R. Lewontin, The Genetic Basis of Evolutionary Change (Columbia Univ, 1974.

E. M. Leffler, Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?, PLoS Biology, vol.10, issue.9, p.1001388, 2012.
DOI : 10.1371/journal.pbio.1001388.s007

L. F. Keller and D. M. Waller, Inbreeding effects in wild populations, Trends in Ecology & Evolution, vol.17, issue.5, pp.19-23, 2002.
DOI : 10.1016/S0169-5347(02)02489-8

T. B. Reusch, A. Ehlers, A. Hämmerli, and B. Worm, Ecosystem recovery after climatic extremes enhanced by genotypic diversity, Proc. Natl Acad. Sci. USA, pp.2826-2831, 2005.
DOI : 10.1073/pnas.0500008102

A. R. Hughes, B. D. Inouye, M. T. Johnson, N. Underwood, and M. Vellend, Ecological consequences of genetic diversity, Ecology Letters, vol.406, issue.6, pp.609-623, 2008.
DOI : 10.1111/j.1461-0248.2008.01179.x

W. E. Johnson, Genetic Restoration of the Florida Panther, Science, vol.329, issue.5999, pp.1641-1645, 2010.
DOI : 10.1126/science.1192891

P. Nair, Conservation genomics, Proc. Natl Acad. Sci. USA, p.569, 2014.
DOI : 10.1073/pnas.1323086111

E. Bazin, S. Glémin, and N. Galtier, Population Size Does Not Influence Mitochondrial Genetic Diversity in Animals, Science, vol.312, issue.5773, pp.570-572, 2006.
DOI : 10.1126/science.1122033

URL : https://hal.archives-ouvertes.fr/halsde-00339540

B. Nabholz, J. Mauffrey, E. Bazin, N. Galtier, and S. Glemin, Determination of Mitochondrial Genetic Diversity in Mammals, Genetics, vol.178, issue.1, pp.351-361, 2008.
DOI : 10.1534/genetics.107.073346

G. Perry, Comparative RNA sequencing reveals substantial genetic variation in endangered primates, Genome Research, vol.22, issue.4, pp.602-610, 2012.
DOI : 10.1101/gr.130468.111

S. C. Banks, How does ecological disturbance influence genetic diversity?, Trends in Ecology & Evolution, vol.28, issue.11, pp.670-679, 2013.
DOI : 10.1016/j.tree.2013.08.005

G. Hewitt, The genetic legacy of the Quaternary ice ages, Nature, vol.405, issue.6789, pp.907-913, 2000.
DOI : 10.1038/35016000

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

V. Cahais, Reference-free transcriptome assembly in non-model animals from next-generation sequencing data, Molecular Ecology Resources, vol.19, issue.5, pp.834-845, 2012.
DOI : 10.1111/j.1755-0998.2012.03148.x

URL : https://hal.archives-ouvertes.fr/hal-01267810

G. Tsagkogeorga, V. Cahais, and N. Galtier, The Population Genomics of a Fast Evolver: High Levels of Diversity, Functional Constraint, and Molecular Adaptation in the Tunicate Ciona intestinalis, Genome Biology and Evolution, vol.4, issue.8, pp.740-749, 2012.
DOI : 10.1093/gbe/evs054

P. Gayral, Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate???Invertebrate Gap, PLoS Genetics, vol.335, issue.4, p.1003457, 2013.
DOI : 10.1371/journal.pgen.1003457.s008

URL : https://hal.archives-ouvertes.fr/hal-00866204

R. H. Macarthur and E. Wilson, The Theory of Island Biogeography, 1967.
DOI : 10.1515/9781400881376

M. Lynch, Evolution of the mutation rate, Trends in Genetics, vol.26, issue.8, pp.345-352, 2010.
DOI : 10.1016/j.tig.2010.05.003

T. Ohta, Slightly Deleterious Mutant Substitutions in Evolution, Nature, vol.68, issue.5428, pp.96-98, 1973.
DOI : 10.1038/246096a0

M. L. Pinsky, Unexpected patterns of fisheries collapse in the world's oceans, Proc. Natl Acad. Sci. USA, pp.8317-8322, 2011.
DOI : 10.1073/pnas.1015313108

F. Delsuc, E. Douzery, M. Tilak, G. Dugas, S. Harispe et al., Flaven (brine shrimps), Rotterdam Zoo, Acknowledgements We thank the following for providing samples J. Do Nascimento, C. Daguin-Thiébaut, M. Cantou (crabs), L. Bonnaud (cuttlefish), D. Aurelle (gorgonians), F. Viard, Y. Pechenik, A. Cahill, R. Colins (slipper limpets) M. de Dinechin, B. Rey (penguins), Z. Melo-Fereira, P. Alves (hares) Service Modèle Biologique Station Marine Roscoff (ciona), L. Excoffier, G. Heckel (voles), F. Dedeine (termites), C. Atyame, O. Duron, M. Weill (mosquitoes), M. Cantou, H. Violette, F. Batista, J. Hondeville (seahorses), C. Fra?¨sseFra?¨sse, G. Pogson, N. Saarman, J. Normand (mussels), E. Poulin, C. Gonzalez-Weivar, and J. P. Feral (sea urchins). This work was supported by European Research Council advanced grant, p.232971

A. Contributions, N. G. Conceived-the-project, M. B. , N. F. , Y. C. et al., performed sampling and laboratory work

J. , R. J. , A. B. , V. C. , L. D. et al., provided interpretations and models