Abbiati, M. and Maltagliati, F. (1992) Genetic population structure of Neanthes succinea (Polychaeta: Nereididae). Journal of the Marine Biological Association of the United Kingdom 72, 511–517.
Alvarado-Bremer, J., Viñas, J., Mejuto, J., Ely, B. and Pla, C. (2005) Comparative phylogeography of Atlantic bluefin tuna and swordfish: the combined effects of vicariance, secondary contact, introgression, and population expansion. Molecular Phylogenetics and Evolution 36, 169–187.
Anderson, M.J. (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecology 26, 32–46.
Aylagas, E., Borja, A. and Rodríguez-Ezpeleta, N. (2014) Environmental status assessment using DNA metabarcoding: towards a genetics based marine biotic index (gAMBI). PLoS ONE 9, e90529.
Barnes, R. (1995) European coastal lagoons: macrotidal versus microtidal contrasts. Biologia Marina Mediterranea 2, 3–7.
Baselga, A. and Fujisawa, T. (2013) Whole-community DNA barcoding reveals a spatio-temporal continuum of biodiversity at species and genetic levels. Nature Communications 4, 1892.
Bilton, D.T., Paula, J. and Bishop, J.D.D. (2002) Dispersal, genetic differentiation and speciation in estuarine organisms. Estuarine, Coastal and Shelf Science 55, 937–952.
Birky, C.W. (2013) Species detection and identification in sexual organisms using population genetic theory and DNA sequences. PLoS ONE 8, e52544.
Bisol, P.M., Gallini, A., Prevedello, S., Rianna, E., Bernardinelli, E., Franco, A. and Zane, L. (2007) Low variation at allozyme loci and differences between age classes at microsatellites in grass goby (Zosterisessor ophiocephalus) populations. Hydrobiologia 577, 151–159.
Bray, J.R. and Curtis, J.T. (1957) An ordination of the upland forest community of southern Wisconsin. Ecology Monographs 27, 325–349.
Cancela da Fonseca, L., Costa, A.M. and Bernardo, J.M. (1989) Seasonal variation of benthic and fish communities in a shallow land-locked coastal lagoon (St Andre, SW Portugal). Scientia Marina 53, 663–669.
Chust, G., Albaina, A., Aranburu, A., Borja, Á., Diekmann, O.E., Estonba, A., Franco, J., Garmendia, J.M., Iriondo, M., Muxika, I., Rendo, F., Rodríguez, J.G., Ruiz-Larrañaga, O., Serrão, E.A. and Valle, M. (2013) Connectivity, neutral theories and the assessment of species vulnerability to global change in temperate estuaries. Estuarine, Coastal and Shelf Science 131, 52–63.
Cimmaruta, R., Bondanelli, P. and Nascetti, G. (2005) Genetic structure and environmental heterogeneity in the European hake (Merluccius merluccius). Molecular Ecology 14, 2577–2591.
Clarke, K. and Gorley, R. (2006) PRIMER v6: user manual/tutorial. Plymouth: PRIMER-E UK.
Clarke, K.R. and Ainsworth, M. (1993) A method of linking multivariate community structure to environmental variables. Marine Ecology Progress Series 92, 205–219.
Cognetti, G. and Maltagliati, F. (2004) Strategies of genetic biodiversity conservation in the marine environment. Marine Pollution Bulletin 48, 811–812.
Como, S. and Magni, P. (2009) Temporal changes of a macrobenthic assemblage in harsh lagoon sediments. Estuarine, Coastal and Shelf Science 83, 638–646.
Excoffier, L. (2004) Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model. Molecular Ecology 13, 853–864.
Excoffier, L. and Lischer, H.E.L. (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10, 564–567.
Fontaneto, D., Flot, J.F. and Tang, C.Q. (2015) Guidelines for DNA taxonomy, with a focus on the meiofauna. Marine Biodiversity 45, 433–451.
Fu, Y.X. (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147, 915–925.
Galindo, H.M., Olson, D.B. and Palumbi, S.R. (2006) Seascape genetics: a coupled oceanographic-genetic model predicts population structure of Caribbean corals. Current Biology 16, 1622–1626.
Galindo, H.M., Pfeiffer-Herbert, A.S., McManus, M.A., Chao, Y., Chai, F. and Palumbi, S.R. (2010) Seascape genetics along a steep cline: using genetic patterns to test predictions of marine larval dispersal. Molecular Ecology 19, 3692–3707.
Gamfeldt, L. and Källström, B. (2007) Increasing intraspecific diversity increases predictability in population survival in the face of perturbations. Oikos 116, 700–705.
Gamfeldt, L., Wallén, J., Jonsson, P.R., Berntsson, K.M. and Havenhand, J.N. (2005) Increasing intraspecific diversity enhances settling success in a marine invertebrate. Ecology 86, 3219–3224.
Gouvis, N., Kevrekidis, T. and Koukouras, A. (1997) Temporal changes of a macrobenthic assemblage in Evros Delta (North Aegean Sea). Internationale Revue der gesamten Hydrobiologie und Hydrographie 82, 67–80.
Grasshoff, K., Ehrhardt, M. and Kremling, K. (1983) Methods of seawater analysis. Berlin: Wiley-VHC Verlag.
Gravina, M.F., Ardizzone, G.D., Scaletta, F. and Chimenez, C. (1989) Descriptive analysis and classification of benthic communities in some Mediterranean coastal lagoons (Central Italy). Marine Ecology 10, 141–166.
Gray, J.S. and Elliott, M. (2009) Ecology of marine sediments: from science to management. Oxford: Oxford University Press.
Guelorget, O. and Perthuisot, J. (1983) Le domaine paralique: expressions géologiques, biologiques et économiques du confinement. Paris: Ecole Normale Superieure de Paris .
Hamilton, M.B. (2009) Population genetics. Chichester: Wiley-Blackwell.
Hedges, J.I. and Stern, J.H. (1984) Carbon and nitrogen determinations of carbonate-containing solids. Limnology and Oceanography 29, 657–663.
Katselis, G.N., Moutopoulos, D.K., Dimitriou, E.N. and Koutsikopoulos, C. (2013) Long-term changes of fisheries landings in enclosed gulf lagoons (Amvrakikos gulf, W Greece): influences of fishing and other human impacts. Estuarine, Coastal and Shelf Science 131, 31–40.
Kevrekidis, T. (2004) Seasonal variation of the macrozoobenthic community structure at low salinities in a Mediterranean lagoon (Monolimni Lagoon, Northern Aegean). International Review of Hydrobiology 89, 407–425.
Kormas, K.A., Nicolaidou, A. and Reizopoulou, S. (2001) Temporal variations of nutrients, chlorophyll a and particulate matter in three coastal lagoons of Amvrakikos Gulf (Ionian Sea, Greece). Marine Ecology 22, 201–213.
Lande, R. (1988) Genetics and demography in biological conservation. Science 241, 1455–1460.
Lawrence, A.J. and Soame, J.M. (2004) The effects of climate change on the reproduction of coastal invertebrates. Ibis 146, 29–39.
Librado, P. and Rozas, J. (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451–1452.
Liggins, L., Treml, E.A. and Riginos, C. (2013) Taking the plunge: an introduction to undertaking seascape genetic studies and using biophysical models. Geography Compass 7, 173–196.
Loh, P.S., Miller, A.E.J., Reeves, A.D., Harvey, S.M. and Overnell, J. (2008) Assessing the biodegradability of terrestrially-derived organic matter in Scottish sea loch sediments. Hydrology and Earth System Sciences 12, 811–823.
Lorenzo-Carballa, M., Hadrys, H., Cordero-Rivera, A. and Andrés, J.A. (2011) Population genetic structure of sexual and parthenogenetic damselflies inferred from mitochondrial and nuclear markers. Heredity 108, 386–395.
Mallet, B., Martos, F., Blambert, L., Pailler, T. and Humeau, L. (2014) Evidence for isolation-by-habitat among populations of an epiphytic orchid species on a small oceanic island. PLoS ONE 9, e87469.
Maltagliati, F. (2002) Genetic monitoring of brackish-water populations: the Mediterranean toothcarp Aphanius fasciatus (Cyprinodontidae) as a model. Marine Ecology Progress Series 235, 257–262.
Mathivat-Lallier, M.H. and Cazaux, C. (1991) Life-history of Nephtys hombergii in Arachon Bay. Estuarine, Coastal and Shelf Science 32, 1–9.
Olive, P.J.W., Garwood, P.R., Bentley, M.G. and Wright, N. (1981) Reproductive success, relative abundance and population structure of two species of Nephtys in an estuarine beach. Marine Biology 63, 189–196.
Palumbi, S.R. (1992) Marine speciation on a small planet. Trends in Ecology and Evolution 7, 114–118.
Parsons, T.R., Maita, Y. and Lalli, C.M. (1984) Manual of chemical and biological methods for seawater analysis. Oxford: Pergamon Press.
Patarnello, T., Volckaert, F.A.M.J. and Castilho, R. (2007) Pillars of Hercules: is the Atlantic-Mediterranean transition a phylogeographical break? Molecular Ecology 16, 4426–4444.
Pérez-Ruzafa, A., Fernández, A.I., Marcos, C., Gilabert, J., Quispe, J.I. and García-Charton, J.A. (2005) Spatial and temporal variations of hydrological conditions, nutrients and chlorophyll a in a Mediterranean coastal lagoon (Mar Menor, Spain). Hydrobiologia 550, 11–27.
Pérez-Ruzafa, A., Marcos, C., Pérez-Ruzafa, I.M., Barcala, E., Hegazi, M.I. and Quispe, J. (2007) Detecting changes resulting from human pressure in a naturally quick-changing and heterogeneous environment: spatial and temporal scales of variability in coastal lagoons. Estuarine, Coastal and Shelf Science 75, 175–188.
Posada, D. and Crandall, K. (2001) Intraspecific gene genealogies: trees grafting into networks. Trends in Ecology and Evolution 16, 37–45.
Prado, P., Caiola, N. and Ibáñez, C. (2014a) Freshwater inflows and seasonal forcing strongly influence macrofaunal assemblages in Mediterranean coastal lagoons. Estuarine, Coastal and Shelf Science 147, 68–77.
Prado, P., Vergara, C., Caiola, N. and Ibáñez, C. (2014b) Influence of salinity regime on the food-web structure and feeding ecology of fish species from Mediterranean coastal lagoons. Estuarine, Coastal and Shelf Science 139, 1–10.
Puillandre, N., Lambert, A., Brouillet, S. and Achaz, G. (2011) ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular Ecology 21, 1864–1877.
Rainer, S.F. (1991) The genus Nephtys (Polychaeta: Phyllodocida) of northern Europe: a review of species, including the description of N. pulchra sp. n. and a key to the Nephtyidae. Helgoländer Meeresuntersuchungen 45, 65–96.
Ray, N., Currat, M. and Excoffier, L. (2003) Intra-deme molecular diversity in spatially expanding populations. Molecular Biology and Evolution 20, 76–86.
Reizopoulou, S., Thessalou-Legaki, M. and Nicolaidou, A. (1996) Assessment of disturbance in Mediterranean lagoons: an evaluation of methods. Marine Biology 125, 189–197.
Reusch, T.B.H., Ehlers, A., Hämmerli, A. and Worm, B. (2005) Ecosystem recovery after climatic extremes enhanced by genotypic diversity. Proceedings of the National Academy of Sciences USA 102, 2826–2831.
Riginos, C. and Liggins, L. (2013) Seascape genetics: populations, individuals and genes marooned and adrift. Geography Compass 7, 197–216.
Rodrigues, F., Valente, S. and González-Wanguemert, M. (2015) Genetic diversity across geographical scales in marine coastal ecosystems: Holothuria arguinensis a model species. Journal of Experimental Marine Biology and Ecology 463, 158–167.
Sanford, E. and Kelly, M.W. (2011) Local adaptation in marine invertebrates. Annual Review of Marine Science 3, 509–535.
Schmidt, H. and Westheide, W. (1994) Isozymes and general protein patterns as taxonomic markers in the taxon Nephtyidae (Annelida Polychaeta). Marine Biology 119, 31–38.
Selkoe, K.A., Watson, J.R., White, C., Ben Horin, T., Iacchei, M., Mitarai, S., Siegel, D.A., Gaines, S.D. and Toonen, R.J. (2010) Taking the chaos out of genetic patchiness: seascape genetics reveals ecological and oceanographic drivers of genetic patterns in three temperate reef species. Molecular Ecology 19, 3708–3726.
Sfriso, A., Birkemeyer, T. and Ghetti, P.F. (2001) Benthic macrofauna changes in areas of Venice lagoon populated by seagrasses or seaweeds. Marine Environmental Research 52, 323–349.
Shafer, A.B.A. and Wolf, J.B.W. (2013) Widespread evidence for incipient ecological speciation: a meta-analysis of isolation-by-ecology. Ecology Letters 16, 940–950.
Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595.
Tamura, K., Peterson, D. and Peterson, N. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28, 2731–2739.
Vandamme, S.G., Maes, G.E., Raeymaekers, J.A., Cottenie, K., Imsland, A.K., Hellemans, B., Lacroix, G., Mac Aoidh, E., Martinsohn, J.T., Martínez, P., Robbens, J., Vilas, R. and Volckaert, F.A. (2014) Regional environmental pressure influences population differentiation in turbot (Scophthalmus maximus). Molecular Ecology 23, 618–636.
Vergara-Chen, C., Gonzalez-Wanguemert, M., Marcos, C. and Perez-Ruzafa, A. (2013) Small-scale genetic structure of Cerastoderma glaucum in a lagoonal environment: potential significance of habitat discontinuity and unstable population dynamics. Journal of Molluscan Studies 79, 230–240.
Vignes, F., Barbone, E., Breber, P., Adamo, R.D., Leonilde, R., Ungaro, N., Focardi, S., Renzi, M. and Basset, A. (2009) Spatial and temporal description of the dystrophic crisis in Lesina lagoon during summer 2008. Transitional Waters Bulletin 3, 47–62.
Yentsch, C.S. and Menzel, D.W. (1963) A method for the determination of phytoplankton chlorophyll and phaeophytin by fluorescence. Deep Sea Research and Oceanographic Abstracts 10, 221–231.