A. Alberti, J. Poulain, and S. Engelen, Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition, 2017.
DOI : 10.1038/sdata.2017.93

URL : https://hal.archives-ouvertes.fr/hal-01771844

J. C. Avise, Molecular Markers, Natural History and Evolution, 2004.

G. Beaugrand, K. M. Brander, A. Lindley, J. Souissi, S. Reid et al., Plankton effect on cod recruitment in the North Sea, Nature, vol.426, pp.661-664, 2003.
DOI : 10.1038/nature02164

G. Beaugrand, P. C. Reid, F. Ibanez, J. A. Lindley, and M. Edwards, Reorganization of North Atlantic marine copepod biodiversity and climate, Science, vol.296, pp.1692-1694, 2002.

L. Blanco-bercial and A. Bucklin, New view of population genetics of zooplankton: RAD-seq analysis reveals population structure of the North Atlantic planktonic copepod Centropages typicus, Mol Ecol, vol.25, pp.1566-1580, 2016.

L. Blanco-bercial, A. Cornils, N. Copley, and A. Bucklin, DNA barcoding of marine copepods: assessment of analytical approaches to species identification, PLoS Curr, vol.6, 2014.

M. Bonhomme, C. Chevalet, and B. Servin, Detecting selection in population trees: the Lewontin and Krakauer test extended, Genetics, vol.186, pp.241-262, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00842515

Q. Carradec, E. Pelletier, D. Silva, and C. , A global ocean atlas of eukaryotic genes, Nat Commun, vol.9, p.373, 2018.
URL : https://hal.archives-ouvertes.fr/cea-01874711

G. D. Cepeda, L. Blanco-bercial, A. Bucklin, C. M. Beron, and M. D. Vinas, Molecular systematic of three species of Oithona (Copepoda, Cyclopoida) from the Atlantic Ocean: comparative analysis using 28S rDNA, PLoS One, vol.7, p.35861, 2012.

P. Cingolani, A. Platts, and L. Wang-le, A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3, Fly (Austin), vol.6, pp.80-92, 2012.

P. I. Costea, R. Munch, and L. P. Coelho, metaSNV: A tool for metagenomic strain level analysis, PLoS One, vol.12, p.182392, 2017.

T. O. Delmont, E. Kiefl, and O. Kilinc, The global biogeography of amino acid variants within a single SAR11 population is governed by natural selection, 2017.

J. J. Freer, J. C. Partridge, G. A. Tarling, M. A. Collins, and M. J. Genner, Predicting ecological responses in a changing ocean: the effects of future climate uncertainty, Mar Biol, vol.165, p.7, 2018.

E. Karsenti, S. G. Acinas, and P. Bork, A holistic approach to marine eco-systems biology, PLoS Biol, vol.9, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01893669

R. C. Lewontin and J. Krakauer, Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms, Genetics, vol.74, pp.175-195, 1973.

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, pp.1754-1760, 2009.

H. Li, B. Handsaker, and A. Wysoker, The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009.

M. A. Madoui, J. Poulain, and K. Sugier, New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod Oithona, Mol Ecol, vol.26, pp.4467-4482, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01621969

E. W. Myers, The fragment assembly string graph, Bioinformatics, vol.21, issue.2, pp.79-85, 2005.

K. T. Peijnenburg and E. Goetze, High evolutionary potential of marine zooplankton, Ecol Evol, vol.3, pp.2765-2781, 2013.

C. Pelejero, E. Calvo, and O. Hoegh-guldberg, Paleo-perspectives on ocean acidification, Trends Ecol Evol, vol.25, pp.332-344, 2010.

S. Pesant, F. Not, and M. Picheral, Open science resources for the discovery and analysis of Tara Oceans data, Sci Data, vol.2, p.150023, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01253984

P. Peterlongo, C. Riou, E. Drezen, and C. Lemaitre, DiscoSnp++: de novo detection of small variants from raw unassembled read set(s) bioRxiv 209965, 2017.

P. A. Pevzner, H. Tang, and G. Tesler, De novo repeat classification and fragment assembly, Genome Res, vol.14, pp.1786-1796, 2004.

S. Schloissnig, M. Arumugam, and S. Sunagawa, Genomic variation landscape of the human gut microbiome, Nature, vol.493, pp.45-50, 2013.

R. Uricaru, G. Rizk, and V. Lacroix, Reference-free detection of isolated SNPs, Nucleic Acids Res, vol.43, p.11, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01083715

S. Wright, The genetical structure of populations, Ann Eugen, vol.15, pp.323-354, 1951.

G. A. Wyngaard and E. M. Rasch, Patterns of genome size in the copepoda, Hydrobiologia, vol.417, pp.43-56, 2000.

G. A. Wyngaard, E. M. Rasch, N. M. Manning, K. Gasser, and K. Domangue, The relationship between genome size, development rate, and body size in copepods, Hydrobiologia, vol.532, pp.123-137, 2005.