D. Anderson, T. Alpermann, and A. Cembella, The globally distributed genus 493, 2012.

D. Anderson, A. Cembella, and G. Hallegraeff, Progress in understanding harmful algal 496 blooms: Paradigm shifts and new technologies for research, monitoring, and management, Annual Review of Marine Science, vol.4, pp.497-143, 2012.

N. Bierne, F. Bonhomme, and P. David, Habitat preference and the marine-speciation paradox, Proceedings of the Royal Society B: Biological Sciences, vol.270, issue.1522, pp.1399-1406, 2003.
DOI : 10.1098/rspb.2003.2404

S. Casabianca, A. Penna, E. Pecchioli, A. Jordi, G. Basterretxea et al., Population genetic 501 structure and connectivity of the harmful dinoflagellate Alexandrium minutum in the 502, 2011.

G. Casteleyn, F. Leliaert, and T. Backeljau, Limits to gene flow in a cosmopolitan marine 504 planktonic diatom, Proceedings of the National Academy of Sciences of the United States of 505 America, pp.12952-12957, 2010.

K. Cusick and G. Sayler, An Overview on the Marine Neurotoxin, Saxitoxin: Genetics, Molecular Targets, Methods of Detection and Ecological Functions, Marine Drugs, vol.11, issue.4, pp.991-1018, 2013.
DOI : 10.3390/md11040991

P. Danecek, A. Auton, and G. Abecasis, The variant call format and VCFtools, Bioinformatics, vol.27, issue.15, pp.27-2156, 2011.
DOI : 10.1093/bioinformatics/btr330

H. Ellegren, Genome sequencing and population genomics in non-model organisms, Trends in Ecology & Evolution, vol.29, issue.1, pp.51-63, 2014.
DOI : 10.1016/j.tree.2013.09.008

J. Fay and C. Wu, Hitchhiking under positive Darwinian selection, Genetics, vol.155, pp.1405-1413, 2000.

J. Feder, S. Flaxman, S. Egan, A. Comeault, and P. Nosil, Geographic Mode of Speciation and Genomic Divergence, Annual Review of Ecology, Evolution, and Systematics, vol.44, issue.1, pp.73-97, 2013.
DOI : 10.1146/annurev-ecolsys-110512-135825

L. Fritz and R. Triemer, A RAPID SIMPLE TECHNIQUE UTILIZING CALCOFLUOR WHITE M2R FOR THE VISUALIZATION OF DINOFLAGELLATE THECAL PLATES1, Journal of Phycology, vol.19, issue.4, pp.662-664, 1985.
DOI : 10.1111/j.0022-3646.1985.00662.x

E. Garrison and M. G. , Haplotype-based variant detection from short-read sequencing, pp.1207-3907, 2012.

B. Giardine, C. Riemer, and R. Hardison, Galaxy: A platform for interactive large-scale genome analysis, Genome Research, vol.15, issue.10, pp.1451-1455, 2005.
DOI : 10.1101/gr.4086505

R. Gutenkunst, R. Hernandez, S. Williamson, and C. Bustamante, Inferring the joint 528 demographic history of multiple populations from multidimensional SNP data, PLoS Genetics, vol.529, issue.5, pp.1000695-530, 2009.

B. Haas, A. Papanicolaou, and M. Yassour, De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Nature Protocols, vol.500, issue.8, pp.1494-1512, 2013.
DOI : 10.1038/ng.2295

G. Hansen, N. Daugbjerg, and J. Franco, Morphology, toxin composition and LSU rDNA phylogeny of Alexandrium minutum (Dinophyceae) from Denmark, with some morphological observations on other European strains, Harmful Algae, vol.2, issue.4, pp.317-335, 2003.
DOI : 10.1016/S1568-9883(03)00060-X

G. Hutchinson, The Paradox of the Plankton, The American Naturalist, vol.95, issue.882, pp.137-145, 1961.
DOI : 10.1086/282171

M. Iglesias-rodríguez, O. Schofield, J. Batley, L. Medlin, and P. Hayes, Intraspecific 538 genetic diversity in the marine coccolithophore Emilianta huxleyi (Primnesiophyceae) : The 539 use of microsatellite analysis in marine phytoplankton population studies, pp.526-536, 2006.

N. Knowlton, Sibling Species in the Sea, Annual Review of Ecology and Systematics, vol.24, issue.1, pp.189-542, 1993.
DOI : 10.1146/annurev.es.24.110193.001201

L. Moan, A. Gagnaire, P. Bonhomme, and F. , Parallel genetic divergence among coastal?marine 544 ecotype pairs of European anchovy explained by differential introgression after secondary 545 contact, Molecular Ecology, 2016.

B. Langmead and S. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-547, 2012.
DOI : 10.1093/bioinformatics/btp352

Y. Lee, C. Langley, and D. Begun, Differential Strengths of Positive Selection Revealed by Hitchhiking Effects at Small Physical Scales in Drosophila melanogaster, Molecular Biology and Evolution, vol.31, issue.4, pp.804-816, 2014.
DOI : 10.1093/molbev/mst270

H. Li, B. Handsaker, and A. Wysoker, The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2079, 2009.
DOI : 10.1093/bioinformatics/btp352

Y. Li, J. Costello, A. Holloway, and M. Hahn, ???REVERSE ECOLOGY??? AND THE POWER OF POPULATION GENOMICS, Evolution, vol.24, issue.12, pp.2984-2994, 2008.
DOI : 10.1111/j.1558-5646.2008.00486.x

M. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA- 556 seq data with DESeq2, Genome Biology, vol.15, p.557, 2014.

T. Magoc and S. Salzberg, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, vol.27, issue.21, pp.2957-2963, 2011.
DOI : 10.1093/bioinformatics/btr507

E. Masseret, D. Grzebyk, and S. Nagai, Unexpected Genetic Diversity among and within Populations of the Toxic Dinoflagellate Alexandrium catenella as Revealed by Nuclear Microsatellite Markers, Applied and Environmental Microbiology, vol.75, issue.7, pp.2037-2045, 2009.
DOI : 10.1128/AEM.01686-08
URL : https://hal.archives-ouvertes.fr/halsde-00372215

K. Matsumura, Tetrodotoxin as a pheromone, Nature, vol.378, issue.6557, pp.563-564, 1995.
DOI : 10.1038/378563b0

J. Mcdonald and M. Kreitman, Adaptive protein evolution at the Adh locus in Drosophila, Nature, vol.351, issue.6328, pp.351-652, 1991.
DOI : 10.1038/351652a0

S. Murray, R. Diwan, R. Orr, G. Kohli, and U. John, Gene duplication, loss and selection in the evolution of saxitoxin biosynthesis in alveolates, Molecular Phylogenetics and Evolution, vol.92, issue.567, pp.165-180, 2015.
DOI : 10.1016/j.ympev.2015.06.017

V. Nguyen and D. Lavenier, PLAST: parallel local alignment search tool for database comparison, BMC Bioinformatics, vol.10, issue.1, p.569, 2009.
DOI : 10.1186/1471-2105-10-329
URL : https://hal.archives-ouvertes.fr/inria-00425301

R. Nielsen, Molecular Signatures of Natural Selection, Annual Review of Genetics, vol.39, issue.1, pp.197-218, 2005.
DOI : 10.1146/annurev.genet.39.073003.112420

B. Palenik, J. Grimwood, and A. Aerts, The tiny eukaryote Ostreococcus provides genomic 572 insights into the paradox of plankton speciation, Proceedings of the National Academy of 573 Sciences of the United States of America, pp.7705-7710, 2007.

S. Palumbi, Marine speciation on a small planet, Trends in Ecology & Evolution, vol.7, issue.4, pp.114-118, 1992.
DOI : 10.1016/0169-5347(92)90144-Z

G. Peers and N. Price, Copper-containing plastocyanin used for electron transport by an oceanic diatom, Nature, vol.49, issue.7091, pp.341-344, 2006.
DOI : 10.1021/es001213r

M. Przeworski, G. Coop, and J. Wall, THE SIGNATURE OF POSITIVE SELECTION ON STANDING GENETIC VARIATION, Evolution, vol.59, issue.11, pp.2312-2323, 2005.
DOI : 10.1554/05-273.1

M. Ritchie, B. Phipson, D. Wu, Y. Hu, C. Law et al., limma powers 580 differential expression analyses for RNA-sequencing and microarray studies, Nucleic Acids 581 Research 43, pp.47-582, 2015.

M. Robinson, D. Mccarthy, and G. Smyth, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.26, issue.1, pp.139-140, 2010.
DOI : 10.1093/bioinformatics/btp616

G. Rocap, F. Larimer, and J. Lamerdin, Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation, Nature, vol.424, issue.6952, pp.1042-1047, 2003.
DOI : 10.1038/nature01947

C. Roux, G. Tsagkogeorga, N. Bierne, and N. Galtier, Crossing the Species Barrier: Genomic Hotspots of Introgression between Two Highly Divergent Ciona intestinalis Species, Molecular Biology and Evolution, vol.30, issue.7, pp.1574-1587, 2013.
DOI : 10.1093/molbev/mst066

C. Roux, C. Fraïsse, V. Castric, X. Vekemans, G. Pogson et al., hybrid zone, Journal of Evolutionary Biology, vol.14, issue.8, pp.1662-1675, 2014.
DOI : 10.1111/jeb.12425
URL : https://hal.archives-ouvertes.fr/hal-01110882

S. Roy and J. Chattopadhyay, Towards a resolution of ???the paradox of the plankton???: A brief overview of the proposed mechanisms, Ecological Complexity, vol.4, issue.1-2, pp.26-33, 2007.
DOI : 10.1016/j.ecocom.2007.02.016

T. Rynearson and A. Ve, GENETIC DIFFERENTIATION AMONG POPULATIONS OF THE PLANKTONIC MARINE DIATOM DITYLUM BRIGHTWELLII (BACILLARIOPHYCEAE)1, Journal of Phycology, vol.23, issue.1, pp.34-43, 2004.
DOI : 10.1046/j.1529-8817.2004.03089.x

O. Seehausen, R. Butlin, and I. Keller, Genomics and the origin of species, Nature Reviews Genetics, vol.139, issue.3, pp.176-192, 2014.
DOI : 10.1111/j.1558-5646.2010.01096.x

N. Shoresh, M. Hegreness, and R. Kishony, Evolution exacerbates the paradox of the plankton, Proceedings of the National Academy of Sciences, vol.105, issue.34, pp.12365-604, 2008.
DOI : 10.1073/pnas.0803032105

M. Stomp, J. Huisman, and F. De-jongh, Adaptive divergence in pigment composition promotes phytoplankton biodiversity, Nature, vol.79, issue.7013, pp.104-107, 2004.
DOI : 10.1016/0273-1223(95)00696-6

A. Stüken, R. Orr, and R. Kellmann, Discovery of nuclear-encoded genes for the neurotoxin 608 saxitoxin in dinoflagellates, Plos One, vol.6, issue.12, p.609, 2011.

M. Tine, H. Kuhl, and P. Gagnaire, European sea bass genome and its variation provide 610 insights into adaptation to euryhalinity and speciation, Nature Communications, vol.5, issue.5770, p.611, 2014.

T. Turner, M. Hahn, and S. Nuzhdin, Genomic Islands of Speciation in Anopheles gambiae, PLoS Biology, vol.20, issue.9, pp.1572-1578, 2005.
DOI : 10.1371/journal.pbio.0030285.st001

F. Verret, G. Wheeler, A. Taylor, G. Farnham, and C. Brownlee, Calcium channels in photosynthetic eukaryotes: implications for evolution of calcium-based signalling, New Phytologist, vol.120, issue.31, pp.23-615, 2010.
DOI : 10.1111/j.1469-8137.2010.03271.x

A. Weiner, R. Aurahs, A. Kurasawa, H. Kitazato, and M. Kucera, Vertical niche partitioning between 617 cryptic sibling species of a cosmopolitan marine planktonic protist, Molecular Ecology, vol.21, pp.618-4063, 2012.

J. Wisecaver and J. Hackett, Dinoflagellate Genome Evolution, Annual Review of Microbiology, vol.65, issue.1, pp.369-387, 2011.
DOI : 10.1146/annurev-micro-090110-102841

T. Wyatt and I. Jenkinson, population dynamics, Journal of Plankton Research, vol.19, issue.5, pp.551-575, 1997.
DOI : 10.1093/plankt/19.5.551

H. Zhang, Y. Hou, and L. Miranda, Spliced leader RNA trans-splicing in dinoflagellates, 624 Proceedings of the National Academy of Sciences of the United States of America, pp.4618-625, 2007.
DOI : 10.1073/pnas.0700258104

Z. Zhang, S. Schwartz, L. Wagner, and W. Miller, A Greedy Algorithm for Aligning DNA Sequences, Journal of Computational Biology, vol.7, issue.1-2, pp.203-214, 2000.
DOI : 10.1089/10665270050081478

R. Reads and R. Transcriptome, European Nucleotide Archive 633 http://www.ebi.ac.uk/ena/data/view/PRJEB15046 634 635 SNP and differential expression information: SEANOE database http, p.45445