Sea case study. Biard V., Gol’din P. E., Gladilina E., Vishnyakova K., McGarth K., Vieira F. G., Wales N., Fontaine M. C., Speller C., Olsen M. T. Journal of Archeological Science, 15: 262–271. (https://doi.org/10.1016/j.jasrep.2017.07.008).
[41]. Ecological and environmental factors associated with heterogeneous patterns of genomic divergence across a butterfly hybrid zone: climate being the most salient. Ryan S., Fontaine M. C., Scriber M., O’Neil S., Pfrender M. E., Hellman J. Molecular Ecology, 26: 4725-4742. (https://doi.org/10.1111/mec.14236).
[40]. Mixing of Porpoise Ecotypes in South Western UK Waters Revealed by Genetic Profiling. Fontaine MC, O Tatcher, N Ray, S Piry, A Brownlow, NJ Davison, P Jepson, R Deaville, SJ Goodman. R. Soc. open sci. 4: 160992. (http://dx.doi.org/10.1098/rsos.160992)
[39]. Spatial variations in concentrations of mercury and persistent organic pollutants in coastal bottlenose dolphins, Tursiops truncatus from the Lower Florida Keys and the coastal Everglades (South Florida). Damseaux F., Kiszka J. J., Heithaus M. R., George S., Eppe G., Thomé J.-P., Lewis J., Hao W., Fontaine M. C., Das K. (2017) Environmental Pollution 220 (Pt A): 577-587. (link) [MEDIA coverage] FIU-News: Mercury contamination found in Everglades dolphins
2016
[38]. Harbour porpoises, Phocoena phocoena, in the Mediterranean Sea and adjacent regions: biogeographic relicts of the last glacial period Fontaine M.C. (2016) Advances in Marine Biology 75: 333-358.(link)
[37]. Chromosomal inversions and ecotypic differentiation in Anopheles gambiae: the perspective from whole-genome sequencing. Love R. R., Steele A., Coulibaly M. B., Traoré S., Emrich S. J., Fontaine M. C.*, Besansky N. J.* (2016) Molecular Ecology, 25: 5889–5906 (link). *Co-supervise this work.
2015
[36]. Scaffold assembly based on genome rearrangement analysis. Aganezov, S., Sitdykova, N., AGC Consortium*, Alekseyev, M. A. (2015). Computational biology and chemistry. 57: 46-53. * As part of the AGC Consortium. (link)
[35]. Enhanced computational methods for quantifying the effect of geographic and environmental isolation on genetic differentiation. Botta F., Eriksen C., Fontaine M. C., Guillot G., 2015 Method in Ecology and Evolution 6: 1270-1277 (link, SUNDER R package).
[34]. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Fontaine M.C.*, Pease J. B.*., Steele A., Waterhouse R. M., Neafsey D. E., Sharakhov I. V., Jiang X., Hall A. B., Kakani E., Mitchell S. N., Wu Y.-C., Smith H. A., Love R. R., Lawniczak M. K. N., Slotman M. A., Emrich S. J., Hahn M. W., Besansky N. J. Science vol. 347 (no. 6217), DOI: 10.1126/science.1258524 (link). *Contributed equally.
[33]. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Neafsey DE*, Waterhouse RM*, Abai MR, Aganezov SS, Alekseyev MA, […], Fontaine MC, […], Besansky NJ. Science, vol. 347 (no. 6217). DOI: 10.1126/science.1258522 (link). *Contributed equally.
2014
[32]. Tools and Methods Derived from the Anopheline 16 Genome project Steele A, Fontaine MC, Martin A, Emrich SJ. (2014) bioRXiv. (NGSTools)
[31]. Ecological opportunities and specializations shaped genetic divergence in a highly mobile marine top predator. Louis M., Fontaine M. C., Spitz J., Schlund E., Dabin W., Deaville R., Caurant F., Cherel Y., Guinet C., Simon-Bouhet B. 2014. Proceedings of the Royal Society B: Biology, 281: 1795 (link).
[30]. Postglacial climate changes and rise of three ecotypes of harbor porpoises, Phocoena phocoena, in western Palearctic waters. Fontaine M. C., Roland K., Calves I., Austerlitz F., Palstra F. P., Tolley K. A., Ryan S., Ferreira M., Jauniaux T., Llavona Á., Öztürk B., Oztürk A. A., Ridoux V., Rogan E., Sequeira M., Siebert U., Vikingsson G. A., Borrell A., Michaux J. R., Aguilar A., 2014 Molecular Ecology 23, 3306–3321. (link)
2013
[29]. The evolution of the Anopheles 16 genomes project. Neafsey D., Christophides G. K., Collins F. H., Emrich S. J., Fontaine M. C., Gelbart W., Hahn M. W., Howell P. I., Kafatos F. C., Lawson D., Muskavitch M. A. T., Waterhouse R. M., Williams L. J., Besansky N. J., 2013. G3: Genes, Genomes, Genetics 3: 1191–1194. (link)
[28]. Antennal transcriptome profiles of anopheline mosquitoes reveal human host olfactory specialization in Anopheles gambiae. Rinker D. C., Zhou X., Pitts R. J., AGC Consortium*, Rokas A., Zwiebel L. J., 2013. BMC Genomics 14: 749. *As part of the AGC Consortium. (link)
[27]. Complex speciation process in the Anopheles gambiae species complex revealed by whole genome sequencing. (Conference abstract) Fontaine M. C., Steele A., Emrich S. J., Smith H. A., Hahn M. W., Besansky N. J., 2013 Pathogens and Global Health 107: 428–429.
[26]. Genetic signature of a range expansion and leap-frog event after the recent invasion of Europe by the grapevine downy mildew pathogen Plasmopara viticola. Fontaine M. C., Austerlitz F., Giraud T., Labbé F., Papura D., Richard-Cervera S., Delmotte F., 2013. Molecular Ecology22: 2771–2786. (link)
[25]. History of the invasion of the anther smut pathogen on Silene latifolia in North America. Fontaine M. C., Gladieux P., Hood M. E., Giraud T., 2013. New Phytol. 198: 946–956. (link)
[24]. Polymorphism pattern at a miniature inverted-repeat transposable element locus downstream of the domestication gene Teosinte-branched1 in wild and domesticated pearl millet Dussert Y., Remigereau M. S., Fontaine M. C., Snirc A., Lakis G., Stoeckel S., Langin T., Sarr A., Robert T., 2013. Molecular Ecology 22: 327–340. (link)
2012
[23]. Une nouvelle espèce de dauphin. Fontaine M.C. (2012) Encyclopaedia Universalis France. Pp. 330-331. (In French).
[22]. A European Melting Pot of Harbour Porpoise in the French Atlantic Coasts Inferred from Mitochondrial and Nuclear Data Alfonsi E., Hassani S., Carpentier F.-G., Le Clec’h J.-Y., Dabin W., Van Canneyt O., Fontaine M. C.*, Jung J.-L.*, 2012. PLoS ONE 7: e44425. *Co-supervise this work. (link)
[21]. Genetic structure in a dynamic baboon hybrid zone corroborates behavioural observations in a hybrid population Charpentier M.*, Fontaine M. C.*, Cherel E., Renoult J. P., Jenkins T., Benoit L., Barthès N., Alberts S. C., Tung J., 2012. Molecular Ecology 21: 715–731. *Contributed equally (link)
[20]. History of expansion and anthropogenic collapse in a top marine predator of the Black Sea estimated from genetic data. Fontaine M. C., Snirc A., Frantzis A., Koutrakis E., Öztürk B., Oztürk A. A., Austerlitz F., 2012. Proceedings of the National Academy of Sciences 109: E2569–76. (link)
[19]. Factors shaping gene flow in red deer (Cervus elaphus) in seminatural landscapes of central Europe. Niedziałkowska M., Fontaine M.C., Jędrzejewska B., 2012. Can. J. Zool. 90: 150–162. (link)
[18]. Different biogeographic patterns of prokaryotes and microbial eukaryotes in epilithic biofilms. Ragon M.*, Fontaine M. C.*, Moreira D., López-Garcia P., 2012. Molecular Ecology 21: 3852–3868. *Contributed equally. (link)
[17]. Barriers To Gene Flow In The Marine Environment: Insights From Two Common Intertidal Limpet Species Of The Atlantic And Mediterranean Sà Pinto A., Simas Branco M., Barros Alexandrino P., Fontaine M. C., Baird S. J. E., 2012. PLoS ONE 7: e50330.
2011
[16]. Chromosomal inversions, natural selection and adaptation in the malaria vector Anopheles funestus. Ayala D., Fontaine M. C., Cohuet A., Fontenille D., Vitalis R., Simard F., 2011 Molecular Biology and Evolution 28: 745–758.
[15]. Maintenance of fungal pathogen species that are specialized to different hosts: allopatric divergence and introgression through secondary contact. Gladieux P., Vercken E., Fontaine M. C., Hood M. E., Jonot O., Couloux A., Giraud T., 2011 Molecular Biology and Evolution 28: 459–471.
[14]. Cytochrome P450 1A1 expression in cetacean skin biopsies from the Indian Ocean. Jauniaux T., Farnir F., Fontaine M. C., Kiszka J., Sarlet M., Coignoul F., 2011 Mar. Pollut. Bull. 62: 1317–1319.
[13]. Temporal isolation explains host-related genetic differentiation in a group of widespread mycoparasitic fungi. Kiss L., Pintye A., Kovács G. M., Jankovics T., Fontaine M. C., Harvey N., Xu X., Nicot P. C., Bardin M., Shykoff J. A., Giraud T., 2011 Molecular Ecology 20: 1492–1507.
[12]. Cereal domestication and evolution of branching: evidence for soft selection in the Tb1 orthologue of pearl millet (Pennisetum glaucum [L.] R. Br.). Remigereau M.-S., Lakis G., Rekima S., Leveugle M., Fontaine M. C., Langin T., Sarr A., Robert T., 2011 PLoS ONE 6: e22404.
2010
[11]. Finding candidate genes under positive selection in Non-model species: examples of genes involved in host specialization in pathogens. Aguileta G., Lengelle J., Marthey S., Chiapello H., Rodolphe F., Gendrault A., Yockteng R., Vercken E., Devier B., Fontaine M. C., Wincker P., Dossat C., Cruaud C., Couloux A., Giraud T., 2010. Molecular Ecology 19: 292–306.
[10]. Genetic and historic evidence for climate-driven population fragmentation in a top cetacean predator: the harbour porpoises in European water. Fontaine M. C., Tolley K. A., Michaux J. R., Birkun A., Ferreira M., Jauniaux T., Llavona Á., Öztürk B., Oztürk A. A., Ridoux V., Rogan E., Sequeira M., Bouquegneau J.-M., Baird S. J. E., 2010. Proceedings of the Royal Society B: Biological Sciences 277: 2829–2837.
[9]. Glacial refugia in pathogens: European genetic structure of anther smut pathogens on Silene latifolia and Silene dioica. Vercken E.*, Fontaine M. C.*, Gladieux P., Hood M. E., Jonot O., Giraud T., 2010. PLoS Pathog 6: e1001229. *Contributed equally.
2008 –> 2009
[8]. A relict bank vole lineage highlights the biogeographic history of the Pyrenean region in Europe. Deffontaine V., Ronan L., Fontaine M. C., Quéré J.-P., Renaud S., Libois R., Michaux J. R., 2009. Molecular Ecology 18: 2489–2502.
[7]. Structure et evolution des populations de marsouins communs des eaux Palearctiques occidentales. Fontaine M. C., 2008 PhD Thesis defended the in March 2008 at the University of Liège (Belgium). (link)
2007
[6]. Rise of oceanographic barriers in continuous populations of a cetacean: the genetic structure of harbour porpoises in Old World waters. Fontaine M. C., Baird S. J. E., Piry S., Ray N., Tolley K. A., Duke S., Birkun A., Ferreira M., Jauniaux T., Llavona Á., Öztürk B., A Öztürk A., Ridoux V., Rogan E., Sequeira M., Siebert U., Vikingsson G. A., Bouquegneau J.-M., Michaux J. R., 2007a. BMC Biol 5: 30.
[5]. Long-term feeding ecology and habitat use in harbour porpoises Phocoena phocoena from Scandinavian waters inferred from trace elements and stable isotopes. Fontaine M. C., Tolley K. A., Siebert U., Gobert S., Lepoint G., Bouquegneau J.-M., Das K., 2007b. BMC Ecol 7: 1.
[4]. Genetic pattern of the recent recovery of European otters in southern France. Janssens X.*, Fontaine M. C.*, Michaux J. R. , Libois R., de Kermabon J., Defourny P., Baret P. V., 2007. Ecography 31: 176–186. *Contributed equally.
2003 -> 2006
[3]. Ecological and pathological factors related to trace metal concentrations in harbour porpoises Phocoena phocoena from the North Sea and adjacent areas. Das K., Siebert U., Fontaine M., Jauniaux T., Holsbeek L., Bouquegneau J. M., 2004 Mar. Ecol. Prog. Ser. 281.
[2]. Fluorescent Multiplex Polymerase Chain Reactions (PCRs) for Rapid Genotyping of Harbour Porpoises (Phocoena phocoena) with 11 Microsatellite Loci. Fontaine M. C., Galan M., Bouquegneau J.-M., Michaux J. R., 2006 Aquatic mammals 32: 301–304.
[1]. Carbon and Nitrogen Isotopic Ratios of the Seagrass Posidonia oceanica: Depth-related Variations. Lepoint G., Dauby P., Fontaine M., Bouquegneau J. M., Gobert S., 2003. Botanica Marina 46: 555–561.