D. Gaskin, The harbour porpoise Phocoena phocoena (L.): Regional populations, status, and information on direct and indirect catches, Rep Int Whal Comm, vol.34, pp.569-586, 1984.

A. Read, Harbour porpoise -Phocoena phocoena (Linnaeus, 1758) Handbook of marine mammals: the second book of dolphins and porpoises, pp.323-356, 1999.

P. Hammond, P. Berggren, H. Benke, D. Borchers, and A. Collet, Abundance of harbour porpoise and other cetaceans in the North Sea and adjacent waters, Journal of Applied Ecology, vol.52, issue.244, pp.361-376, 2002.
DOI : 10.1046/j.1365-2664.2002.00713.x

S. Kiska, S. Hassani, and S. Pezeril, Distribution and status of small cetaceans along the French Channel coasts: using opportunistic records for a preliminary assessment, Lutra, vol.47, pp.33-46, 2004.

F. Thomsen, M. Laczny, and W. Piper, A recovery of harbour porpoises (Phocoena phocoena) in the southern North Sea? A case study off Eastern Frisia, Germany, Helgoland Marine Research, vol.40, issue.3, pp.189-195, 2006.
DOI : 10.1007/s10152-006-0021-z

S. Van-der-meij and K. Camphuysen, The distribution and diversity of whales and dolphins (Cetacea) in the southern North Sea, Lutra, vol.49, pp.1970-2005, 2006.

J. Jung, E. Stéphan, M. Louis, E. Alfonsi, and C. Liret, Harbour porpoises ( Phocoena phocoena) in north-western France: aerial survey, opportunistic sightings and strandings monitoring, Journal of the Marine Biological Association of the United Kingdom, vol.6, issue.05, pp.1045-1050, 2009.
DOI : 10.1016/j.seares.2006.01.003

URL : https://hal.archives-ouvertes.fr/hal-01072192

R. Duguy, Notes on the small cetaceans off the coasts of France, Rep Int Whal Comm, vol.27, pp.500-501, 1977.

P. Reijnders, Harbour porpoisesPhocoena phocoena in the North Sea: Numerical responses to changes in environmental conditions, Netherlands Journal of Aquatic Ecology, vol.25, issue.1, pp.75-85, 1992.
DOI : 10.1007/BF02298029

K. Camphuysen, The return of the harbour porpoise (Phocoena phocoena) in Dutch coastal waters, Lutra, vol.47, pp.113-122, 2004.

U. Siebert, A. Gilles, K. Lucke, M. Ludwig, and H. Benke, A decade of harbour porpoise occurrence in German waters???Analyses of aerial surveys, incidental sightings and strandings, Journal of Sea Research, vol.56, issue.1, 2006.
DOI : 10.1016/j.seares.2006.01.003

S. Pikesley, M. Witt, T. Hardy, and J. Loveridge, Cetacean sightings and strandings: evidence for spatial and temporal trends?, Journal of the Marine Biological Association of the United Kingdom, vol.16, issue.08, pp.10-1017, 2011.
DOI : 10.1016/j.seares.2006.01.003

C. Lockyer, All creatures great and smaller: a study in cetacean life history energetics, Journal of the Marine Biological Association of the UK, vol.87, issue.04, pp.1035-1045, 2007.
DOI : 10.1017/S0025315407054720

M. Fontaine, S. Baird, S. Piry, N. Ray, and K. Tolley, Rise of oceanographic barriers in continuous populations of a cetacean: the genetic structure of harbour porpoises in Old World waters, BMC Biology, vol.5, issue.1, pp.30-40, 2007.
DOI : 10.1186/1741-7007-5-30

M. Fontaine, K. Tolley, J. Michaux, A. Birkun, and M. Ferreira, Genetic and historic evidence for climate-driven population fragmentation in a top cetacean predator: the harbour porpoises in European water, Proceedings of the Royal Society B: Biological Sciences, vol.325, issue.5940, pp.2829-2837, 2010.
DOI : 10.1126/science.1173146

C. Lockyer, Harbour porpoises (<i>Phocoena phocoena</i>) in the North Atlantic: Biological parameters, NAMMCO Scientific Publications, vol.5, pp.71-90, 2003.
DOI : 10.7557/3.2740

H. Koopman, D. Pabst, W. Mclellan, R. Dillaman, and A. Read, ): Evidence for Regional Differences in Blubber Structure and Function, Physiological and Biochemical Zoology, vol.75, issue.5, pp.498-512, 2002.
DOI : 10.1086/342799

C. Macleod, M. Santos, R. Reid, B. Scott, and G. Pierce, Linking sandeel consumption and the likelihood of starvation in harbour porpoises in the Scottish North Sea: could climate change mean more starving porpoises?, Biology Letters, vol.163, issue.2, pp.185-188, 2007.
DOI : 10.1098/rsbl.2006.0588

M. Santos, G. Pierce, J. Learmonth, R. Reid, and H. Ross, VARIABILITY IN THE DIET OF HARBOR PORPOISES (PHOCOENA PHOCOENA) IN SCOTTISH WATERS 1992???2003, Marine Mammal Science, vol.88, issue.1, pp.1-27, 1992.
DOI : 10.1016/S0165-7836(00)00219-8

D. Johnston, A. Westgate, and A. Read, Effects of fine-scale oceanographic features on the distribution and movements of harbour porpoises Phocoena phocoena in the Bay of Fundy, Marine Ecology Progress Series, vol.295, pp.279-293, 2005.
DOI : 10.3354/meps295279

M. Santos and G. Pierce, The diet of harbour porpoise (phocoena phocoena) in the northeast atlantic, Oceanogr Mar Biol: Ann Rev, vol.41, pp.335-390, 2003.

H. Herr, H. Fock, and U. Siebert, Spatio-temporal associations between harbour porpoise Phocoena phocoena and specific fisheries in the German Bight, Biological Conservation, vol.142, issue.12, pp.2962-2972, 2009.
DOI : 10.1016/j.biocon.2009.07.025

N. Tregenza, S. Berrow, P. Hammond, and R. Leaper, Harbour porpoise (Phocoena phocoenaL.) by-catch in set gillnets in the Celtic Sea, ICES Journal of Marine Science, vol.54, issue.5, pp.896-904, 1997.
DOI : 10.1006/jmsc.1996.0212

S. Northridge and P. Hammond, Estimation of porpoise mortality in UK gill and tangle net fisheries in the North Sea and west of Scotland. Paper presented to the Scientific Committee of the international whaling Commission Paper SC/ 51, 1999.

P. Berggren, P. Wade, J. Carlström, and A. Read, Potential limits to anthropogenic mortality for harbour porpoises in the Baltic region, Biological Conservation, vol.103, issue.3, pp.313-322, 2002.
DOI : 10.1016/S0006-3207(01)00142-2

G. Stenson, T. Haug, G. Desportes, G. Vikingsson, and L. Witting, Harbour porpoise (<i>Phocoena phocoena</i>) in the North Atlantic: Abundance, removals, and sustainability of removals, Harbour porpoises in the North Atlantic, pp.271-302, 2003.
DOI : 10.7557/3.2830

D. Gambaiani, P. Mayol, S. Isaac, and M. Simmonds, Potential impacts of climate change and greenhouse gas emissions on Mediterranean marine ecosystems and cetaceans, Journal of the Marine Biological Association of the United Kingdom, vol.7, issue.01, pp.179-201, 2008.
DOI : 10.1126/science.1071281

M. Simmonds and W. Eliott, Climate change and cetaceans: concerns and recent developments, Journal of the Marine Biological Association of the United Kingdom, vol.44, issue.01, pp.203-210, 2009.
DOI : 10.1098/rsbl.2007.0076

M. Fontaine, A. Snirc, A. Frantzis, E. Koutrakis, O. ¨. et al., History of expansion and anthropogenic collapse in a top marine predator of the Black Sea estimated from genetic data, Proceedings of the National Academy of Sciences, vol.109, issue.38, 2012.
DOI : 10.1073/pnas.1201258109

M. Walton, Population structure of harbour porpoises Phocoena phocoena in the seas around the UK and adjacent waters, Proceedings of the Royal Society B: Biological Sciences, vol.264, issue.1378, pp.89-94, 1997.
DOI : 10.1098/rspb.1997.0013

R. Tiedemann, J. Harder, C. Gmeiner, and E. Haase, Mitochondrial DNA sequence patterns of Harbour porpoises (Phocoena phocoena) from the North and the Baltic sea, Zeit Saugetierkunde, vol.61, pp.104-111, 1996.

P. Rosel, A. Dizon, and M. Haygood, , on interoceanic and regional scales, Canadian Journal of Fisheries and Aquatic Sciences, vol.52, issue.6, pp.1210-1219, 1995.
DOI : 10.1139/f95-118

S. Chivers, A. Dizon, P. Gearin, and K. Robertson, Small-scale population structure of eastern North Pacific harbour porpoises (Phocoena phocoena) indicated by molecular genetic analyses, J Cetacean Res Manage, vol.4, pp.111-122, 2002.

K. Tolley, P. Rosel, M. Walton, A. Bjørge, and N. Øien, Genetic population structure of harbour porpoises (Phocoena phocoena) in the North Sea and Norvegian waters, J Cetacean Res Manage, vol.1, pp.265-274, 2001.

K. Tolley, G. Vikingsson, and P. Rosel, Mitochondrial DNA sequence variation and phylogeographic patterns in harbour porpoises (Phocoena phocoena) from the North Atlantic, Conservation Genetics, vol.2, issue.4, pp.349-361, 2001.
DOI : 10.1023/A:1012561811074

L. Andersen, D. Ruzzante, M. Walton, P. Berggren, and A. Bjørge, Conservation genetics of harbour porpoises, Phocoena phocoena, in eastern and central North Atlantic, Conservation Genetics, vol.2, issue.4, pp.309-324, 2001.
DOI : 10.1023/A:1012534212853

A. Wiemann, L. Andersen, P. Berggren, U. Siebert, and H. Benke, Mitochondrial Control Region and microsatellite analyses on harbour porpoise (Phocoena phocoena) unravel population differentiation in the Baltic Sea and adjacent waters, Conservation Genetics, vol.55, issue.3, pp.195-211, 2010.
DOI : 10.1007/s10592-009-0023-x

K. Tolley and P. Rosel, Population structure and historical demography of eastern North Atlantic harbour porpoises inferred through mtDNA sequences, Marine Ecology Progress Series, vol.327, pp.297-308, 2006.
DOI : 10.3354/meps327297

K. Viaud-martinez, M. Vergara, P. Gol-'din, V. Ridoux, and A. Ozturk, Morphological and genetic differentiation of the Black Sea harbour porpoise Phocoena phocoena, Marine Ecology Progress Series, vol.338, pp.281-294, 2007.
DOI : 10.3354/meps338281

P. Rosel, S. France, J. Wang, and T. Kocher, Genetic structure of harbour porpoise Phocoena phocoena populations in the northwest Atlantic based on mitochondrial and nuclear markers, Molecular Ecology, vol.14, issue.s1, pp.41-54, 1999.
DOI : 10.1139/cjfas-53-7-1632

R. Hudson, D. Boos, and N. Kaplan, A Statistical Test for Detecting Geographic Subdivision, Mol Biol Evol, vol.9, pp.138-151, 1998.

R. Hudson, A New Statistic for Detecting Genetic Differentiation, Genetics, vol.155, pp.2011-2014, 2000.

J. Pritchard, M. Stephens, and P. Donnelly, Inference of Population Structure Using Multilocus Genotype Data, Genetics, vol.155, pp.945-959, 2000.

D. Falush, M. Stephens, and J. Pritchard, Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies, Genetics, vol.164, pp.1567-1587, 2003.

M. Hubisz, D. Falush, M. Stephens, and J. Pritchard, Inferring weak population structure with the assistance of sample group information, Molecular Ecology Resources, vol.101, issue.5, pp.1322-1332, 2009.
DOI : 10.1111/j.1755-0998.2009.02591.x

N. Ryman and S. Palm, POWSIM: a computer program for assessing statistical power when testing for genetic differentiation, Molecular Ecology Notes, vol.86, issue.3, pp.600-602, 2006.
DOI : 10.1111/j.1471-8286.2004.00693.x

G. Donovan and A. Bjørge, Harbour porpoises in the North Atlantic, Biology of the Phocoenids. Rep Int Whal Comm, pp.3-25, 1995.

D. Hartl and A. Clark, Principles of Population Genetics, 2007.

P. Reijnders, G. Donovan, A. Bjørge, K. Koch, and S. Eisfeld, ASCOBANS Conservation Plan for Harbour Porpoises (Phocoena phocoena L.) in the North Sea, pp.20-24, 1921.

A. Southward, S. Hawkins, and M. Burrows, Seventy years' observations of changes in distribution and abundance of zooplankton and intertidal organisms in the western English Channel in relation to rising sea temperature, Journal of Thermal Biology, vol.20, issue.1-2, pp.127-155, 1995.
DOI : 10.1016/0306-4565(94)00043-I

J. Poulard and F. Blanchard, The impact of climate change on the fish community structure of the eastern continental shelf of the Bay of Biscay, ICES Journal of Marine Science, vol.62, issue.7, pp.1436-1443, 2005.
DOI : 10.1016/j.icesjms.2005.04.017

A. Perry, Climate Change and Distribution Shifts in Marine Fishes, Science, vol.308, issue.5730, pp.1912-1915, 2005.
DOI : 10.1126/science.1111322

D. Palacios, S. Salazar, and F. Vargas, Galápagos Marine Vertebrates: Responses to Environmental Variability and Potential Impacts of Climate Change, Climate Change Vulnerability Assessment of the Galápagos Islands. USA: WWF and Conservation International, pp.69-80, 2011.

P. Rosel, PCR-based sex determination in Odontocete cetaceans, Conservation Genetics, vol.4, issue.5, pp.647-649, 2003.
DOI : 10.1023/A:1025666212967

P. Jayasankar, B. Anoop, and M. Rajagopalan, PCR-based sex determination of cetaceans and dugong from the Indian seas, Current Sci, vol.94, pp.1513-1516, 2008.

T. Kocher, W. Thomas, A. Meyer, S. Edwards, and S. Pââbo, Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers., Proceedings of the National Academy of Sciences, vol.86, issue.16, pp.6196-6200, 1989.
DOI : 10.1073/pnas.86.16.6196

T. Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symp Ser, vol.41, pp.95-98, 1999.

L. Excoffier, G. Laval, and S. Schneider, Arlequin (version 3.0): An integrated software package for population genetics data analysis, Evolutionary Bioinformatics Online, vol.1, pp.47-50, 2005.

P. Librado and J. Rozas, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data, Bioinformatics, vol.25, issue.11, pp.1451-1452, 2009.
DOI : 10.1093/bioinformatics/btp187

F. Tajima, Statistical Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism, Genetics, vol.123, pp.585-595, 1989.

A. Dereeper, V. Guignon, G. Blanc, S. Audic, and S. Buffet, Phylogeny.fr: robust phylogenetic analysis for the non-specialist, Nucleic Acids Research, vol.36, issue.Web Server, pp.465-469, 2008.
DOI : 10.1093/nar/gkn180

URL : https://hal.archives-ouvertes.fr/lirmm-00324099

R. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-70410, 1080.
DOI : 10.1080/10635150390235520

F. Chevenet, C. Brun, A. Bañ-uls, B. Jacq, and C. R. , TreeDyn: towards dynamic graphics and annotations for analyses of trees, BMC Bioinformatics, vol.7, issue.1, pp.439-448, 2006.
DOI : 10.1186/1471-2105-7-439

URL : https://hal.archives-ouvertes.fr/hal-00321061

M. Anisimova and O. Gascuel, Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative, Systematic Biology, vol.55, issue.4, pp.539-552, 2006.
DOI : 10.1080/10635150600755453

URL : https://hal.archives-ouvertes.fr/lirmm-00136658

P. Goloboff, J. Farris, and K. Nixon, TNT, a free program for phylogenetic analysis, Cladistics, vol.183, issue.5, pp.774-786, 2008.
DOI : 10.1111/j.1096-0031.2008.00217.x

O. Gascuel, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Molecular Biology and Evolution, vol.14, issue.7, pp.685-695, 1998.
DOI : 10.1093/oxfordjournals.molbev.a025808

URL : https://hal.archives-ouvertes.fr/lirmm-00730410

J. Felsenstein, PHYLIP -Phylogeny Inference Package (Version 3.2), Cladistics, vol.5, pp.164-166, 1989.

M. Schuelke, An economic method for the fluorescent labeling of PCR fragments, Nature Biotechnology, vol.252, issue.2, pp.233-234, 2000.
DOI : 10.1038/72708

Z. Szpiech, M. Jakobsson, and N. Rosenberg, ADZE: a rarefaction approach for counting alleles private to combinations of populations, Bioinformatics, vol.24, issue.21, pp.2498-2504, 2008.
DOI : 10.1093/bioinformatics/btn478

J. Goudet, FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3) Available at http, 2001.

M. Raymond and F. Rousset, GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism, Journal of Heredity, vol.86, issue.3, pp.248-249, 1995.
DOI : 10.1093/oxfordjournals.jhered.a111573

URL : https://hal.archives-ouvertes.fr/halsde-00186383

B. Weir and C. Cockerham, Estimating F-Statistics for the Analysis of Population Structure, Evolution, vol.38, issue.6, pp.1358-1370, 1984.
DOI : 10.2307/2408641

G. Evanno, S. Regnaut, and J. Goudet, Detecting the number of clusters of individuals using the software structure: a simulation study, Molecular Ecology, vol.16, issue.8, 2005.
DOI : 10.1098/rspb.2001.1600