Michael Fontaine

Chargé de recherche du CNRS dans l'UMR MIVEGEC, Montpellier, France. | Prof. honoraire au Groningen Institute for Evolutionary Life Sciences (GELIFES), U. Groningen, Pays Bas.
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Documents

Présentation

MIVEGEC [UMR CNRS / U. Montpellier / IRD] Institut de Recherche pour le Développement
911, Avenue Agropolis, BP 64501 34394 Montpellier Cedex 5, France Tel: +33-(0)4 67 41 61 06 Email: michael.fontaine@cnrs.fr

Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands Email: m.c.fontaine@rug.nl


Compétences

Bioinformatics Molecular Ecology and Evolution Statistical genetics Phylogenetics/genomics Population genetics/genomics Computational biology Data sciences FAIR principles

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Publications

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A comparison of genomic diversity and demographic history of the North Atlantic and Southwest Atlantic southern right whales

Carla A Crossman , Michael C. Fontaine , Timothy R Frasier
Molecular Ecology, 2024, 33, pp.e17099. ⟨10.1111/mec.17099⟩
Article dans une revue hal-04299475 v2
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High dispersal ability versus migratory traditions: Fine‐scale population structure and post‐glacial colonisation in bar‐tailed godwits

Jesse R Conklin , Yvonne I Verkuil , Margaux J M Lefebvre , Phil F Battley , Roeland A Bom et al.
Molecular Ecology, 2024, 33 (15), pp.e17452. ⟨10.1111/mec.17452⟩
Article dans une revue hal-04779401 v1
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Mitochondrial variation in <i>Anopheles gambiae</i> and <i>An. coluzzii</i> : phylogeographic legacy and mitonuclear associations with metabolic resistance to pathogens and insecticides

Jorge E Amaya Romero , Clothilde Chenal , Yacine Ben Chehida , Alistair Miles , Chris S Clarkson et al.
Genome Biology and Evolution, 2024, 16 (9), pp.evae172. ⟨10.1093/gbe/evae172⟩
Article dans une revue hal-04300269 v2
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A genotyping array for the globally invasive vector mosquito, Aedes albopictus

Luciano Veiga Cosme , Margaret Corley , Thomas Johnson , Dave W Severson , Guiyun Yan et al.
Parasites & Vectors, 2024, 17, pp.106. ⟨10.1186/s13071-024-06158-z⟩
Article dans une revue hal-04779465 v1
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Harbor porpoise losing its edges: genetic time series suggests a rapid population decline in Iberian waters over the last 30 years

Yacine Ben Chehida , Tjibbe Stelwagen , Jeroen P A Hoekendijk , Marisa Ferreira , Catarina Eira et al.
Ecology and Evolution, 2023, 13 (12), pp.e10819. ⟨10.1002/ece3.10819⟩
Article dans une revue hal-03415287 v3
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Population genomic evidence of adaptive response during the invasion history of Plasmodium falciparum in the Americas

Margaux J M Lefebvre , Josquin Daron , Eric Legrand , Michael C. Fontaine , Virginie Rougeron et al.
Molecular Biology and Evolution, 2023, 40 (5), pp.msad082. ⟨10.1093/molbev/msad082⟩
Article dans une revue hal-03836777 v2
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Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Marie Louis , Petra Korlević , Milaja Nykänen , Frederick Archer , Simon Berrow et al.
Nature Communications, 2023, 14 (1), pp.4020. ⟨10.1038/s41467-023-39532-z⟩
Article dans une revue hal-04300188 v1
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Models based on best-available information support a low inbreeding load and potential for recovery in the vaquita

Christopher Kyriazis , Jacqueline Robinson , Sergio Nigenda-Morales , Annabel Beichman , Lorenzo Rojas-Bracho et al.
Heredity, 2023, 130, pp.183-187. ⟨10.1038/s41437-023-00608-7⟩
Article dans une revue hal-04047612 v1
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Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria vector

Scott T Small , Carlo Costantini , N’fale Sagnon , Moussa W Guelbeogo , Scott J Emrich et al.
Proceedings of the National Academy of Sciences of the United States of America, 2023, 120 (11), ⟨10.1073/pnas.2219835120⟩
Article dans une revue hal-03871937 v2
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Microbiome composition is shaped by geography and population structure in the parasitic wasp Asobara japonica , but not in the presence of the endosymbiont Wolbachia

Pina Brinker , Fangying Chen , Yacine Ben Chehida , Leo Beukeboom , Michael C. Fontaine et al.
Molecular Ecology, 2022, ⟨10.1111/mec.16699⟩
Article dans une revue hal-03782865 v1
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Reticulated evolution marks the rapid diversification of the Delphinoidae

Michael C. Fontaine
Peer Community In Evolutionary Biology, 2022, ⟨10.24072/pci.evolbiol.100139⟩
Article dans une revue hal-03748477 v1
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Global flyway evolution in red knots Calidris canutus and genetic evidence for a Nearctic refugium

Jesse R Conklin , Yvonne I Verkuil , Philip Battley , Chris J Hassell , Job Ten Horn et al.
Molecular Ecology, 2022, 31 (7), pp.2124-2139. ⟨10.1111/mec.16379⟩
Article dans une revue hal-03408091 v2
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Evolutionary history of Plasmodium vivax and Plasmodium simium in the Americas

Virginie Rougeron , Josquin Daron , Michael C. Fontaine , Franck Prugnolle
Malaria Journal, 2022, 21 (1), pp.141. ⟨10.1186/s12936-022-04132-7⟩
Article dans une revue hal-03748455 v1
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The critically endangered vaquita is not doomed to extinction by inbreeding depression

Jacqueline Robinson , Christopher Kyriazis , Sergio Nigenda-Morales , Annabel Beichman , Lorenzo Rojas-Bracho et al.
Science, 2022, 376 (6593), pp.635-639. ⟨10.1126/science.abm1742⟩
Article dans une revue hal-03748473 v1
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Population structure in a continuously distributed coastal marine species, the harbor porpoise, based on microhaplotypes derived from poor quality samples

Phillip A. Morin , Brenna R. Forester , Karin A. Forney , Carla A. Crossman , Brittany L. Hancock-Hanser et al.
Molecular Ecology, 2021, 30 (6), pp.1457-1476. ⟨10.1111/mec.15827⟩
Article dans une revue hal-03088621 v1
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Discovery of Ongoing Selective Sweeps within Anopheles Mosquito Populations Using Deep Learning

Alexander Xue , Daniel Schrider , Andrew Kern , Alessandra Della Torre , Beniamino Caputo et al.
Molecular Biology and Evolution, 2021, 38 (3), pp.1168-1183. ⟨10.1093/molbev/msaa259⟩
Article dans une revue hal-03420515 v1
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Population genomic evidence of Plasmodium vivax Southeast Asian origin

J. Daron , A. Boissiere , L. Boundenga , B. Ngoubangoye , S. Houze et al.
Science Advances , 2021, 7, pp.eabc3713. ⟨10.1126/sciadv.abc3713⟩
Article dans une revue hal-02915422 v1
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Habitat segregation of plate phenotypes in a rapidly expanding population of three-spined stickleback

Britas Klemens Eriksson , Casey Yanos , Sarah Bourlat , Serena Donadi , Michael C. Fontaine et al.
Ecosphere, 2021, 12 (6), pp.e03561. ⟨10.1002/ecs2.3561⟩
Article dans une revue hal-02915393 v1
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The genetic architecture of target‐site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii

Chris Clarkson , Alistair Miles , Nicholas Harding , Andrias O’reilly , David Weetman et al.
Molecular Ecology, 2021, ⟨10.1111/mec.15845⟩
Article dans une revue hal-03420486 v1
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Genetic variation at the Cyp6m2 putative insecticide resistance locus in Anopheles gambiae and Anopheles coluzzii

Martin G Wagah , Petra Korlević , Christopher Clarkson , Alistair Miles , Mara K N Lawniczak et al.
Malaria Journal, 2021, 20 (1), pp.234. ⟨10.1186/s12936-021-03757-4⟩
Article dans une revue hal-03861207 v1
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Europe as a bridgehead in the worldwide invasion history of grapevine downy mildew, Plasmopara viticola

Michaël Fontaine , Frédéric Labbé , Yann Dussert , Laurent Delière , Sylvie Richart-Cervera et al.
Current Biology, 2021, 31 (10), pp.2155-2166.e4. ⟨10.1016/j.cub.2021.03.009⟩
Article dans une revue hal-03184119 v1
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Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins

Marie Louis , M Galimberti , Frederick Archer , Simon Berrow , Andrew Brownlow et al.
Science Advances , 2021, 7, pp.eabg1245. ⟨10.1126/sciadv.abg1245⟩
Article dans une revue hal-03020428 v1
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No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications

Yacine Ben Chehida , Roisin Loughnane , Julie Thumloup , Kristin Kaschner , Cristina Garilao et al.
Evolutionary Applications, 2021, 14 (6), pp.1588-1611. ⟨10.1111/eva.13227⟩
Article dans une revue hal-03015895 v1
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Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus

Xavier Grau-Bové , Eric Lucas , Dimitra Pipini , Emily Rippon , Arjèn Van’t Hof et al.
PLoS Genetics, 2021, 17 (1), pp.e1009253. ⟨10.1371/journal.pgen.1009253⟩
Article dans une revue hal-02915392 v1
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Predator biomass and vegetation influence the coastal distribution of threespine stickleback morphotypes

Casey L Yanos , Eeke P Haanstra , Fiona Colgan Carey , Sorsha A Passmore , Johan S Eklöf et al.
Ecology and Evolution, 2021, 11 (18), pp.12485-12496. ⟨10.1002/ece3.7993⟩
Article dans une revue hal-03408086 v1
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Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum.

Yacine Ben Chehida , Julie Thumloup , Cassie Schumacher , Timothy Harkins , Alex Aguilar et al.
Scientific Reports, 2020, 10 (1), pp.15190. ⟨10.1038/s41598-020-71603-9⟩
Article dans une revue hal-03020351 v1
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Assessing connectivity despite high diversity in island populations of a malaria mosquito

Christina M. Bergey , Martin Lukindu , Rachel Wiltshire , Michael C. Fontaine , Jonathan Kayondo et al.
Evolutionary Applications, 2020, 13 (2), pp.417-431. ⟨10.1111/eva.12878⟩
Article dans une revue hal-02915424 v1
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Genetic homogeneity in the face of morphological heterogeneity in the harbor porpoise from the Black Sea and adjacent waters (Phocoena phocoena relicta)

Yacine Ben Chehida , Julie Thumloup , Karina Vishnyakova , Pavel Gol’din , Michael C. Fontaine
Heredity, 2020, 124 (3), pp.469-484. ⟨10.1038/s41437-019-0284-1⟩
Article dans une revue hal-02915495 v1
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Evolution of the Insecticide Target Rdl in African Anopheles Is Driven by Interspecific and Interkaryotypic Introgression

Xavier Grau-Bové , Sean Tomlinson , Andrias O’reilly , Nicholas Harding , Alistair Miles et al.
Molecular Biology and Evolution, 2020, 37 (10), pp.2900-2917. ⟨10.1093/molbev/msaa128⟩
Article dans une revue hal-02915420 v1
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Building genomic infrastructure: Sequencing platinum-standard reference-quality genomes of all cetacean species

Phillip A. Morin , Alana Alexander , Mark Blaxter , Susana Caballero , Olivier Fedrigo et al.
Marine Mammal Science, 2020, ⟨10.1111/mms.12721⟩
Article dans une revue hal-03020344 v1
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Radiation with reticulation marks the origin of a major malaria vector

Scott T. Small , Frédéric Labbé , Neil F. Lobo , Lizette L. Koekemoer , Chadwick H. Sikaala et al.
Proceedings of the National Academy of Sciences of the United States of America, 2020, 117 (50), pp.31583-31590. ⟨10.1073/pnas.2018142117⟩
Article dans une revue hal-03088085 v1
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Genome variation and population structure among 1,142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii

Chris C.S. Clarkson , Alistair Miles , Nicholas J Harding , Eric R Lucas , C J Battey et al.
Genome Research, 2020, 30 (10), pp.1533-1546. ⟨10.1101/gr.262790.120⟩
Article dans une revue hal-02446284 v1
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Whole-genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes

Eric Lucas , Alistair Miles , Nicholas Harding , Chris Clarkson , Mara K.N. Lawniczak et al.
Genome Research, 2019, 29 (8), pp.1250-1261. ⟨10.1101/gr.245795.118⟩
Article dans une revue hal-02915503 v1
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In Silico Karyotyping of Chromosomally Polymorphic Malaria Mosquitoes in the Anopheles gambiae Complex

R. Rebecca Love , Seth Redmond , Marco Pombi , Beniamino Caputo , Vincenzo Petrarca et al.
G3, 2019, 9 (10), pp.3249-3262. ⟨10.1534/g3.119.400445⟩
Article dans une revue hal-02915499 v1
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Population structure, connectivity, and demographic history of an apex marine predator, the bull shark Carcharhinus leucas

Agathe Pirog , Virginie Ravigné , Michael C. Fontaine , Adrien Rieux , Aude Gilabert et al.
Ecology and Evolution, 2019, 9 (23), pp.12980-13000. ⟨10.1002/ece3.5597⟩
Article dans une revue hal-02915501 v1
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Host, Symbionts, and the Microbiome: The Missing Tripartite Interaction

Pina Brinker , Michael C. Fontaine , Leo Beukeboom , Joana Falcão Salles
Trends in Microbiology, 2019, ⟨10.1016/j.tim.2019.02.002⟩
Article dans une revue hal-02104428 v1

Resilience of harbor porpoises to anthropogenic disturbance: Must they really feed continuously?

Jeroen Hoekendijk , Jérôme Spitz , Andrew Read , Mardik Leopold , Michael C. Fontaine
Marine Mammal Science, 2018, 34 (1), pp.258-264. ⟨10.1111/mms.12446⟩
Article dans une revue hal-02915504 v1
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Genetic diversity of the African malaria vector Anopheles gambiae

Alistair Miles , Mara K. N. Lawniczak , Martin J Donnelly , Dominic P Kwiatkowski , Nicholas J Harding et al.
Nature, 2017, 552 (7683), pp.96-100. ⟨10.1038/nature24995⟩
Article dans une revue hal-02915878 v1
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Genetic footprint of population fragmentation and contemporary collapse in a freshwater cetacean

Minmin Chen , Michael C. Fontaine , Yacine Ben Chehida , Jinsong Zheng , Frédéric Labbe et al.
Scientific Reports, 2017, 7 (1), pp.14449. ⟨10.1038/s41598-017-14812-z⟩
Article dans une revue hal-02915513 v1

Genetic signatures of variation in population size in a native fungal pathogen after the recent massive plantation of its host tree

F Labbé , Michael C. Fontaine , C. Robin , C. Dutech
Heredity, 2017, 119 (6), pp.402-410. ⟨10.1038/hdy.2017.58⟩
Article dans une revue hal-02915508 v1
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Mixing of porpoise ecotypes in southwestern UK waters revealed by genetic profiling

Michael C. Fontaine , Oliver Thatcher , Nicolas Ray , Sylvain Piry , Andrew Brownlow et al.
Royal Society Open Science, 2017, 4 (3), ⟨10.1098/rsos.160992⟩
Article dans une revue hal-01602775 v1

Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient

Sean Ryan , Michael C. Fontaine , J. Mark Scriber , Michael Pfrender , Shawn O'Neil et al.
Molecular Ecology, 2017, 26 (18), pp.4725-4742. ⟨10.1111/mec.14236⟩
Article dans une revue hal-02915518 v1

Spatial variation in the accumulation of POPs and mercury in bottlenose dolphins of the Lower Florida Keys and the coastal Everglades (South Florida)

France Damseaux , Jérémy Kiszka , Michael R Heithaus , George Scholl , Gauthier Eppe et al.
Environmental Pollution, 2017, 220, pp.577-587. ⟨10.1016/j.envpol.2016.10.005⟩
Article dans une revue hal-02915882 v1

Genomic and proteomic identification of Late Holocene remains: Setting baselines for Black Sea odontocetes

Vincent Biard , Pavel Gol'Din , Elena Gladilina , Karina Vishnyakova , Krista Mcgrath et al.
Journal of Archaeological Science: Reports, 2017, 15, pp.262-271. ⟨10.1016/j.jasrep.2017.07.008⟩
Article dans une revue hal-02915879 v1

Chromosomal inversions and ecotypic differentiation in Anopheles gambiae : the perspective from whole-genome sequencing

R. Rebecca Love , Aaron Steele , Mamadou Lamine Coulibaly , Sékou F Traoré , Scott Emrich et al.
Molecular Ecology, 2016, 25 (23), pp.5889-5906. ⟨10.1111/mec.13888⟩
Article dans une revue hal-02915883 v1

Harbour Porpoises, Phocoena phocoena, in the Mediterranean Sea and Adjacent Regions: Biogeographic Relicts of the Last Glacial Period

Michael C. Fontaine
Advances in Marine Biology, 2016, 75, pp.333-358. ⟨10.1016/bs.amb.2016.08.006⟩
Article dans une revue hal-02915884 v1

Scaffold assembly based on genome rearrangement analysis

Sergey Aganezov , Nadia Sitdykova , Max Alekseyev , The Anopheles Gambiae Consortium (including Michael C Fontaine)
Computational Biology and Chemistry, 2015, 57, pp.46-53. ⟨10.1016/j.compbiolchem.2015.02.005⟩
Article dans une revue hal-02915885 v1

Ecological opportunities and specializations shaped genetic divergence in a highly mobile marine top predator

Louis Marie , Michael C. Fontaine , Jérôme Spitz , Schlund Erika , Willy Dabin et al.
Proceedings of the Royal Society B: Biological Sciences, 2014, 281, pp.20141558. ⟨10.1098/rspb.2014.1558⟩
Article dans une revue hal-01075773 v1

Postglacial climate changes and rise of three ecotypes of harbour porpoises, Phocoena phocoena, in western Palearctic waters.

Michaël C Fontaine , Kathleen Roland , Isabelle Calves , Frederic Austerlitz , Friso P Palstra et al.
Molecular Ecology, 2014, 23 (13), pp.3306-21. ⟨10.1111/mec.12817⟩
Article dans une revue hal-01019023 v1
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A European Melting Pot of Harbour Porpoise in the French Atlantic Coasts Inferred from Mitochondrial and Nuclear Data

Eric Alfonsi , Sami Hassani , François-Gilles Carpentier , Jean-Yves Le Clec'H , Willy Dabin et al.
PLoS ONE, 2012, 7 (9), pp.e44425. ⟨10.1371/journal.pone.0044425.t001⟩
Article dans une revue hal-01066281 v1
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Chromosomal Inversions, Natural Selection and Adaptation in the Malaria Vector Anopheles funestus

Diego Ayala , Michael C. Fontaine , Anna Cohuet , Didier Fontenille , Renaud Vitalis et al.
Molecular Biology and Evolution, 2011, 28 (1), pp.745-758. ⟨10.1093/molbev/msq248⟩
Article dans une revue hal-02651247 v1
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Cytochrome P450 1A1 expression in cetacean skin biopsies from the Indian Ocean

Thierry Jauniaux , Frédéric Farnir , Michaël Fontaine , Jeremy Kiszka , Michael Sarlet et al.
Marine Pollution Bulletin, 2011, 62 (6), pp.1317-1319. ⟨10.1016/j.marpolbul.2011.04.005⟩
Article dans une revue hal-00608678 v1

Blackwell Publishing LtdA relict bank vole lineage highlights the biogeographic history of the Pyrenean region in Europe

V. Deffontaine , R. Ledevin , M. C. Fontaine , J-P. Quéré , Sabrina Renaud et al.
Molecular ecology, 2009, 18, pp.2489-2502
Article dans une revue hal-02307068 v1

Genomic diversity, evolution, and adaptation of Anopheles bwambae to the extreme thermal spring waters in Uganda

Michael C. Fontaine , Frédéric Labbé , R. Rebecca Love , Loïc Talignani , Adeyemi T. Akinade et al.
ESOVE 2024 - 23rd European Society for Vector Ecology Conference, Vectopole Sud; SOVE (Society for Vector Ecology), Oct 2024, Montpellier, France. pp.S1-3
Communication dans un congrès hal-05006360 v1

Pangenomic variations and differentiation between the two African malaria vector sister species Anopheles gambiae and Anopheles coluzzii

Clothilde Chenal , Corentin Marco , Francois Sabot , Chris S Clarkson , Alistair Miles et al.
ESOVE 2024 - 23rd European Society for Vector Ecology Conference, Vectopole Sud; SOVE (Society for Vector Ecology), Oct 2024, Montpellier, France. pp.S1-1
Communication dans un congrès hal-05006323 v1

Mitochondrial variation in Anopheles gambiae and An. coluzzii: phylogeographic legacy and associations with metabolic resistance to pathogens and insecticides

Michael C. Fontaine , Clothilde Chenal , Yacine Ben Chehida , Alistair Miles , Chris S Clarkson et al.
ESOVE 2024 - 23rd European Society for Vector Ecology Conference, Oct 2024, Montpellier, France. , ESOVE 2024 - the 23rd European Society for Vector Ecology Conference. Book of Abstracts, pp.S1-P08
Poster de conférence hal-05007034 v1
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Genomic insights into Plasmodium vivax and Plasmodium simium host shifts in Latin America

Margaux J M Lefebvre , Fanny Degrugillier , Céline Arnathau , Camila González , Silvia Rondón et al.
2025
Pré-publication, Document de travail hal-04867637 v1
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Genomic Signatures of Microgeographic Adaptation in Anopheles coluzzii Along an Anthropogenic Gradient in Gabon

Josquin Daron , Lemonde Bouafou , Jacob A Tennessen , Nil Rahola , Boris Makanga et al.
2024
Pré-publication, Document de travail hal-04782274 v1
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Population structure of the invasive Asian tiger mosquito, Aedes albopictus, in Europe

Margaret K Corley , Luciano Cosme , Peter A Armbruster , Maria Sharakhova , Alessandra Della Torre et al.
2024
Pré-publication, Document de travail hal-04782404 v1
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Genomic exploration of the complex journey of Plasmodium vivax in Latin America

M J M Lefebvre , Fanny Degrugillier , C. Arnathau , G A Fontecha , O. Noya et al.
2024
Pré-publication, Document de travail hal-04782302 v1
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Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Marie Louis , Petra Korlevic , Milaja Nykanen , Frederick Archer , Simon Berrow et al.
2022
Pré-publication, Document de travail hal-03842461 v1
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Evolutionary implications of recombination differences across diverging populations of Anopheles

Joel T Nelson , Omar E Cornejo , The Anopheles Gambiae 1000 Genomes Consortium (including Mc Fontaine)
2021
Pré-publication, Document de travail hal-03415333 v1
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Joint inference of species histories and gene flow

Nicola F Müller , Huw A Ogilvie , Chi Zhang , Michael C. Fontaine , Jorge E Amaya-Romero et al.
2021
Pré-publication, Document de travail hal-03415337 v1

Evolutionary history of the porpoises ( Phocoenidae ) across the speciation continuum: a mitogenome phylogeographic perspective

Yacine Ben Chehida , Julie Thumloup , Cassie Schumacher , Timothy Harkins , Alex Aguilar et al.
2020
Pré-publication, Document de travail (preprint/prepublication) hal-02915433 v1