Grummer, J. A. et al. Aquatic landscape genomics and environmental effects on genetic variation. Trends Ecol. Evol. 34, 641–654 (2019).
Ahrens, C. W. et al. The search for loci under selection: trends, biases and progress. Mol. Ecol. 27, 1342–1356 (2018).
Benestan, L. et al. Seascape genomics provides evidence for thermal adaptation and current-mediated population structure in American lobster (Homarus americanus). Mol. Ecol. 25, 5073–5092 (2016).
Xuereb, A., Kimber, C. M., Curtis, J. M. R., Bernatchez, L. & Fortin, M. J. Putatively adaptive genetic variation in the giant California sea cucumber (Parastichopus californicus) as revealed by environmental association analysis of restriction-site associated DNA sequencing data. Mol. Ecol. 27, 5035–5048 (2018).
Hasan, M. M. et al. Sticklebacks adapted to divergent osmotic environments show differences in plasticity for kidney morphology and candidate gene expression. J. Exp. Biol. 220, 2175–2186 (2017).
Carreras, C. et al. East is East and West is West: Population genomics and hierarchical analyses reveal genetic structure and adaptation footprints in the keystone species Paracentrotus lividus (Echinoidea). Divers. Distrib. 26, 382–398 (2020).
Hansen, M. M., Olivieri, I., Waller, D. M. & Nielsen, E. E. Monitoring adaptive genetic responses to environmental change. Mol. Ecol. 21, 1311–1329 (2012).
Elshire, R. J. et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6, e19379 (2011).
Stapley, J. et al. Adaptation genomics: the next generation. Trends Ecol. Evol. 25, 705–712 (2010).
Carreras, C. et al. Population genomics of an endemic Mediterranean fish: differentiation by fine scale dispersal and adaptation. Sci. Rep. 7, 43417 (2017).
Babbucci, M. et al. An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax). Sci. Rep. 6, 1–11 (2016).
Gonzalez-Pena, D. et al. Genome-wide association study for identifying loci that affect fillet yield, carcass, and body weight traits in rainbow trout (Oncorhynchus mykiss). Front. Genet. 7, 203 (2016).
Zhong, X. et al. Genome-wide association study reveals multiple novel QTL associated with low oxygen tolerance in hybrid catfish. Mar. Biotechnol. 19, 379–390 (2017).
Schweizer, R. M. et al. Genetic subdivision and candidate genes under selection in North American grey wolves. Mol. Ecol. 25, 380–402 (2016).
Planes, S. & Lenfant, P. Temporal change in the genetic structure between and within cohorts of a marine fish, Diplodus sargus, induced by a large variance in individual reproductive success. Mol. Ecol. 11, 1515–1524 (2002).
Schunter, C. et al. Matching genetics with oceanography: Directional gene flow in a Mediterranean fish species. Mol. Ecol. 20, 5167–5181 (2011).
Treml, E. A. et al. Reproductive output and duration of the pelagic larval stage determine seascape-wide connectivity of marine populations. Integr. Comp. Biol. 52, 525–537 (2012).
Aspillaga, E. et al. Ordinary and extraordinary movement behaviour of small resident fish within a mediterranean marine protected area. PLoS ONE 11, 1–19 (2016).
Garrido, S. et al. Born small, die young: Intrinsic, size-selective mortality in marine larval fish. Sci. Rep. 5, 17065 (2015).
Raventos, N., Macpherson, E. & García-Rubiés, A. Effect of brine discharge from a desalination plant on macrobenthic communities in the NW Mediterranean. Mar. Environ. Res. 62, 1–14 (2006).
Schunter, C. et al. A novel integrative approach elucidates fine-scale dispersal patchiness in marine populations. Sci. Rep. 9, 10796 (2019).
Warner, R. R. Evolutionary ecology: how to reconcile pelagic dispersal with local adaptation. Coral Reefs 16, S115–S120 (1997).
Warner, R. R. & Lejeune, P. Sex change limited by paternal care: a test using four Mediterranean labrid fishes, genus Symphodus. Mar. Biol. 87, 89–99 (1985).
Raventos, N. Nest site characteristics and nesting success of the five- spotted wrasse Symphodus roissali in the north-western Mediterranean Sea. J. Fish Biol. 68, 305–309 (2006).
Raventos, N. & Macpherson, E. Planktonic larval duration and settlement marks on the otoliths of Mediterranean littoral fishes. Mar. Biol. 138, 1115–1120 (2001).
Lejeune, P. L. comportement social des Labridés méditerranéens. Cah. d’Ethologie Appliqué 5, 1–208 (1985).
Froese, R. & Pauly, D. FishBase. World Wide Web electronic publication. www.fishbase.org, version (10/2016) (2016).
Gordoa, A., Molí, B. & Raventos, N. Growth performance of four wrasse species on the north-western Mediterranean coast. Fish. Res. 45, 43–50 (2000).
Pascual, M., Rives, B., Schunter, C. & Macpherson, E. Impact of life history traits on gene flow: a multispecies systematic review across oceanographic barriers in the Mediterranean Sea. PLoS ONE 12, 1–20 (2017).
Galarza, J. A. et al. The influence of oceanographic fronts and early-life-history traits on connectivity among littoral fish species. Proc. Natl. Acad. Sci. 106, 1473–1478 (2009).
Balbín, R. et al. Interannual variability of the early summer circulation around the Balearic Islands: driving factors and potential effects on the marine ecosystem. J. Mar. Syst. 138, 70–81 (2014).
Fernández, V., Dietrich, D. E., Haney, R. L. & Tintoré, J. Mesoscale, seasonal and interannual variability in the Mediterranean Sea using a numerical ocean model. Prog. Oceanogr. 66, 321–340 (2005).
Pascual, M. et al. Temporal and spatial genetic differentiation in the crab Liocarcinus depurator across the Atlantic-Mediterranean transition. Sci. Rep. 6, 1–10 (2016).
Izaguirre, C., Méndez, F. J., Menéndez, M. & Losada, I. J. Global extreme wave height variability based on satellite data. Geophys. Res. Lett. 38, 1–6 (2011).
Álvarez, I. et al. Drivers of larval fish assemblage shift during the spring-summer transition in the coastal Mediterranean. Estuar. Coast. Shelf Sci. 97, 127–135 (2012).
Guillén, J. et al. Coastal oceanographic signatures of heat waves and extreme events of dense water formation during the period 2002–2012 (Barcelona, NW Mediterranean). Sci. Mar. 82, 189–206 (2019).
Patarnello, T., Volckaert, F. & Castilho, R. Pillars of Hercules: is the Atlantic-Mediterranean transition a phylogeographical break?. Mol. Ecol. 16, 4426–4444 (2007).
Pérez-Portela, R. et al. Spatio-temporal patterns of genetic variation in Arbacia lixula, a thermophilous sea urchin in expansion in the Mediterranean. Heredity (Edinb). 122, 244–259 (2019).
Calderón, I., Pita, L., Brusciotti, S., Palacín, C. & Turon, X. Time and space: genetic structure of the cohorts of the common sea urchin Paracentrotus lividus in Western Mediterranean. Mar. Biol. 159, 187–197 (2012).
Renault, L., Oguz, T., Pascual, A., Vizoso, G. & Tintore, J. Surface circulation in the Alborn Sea (western Mediterranean) inferred from remotely sensed data. J. Geophys. Res. Ocean. 117, 1–12 (2012).
Bradbury, I. R. et al. Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature. Proc. R. Soc. Lond. B Biol. Sci. 277, 3725–34 (2010).
Forester, B. R., Lasky, J. R., Wagner, H. H. & Urban, D. L. Comparing methods for detecting multilocus adaptation with multivariate genotype–environment associations. Mol. Ecol. 27, 2215–2233 (2018).
Excoffier, L., Hofer, T. & Foll, M. Detecting loci under selection in a hierarchically structured population. Heredity (Edinb). 103, 285–298 (2009).
Franch-Gras, L. et al. Genomic signatures of local adaptation to the degree of environmental predictability in rotifers. Sci. Rep. 8, 16051 (2018).
Lamichhaney, S. et al. Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring. Proc. Natl. Acad. Sci. USA 109, 19345–19350 (2012).
Sanford, E. & Kelly, M. W. Local adaptation in marine invertebrates. Ann. Rev. Mar. Sci. 3, 509–535 (2010).
Font, J., Garcialadona, E. & Gorriz, E. The seasonality of mesoscale motion in the Northern Current of the western Mediterranean: several years of evidence. Oceanol. Acta 18, 207–219 (1995).
Warner, R. R., Wernerus, F., Lejeune, P. & Van Den Berghe, E. Dynamics of female choice for parental care in a fish species where care is facultative. Behav. Ecol. 6, 73–81 (1995).
Cargnelli, L. M. & Gross, M. R. The temporal dimension in fish recruitment: birth date, body size, and size-dependent survival in a sunfish (bluegill: Lepomis macrochirus). Can. J. Fish. Aquat. Sci. 53, 360–367 (1996).
Fagundes, T. et al. Birth date predicts alternative life-history pathways in a fish with sequential reproductive tactics. Funct. Ecol. 29, 1533–1542 (2015).
Moginie, B. F. & Shima, J. S. Hatch date and growth rate drives reproductive success in nest-guarding males of a temperate reef fish. Mar. Ecol. Prog. Ser. 592, 197–206 (2018).
Hare, J. A. & Cowen, R. K. Size, growth, development, and survival of the planktonic larvae of Pomatomus saltatrix (Pisces: Pomatomidae). Ecology 78, 2415–2431 (1997).
Searcy, S. & Sponaugle, S. Selective mortality during the larval-juvenile transition in two coral reef fishes. Ecology 82, 2452–2470 (2001).
Raventos, N. & Macpherson, E. Effect of pelagic larval growth and size-at-hatching on post-settlement survivorship in two temperate labrid fish of the genus Symphodus. Mar. Ecol. Prog. Ser. 285, 205–211 (2005).
Raventos, N. Relationships between adult population size, recruitment, and year-class strength in a labrid fish in the Mediterranean Sea. Estuar. Coast. Shelf Sci. 85, 167–172 (2009).
García Rubies, A. & Zabala, M. Effects of total fishing prohibition on the rocky fish assemblages of Medes Islands marine reserve (NW Mediterranean). Scientia Marina 54, 317–328 (1990).
Macpherson, E., Gordoa, A. & García-Rubies, A. Biomass size spectra in littoral fishes in protected and unprotected areas in the NW mediterranean. Estuar. Coast. Shelf Sci. 55, 777–788 (2002).
Wilson, D. T. & McCormick, M. I. Microstructure of settlement-marks in the otoliths of tropical reef fishes. Mar. Biol. 134, 29–41 (1999).
Raventos, N. & Macpherson, E. Environmental influences on temporal patterns of settlement in two littoral labrid fishes in the Mediterranean Sea. Estuar. Coast. Shelf Sci. 63, 479–487 (2005).
R Core Team. R: A Language and Environment for Statistical Computing. http://www.r-project.org. (R Foundation for Statistical Computing, 2020).
Pierce, D. ncdf4: Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files. R package version 1.16.1. (2019).
Wickham, H. ggplot2: Elegant Graphics for Data Analysis. (Springer, New York, 2016).
Juza, M. et al. Operational SOCIB forecasting system and multi-platform validation in the Western Mediterranean. J. Oper. Ocean. 9, 9231 (2016).
Acker, J. G. & Leptoukh, G. Online analysis enhances use of NASA Earth Science Data. Eos, Trans. Am. Geophys. Union. 88, 14–17 (2007).
Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.5–2. https://CRAN.R-project.org/package=vegan (2018).
Dray, S. & Dufour, A. B. The ade4 Package: Implementing the Duality Diagram for Ecologists. J. Stat. Softw. 22, 1–20 (2007).
Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A. & Cresko, W. A. Stacks: An analysis tool set for population genomics. Mol. Ecol. 22, 3124–3140 (2013).
Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).
Jombart, T. Adegenet: A R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405 (2008).
Goudet, J. & Jombart, T. hierfstat: estimation and tests of hierarchical F-statistics. R package version 0.04–22. (2015).
Narum, S. R. Beyond Bonferroni: Less conservative analyses for conservation genetics. Conserv. Genet. 7, 783–787 (2006).
Foll, M. & Gaggiotti, O. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 180, 977–993 (2008).
Lotterhos, K. E. & Whitlock, M. C. Evaluation of demographic history and neutral parameterization on the performance of FST outlier tests. Mol. Ecol. 23, 2178–2192 (2014).
Purcell, S. et al. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
Warnes, M. G. R., Bolker, B., Bonebakker, L. & Gentleman, R. gplots: Various R Programming Tools for Plotting Data. R package version 3.0.1. (2016).
Lie, K. K. et al. Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish. BMC Genomics 19, 186 (2018).
Supek, F., Bošnjak, M., Škunca, N. & Šmuc, T. REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms. PLoS ONE 6, e21800 (2011).
Source: Ecology - nature.com