[1] | Maggs CA, Castilho R, Foltz D, Henzler C, Jolly MT, et al. (2008) Evaluating signatures of glacial refugia for North Atlantic Benthic marine taxa. Ecology 89: S108–S122.
|
[2] | Riginos D, Nachman MW (2001) Population subdivision in marine environments: the contributions of biogeography, geographical distance and discontinuous habitat to genetic differentiation in a blennioid fish, Axoclinus nigricaudus. Mol Ecol 10: 1439–1453.
|
[3] | Patarnello T, Volckaert FAMJ, Castilho R (2007) Pillars of Hercules: is the Atlantic-Mediterranean transition a phylogeographical break? Mol Ecol 16: 4426–4444.
|
[4] | Galindo HM, Olson DB, Palumbi SR (2006) Seascape genetics: a coupled oceanographic-genetic model predicts population structure of Caribbean corals. Curr Biol 16: 1622–1626.
|
[5] | J?rgensen HBH, Hansen MM, Bekkevold D, Ruzzante DE, Loeschke V (2005) Marine landscapes and population genetic structure of herring (Clupea harengus L.) in the Baltic Sea. Mol Ecol 14: 3219–3234.
|
[6] | Cowen RK, Sponaugle S (2009) Larval dispersal and marine population connectivity. Ann Rev Mar Sci 1: 443–466.
|
[7] | Small MP, Loxterman JL, Frye AE, Von Bargen JF, Bowman C, et al. (2005) Temporal and spatial genetic structure among some Pacific herring populations in Puget Sound and the southern Strait of Georgia. Trans Am Fish Soc 134: 1329–1341.
|
[8] | Reeb CA, Avise JC (1990) A genetic discontinuity in a continuously distributed species: mitochondrial DNA in the American oyster, Crassostrea virginica. Genetics 124: 397–406.
|
[9] | Neiva J, Pearson GA, Valero M, Serr?o SA (2012) Fine-scale genetic breaks driven by historical range dynamics and ongoing density-barrier effects in the estuarine seaweed Fucus ceranoides L. BMC Evol Biol. 12: 78.
|
[10] | Roman J, Palumbi SR (2004) A global invader at home: population structure of the green crab, Carcinus maenus, in Europe. Mol Ecol 13: 2891–2898.
|
[11] | Toews DPL, Brelsford A (2012) The biogeography of mitochondrial and nuclear discordance in animals. Mol Ecol 21: 3907–3930.
|
[12] | Waters JM (2011) Competitive exclusion: phylogeography's ‘elephant in the room’? Mol Ecol 20: 4388–4394.
|
[13] | Grant WS, Utter FM (1984) Biochemical population genetics of Pacific herring (Clupea pallasi). Can J Fish Aquat Sci 41: 856–864.
|
[14] | Kobayashi T (1993) Biochemical analyses of genetic variability and divergence of populations in Pacific herring (Clupea pallasii). Bull Nat Res Inst Far Seas Fish 30: 1–77. [Japanese: English abstract].
|
[15] | Liu JX, Tatarenkov A, Beacham TD, Gorbachev V, Wildes S, et al. (2011) Effects of Pleistocene climate fluctuations on the phylogeographic and demographic histories of Pacific herring (Clupea pallasii). Mol Ecol 20: 3879–3893.
|
[16] | Grant WS, Liu M, Gao TX, Yanagimoto T (2012) Limits of Bayesian skyline plot analysis of mtDNA sequences to infer historical demographies in Pacific herring (and other species). Mol Phylogen Evol 65: 203–212.
|
[17] | Beacham TD, Schweigert JF, MacConnachie C, Le KD, Flostrand L (2008) Use of microsatellites to determine population structure and migration of Pacific herring in British Columbia and adjacent regions. Trans Am Fish Soc 137: 1795–1811.
|
[18] | O'Connell M, Dillon MC, Wright JM, Bentzen P, Merkouris S, et al. (1998) Genetic structuring among Alaskan Pacific herring populations identified using microsatellite variation. J Fish Biol 53: 150–163.
|
[19] | Wildes SL, Vollenweider JJ, Nguyen HT, Guyon JR (2011) Genetic variation between outer-coastal and fjord populations of Pacific herring (Clupea pallasii) in the eastern Gulf of Alaska. Fish Bull 109: 382–393.
|
[20] | Hay DE, Rose KA, Schweigert J, Megrey BA (2008) Geographic variation in North Pacific herring populations: Pan-Pacific comparisons and implications for climate change impacts. Prog Oceanogr 77: 233–240.
|
[21] | Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2d ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
|
[22] | Liu JX, Gao TX, Wu SF, Zhang YP (2007) Pleistocene isolation in the Northwestern Pacific marginal seas and limited dispersal in a marine fish, Chelon haemotocheilus (Temminck and Schlegel, 1845). Mol Ecol 16: 275–288.
|
[23] | Olson JB, Lewis CJ, Kretschmer EJ, Wilson SL, Seeb JE (2002) Characterization of 14 tetranucleotide microsatellite loci derived from Pacific herring. Mol Ecol Resour 2: 101–103.
|
[24] | Bassam BJ, Caetano-Anollés G, Gresshoff PM (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196: 80–83.
|
[25] | Jiang X, Yang GP, Liao MJ, Liu Y, Gao TX, et al. (2007) Microsatellite DNA polymorphism of Japanese sea bass (Laterolabrax japonicus) inhabiting Chinese and Japanese coasts. J Appl Ichthyol 24: 180–186.
|
[26] | Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform 1: 47–50.
|
[27] | Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinform. 14: 817–818.
|
[28] | Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512–526.
|
[29] | Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9: 1657–1659.
|
[30] | Excoffier L, Smouse P, Quattro J (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479–491.
|
[31] | Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915–925.
|
[32] | Excoffier L (2004) Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model. Mol Ecol 13: 853–864.
|
[33] | Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise differences. Mol Biol Evol 9: 552–569.
|
[34] | Ray N, Currat M, Excoffier L (2003) Intra-deme molecular diversity in spatially expanding populations. Mol Biol Evol 20: 76–86.
|
[35] | Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145: 1219–1228.
|
[36] | Jensen JL, Bohonak AJ, Kelley ST (2005) Isolation by distance, web service. BMC Genetics 6: 13. v.3.23 http://ibdws.sdsu.edu/. Accessed 2012 March 25.
|
[37] | Yeh FC, Yang RC, Boyle T (1999) POPGENE, version 1.32: the user friendly software for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton, AB, Canada.
|
[38] | Rousset F (2008) GENEPOP '007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Resour 8: 103–106.
|
[39] | Pritchard JK, Stephens M, Donnelly P (2000) Inference on population structure using multilocus genotype data. Genetics 155: 945–959.
|
[40] | Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611–2620.
|
[41] | Ryman N, Palm S, André C, Carvalho GR, Dahlgren TG, et al. (2006) Power for detecting genetic divergence: differences between statistical methods and marker loci. Mol Ecol 15: 2031–2045.
|
[42] | Slatkin M (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47: 264–279.
|
[43] | Akaike S, Takahashi K, Hoshikawa H, Takiya A, Tsuda F, et al.. (2010) Distribution and abundance of the Ishikari Bay herring (Clupea pallasii) natural spawning beds and the seaweed beds on the northwestern coast of Hokkaido. Sci Reps Hokk Fish Exp Sta 77: 29–33. [Japanese with English abstract].
|
[44] | Hay DE (1985) Reproductive biology of Pacific herring (Clupea harengus pallasi). Can J Fish Aquat Sci 42: 111–126.
|
[45] | Tojo N, Kruse GH, Funk FC (2007) Migration dynamics of Pacific herring (Clupea pallasii) and response to spring environmental variability in the southeastern Bering Sea. Deep Sea Res II 54: 2832–2848.
|
[46] | Kanno Y (1989) Variations in meristic and morphometric characters among populations of herring Clupea pallasii in the far eastern waters. Bull Jap Soc Sci Fish 55: 431–439.
|
[47] | Hotta T, Matsuishi T, Sakano H, Kanno Y (1999) Population structure of Pacific herring Clupea pallasii in the eastern Hokkaido waters. Nip Sui Gakk 65: 655–660.
|
[48] | Yamane K, Shirai K, Nagakura Y, Yamaguchi M, Takiya A, et al. (2010) Spatial variation in otolith elemental composition of the Pacific herring Clupea pallasii in northern Japan. Aquat Biol 10: 283–290.
|
[49] | Zebdi A, Collie JS (1995) Effect of climate on herring (Clupea pallasi) population dynamics in the Northeast Pacific Ocean, in: Beamish, RJ, editor. Climate change and northern fish populations. Can Spec Pubs Fish Aquat Sci 121: 277–290.
|
[50] | Nagasawa K (2001) Long-term variation in abundance of Pacific herring (Clupea pallasi) in Hokkaido and Sakhalin related to changes in environmental conditions. Prog Oceanogr 49: 551–564.
|
[51] | Liu M, Gao TX, Sakurai Y, Jia N, Zhao LL, et al. (2011) Mitochondrial DNA control region diversity and population structure of Pacific herring (Clupea pallasii) in the Yellow Sea and Sea of Japan. Chin J Oceanol Limnol 29: 317–325.
|
[52] | Johannesson K, André C (2006) Life on the margin: genetic isolation and diversity loss in a peripheral marine ecosystem, the Baltic Sea. Mol Ecol 15: 2013–2029.
|
[53] | Eckert CG, Samis KE, Lougheed SC (2008) Genetic variation across species' geographical ranges: the central-marginal hypothesis and beyond. Mol Ecol 17: 1170–1188.
|
[54] | Sancetta C (1983) Effect of Pleistocene glaciation upon oceanographic characteristics of the North Pacific Ocean and Bering Sea. Deep-Sea Res 30: 851–869.
|
[55] | Mann DH, Hamilton TD (1995) Late Pleistocene and Holocene paleoenvironments of the North Pacific coast. Quat Sci Revs 14: 449–471.
|
[56] | Harrison PJ, Boyd PW, Vaela DE, Takeda S, Shiomoto A, et al. (1999) Comparison of factors controlling phytoplankton productivity in the NE and NW subarctic Pacific gyres. Prog Oceanogr 43: 205–234.
|
[57] | Gorbarenko SA, Southon JR (2000) Detailed Japan Sea paleoceanography during the last 25 kyr: constraints from AMS dating and d18O of planktonic foraminifera. Palaeogeogr Palaeoclim Palaeoecol 156: 177–193.
|
[58] | Payne MC, Brown CA, Reusser DA, Lee HII (2012) Ecoregional analysis of nearshore sea-surface temperature in the North Pacific. PLoS One 7(1): e30105.
|
[59] | Zarraonaindia I, Iriondo M, Albaina A, Pardo MA, Manzano C, et al. (2012) Multiple SNP markers reveal fine-scale population and deep phylogeographic structure in European anchovy (Engraulis encrasicolus L.). PLoS One 7(7): e42201.
|
[60] | Mantua NJ, Hare SR (2002) The Pacific Decadal Oscillation. J Oceanogr 58: 35–44.
|
[61] | Swanson WJ, Vacquier VD (2002) The rapid evolution of reproductive proteins. Nat Revs 3: 137–144.
|
[62] | Springer SA, Crespi BJ (2007) Adaptive gamete-recognition divergence in a hybriding Mytilus population. Evolution 61: 772–783.
|
[63] | Binks RM, Prince J, Evans JP, Kennington WJ (2012) More than bindin divergence: reproductive isolation between sympatric subspecies of a sea urchin by asynchronous spawning. Evolution 66: 3545–3557.
|