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Individual-based population genomics reveal different drivers of adaptation in sympatric fish

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  • 1.

    Grummer, J. A. et al. Aquatic landscape genomics and environmental effects on genetic variation. Trends Ecol. Evol. 34, 641–654 (2019).

    PubMed  Google Scholar 

  • 2.

    Ahrens, C. W. et al. The search for loci under selection: trends, biases and progress. Mol. Ecol. 27, 1342–1356 (2018).

    PubMed  Google Scholar 

  • 3.

    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).

    PubMed  Google Scholar 

  • 4.

    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).

    CAS  PubMed  Google Scholar 

  • 5.

    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).

    PubMed  Google Scholar 

  • 6.

    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).

    Google Scholar 

  • 7.

    Hansen, M. M., Olivieri, I., Waller, D. M. & Nielsen, E. E. Monitoring adaptive genetic responses to environmental change. Mol. Ecol. 21, 1311–1329 (2012).

    PubMed  Google Scholar 

  • 8.

    Elshire, R. J. et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6, e19379 (2011).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • 9.

    Stapley, J. et al. Adaptation genomics: the next generation. Trends Ecol. Evol. 25, 705–712 (2010).

    PubMed  Google Scholar 

  • 10.

    Carreras, C. et al. Population genomics of an endemic Mediterranean fish: differentiation by fine scale dispersal and adaptation. Sci. Rep. 7, 43417 (2017).

    ADS  PubMed  PubMed Central  Google Scholar 

  • 11.

    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).

    Google Scholar 

  • 12.

    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).

    PubMed  PubMed Central  Google Scholar 

  • 13.

    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).

    CAS  PubMed  Google Scholar 

  • 14.

    Schweizer, R. M. et al. Genetic subdivision and candidate genes under selection in North American grey wolves. Mol. Ecol. 25, 380–402 (2016).

    CAS  PubMed  Google Scholar 

  • 15.

    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).

    CAS  PubMed  Google Scholar 

  • 16.

    Schunter, C. et al. Matching genetics with oceanography: Directional gene flow in a Mediterranean fish species. Mol. Ecol. 20, 5167–5181 (2011).

    CAS  PubMed  Google Scholar 

  • 17.

    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).

    PubMed  Google Scholar 

  • 18.

    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).

    Google Scholar 

  • 19.

    Garrido, S. et al. Born small, die young: Intrinsic, size-selective mortality in marine larval fish. Sci. Rep. 5, 17065 (2015).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • 20.

    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).

    CAS  PubMed  Google Scholar 

  • 21.

    Schunter, C. et al. A novel integrative approach elucidates fine-scale dispersal patchiness in marine populations. Sci. Rep. 9, 10796 (2019).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • 22.

    Warner, R. R. Evolutionary ecology: how to reconcile pelagic dispersal with local adaptation. Coral Reefs 16, S115–S120 (1997).

    Google Scholar 

  • 23.

    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).

    Google Scholar 

  • 24.

    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).

    Google Scholar 

  • 25.

    Raventos, N. & Macpherson, E. Planktonic larval duration and settlement marks on the otoliths of Mediterranean littoral fishes. Mar. Biol. 138, 1115–1120 (2001).

    Google Scholar 

  • 26.

    Lejeune, P. L. comportement social des Labridés méditerranéens. Cah. d’Ethologie Appliqué 5, 1–208 (1985).

    Google Scholar 

  • 27.

    Froese, R. & Pauly, D. FishBase. World Wide Web electronic publication. www.fishbase.org, version (10/2016) (2016).

  • 28.

    Gordoa, A., Molí, B. & Raventos, N. Growth performance of four wrasse species on the north-western Mediterranean coast. Fish. Res. 45, 43–50 (2000).

    Google Scholar 

  • 29.

    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).

    Google Scholar 

  • 30.

    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).

    ADS  CAS  PubMed  Google Scholar 

  • 31.

    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).

    Google Scholar 

  • 32.

    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).

    ADS  Google Scholar 

  • 33.

    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).

    Google Scholar 

  • 34.

    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).

    Google Scholar 

  • 35.

    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).

    ADS  Google Scholar 

  • 36.

    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).

    Google Scholar 

  • 37.

    Patarnello, T., Volckaert, F. & Castilho, R. Pillars of Hercules: is the Atlantic-Mediterranean transition a phylogeographical break?. Mol. Ecol. 16, 4426–4444 (2007).

    PubMed  Google Scholar 

  • 38.

    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).

    PubMed  Google Scholar 

  • 39.

    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).

    Google Scholar 

  • 40.

    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).

    Google Scholar 

  • 41.

    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).

    Google Scholar 

  • 42.

    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).

    CAS  PubMed  Google Scholar 

  • 43.

    Excoffier, L., Hofer, T. & Foll, M. Detecting loci under selection in a hierarchically structured population. Heredity (Edinb). 103, 285–298 (2009).

    CAS  PubMed  Google Scholar 

  • 44.

    Franch-Gras, L. et al. Genomic signatures of local adaptation to the degree of environmental predictability in rotifers. Sci. Rep. 8, 16051 (2018).

    ADS  PubMed  PubMed Central  Google Scholar 

  • 45.

    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).

    ADS  CAS  PubMed  Google Scholar 

  • 46.

    Sanford, E. & Kelly, M. W. Local adaptation in marine invertebrates. Ann. Rev. Mar. Sci. 3, 509–535 (2010).

    Google Scholar 

  • 47.

    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).

    Google Scholar 

  • 48.

    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).

    Google Scholar 

  • 49.

    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).

    Google Scholar 

  • 50.

    Fagundes, T. et al. Birth date predicts alternative life-history pathways in a fish with sequential reproductive tactics. Funct. Ecol. 29, 1533–1542 (2015).

    Google Scholar 

  • 51.

    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).

    ADS  Google Scholar 

  • 52.

    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).

    Google Scholar 

  • 53.

    Searcy, S. & Sponaugle, S. Selective mortality during the larval-juvenile transition in two coral reef fishes. Ecology 82, 2452–2470 (2001).

    Google Scholar 

  • 54.

    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).

    ADS  Google Scholar 

  • 55.

    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).

    ADS  Google Scholar 

  • 56.

    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).

    Google Scholar 

  • 57.

    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).

    ADS  Google Scholar 

  • 58.

    Wilson, D. T. & McCormick, M. I. Microstructure of settlement-marks in the otoliths of tropical reef fishes. Mar. Biol. 134, 29–41 (1999).

    Google Scholar 

  • 59.

    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).

    ADS  Google Scholar 

  • 60.

    R Core Team. R: A Language and Environment for Statistical Computing. http://www.r-project.org. (R Foundation for Statistical Computing, 2020).

  • 61.

    Pierce, D. ncdf4: Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files. R package version 1.16.1. (2019).

  • 62.

    Wickham, H. ggplot2: Elegant Graphics for Data Analysis. (Springer, New York, 2016).  

    Google Scholar 

  • 63.

    Juza, M. et al. Operational SOCIB forecasting system and multi-platform validation in the Western Mediterranean. J. Oper. Ocean. 9, 9231 (2016).

    Google Scholar 

  • 64.

    Acker, J. G. & Leptoukh, G. Online analysis enhances use of NASA Earth Science Data. Eos, Trans. Am. Geophys. Union. 88, 14–17 (2007).

    ADS  Google Scholar 

  • 65.

    Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.5–2. https://CRAN.R-project.org/package=vegan (2018).

  • 66.

    Dray, S. & Dufour, A. B. The ade4 Package: Implementing the Duality Diagram for Ecologists. J. Stat. Softw. 22, 1–20 (2007).

    Google Scholar 

  • 67.

    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).

    PubMed  PubMed Central  Google Scholar 

  • 68.

    Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 69.

    Jombart, T. Adegenet: A R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405 (2008).

    CAS  Google Scholar 

  • 70.

    Goudet, J. & Jombart, T. hierfstat: estimation and tests of hierarchical F-statistics. R package version 0.04–22. (2015).

  • 71.

    Narum, S. R. Beyond Bonferroni: Less conservative analyses for conservation genetics. Conserv. Genet. 7, 783–787 (2006).

    CAS  Google Scholar 

  • 72.

    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).

    PubMed  PubMed Central  Google Scholar 

  • 73.

    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).

    PubMed  PubMed Central  Google Scholar 

  • 74.

    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).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 75.

    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).

  • 76.

    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).

    PubMed  PubMed Central  Google Scholar 

  • 77.

    Supek, F., Bošnjak, M., Škunca, N. & Šmuc, T. REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms. PLoS ONE 6, e21800 (2011).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 


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