Population connectivity of an overexploited coastal fish, Argyrosomus coronus (Sciaenidae), in an ocean-warming hotspot

References

• Allendorf FW, Berry O, Ryman N. 2014. So long to genetic diversity, and thanks for all the fish. Molecular Ecology 23: 23–25.
   PubMed Web of Science ®Google Scholar
• Apte S, Gardner JPA. 2002. Population genetic subdivision in the New Zealand greenshell mussel (Perna canaliculus) inferred from single-strand conformation polymorphism analysis of mitochondrial DNA. Molecular Ecology 11: 1617–1628.
   PubMed Web of Science ®Google Scholar
• Archangi B, Chand V, Mather PB. 2009. Isolation and characterization of 15 polymorphic microsatellite DNA loci from Argyrosomus japonicus (mulloway), a new aquaculture species in Australia. Molecular Ecology Resources 9: 412–414.
   PubMedGoogle Scholar
• Avise JC. 2000. Phylogeography: the history and formation of species. Cambridge, Massachusetts: Harvard University Press.
   Google Scholar
• Bandelt HJ, Forster P, Rohl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16: 37–48.
   PubMed Web of Science ®Google Scholar
• Beckensteiner J, Kaplan D, Potts WM, Santos CV, O’Farrell MR. 2016. Data-limited population status evaluation of two coastal fishes in southern Angola using recreational catch length-frequency data. PLoS ONE 11: e0147834.
   PubMed Web of Science ®Google Scholar
• Belkhir K, Borsa P, Chiki L, Refaust N, Bonhomme F. 2000. GENETIX 4.0.1, logiciel sous Windows pour la génétique des populations. Université de Montpellier, France: Laboratoire Génome Populations Interactions.
   Google Scholar
• Bowen BW, Muss A, Rocha LA, Grant WS. 2006. Shallow mtDNA coalescence in Atlantic pigmy angelfish (genus Centropyge) indicates a recent invasion from the Indian Ocean. Journal of Heredity 97: 1–12.
   PubMed Web of Science ®Google Scholar
• Briggs JC. 2011. Marine extinctions and conservation. Marine Biology 158: 485–488.
   Web of Science ®Google Scholar
• Canino MF, O’Reilly PT, Hauser L, Bentzen P. 2005. Genetic differentiation in walleye pollock (Theragra chalcogramma) in response to selection at the pantophysin (PanI) locus. Canadian Journal of Fisheries and Aquatic Sciences 62: 2519–2529.
   Web of Science ®Google Scholar
• Carvalho GR, Hauser L. 1994. Molecular genetics and the stock concept in fisheries. Reviews in Fish Biology and Fisheries 4: 326–350.
   Web of Science ®Google Scholar
• Chapuis M-P, Estoup A. 2007. Microsatellite null alleles and estimation of population differentiation. Molecular Biology and Evolution 24: 621–631.
   PubMed Web of Science ®Google Scholar
• Clark PU, Dyke AS, Shakun JD, Carlson AE, Clark J, Wohlfarth B et al. 2009. The Last Glacial Maximum. Science 325: 710–714.
   PubMed Web of Science ®Google Scholar
• Coleman RR, Gaither MR, Kimokeo B, Stanton FG, Bowen BW, Toonen RJ. 2014. Large-scale introduction of the Indo-Pacific damselfish Abudefduf vaigiensis into Hawaii promotes genetic swamping of the endemic congener A. abdominalis. Molecular Ecology 23: 5552–5565.
   PubMed Web of Science ®Google Scholar
• Cornuet JM, Piry S, Luikart G, Estoup A, Solignac M. 1999. New methods employing multilocus to select or exclude populations as origins of individuals. Genetics 153: 1989–2000.
   PubMed Web of Science ®Google Scholar
• Crawford NG. 2010. smogd: software for the measurement of genetic diversity. Molecular Ecology Resources 10: 556–557.
   PubMed Web of Science ®Google Scholar
• Diaz-Jaimes P, Uribe-Alcocer M, Rocha-Olivares A, Garcia-de-Leon FJ, Nortmoon P, Durand JD. 2010. Global phylogeography of the dolphinfish (Coryphaena hippurus): the influence of large effective population size and recent dispersal on the divergence of a marine pelagic cosmopolitan species. Molecular Phylogenetics and Evolution 57: 1209–1218.
   PubMed Web of Science ®Google Scholar
• Do C, Waples RS, Peel D, Macbeth GM, Tillett BJ, Ovenden JR. 2014. NEESTIMATOR v2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources 14: 209–214.
   PubMed Web of Science ®Google Scholar
• Donaldson KA, Wilson RR. 1999. Amphi-panamic geminates of snook (Percoidei: Centropomidae) provide a calibration of the divergence rate in the mitochondrial DNA central region of fishes. Molecular Phylogenetics and Evolution 13: 208–213.
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214–221.
   PubMed Web of Science ®Google Scholar
• Earl DA, von Holdt BM. 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4: 359–361.
   Web of Science ®Google Scholar
• Edworthy C, James NC, Erasmus B, Kemp JOG, Kaiser H, Potts WM. 2018. Metabolic activity throughout early development of dusky kob Argyrosomus japonicus. African Journal of Marine Science 40 [this issue].
   Google Scholar
• Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611–2620.
   PubMed Web of Science ®Google Scholar
• Excoffier L, Laval G, Schneider S. 2005. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics 1: 47–50.
   PubMed Web of Science ®Google Scholar
• Faria R, Weiss S, Alexandrino P. 2012. Comparative phylogeography and demographic history of European shads (Alosa alosa and A. fallax) inferred from mitochondrial DNA. BMC Evolutionary Biology 12: 194.
   Google Scholar
• Francisco SM, Faria C, Lengkeek W, Vieira MN, Velasco EM, Almada VC. 2011. Phylogeography of the shanny Lipophrys pholis (Pisces: Blenniidae) in the NE Atlantic records signs of major expansion event older than the last glaciation. Journal of Experimental Marine Biology and Ecology 403: 14–20.
   Web of Science ®Google Scholar
• Frankham R. 2005. Stress and adaptation in conservation genetics. Journal of Evolutionary Biology 18: 750–755.
   PubMed Web of Science ®Google Scholar
• Fu YX. 1997. Statistical tests of neutrality of mutations against population growth hitchhiking and background selection. Genetics 147: 915–925.
   PubMed Web of Science ®Google Scholar
• Galarza JA, Carreras-Carbonell J, Macpherson E, Pascual M, Roques S, Turner GF, Rico C. 2009. The influence of oceanographic fronts and early-life-history traits on connectivity among littoral fish species. Proceedings of the National Academy of Sciences of the United States of America 106: 1473–1478.
   PubMed Web of Science ®Google Scholar
• Garroway CJ, Bowman J, Holloway GL, Malcolm JR, Wilson PJ. 2011. The genetic signature of rapid range expansion by flying squirrels in response to contemporary climate warming. Global Change Biology 17: 1760–1769.
   Web of Science ®Google Scholar
• Goudet J. 1995. FSTAT (Version 1.2): a computer program to calculate F-statistics. Journal of Heredity 86: 485–486.
   Web of Science ®Google Scholar
• Grant WS, Bowen BW. 2006. Living in a tilted world: climate change and geography limit speciation in Old World anchovies (Engraulis; Engraulidae). Biological Journal of the Linnean Society 88: 673–689.
   Web of Science ®Google Scholar
• Griffiths MH. 1996. Life history of the dusky kob Argyrosomus japonicus (Sciaenidae) off the east coast of South Africa. South African Journal of Marine Science 17: 135–154.
   Google Scholar
• Griffiths MH, Heemstra PC. 1995. A contribution to the taxonomy of the marine fish genus Argyrosomus (Perciformes: Sciaenidae) with description of two new species from southern Africa. Ichthyological Bulletin of the JLB Smith Institute of Ichthyology 65: 1–40.
   Google Scholar
• Hall T. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95–98. Available at http://www.mbio.ncsu.edu/BioEdit/bioedit.html [accessed January 2008].
   Google Scholar
• Henriques R, Nielsen ES, Durholtz D, Japp DW, von der Heyden S. 2017. Genetic population substructuring of kingklip (Genypterus capensis – Ophidiidiae), a commercially exploited demersal fish off South Africa. Fisheries Research 187: 86–95.
   Web of Science ®Google Scholar
• Henriques R, Potts WM, Santos CV, Sauer WHH, Shaw PW. 2014. Population connectivity and phylogeography of a coastal fish, Atractoscion aequidens (Sciaenidae), across the Benguela Current region: evidence of an ancient vicariant event. PLoS ONE 9: e87907.
   PubMed Web of Science ®Google Scholar
• Henriques R, Potts WM, Sauer WHH, Shaw PW. 2012. Evidence of deep genetic divergence between populations of an important recreational fishery species, Lichia amia L. 1758 around southern Africa. African Journal of Marine Science 34: 585–591.
   Google Scholar
• Henriques R, Potts WM, Sauer WHH, Shaw PW. 2015. Incipient genetic isolation of a temperate migratory coastal sciaenid fish (Argyrosomus inodorus) within the Benguela Cold Current system. Marine Biology Research 11: 423–429.
   Web of Science ®Google Scholar
• Henriques R, von der Heyden S, Lipiński MR, du Toit N, Kainge P, Bloomer P, Matthee CA. 2016. Spatio-temporal genetic structure and the effects of long-term fishing in two partially sympatric offshore demersal fishes. Molecular Ecology 25: 5843–5861.
   PubMed Web of Science ®Google Scholar
• Hill JK, Griffiths HM, Thomas CD. 2011. Climate change and evolutionary adaptations at species’ range margins. Annual Review of Entomology 56: 143–159.
   PubMed Web of Science ®Google Scholar
• Hobday AJ, Pecl GT. 2014. Identification of global marine hotspots: sentinels for change and vanguards for adaptation action. Reviews in Fish Biology and Fisheries 24: 415–425.
   Web of Science ®Google Scholar
• Holtzhausen JA, Kirchner CH, Voges SF. 2001. Observations on the linefish resources of Namibia 1990–2000 with special reference to West Coast steenbras and silver kob. South African Journal of Marine Science 23: 135–144.
   Google Scholar
• Jahn B, Donner B, Muller PJ, Rohl U, Schneider RR, Wefer G. 2003. Pleistocene variations in dust input and marine productivity in the northern Benguela Current: evidence of evolution of global glacial-interglacial cycles. Palaeogeography, Palaeoclimatology, Palaeoecology 193: 515–533.
   Web of Science ®Google Scholar
• Jost L. 2008. GST and its relatives do not measure differentiation. Molecular Ecology 17: 4015–4026.
   PubMed Web of Science ®Google Scholar
• Kirkman SP, Blamey L, Lamont T, Field JG, Bianchi G, Huggett JA et al. 2016. Spatial characterisation of the Benguela ecosystem for ecosystem-based management. African Journal of Marine Science 38: 7–22.
   Web of Science ®Google Scholar
• Kirst GJ, Schneider RR, Muller PJ, von Storch I, Wefer G. 1999. Late Quaternary temperature variability in the Benguela Current System derived from alkenones. Quaternary Research 52: 92–103.
   Web of Science ®Google Scholar
• Last PR, White WT, Gledhill DC, Hobday AJ, Brown R, Edgar GJ, Pecl G. 2011. Long-term shifts in abundance and distribution of a temperate fish fauna: a response to climate change and fishing practices. Global Ecology and Biogeography 20: 58–72.
   Web of Science ®Google Scholar
• Latch EK, Dharmarajan G, Glaubitz JC, Rhodes OE. 2006. Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation. Conservation Genetics 7: 295–302.
   Web of Science ®Google Scholar
• Luiz JO, Madin JS, Robertson DR, Rocha LA, Wirtz P, Floeter SR. 2012. Ecological traits influencing range expansion across large oceanic dispersal barriers: insights from tropical Atlantic reef fishes. Proceedings of the Royal Society B 279: 1033–1040.
   Google Scholar
• Matthee CA, Cockcroft AC, Gopal K, von der Heyden S. 2007. Mitochondrial DNA variation of the west-coast rock lobster Jasus lalandii: marked genetic diversity differences among sampling sites. Marine and Freshwater Research 58: 1130–1135.
   Web of Science ®Google Scholar
• McKeown NJ, Arkhipkin A, Shaw PW. 2015. Integrating genetic and otolith microchemistry data to understand population structure in the Patagonian hoki (Macruronus magellanicus). Fisheries Research 164: 1–7.
   Web of Science ®Google Scholar
• Miethe T, Dytham C, Dieckmann U, Pitchford JW. 2010. Marine reserves and the evolutionary effects of fishing on size at maturation. ICES Journal of Marine Science 67: 412–425.
   Web of Science ®Google Scholar
• Monteiro PMS, van der Plas AK, Melice JL, Florenchie P. 2008. Interannual hypoxia variability in a coastal upwelling system: ocean-shelf exchange climate and ecosystem-state implications. Deep-Sea Research Part I 55: 435–450.
   Google Scholar
• Mullen SP, Little K, Draud M, Brozek J, Itzkowitz M. 2012. Hybridization among Caribbean damselfish species correlates with habitat degradation. Journal of Experimental Marine Biology and Ecology 416: 221–229.
   Web of Science ®Google Scholar
• Nei M, Li WH. 1973. Linkage disequilibrium in subdivided populations. Genetics 75: 213–219.
   PubMed Web of Science ®Google Scholar
• Pauly D, Watson R, Alder J. 2005. Global trends in world fisheries: impacts on marine ecosystems and food security. Philosophical Transactions of the Royal Society B 360: 5–12.
   PubMed Web of Science ®Google Scholar
• Pinsky ML, Palumbi SR. 2014. Meta-analysis reveals lower genetic diversity in overfished populations. Molecular Ecology 23: 29–39.
   PubMed Web of Science ®Google Scholar
• Poll M. 1954. Résultats scientifiques de l’expédition océanographie belge dans les eaux côtières africaines de l‘Atlantique sud (1948–1949). IV. Téléostéens acanthoptérygiens (1ère partie). Institute royal des Sciences naturelles de Belgique 4: 1–390.
   Google Scholar
• Posada D. 2008. jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25: 1253–1256.
   PubMed Web of Science ®Google Scholar
• Potts WM, Childs A-R, Sauer WHH, Duarte ADC. 2009. Characteristics and economic contribution of a developing recreational fishery in southern Angola. Fisheries Management and Ecology 16: 14–20.
   Web of Science ®Google Scholar
• Potts WM, Henriques R, Santos CV, Munnik K, Ansorge I, Dufois F et al. 2014. Ocean warming, a rapid distributional shift, and the hybridization of a coastal fish species. Global Change Biology 20: 2765–2777.
   PubMed Web of Science ®Google Scholar
• Potts WM, Sauer WHH, Henriques R, Sequesseque S, Santos CV, Shaw PW. 2010. The biology, life history and management needs of a large sciaenid fish Argyrosomus coronus in Angola. African Journal of Marine Science 32: 247–258.
   Web of Science ®Google Scholar
• Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945–959.
   PubMed Web of Science ®Google Scholar
• Pusack TJ, Christie MR, Johnson DW, Stallings CD, Hixon MA. 2014. Spatial and temporal patterns of larval dispersal in a coral-reef fish metapopulation: evidence of variable reproductive success. Molecular Ecology 23: 3396–3408.
   PubMed Web of Science ®Google Scholar
• Rambaut A, Suchard MA, Xie D, Drummond AJ. 2014. Tracer v1.6. Available at http://beast.bio.ed.ac.uk/Tracer [accessed March 2017].
   Google Scholar
• Raymond M, Rousset F. 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity 86: 248–249.
   Web of Science ®Google Scholar
• Riccioni G, Landi M, Ferrara G, Milano I, Cariani A, Zane L et al. 2010. Spatio-temporal population structuring and genetic diversity retention in depleted Atlantic bluefin tuna of the Mediterranean Sea. Proceedings of the National Academy of Sciences of the United States of America 107: 2102–2107.
   Google Scholar
• Roberts DG, Gray CA, West RJ, Ayre DJ. 2009. Evolutionary impacts of hybridization and interspecific gene flow on an obligately estuarine fish. Journal of Evolutionary Biology 22: 27–35.
   PubMed Web of Science ®Google Scholar
• Roberts DG, Gray CA, West RJ, Ayre DJ. 2010. Marine genetic swamping: hybrids replace an obligately estuarine fish. Molecular Ecology 19: 508–520.
   PubMed Web of Science ®Google Scholar
• Ryman N, Palm S. 2006. POWSIM: a computer program for assessing statistical power when testing for genetic differentiation. Molecular Ecology Notes 6: 600–602.
   Web of Science ®Google Scholar
• Sala E, Knowlton N. 2006. Global marine biodiversity trends. Annual Review of Environment and Resources 31: 93–122.
   Web of Science ®Google Scholar
• Sambrook J, Fritscher EF, Maniatis T. 1989. Molecular cloning: a laboratory manual. Woodbury, New York: Cold Spring Harbor Laboratory Press.
   Google Scholar
• Silberschneider V, Gray CA. 2008. Synopsis of biological fisheries and aquaculture-related information on mulloway Argyrosomus japonicus (Pisces: Sciaenidae) with particular reference to Australia. Journal of Applied Ichthyology 24: 7–17.
   Web of Science ®Google Scholar
• Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585–595.
   PubMed Web of Science ®Google Scholar
• Tamura K, Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10: 512–526.
   PubMed Web of Science ®Google Scholar
• Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25: 4876–4882.
   PubMed Web of Science ®Google Scholar
• van Oosterhout C, Weetman D, Hutchinson WF. 2006. Estimation and adjustment of microsatellite null alleles in nonequilibrium populations. Molecular Ecology Notes 6: 255–256.
   Web of Science ®Google Scholar
• von der Heyden S, Lipiński MR, Matthee CA. 2007. Mitochondrial DNA analyses of the Cape hakes reveal an expanding panmictic population for Merluccius capensis and population structuring for mature fish in Merluccius paradoxus. Molecular Phylogenetics and Evolution 42: 517–527.
   PubMed Web of Science ®Google Scholar
• von der Heyden S, Prochazka K, Bowie RCK. 2008. Significant population structure and asymmetric gene flow patterns amidst expanding populations of Clinus cottoides (Perciformes, Clinidae): application of molecular data to marine conservation planning in South Africa. Molecular Ecology 17: 4812–4826.
   PubMed Web of Science ®Google Scholar
• von der Heyden S, Lipiński MR, Matthee CA. 2010. Remarkably low mtDNA control region diversity in an abundant demersal fish. Molecular Phylogenetics and Evolution 55: 1183–1188.
   PubMed Web of Science ®Google Scholar
• von der Heyden S, Bowie RCK, Prochazka K, Bloomer P, Crane NL, Bernardi G. 2011. Phylogeographic patterns and cryptic speciation across oceanographic barriers in South African intertidal fishes. Journal of Evolutionary Biology 24: 2505–2519.
   PubMed Web of Science ®Google Scholar
• Waples RS, Do C. 2010. Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evolutionary Applications 3: 244–262.
   PubMed Web of Science ®Google Scholar
• Weir BS, Cockerham CC. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38: 1358–1370.
   PubMed Web of Science ®Google Scholar