A. Acou, E. Lasne, and E. Feunteun, Programme de connaissance Natura2000 en mer : les habitats marins des espèces amphihalines Evaluation de la cohérence du réseau Natura2000 en mer pour la grande alose (Alosa alosa), l'alose feinte (A. fallax sp.), la lamproie marine (Petromyzon marinus) et la lamproie fluviatile (Lampetra fluviatilis), 2013.

P. Alexandrino, R. Faria, D. Linhares, F. Castro, L. Corre et al., Interspecific differentiation and intraspecific substructure in two closely related clupeids with extensive hybridization, Alosa alosa and Alosa fallax, Journal of Fish Biology, vol.125, issue.sb, pp.242-259, 2006.
DOI : 10.2307/2408641

URL : https://hal.archives-ouvertes.fr/hal-01453704

S. Altschul, T. Madden, A. Schäffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-402, 1997.
DOI : 10.1093/nar/25.17.3389

R. Anderson, A. Chabaud, and S. Willmott, Keys to the nematode parasites of vertebrates, 2009.

T. Anderson and M. Sukhdeo, Abiotic versus biotic hierarchies in the assembly of parasite populations, Parasitology, vol.3, issue.04, pp.743-754, 2010.
DOI : 10.1017/CBO9780511623387

M. Aprahamian, The effect of the migration of Alosa fallax fallax (Laecpede) into fresh water, on branchial and gut parasites, Journal of Fish Biology, vol.1, issue.2, pp.521-532, 1985.
DOI : 10.1139/f78-230

M. Aprahamian, C. Aprahamian, J. Baglinière, R. Sabatié, and P. Alexandrino, Alosa alosa and Alosa fallax spp. Literature Review and Bibliography, 2003.

M. Aprahamian, J. Baglinière, M. Sabatié, P. Alexandrino, R. Thiel et al., Biology, status, and conservation of the anadromous Atlantic twaite shad Alosa fallax fallax, American Fisheries Society Symposium, vol.35, pp.103-124, 2003.

C. Assis, P. Almeida, F. Moreira, J. Costa, and M. Costa, Diet of the twaite shad Alosa fallax (Lacepede) (Clupeidae) in the River Tagus Estuary, Portugal, Journal of Fish Biology, vol.1, issue.6, pp.1049-1050, 1992.
DOI : 10.1007/BF00007604

J. Baglinière and P. Elie, Les aloses (Alosa alosa et Alosa fallax spp.): Ecobiologie et variabilité des populations, 2000.

J. Baglinière, R. Sabatié, E. Rochard, P. Alexandrino, and M. Aprahamian, The allis shad Alosa alosa: biology, ecology, range, and status of populations, American Fisheries Society Symposium, vol.35, pp.85-102, 2003.

M. Bao, M. Mota, D. Nachón, C. Antunes, F. Cobo et al., Anisakis infection in allis shad, Alosa alosa (Linnaeus, 1758), and twaite shad, Alosa fallax (Lac??p??de, 1803), from Western Iberian Peninsula Rivers: zoonotic and ecological implications, Parasitology Research, vol.1, issue.1, pp.2143-2154, 2015.
DOI : 10.1111/j.2041-210X.2009.00001.x

M. Bao, A. Roura, M. Mota, D. Nachón, C. Antunes et al., Macroparasites of allis shad (Alosa alosa) and twaite shad (Alosa fallax) of the Western Iberian Peninsula Rivers: ecological, phylogenetic and zoonotic insights, Parasitology Research, vol.86, issue.363, pp.3721-3739, 2015.
DOI : 10.1007/PL00008561

C. Barnes, C. Sweeting, S. Jennings, J. Barry, and N. Polunin, Effect of temperature and ration size on carbon and nitrogen stable isotope trophic fractionation, Functional Ecology, vol.130, issue.3, pp.356-362, 2007.
DOI : 10.1007/s00442-003-1270-z

T. Bolger and P. Connolly, The selection of suitable indices for the measurement and analysis of fish condition, Journal of Fish Biology, vol.14, issue.26, pp.171-198, 1989.
DOI : 10.1577/1548-8659(1982)111<761:GACOBI>2.0.CO;2

A. Bouchut, E. Roger, B. Gourbal, C. Grunau, C. Coustau et al., The compatibility polymorphism in invertebrate host/trematodes interactions: research of molecular determinants, Parasite, vol.15, issue.3, pp.304-309, 2008.
DOI : 10.1051/parasite/2008153304

URL : https://hal.archives-ouvertes.fr/halsde-00344425

A. Bush, K. Lafferty, J. Lotz, and A. Shostak, Parasitology Meets Ecology on Its Own Terms: Margolis et al. Revisited, The Journal of Parasitology, vol.83, issue.4, pp.575-583, 1997.
DOI : 10.2307/3284227

R. Bray and D. Gibson, The Fellodistomidae (Digenea) of fishes from the NE Atlantic, Bull Br Mus nat Hist, vol.37, pp.199-293, 1980.

B. Bychowsky, Monogenetic Trematodes, their systematics and phylogeny. (Hargis Jr WJ Editor) Translated by Oustinoff PC, 1957.

N. Campbell, M. Cross, J. Chubb, C. Cunningham, E. Hatfield et al., Spatial and temporal variations in parasite prevalence and infracommunity structure in herring (Clupea harengus L.) caught to the west of the British Isles and in the North and Baltic Seas: implications for fisheries science, Journal of Helminthology, vol.81, issue.02, pp.137-146, 2007.
DOI : 10.1017/S0022149X07747454

J. Carney and T. Dick, Enteric Helminths of Perch (Perca fluviatilis L.) and Yellow Perch (Perca flavescens Mitchill): Stochastic or Predictable Assemblages?, The Journal of Parasitology, vol.85, issue.5, pp.785-795, 1999.
DOI : 10.2307/3285812

T. Ceyhan, O. Akyol, T. Sever, and A. Kara, Diet composition of adult twaite shad (Alosa fallax) in the Aegean Sea (Izmir Bay, Turkey), Journal of the Marine Biological Association of the United Kingdom, vol.4, issue.03, pp.601-604, 2012.
DOI : 10.1111/j.1095-8649.2007.01610.x

E. Chiriac and M. Udrescu, Fauna Republicii Socialiste România, Plathelminthes. Volumul II Fascicula, vol.4, 1973.

M. Correia, J. Costa, C. Teixeira, P. Almeida, I. Domingos et al., FEEDING HABITS AND CONDITION OF TWO LANDLOCKED POPULATIONS OF ALLIS SHAD (ALOSA ALOSA) IN PORTUGAL., Bulletin Fran??ais de la P??che et de la Pisciculture, vol.362362, issue.362-363, pp.823-835, 2001.
DOI : 10.1051/kmae:2001021

A. Dessier, C. Dupuy, T. Trancart, A. Audras, P. Bustamante et al., Low diversity of helminth parasites in Sardina pilchardus and Engraulis encrasicolus (Clupeidae) from the Bay of Biscay, Marine and Freshwater Research, vol.67, issue.10, pp.1583-1588, 2016.
DOI : 10.1071/MF15147

URL : https://hal.archives-ouvertes.fr/hal-01377895

V. Dogiel, G. Petrushevski, and Y. Polyanski, Parasitology of Fishes, Leningrad. Translated from the Russian by Kabata Z, 1958.

D. Doherty and T. Mccarthy, Chapter 10 Aspects of the ecology, parasites and future conservation of twaite shad, Alosa fallax, and allis shad, Alosa alosa, in south-eastern Ireland, 2002.

I. G. Coelho and . Cowx, Conservation of freshwater fishes: options for the future. Fishing News Books

G. Esch, E. Wetzel, D. Zelmer, and A. Schotthoeffer, Long-term Changes in Parasite Population and Community Structure: A Case History, American Midland Naturalist, vol.137, issue.2, pp.369-387, 1997.
DOI : 10.2307/2426856

H. Fagerholm, Systematic implications of male caudal morphology in ascaridoid nematode parasites, Systematic Parasitology, vol.16, issue.2, pp.215-228, 1991.
DOI : 10.1007/978-1-4612-5938-1

R. Faria, S. Weiss, and P. Alexandrino, Comparative phylogeography and demographic history of European shads (Alosa alosa and A. fallax) inferred from mitochondrial DNA, BMC Evolutionary Biology, vol.12, issue.1, pp.194-204, 2012.
DOI : 10.1186/1471-2148-12-194

J. Freyhof and M. Kottelat, Alosa alosa. The IUCN Red List of Threatened Species, 2008.

J. Freyhof and M. Kottelat, Alosa fallax. The IUCN Red List of Threatened Species, 2008.

C. Gérard, E. Amilhat, T. Trancart, E. Faliex, L. Virag et al., Influence of introduced vs. native parasites on the body condition of migrant silver eels, Parasite, vol.20, 2013.
DOI : 10.1051/parasite/2013040

C. Gérard, V. Verrez-bagnis, M. Jérôme, and E. Lasne, Petromyzon marinus (Petromyzontidae), an unusual host for helminth parasites in western Europe, Diseases of Aquatic Organisms, vol.113, issue.3, pp.263-267, 2015.
DOI : 10.3354/dao02842

C. Gérard, M. Hervé, E. Réveillac, and A. Acou, Spatial distribution and impact of the gill-parasitic Mazocraes alosae (Monogenea Polyopisthocotylea) on Alosa alosa and A. fallax (Actinopterygii, Clupeidae), Monogenea Polyopisthocotylea) on Alosa alosa (Linnaeus, 1758) and Alosa fallax (Lacépède, 1803) (Clupeidae), pp.371-379, 1782.
DOI : 10.3147/jsfp.19.119

D. Gibson and R. Bray, The Hemiuridae (Digenea) of fishes from the north-east Atlantic, Bull Br Mus nat Hist, vol.36, pp.55-146, 1986.

Y. Golvan, Systématique des Acanthocéphales (Acanthocephala Rudolphi 1801), Mém Mus Natn Hist Nat, vol.57, 1969.

M. Grano-maldonado, E. Gisbert, J. Hirt-chabbert, G. Paladini, A. Roque et al., An infection of Gyrodactylus anguillae Ergens, 1960 (Monogenea) associated with the mortality of glass eels (Anguilla anguilla L.) on the north-western Mediterranean Sea board of Spain, Veterinary Parasitology, vol.180, issue.3-4, pp.323-331, 2011.
DOI : 10.1016/j.vetpar.2011.03.004

M. Hatcher, J. Dick, and A. Dunn, Diverse effects of parasites in ecosystems: linking interdependent processes, Frontiers in Ecology and the Environment, vol.7, issue.4, pp.186-194, 2012.
DOI : 10.1890/0012-9658(2003)084[1083:AROTII]2.0.CO;2

R. Hechinger, A Metabolic and Body-Size Scaling Framework for Parasite Within-Host Abundance, Biomass, and Energy Flux, The American Naturalist, vol.182, issue.2, pp.234-248, 2013.
DOI : 10.1086/670820

M. Hervé, RVAideMemoire: Diverse basic statistical and graphical functions. R package version 0, pp.9-55, 2016.

E. Jakob, S. Marshall, and G. Uets, Estimating Fitness: A Comparison of Body Condition Indices, Oikos, vol.77, issue.1, pp.61-67, 1996.
DOI : 10.2307/3545585

M. Jolly, M. Aprahamian, S. Hawkins, P. Henderson, R. Hillman et al., Population genetic structure of protected allis shad (Alosa alosa) and twaite shad (Alosa fallax), Marine Biology, vol.56, issue.Supp C, pp.675-687, 2012.
DOI : 10.1111/j.1095-8649.2000.tb00760.x

P. Johnson, A. Dobson, K. Lafferty, D. J. Marcogliese, J. Memmott et al., When parasites become prey: ecological and epidemiological significance of eating parasites, Trends in Ecology & Evolution, vol.25, issue.6, pp.362-371, 2010.
DOI : 10.1016/j.tree.2010.01.005

Z. Kabata, Clavellisa Emarginata (Kr??Yer, 1873): Morphological Study of a Parasitic Copepod, Crustaceana, vol.7, issue.1, pp.1-10, 1964.
DOI : 10.1163/156854064X00191

P. Kania, H. Taraschewski, Y. Han, D. Cone, and K. Buchmann, Divergence between Asian, European and Canadian populations of the monogenean Pseudodactylogyrus bini indicated by ribosomal DNA patterns, Journal of Helminthology, vol.15, issue.04, pp.404-409, 2010.
DOI : 10.1079/JOH2006364

C. Kennedy, The occurrence of Eubothrium fragile (Cestoda: Pseudophyllidae) in twaite shad, Alosa fallax (Lacepede) in the River Severn, Journal of Fish Biology, vol.26, issue.2, pp.171-177, 1981.
DOI : 10.1007/BF00927971

C. Kennedy, The distribution and abundance of the nematode Anguillicola australiensis in eels Anguilla reinhardtii in Queensland, Australia. Folia Parasit, vol.41, pp.279-285, 1994.

C. Kennedy, Ecology of the Acanthocephala, 2006.
DOI : 10.1017/CBO9780511541902

C. Kennedy, The ecology of parasites of freshwater fishes: the search for patterns, Parasitology, vol.109, issue.12, pp.1653-1662, 2009.
DOI : 10.1111/j.0030-1299.2005.13590.x

S. Kleinertz, S. Klimpel, and H. Palm, Parasite communities and feeding ecology of the European sprat (Sprattus sprattus L.) over its range of distribution, Parasitology Research, vol.2, issue.1, pp.1147-1157, 2012.
DOI : 10.1007/BF00042882

S. Klimpel and S. Rückert, Life cycle strategy of Hysterothylacium aduncum to become the most abundant anisakid fish nematode in the North Sea, Parasitology Research, vol.75, issue.2, pp.141-149, 2005.
DOI : 10.1080/00364827.1990.10413445

M. Køie, (Rudolphi, 1802) (Nematoda, Ascaridoidea, Anisakidae), Canadian Journal of Zoology, vol.71, issue.7, pp.1289-1296, 1993.
DOI : 10.1139/z93-178

R. Kuchta, V. Hanzelova, A. Shinn, L. Poddubnaya, and T. Scholz, Redescription of Eubothrium fragile (Rudolphi, 1802) and E. rugosum (Batsch, 1786) (Cestoda: Pseudophyllidea), parasites of fish in the Holarctic Region, Folia Parasitologica, vol.52, issue.2, pp.251-260, 2005.
DOI : 10.14411/fp.2005.033

A. Kuris, R. Hechinger, J. Shaw, K. Whitney, L. Aguirre-macedo et al., Ecosystem energetic implications of parasite and free-living biomass in three estuaries, Nature, vol.83, issue.7203, pp.515-518, 2008.
DOI : 10.1038/nature06970

J. Lambden and P. Johnson, Quantifying the biomass of parasites to understand their role in aquatic communities, Ecology and Evolution, vol.104, issue.7, pp.2310-2321, 2013.
DOI : 10.1073/pnas.0700062104

P. Legendre and L. Legendre, Numerical ecology Elsevier, the Netherlands Lenth R (2016) Least-Squares Means: The R package lsmeans, J Stat Softw, vol.69, pp.1-33, 2012.

S. Locke, J. Mclaughlin, and D. Marcogliese, Predicting the similarity of parasite communities in freshwater fishes using the phylogeny, ecology and proximity of hosts, Oikos, vol.26, issue.1, pp.73-83, 2013.
DOI : 10.2307/1943577

K. Mackenzie, Parasites as biological tags in population studies of marine organisms: an update, Parasitology, vol.124, issue.07, pp.153-163, 2002.
DOI : 10.1017/S0031182002001518

P. Maitland and A. Lyle, Ecology of Allis Shad Alosa alosa and Twaite Shad Alosa fallax in the Solway Firth, Scotland, Hydrobiologia, vol.362, issue.363, pp.205-221, 2005.
DOI : 10.1051/kmae:2001022

D. Marcogliese, Food webs and the transmission of parasites to marine fish, Parasitology, vol.124, issue.07, pp.83-99, 2002.
DOI : 10.1017/S003118200200149X

D. Marcogliese, Parasites: Small Players with Crucial Roles in the Ecological Theater, EcoHealth, vol.1, issue.2, pp.151-164, 2004.
DOI : 10.1007/s10393-004-0028-3

D. Marcogliese, Parasites of the superorganism: Are they indicators of ecosystem health?, International Journal for Parasitology, vol.35, issue.7, pp.705-716, 2005.
DOI : 10.1016/j.ijpara.2005.01.015

J. Martin, Q. Rougemont, H. Drouineau, S. Launey, P. Jatteau et al., Dispersal capacities of anadromous Allis shad population inferred from a coupled genetic and otolith approach, Canadian Journal of Fisheries and Aquatic Sciences, vol.72, issue.7, pp.991-1003, 2015.
DOI : 10.1139/cjfas-2014-0510

URL : https://hal.archives-ouvertes.fr/hal-01557337

S. Mattiucci and G. Nascetti, Dujardin, 1845: an update, Parasite, vol.13, issue.2, pp.99-113, 2006.
DOI : 10.1051/parasite/2006132099

S. Mattiucci and G. Nascetti, Chapter 2 Advances and Trends in the Molecular Systematics of Anisakid Nematodes, with Implications for their Evolutionary Ecology and Host???Parasite Co-evolutionary Processes, 2008.
DOI : 10.1016/S0065-308X(08)00202-9

E. Mcelroy, D. Buron, and I. , Host Performance as a Target of Manipulation by Parasites: A Meta-Analysis, Journal of Parasitology, vol.100, issue.4, pp.399-410, 2014.
DOI : 10.1645/13-488.1

M. Mota and C. Antunes, A preliminary characterisation of the habitat use and feeding of Allis shad (Alosa alosa) juveniles in the Minho River tidal freshwater wetlands, Limnetica, vol.31, pp.165-172, 2012.

M. Mota, A. Bio, M. Bao, S. Pascual, E. Rochard et al., New insights into biology and ecology of the Minho River Allis shad (Alosa alosa L.): contribution to the conservation of one of the last European shad populations, Reviews in Fish Biology and Fisheries, vol.6, issue.2, pp.395-412, 2015.
DOI : 10.1139/d98-023

D. Nachón, J. Sánchez-hernández, R. Vieira-lanero, and F. Cobo, Feeding of twaite shad, Alosa fallax (Lac??p??de, 1803), during the upstream spawning migration in the River Ulla (NW Spain), Marine and Freshwater Research, vol.64, issue.3, pp.233-236, 2013.
DOI : 10.1071/MF12322

S. Nadler and D. Hudspeth, PHYLOGENY OF THE ASCARIDOIDEA (NEMATODA: ASCARIDIDA) BASED ON THREE GENES AND MORPHOLOGY: HYPOTHESES OF STRUCTURAL AND SEQUENCE EVOLUTION, Journal of Parasitology, vol.86, issue.2, pp.380-93, 2000.
DOI : 10.1645/0022-3395(2000)086[0380:POTANA]2.0.CO;2

B. Neff and L. Cargnelli, Relationships between condition factors, parasite load and paternity in bluegill sunfish, Lepomis macrochirus, Environmental Biology of Fishes, vol.12, issue.3, pp.297-304, 2004.
DOI : 10.1007/s10641-004-1263-8

P. Nelson and T. Dick, Walbaum (Osteichthyes: Percopsidae), and the importance of scale, Canadian Journal of Zoology, vol.80, issue.11, pp.1986-1999, 2002.
DOI : 10.1139/z02-188

A. Nunn, R. Noble, and J. Harvey, The diets and parasites of larval and 0+ juvenile twaite shad in the lower reaches and estuaries of the rivers Wye, Usk and Towy, UK, Hydrobiologia, vol.15, issue.363, pp.209-218, 2008.
DOI : 10.1139/f89-129

J. Oksanen, F. Blanchet, R. Kindt, P. Legendre, P. Minchin et al., Vegan: Community ecology package. R package version 2, pp.3-5, 2016.

E. Pante and B. Simon-bouhet, marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R, PLoS ONE, vol.92, issue.9, p.73051, 2013.
DOI : 10.1371/journal.pone.0073051.s001

URL : https://hal.archives-ouvertes.fr/hal-00871853

A. Pasternak, V. Mikheev, and E. Valtonen, Life history characteristics of Argulus foliaceus L. (Crustacea: Branchiura) populations in Central Finland, Ann Zool Fennici, vol.37, pp.25-35, 2000.

R. Poulin, Evolutionary Ecology of Parasites -From individuals to communities, 1998.

R. Poulin, Decay of similarity with host phylogenetic distance in parasite faunas, Parasitology, vol.32, issue.04, pp.733-741, 2010.
DOI : 10.2307/2389732

E. Price, North American monogenetic trematodes. IX. The families Mazocraeidae and Plectanocotylidae, Proc biol Soc Wash, vol.74, pp.453-458, 1961.

P. Price, M. Westoby, B. Rice, P. Atsatt, R. Fritz et al., Parasite Mediation in Ecological Interactions, Annual Review of Ecology and Systematics, vol.17, issue.1, pp.487-505, 1986.
DOI : 10.1146/annurev.es.17.110186.002415

R. Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2014.

L. Råberg, How to Live with the Enemy: Understanding Tolerance to Parasites, PLoS Biology, vol.64, issue.11, 2014.
DOI : 10.1371/journal.pbio.1001989.g001

N. Robar, G. Burness, and D. Murray, Tropics, trophics and taxonomy: the determinants of parasite-associated host mortality, Oikos, vol.21, issue.8, pp.1273-1280, 2010.
DOI : 10.1136/bmj.315.7109.629

S. Rushton-mellor and G. Boxshall, (Crustacea: Branchiura), Journal of Natural History, vol.34, issue.3, pp.763-785, 1994.
DOI : 10.5479/si.00963801.32-1531.411

S. Sekalovic, P. De-ruiter, and H. Heesterbeek, Infectious disease agents mediate interaction in food webs and ecosystems, Proc R Soc B, vol.281, p.20132709, 2014.

B. Shields, P. Bird, W. Liss, K. Groves, R. Olson et al., The Nematode Anisakis simplex in American Shad (Alosa sapidissima) in Two Oregon Rivers, Journal of Parasitology, vol.88, issue.5, pp.1033-1035, 2002.
DOI : 10.1645/0022-3395(2002)088[1033:TNASIA]2.0.CO;2

M. Skóra, M. Sapota, K. Skóra, and A. Pawelec, Abstract, Oceanological and Hydrobiological Studies, vol.7, issue.96, pp.24-32, 2012.
DOI : 10.1007/s10750-008-9293-4

N. Smit, N. Bruce, and K. Hadfield, Global diversity of fish parasitic isopod crustaceans of the family Cymothoidae, International Journal for Parasitology: Parasites and Wildlife, vol.3, issue.2, pp.188-197, 2014.
DOI : 10.1016/j.ijppaw.2014.03.004

C. Taverny and P. Elie, R??PARTITION SPATIO-TEMPORELLE DE LA GRANDE ALOSE ALOSA ALOSA (LINN??, 1766) ET DE L???ALOSE FEINTE ALOSA FALLAX (LAC??P??DE, 1803) DANS LE GOLFE DE GASCOGNE., Bulletin Fran??ais de la P??che et de la Pisciculture, vol.362363, issue.362-363, pp.803-821, 2001.
DOI : 10.1051/kmae:2001020

C. Taverny and P. Elie, R??GIME ALIMENTAIRE DE LA GRANDE ALOSE ALOSA ALOSA (LINN??, 1766) ET DE L???ALOSE FEINTE ALOSA FALLAX (LAC??P??DE, 1803) DANS LE GOLFE DE GASCOGNE., Bulletin Fran??ais de la P??che et de la Pisciculture, vol.362363, issue.362-363, pp.837-852, 2001.
DOI : 10.1051/kmae:2001022

F. Thomas, J. Guégan, and F. Renaud, ?cologie et évolution des systèmes parasités, 2007.

J. Trilles, Les Cymothoidae (Isopoda, Flabellifera) des collections du Muséum national d'Histoire naturelle de Paris. II. Les Anilocridae Schioedte et Meinert, 1881. Genres Anilocra Leach, Bull Mus natn Hist nat, pp.290-303, 1818.

A. Valentini, S. Mattiucci, P. Bondanelli, S. Webb, A. Mignucci-giannone et al., Genetic relationships among Anisakis species (Nematoda : Anisakidae) inferred from mitochondrial, 2006.
DOI : 10.1645/ge-3504.1