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Paradigm Shifts in the Phylogeographic Analysis of Seaweeds

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Seaweed Phylogeography

Abstract

The phylogeographic analysis of seaweeds faces numerous biological, methodological, and conceptual challenges. One challenge is to understand how life-history phases, mating systems, dispersal mechanisms, and physiological tolerances influence the distributions and persistence of local populations. A second challenge has been to develop genetic assay methods that allow us to trace unbroken gene lineages so they can be tested with models using coalescence theory. An integral part of this challenge has been to identify unrecombining sections of DNA with known modes of inheritance. For the most part, seaweed phylogeographic studies have used unrecombining organellar and plastid DNAs, but new methods of phasing haplotypes of nuclear DNA can provide an enormous amount of data to fine-tune hypotheses to distinguish the effects of demography and natural selection. Finally, phylogeography faces conceptual challenges, as we learn ever more about palaeoclimates, the historical shapes of shorelines, and the dynamics of ocean currents. A major advance is the marriage between demographic models and models of natural selection, because both interact to mold the shapes of gene genealogies.

This chapter is dedicated to Bob Vadas (University of Maine) who, by example, taught me to ask questions.

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References

  • Alberto F, Raimondi PT, Reed DC, Coelho NC, Leblois R, Whitmer A, Serrão EA. Habitat continuity and geographic distance predict population genetic differentiation in giant kelp. Ecology. 2010;91:49–56.

    Article  PubMed  Google Scholar 

  • Alheit J, Hagen E. Long-term climate forcing of European herring and sardine populations. Fish Oceanogr. 1997;6:130–9.

    Article  Google Scholar 

  • Amsler CD, Neushul M. Nutrient stimulation of spore settlement in kelps Pterygophora californica and Macrocystis pyrifera. Mar Biol. 1990;107:297–403.

    Article  CAS  Google Scholar 

  • Amsler CD, Searles RB. Vertical distribution of seaweed spores in a water column offshore of North Carolina. J Phycol. 1980;16:617–9.

    Article  Google Scholar 

  • Arbogast B, Kenagy GJ. Comparative phylogeography as an integrative approach to historical biogeography. J Biogeogr. 2001;28:819–25.

    Article  Google Scholar 

  • Avise JC. Phylogeography: the history and formation of species. Cambridge: Harvard University Press; 2000.

    Google Scholar 

  • Avise JC. Phylogeography: retrospect and prospect. J Biogeogr. 2009;36:3–15.

    Article  Google Scholar 

  • Avise JC, Arnold J, Ball RM Jr, Bermingham E, Lamb T, et al. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Ann Rev Ecol Syst. 1987;18:489–522.

    Article  Google Scholar 

  • Barrett SCH, Harder LD, Worley AC. The comparative biology of pollination and mating in flowering plants. Phil Trans R Soc B. 1996;351:1271–80.

    Article  Google Scholar 

  • Beaumont MA. Approximate Bayesian computation in evolution and ecology. Ann Rev Ecol Evol Syst. 2010;41:379–406.

    Article  Google Scholar 

  • Beerli P, Felsenstein J. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc Nat Acad Sci USA. 2001;98:4563–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bellgrove A, Aoki MN. Variation in gametophyte dominance in populations of Chondrus verrucosus (Gigartinaceae, Rhodophyta). Phycol Res. 2008;56:246–54.

    Article  Google Scholar 

  • Berndt M-L, Callo JA, Brawley SH. Gamete concentrations and timing and success of fertilization in a rocky shore seaweed. Mar Ecol Prog Ser. 2002;226:273–85.

    Article  Google Scholar 

  • Bhattacharya D, Druehl LD. Restriction enzyme analysis of variation and taxonomy in the kelp genus Laminaria (Laminariales, Phaeophyta). Hydrobiologia. 1990;204:105–10.

    Article  Google Scholar 

  • Bigg GR, Cunningham CW, Ottersen G, Pogson GH, Wadley MR, Williamson P. Ice-age survival of Atlantic cod: agreement between palaeoecology models and genetics. Proc R Soc B. 2007;275:163–73.

    Article  PubMed Central  Google Scholar 

  • Bilgin R, Òªoraman E, Karatas A, Morales JC. Phylogeography of the greater horseshoe bat, Rhinolophus ferrumequinum (Chiroptera: Rhinolophidae), in southeastern Europe and Anatolia, with a specific focus on whether the Sea of Marmara is a barrier to gene flow. Act Chiropterologica. 2009;11:53–60.

    Article  Google Scholar 

  • Billot C, Engel CR, Rousvoal S, Kloareg B, Valero M. Current patterns, habitat discontinuities and population genetic structure: the case of the kelp Laminaria digitata in the English Channel. Mar Ecol Prog Ser. 2003;253:111–21.

    Article  Google Scholar 

  • Bird CE, Karl SA, Smouse PE, Toonen RJ (2011) Detecting and measuring genetic differentiation. In: Held C, Koenemann S, Schubart CD (eds), Phylogeography and population genetics in Crustacea, vol 19. CRC Press, pp 31–55.

    Google Scholar 

  • Birky CW Jr. Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution. Proc Nat Acad Sci USA. 1995;92:11331–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bock R (2007) Structure, function, and inheritance of plastid genomes. In: Bock R (ed), Cell and molecular biology of plastids. pp. 29–63 (Topics Curr Genet 19).

    Google Scholar 

  • Bond G, Broecker W, Johnsen S, McManus J, Labeyrie L, Jouzel J, Bonani G. Correlations between climate records from North Atlantic sediments and Greenland ice. Nature. 1993;365:143–7.

    Article  Google Scholar 

  • Bond G, Showers W, Cheseby M, Lotti R, Almasi P, de Menocal P, Priore P, Cullen H, Hajdas I, Bonani G. A pervasive millennial-scale cycle in North Altantic Holocene and glacial climates. Science. 1997;278:1257–66.

    Article  CAS  Google Scholar 

  • Boo GH, Lindstrom SC, Klochkova NG, Yotsukura N, Yang EC, Kim HG, Waaland JR, Cho GY, Miller KA, Boo SM. Taxonomy and biogeography of Agarum and Thalassiophyllum (Laminariales, Phaeophyceae) based on nuclear, mitochondrial and plastid gene sequences. Taxon. 2011;60:831–40.

    Google Scholar 

  • Bowen BW, Shanker K, Yasuda N, Malay MCD, von der Heyden S, Paulay G, Rocha LA, Selkoe KA, Barber PH, Lessios HA, Crandall ED, Bernardi G, Meyer CP, Carpenter KE, Toonen RJ. Phylogeography unplugged: comparative surveys in the genomic era. Bull Mar Sci. 2014;90:13–46.

    Article  Google Scholar 

  • BrÃ¥ten T. The ultrastructure of fertilization and zygote formation in the green alga, Ulva mutabilis Føyn. J Cell Sci. 1971;9:621–35.

    PubMed  Google Scholar 

  • BrÃ¥ten T. Autoradiographic evidence for the rapid disintegration of one chloroplast in the zygote of the green alga Ulva mutabilis. J Cell Sci. 1973;12:385–9.

    PubMed  Google Scholar 

  • Brawley SH, Wetherbeee R, Quatrano RS. Fine-structural studies of the gametes and embryo of Fucus vesiculosus L. (Phaeophyta). I. Fertilization and pronuclear fusion. J Cell Sci. 1976;20:233–54.

    CAS  PubMed  Google Scholar 

  • Brennan G, Kregting L, Beatty GE, Cole C, Elsässer B, Savidge G, Provan J. Understanding macroalgal dispersal in a complex hydrodynamic environment: a combined population genetic and physical modelling approach. J Roy Soc Interface. 2014;11:20140197.

    Article  Google Scholar 

  • Brito P, Edwards SV. Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica. 2009;135:439–55.

    Article  PubMed  Google Scholar 

  • Browning SR, Browning BL. Haplotype phasing: existing methods and new developments. Nat Rev Genet. 2011;12:703–14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Burger G, Saint-Louis D, Gray MW, Lang BF. Complete sequence of the mitochondrial DNA of the red alga Porphyra purpurea: cyanobacterial introns and shared ancestry of red and green algae. Plant Cell. 1999;11:1675–94.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bussolini LT, Waters JM. Genetic analyses of rafted macroalgae reveal regional oceanographic connectivity patterns. J Biogeogr. 2015;42:1319–26.

    Article  Google Scholar 

  • Campbell NR, Harmon SA, Narum SR. Genotyping-in-thousands by sequencing (GT-seq): a cost effective SNP genotyping method based on custom amplicon sequencing. Mol Ecol Res. 2015;15:855–67.

    Article  CAS  Google Scholar 

  • Carrington E, Grace SP, Chopin T. Life history phases and the biomechanical properties of the red alga Chondrus crispus (Rhodophyta). J Phycol. 2001;37:699–704.

    Article  Google Scholar 

  • Chan SW, Cheang CC, Chiraart A, Gerung G, Tharith C, Ang P. Homogeneous population of the brown alga Sargassum polycystum in Southeast Asia: possible role of recent expansion and asexual propogation. PLoS ONE. 2013;8:e77662.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chan SW, Heang CC, Yeung CW, Chirapart A, Gerung G, Tharith C, Ang P. Recent expansion led to the lack of genetic structure of Sargassum aquifolium populations in Southeast Asia. Mar Biol. 2014;16:785–95.

    Article  Google Scholar 

  • Charlesworth D, Charlesworth B. Inbreeding depression and its evolutionary consequences. Ann Rev Ecol Syst. 1987;18:237–68.

    Article  Google Scholar 

  • Charlesworth B, Morgan MT, Charlesworth D. The effect of deleterious mutations on neutral molecular variation. Genetics. 1993;134:1289–303.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cheviron ZA, Brumfield RT. Migration-selection balance and local adaptation of mitochondrial haplotypes in rufous-collared sparrows (Zonotrichia capensis) along an elevational gradient. Ecology. 2009;63:1593–605.

    Google Scholar 

  • Chikhi L, Sousa VC, Luisi P, Goossens B, Beaumont MA. The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Genetics. 2010;186:983–95.

    Article  PubMed  PubMed Central  Google Scholar 

  • Choi SJ, Park EJ, Endo H, Kitade Y, Saga N. Inheritance pattern of chloroplast and mitochondrial genomes in artificial hybrids of Porphyra yezoensis (Rhodophyta). Fish Sci. 2008;74:822–9.

    Article  CAS  Google Scholar 

  • Clark JS, Poore AGB, Ralph PJ, Doblin MA. Potential for adaptation in response to thermal stress in an intertidal macroalga. J Phycol. 2013;49:630–9.

    Article  Google Scholar 

  • Clarkston BE, Saunders GW. A comparison of two DNA barcode markers for species discrimination in the red algal family Kallymeniaceae (Gigartinales, Florideophyceae), with a description of Euthora timburnonii sp. nov. Botany. 2010;88:119–31.

    Article  CAS  Google Scholar 

  • Coleman MA, Brawley SH. Are life history characteristics good predictors of genetic diversity and structure? A case study of the intertidal alga Fucus spiralis (Heterokontophyta; Phyaeophyceae). J Phycol. 2005;41:753–62.

    Article  Google Scholar 

  • Coleman AW, Goff LJ. DNA analysis of eukaryotic algal species. J Phycol. 2004;27:463–73.

    Article  Google Scholar 

  • Coleman AW, Kelaher BP. Connectivity among fragmented populations of a habitat-forming alga, Phyllospoa comosa (Phaeophycea, Fucales) on an urbanised coast. Mar Ecol Prog Ser. 2009;381:63–70.

    Article  Google Scholar 

  • Collins CJ, Freaser CI, Ashcroft A, Waters JM. Asymmetric dispersal of southern bull-kelp (Duvillaea antarctica) adults in coastal New Zealand: testing an oceanographic hypothesis. Mol Ecol. 2010;19:4572–80.

    Article  PubMed  Google Scholar 

  • Consuegra S, John E, Versppor E, Garcia de Leaniz C. Patterns of natural selection acting on the mitochondrial genome of a locally adapted fish species. Genet Sel Evol. 2015. doi:10.1186/s12711-015-0138-0.

    PubMed  PubMed Central  Google Scholar 

  • Coyer JA, Olsen JL, Stam WT. Genetic variability and spatial separation in the sea palm kelp Postelsia palmaeformis (Phaeophyceae) as assessed with m13 fingerprint and RAPDS. J Phycol. 1997;33:561–8.

    Article  CAS  Google Scholar 

  • Coyer JA, Smith GJ, Andersen RA. Evolution of Macrocystis spp. (Phaophyceae) as determined by ITS1 and ITS2 sequences. J Phycol. 2001;37:574–85.

    Article  Google Scholar 

  • Coyer JA, Peters AF, Hoarau G, Stam WT, Olsen JL. Inheritance patterns of ITS1, chloroplasts, and mitochondria in artificial hybrids of the marine rockweeds, Fucus serratus and F. evenescens (Heterokontophyta; Fucaceae). Euro J Phycol. 2002;37:173–8.

    Article  Google Scholar 

  • Coyer JA, Peters AF, Stam WT, Olsen JL. Post-ice age recolonization and differentiation of Fucus serratus L. (Phaeophyceae; Fucaceae) populations in Northern Europe. Mol Ecol. 2003;12:1817–29.

    Article  CAS  PubMed  Google Scholar 

  • Coyer JA, Hoarau G, Stam WT, Olsen JL. Geographically specific heteroplasmy of mitochondrial DNA in the seaweed, Fucus serratus (Heterokontophyta: Phaeophyceae, Fucales). Mol Ecol. 2004;13:1323–6.

    Article  CAS  PubMed  Google Scholar 

  • Crandall ED, Sbrocco EJ, Deboer TS, Barber PH, Carpenter KE. Expansion dating: calibrating molecular clocks in marine species from expansions onto the Sunda Shelf following the Last Glacial Macimum. Mol Biol Evol. 2012;29:707–19.

    Article  CAS  PubMed  Google Scholar 

  • Crow JF, Kimura M (1970) An introduction to population genetics theory. New York: Harper and Row, xiv + 591 p.

    Google Scholar 

  • Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet. 2011;12:499–510.

    Article  CAS  PubMed  Google Scholar 

  • Dawson MN, Algar AC, Antonelli A, Dávalos LM, Davis E, Early R, Guisan A, Jansson R, Lessard JP, Marske KA, McGuire JL, Stigall AL, Swenson NG, Zimmermann NE, Gavin DG. An horizon scan of biogeography. Front Biogeogr. 2013;5:130–57.

    Google Scholar 

  • Destombe C, Godin J, Lefebvre C, Dehorter O, Vernet P. Differences in dispersal abilities of haploid and diploid spores of Gracilaria verrucosa (Gracilariales, Rhodophyta). Bot Mar. 1992;35:93–98.

    Google Scholar 

  • Dewsbury DA. The proximate and the ultimate: past, present, and future. Behav Process. 1999;46:189–99.

    Article  CAS  Google Scholar 

  • Deysher L, Norton TA. Dispersal and colonization in Sargassum muticum (Yendo) Fensholt. J Exp Mar Biol Ecol. 1981;56:179–95.

    Article  Google Scholar 

  • Dixon PS. Perennation vegetative propagation and algal life histories, with special reference to Asparagopsis and other Rhodophyta. Bot Gothoburg. 1965;3:67–74.

    Google Scholar 

  • Dowling DK, Friberg U, Lindell J. Evolutionary implications of non-neutral mitochondrial genetic variation. Trends Ecol Evol. 2008;23:546–54.

    Article  PubMed  Google Scholar 

  • Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007;7:214.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Drummond AJ, Rambaut A, Shapiro B, Pybus OG. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 2005;22:1185–92.

    Article  CAS  PubMed  Google Scholar 

  • Dumolin S, Demesure B, Petit RJ. Inheritance of chloroplast and mitochondrial genomes in pedunculate oak investigated with an efficient PCR method. Theor Appl Genet. 1995;91:1253–6.

    Article  CAS  PubMed  Google Scholar 

  • Dyck JL, DeWreede RE. Reproduction and survival in Mazzaella splendens (Gigartinales, Rhodophyta). Phycologia. 2006a;45:302–10.

    Article  Google Scholar 

  • Dyck JL, DeWreede RE. Seasonal and spatial patterns of population density in the marine macroalga Mazzaella splendens (Gigartinales, Rhodophyta). Phycol Res. 2006b;54:21–31.

    Article  Google Scholar 

  • Eckert CG. The loss of sex in clonal plants. Evol Ecol. 2002;15:501–20.

    Article  Google Scholar 

  • Edwards SV, Beerli P. Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution. 2000;54:1839–54.

    CAS  PubMed  Google Scholar 

  • Eldon B, Wakeley J. Coalescent processes when the distribution of offspring number among individuals is highly skewed. Genetics. 2006;172:2621–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eldon B, Birkner M, Blath J, Freund F. Can the site-frequency spectrum distinguish exponential population growth from multiple-merger coalescents? Genetics. 2015;199:841–56.

    Article  PubMed  Google Scholar 

  • Elith J, Leathwick JR. Species distribution models: ecological explanation and prediction across space and time. Ann Rev Ecol Evol Syst. 2009;40:677–97.

    Article  Google Scholar 

  • Ellegren H. Microsatellites: simple sequences with complex evolution. Nat Rev Genet. 2004;5:435–45.

    Article  CAS  PubMed  Google Scholar 

  • Engel CR, Wattier R, Destombe C, Valero M. Performance of non-motile male gametes in the sea: analysis of paternity and fertilization success in a natural population of a red seaweed, Gracilaria gracilis. Proc R Soc B. 1999;266:1879–86.

    Article  PubMed Central  Google Scholar 

  • Engel CR, Destombe C, Valero M. Mating system and gene flow in the red seaweed Gracilaria gracilis: effect of haploid-diploid life history and intertidal rocky shore landscape on fine-scale genetic structure. Heredity. 2004;92:289–98.

    Article  CAS  PubMed  Google Scholar 

  • Fauvelot C, Bernardi G, Planes S. Reductions in the mitochondrial DNA diversity of coral reef fish provide evidence of population bottlenecks resulting from Holocene sea-level change. Evolution. 2003;57:1571–83.

    Article  CAS  PubMed  Google Scholar 

  • Fierst J, ter Horst C, Kübler JE, Dudgeon S. Fertilization success can drive patterns of phase dominance in complex life histories. J Phycol. 2005;41:238–49.

    Article  Google Scholar 

  • Fjeld A, Løvlie A. Genetics of multicellular marine algae. In: Lewin RA, editor. The genetics of algae. Oxford: Blackwell; 1976. p. 219–35.

    Google Scholar 

  • Forrest BM, Brown SN, Taylor MD, Hurd CL, Hay CH. The role of natural dispersal mechanisms in the spread of Undaria pinnatifida (Laminariales, Phaeophyceae). Phycologia. 2000;39:547–53.

    Article  Google Scholar 

  • Francis RC, Hare SR, Hollowed AB, Wooster WS. Effects of interdecadal climate variability on the oceanic ecosystems of the NE Pacific. Fish Oceanogr. 1998;7:1–21.

    Article  Google Scholar 

  • Fraser CI, Nikula R, Spencer HG, Waters JM. Kelp genes reveal effects of subantarctic sea ice during the Last Glacial Maximum. Proc Nat Acad Sci USA. 2009;106:3249–53.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fraser CI, Thiel M, Hamish G, Spencer HG, Waters JM. Contemporary habitat discontinuity and historic glacial ice drive genetic divergence in Chilean kelp. BMC Evol Biol. 2010;10:203.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fraser CI, Nikula R, Water JM. Ocean rafting by a coastal community. Proc Roy Soc B. 2011;278:649–55.

    Article  Google Scholar 

  • Frederica S, Brodie J, Hommersand MH. Developmental morphology of Chondrus crispus (Gigartinaceae, Rhodophyta). Phycologia. 1992;31:542–63.

    Article  Google Scholar 

  • Freshwater DW, Fredericq S, Butler BS, Hommersand MH, Chase MW. A gene phylogeny of the red algae (Rhodophyta) based on plastid rbcL. Proc Nat Acad Sci USA. 1994;91:7281–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fu YX. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 1997;147:915–25.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fu YX, Li WH. Statistical tests of neutrality of mutations. Genetics. 1993;133:693–709.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fu YX, Li WH. Coalescing into the 21st century: an overview and prospects of coalescent theory. Theor Popul Biol. 1999;56:1–10.

    Article  CAS  PubMed  Google Scholar 

  • Gabrielsen TM, Brochmann C, Rueness J. The Baltic Sea as a model system for studying postglacial colonization and ecological differentiation, exemplified by the red alga Ceramium tenuicorne. Mol Ecol. 2002;11:2083–95.

    Article  CAS  PubMed  Google Scholar 

  • Gagnaire P-A, Broquet T, Aurelle D, Viard F, Souissi A, Bohomme F, Arnaud-Haond S, Bierne N. Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era. Evol Appl. 2015;8:769–86.

    Article  PubMed  PubMed Central  Google Scholar 

  • Galindo H, Olson D, Palumbi SR. Seascape genetics: a coupled oceanographic-genetic model predicts population structure of Caribbean corals. Curr Biol. 2006;16:1622–6.

    Article  CAS  PubMed  Google Scholar 

  • Garden CJ, Currie K, Fraser CI, Waters JM. Rafting dispersal constrained by an oceanographic boundary. Mar Ecol Prog Ser. 2014;501:297–302.

    Article  Google Scholar 

  • Garrick RC, Sunnucks P, Dyer RJ. Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation. BMC Evol Biol. 2010;10:118.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gaunt MW, Miles MA. An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks. Mol Biol Evol. 2002;19:748–61.

    Article  CAS  PubMed  Google Scholar 

  • Gaylord B, Reed DC, Raimondi PT, Washburn L, McLean TR. A physically based model of macroalgal spore dispersal in the wave and current-dominated nearshore. Ecology. 2002;83:1239–51.

    Article  Google Scholar 

  • Gedalof Z, Smith DJ. Interdecadal climate variability and regime-scale shifts in Pacific North America. Geophys Res Letts. 2001;28:1515–8.

    Article  Google Scholar 

  • Giles RE, Blanc H, Cann HM, Wallace DC. Genetics maternal inheritance of human mitochondrial DNA. Proc Nat Acad Sci USA. 1980;77:6715–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gill JL, Williams JW, Jackson ST, Lininger KB, Robinson GS. Pleistocene megafaunal collapse, novel plant communities, and enhanced fire regimes in North America. Science. 2009;326:1100–3.

    Article  CAS  PubMed  Google Scholar 

  • Gómez A, Lunt DH. Refugia within refugia: patterns of phylogeographic concordance in the Iberian Peninsula. In: Weiss S, Ferrand N, editors. Phylogeography of southern European refugia. Netherlands: Springer; 2007. p. 155–88.

    Chapter  Google Scholar 

  • Goowille C, Kalisz S, Eckert CG. The evolutionary enigma of mixed mating systems in plants: occurrence, theoretical explanations, and empirical evidence. Ann Rev Ecol Evol Syst. 2005;36:47–79.

    Article  Google Scholar 

  • Gordon R, Brawley SH. Effects of water motion on propagule release from algae with complex life histories. Mar Biol. 2004;145:21–9.

    Article  Google Scholar 

  • Grant WS. Problems and cautions with sequence mismatch analysis and Bayesian skyline plots to infer historical demography. J Hered. 2015. doi:10.1093/jhered/esv020.

    PubMed  Google Scholar 

  • Grant WS, Liu M, Gao TX, Yanagimoto T. Limits of Bayesian skyline plot analysis of mtDNA sequences to infer historical demographies in Pacific herring (and other species). Mol Phylogenet Evol. 2012;65:203–12.

    Article  PubMed  Google Scholar 

  • Habel JC, Zachos FE, Dapporto L, Rödder D, Radespiel U, Tellier A, Schmitt T. Population genetic revisited–toward a mulidisciplinary research field. Biol J Linn Soc. 2015;115:1–12.

    Article  Google Scholar 

  • Han WH, Klochkova TA, Chim J, Nagasato C, Motomura T, Kim GH. Identification of three proteins involved in fertilization and parthenogenetic development of a brown alga, Scytosiphon lomentaria. Planta. 2014;240:1253–67.

    Article  CAS  PubMed  Google Scholar 

  • Hanebuth T, Stattegger K, Grootes PM. Rapid flooding of the Sunda Shelf: a late-glacial sea-level record. Science. 2000;288:1033–5.

    Article  CAS  PubMed  Google Scholar 

  • Hannach G, Santelices B. Ecological differences between the isomorphic reproductive phases of two species if Iridaea (Rhodophyta: Gigartinales). Mar Ecol Prog Ser. 1985;22:291–303.

    Article  Google Scholar 

  • Hannach G, Waaland JR. Environment, distribution and production of Iridaea. Aquat Bot. 1986;26:51–78.

    Article  Google Scholar 

  • Hansen JE, Doyle WT. Ecology and natural history of Iridaea cordata (Rhodophyta, Gigartinaceae): population structure. J Phycol. 1976;12:273–8.

    Google Scholar 

  • Hare JA, Able KW. Mechanistic links between climate and fisheries along the east coast of the United States: explaining population outbursts of Atlantic croaker (Micropogonias undulates). Fish Oceanogr. 2007;16:31–45.

    Article  Google Scholar 

  • Harley CDG, Anderson KM, Demes KW, Jorve JP, Kordas RL, Coyle TA, Graham MH. Effects of climate change on global seaweed communities. J Phycol. 2012;48:1064–78.

    Article  CAS  Google Scholar 

  • Hedgecock D, Pudovkin AI. Sweepstakes reproductive success in high fecund marine fish and shellfish: a review and commentary. Bull Mar Sci. 2011;87:971–1002.

    Article  Google Scholar 

  • Hedrick PW. Perspective: highly variable loci and their interpretation in evolution and conservation. Evolution. 1999;53:313–8.

    Article  Google Scholar 

  • Heled J, Drummond AJ. Bayesian inference of population size history from multiple loci. BMC Evol Biol. 2008;8:289.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hernández-Carmona G, Hughes B, Graham MH. Reproductive longevity of drifting kelp Macocystis pyrifera (Phaeophyceae) in Monterey Bay, USA. J Phycol. 2006;42:1199–207.

    Article  Google Scholar 

  • Hewitt GM. Some genetic consequences of ice ages, and their role in divergence and speciation. Biol J Linn Soc. 1996;58:247–76.

    Article  Google Scholar 

  • Hewitt GM. The genetic legacy of the Quaternary ice ages. Nature. 2000;405:907–13.

    Article  CAS  PubMed  Google Scholar 

  • Hey J, Nielsen R. Multilocus methods for estimating populations sizes, migration rates and divergence time with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics. 2004;167:747–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hickerson MJ, Carstens BC, Cavender-Bares J, Crandall KA, Graham CH, et al. Phylogeography’s past, present, and future: 10 years after Avise, 2000. Mol Phylogenet Evol. 2010;54:291–301.

    Article  CAS  PubMed  Google Scholar 

  • Ho SYW, Phillips MJ, Cooper A, Drummond AJ. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol. 2005;22:1561–8.

    Article  CAS  PubMed  Google Scholar 

  • Ho SYW, Saarma U, Barnett R, Haile J, Shaprio B. The effect of inappropriate calibration: three case studies in molecular ecology. PLoS ONE. 2008;3:e1615.

    Article  PubMed  PubMed Central  Google Scholar 

  • Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A. Time-dependent rates of molecular evolution. Mol Ecol. 2011;20:3087–101.

    Article  PubMed  Google Scholar 

  • Hoarau G, Coyer JA, Veldsink JH, Stam WT, Olsen JL. Glacial refugia and recolonization pathways in the seaweed Fucus serratus. Mol Ecol. 2007;16:3606–16.

    Article  CAS  PubMed  Google Scholar 

  • Hoarau G, Coyer JA, Olsen JL. Paternal leakage of mitochondrial DNA in Fucus (Phaeophyceae). J Phycol. 2009;45:621–4.

    Article  CAS  Google Scholar 

  • Hoffmann AJ. The arrival of seaweed propagules at the shore: a review. Bot Mar. 1987;30:151–65.

    Article  Google Scholar 

  • Hoffmann AJ, Ugarte R. The arrival of propagules of marine macroalgae in the intertidal zone. J Exp Mar Biol Ecol. 1985;92:83–95.

    Article  Google Scholar 

  • Holsinger KE. Next generation population genetics and phylogeography. Mol Ecol. 2010;1:2361–3.

    Article  Google Scholar 

  • Hu ZM, Duan DL. Insufficient geographical sampling could severely influence phylogeographic interpretations. Mar Biol. 2013;160:1521–2.

    Article  Google Scholar 

  • Hu ZM, Guiry MD, Critchley AT, Duan DL. Phylogeographic patterns indicate trans-Atlantic migration from Europe to North America in the red seaweed Chondrus crispus (Gigartinales, Rhodyphyta). J Phycol. 2010;46:889–900.

    Article  Google Scholar 

  • Hu ZM, Uwai S, Yu SH, Komatsu T, Ajisaka T, Duan DL. Phylogeographic heterogeneity of the brown macroalga Sargassum horneri (Fucaceae) in the northwestern Pacific in relation to late Pleistocene glaciation and tectonic configurations. Mol Ecol. 2011;20:3894–909.

    Article  PubMed  Google Scholar 

  • Hu ZM, Zhang J, Lopez-Bautista J, Duan DL. Asymmetric genetic exchange in the brown seaweed Sargassum fusiforme (Phaeophyceae) driven by oceanic currents. Mar Biol. 2013;160:1407–14.

    Article  Google Scholar 

  • Hudson RR. Gene genealogies and the coalescent process. Oxford Surv Evol Biol. 1991;7:1–44.

    Google Scholar 

  • Hurrell JW. Decadal trends in the North Atlantic Oscillation: regional temperatures and precipitation. Science. 1995;269:676–9.

    Article  CAS  PubMed  Google Scholar 

  • Huxley J. Bird-watching and biological science. Auk. 1916;33:256–70.

    Article  Google Scholar 

  • Jezkova T, Leal M, Rodríguez-Robles JA. Genetic drift or natural selection? Hybridization and asymmetric mitochondrial introgression in two Caribbean lizards (Anolis puchellus and Anolis krugi). J Evol Biol. 2013;26:1458–71.

    Article  CAS  PubMed  Google Scholar 

  • Jouzel J, Masson-Delmotte V, Cattani O, Dreyfus G, Falourd S, Hoffmann G, Minster B, Nouet J, Barnola JM, Chappellaz J, Fischer H, Gallet JC, Johnsen S, Leuenberger M, Loulergue L, Luethi D, Oerter H, Parrenin F, Raisbeck G, Raynaud D, Schilt A, Schwander J, Selmo E, Souchez R, Spahni R, Stauffer B, Steffensen JP, Stenni B, Stocker TF, Tison JL, Werner M, Wolff EW. Orbital and millennial Antarctic climate variability over the past 800,000 years. Science. 2007;317:793–6.

    Article  CAS  PubMed  Google Scholar 

  • Jueterbock A, Tyberghein L, Verbruggen H, Coyer JA, Olsen JL, Hoarau G. Climate change impact on seaweed meadow distribution in the North Atlantic rocky intertidal. Ecol Evol. 2013;3:1356–73.

    Article  PubMed  PubMed Central  Google Scholar 

  • Kain JM. The reproductice phenology of nine species of Rhodophyta in the subtidal region of the Isle of Man. Br Phycol J. 1982;17:321–31.

    Article  Google Scholar 

  • Karl SA, Toonen RJ, Grant WS, Bowen BW. Common misconceptions in molecular ecology: echoes of the modern synthesis. Mol Ecol. 2012;21:4171–89.

    Article  CAS  PubMed  Google Scholar 

  • Kato Y, Kogame K, Nagasato C, Motomura T. Inheritance of mitochondrial and chloroplast genomes in the isogamous brown alga Scytosiphon lomentaria (Phaeophyceae). Phycol Res. 2006;54:65–71.

    Article  CAS  Google Scholar 

  • Keigwin LD. The little ice age and medieval warm period in the Sargasso Sea. Science. 1996;274:1504–8.

    Article  CAS  PubMed  Google Scholar 

  • Kendrick GA, Walker DI. Dispersal of propagules of Sargassum spp. (Sargassaceae: Phaeophyta): observations of local patterns of dispersal and consequences for recruitment and population structure. J Exp Mar Biol Ecol. 1995;192:273–88.

    Article  Google Scholar 

  • Ketmaier V, Argano R, Caccone A. Phylogeography and molecular rates of subterranean aquatic Stenasellid isopods with a per-Tyrrhenian distribution. Mol Ecol. 2003;12:547–55.

    Article  CAS  PubMed  Google Scholar 

  • Kimura K, Nagasato C, Uwai S, Motomura T. Sperm mitochondrial DNA elimination in the zygote of the oogamous brown alga Undaria pinnatifida (Laminariales, Phaeophyceae). Cytologia. 2010;75:353–61.

    Article  CAS  Google Scholar 

  • Kingman JFC. The coalescent. Stochast Proc Appl. 1982;13:235–48.

    Article  Google Scholar 

  • Kirkendale L, Saunders GW, Winberg P. A molecular survey of Ulva (Chlorophyta) in temperate Australia reveals enhanced levels of cosmopolitanism. J Phycol. 2013;49:69–81.

    Article  Google Scholar 

  • Knowlton N, Weigt LA. New dates and new rates for divergence across the Isthmus of Panama. Proc R Soc B. 1998;265:2257–63.

    Article  PubMed Central  Google Scholar 

  • Koch M, Bowes G, Ross C, Zhang XH. Climate change and ocean acidification effects on seagrasses and marine macroalgae. Glob Change Biol. 2013;19:103–32.

    Article  Google Scholar 

  • Kraan S, Guiry M. Molecular and morphologial character inheritance in hybrids of Alaria esculenta and A. praelonga (Alariaceae, Phaeophyceae). Phycologia. 2000;39:554–9.

    Article  Google Scholar 

  • Kraft LGK, Kraft GT, Waller RF. Investigation into southern Australian Ulva (Ulvophyceae, Chlorophyta) taxonomy and molecular phylogeny indicate both cosmopolitanism and endemic cryptic species. J Phycol. 2010;46:1257–77.

    Article  Google Scholar 

  • Krueger-Hadfield SA, Collén J, Dauguin-Thiébaut C, Valero M. Genetic population structure and mating system in Chondrus crispus (Rhodophyta). J Phycol. 2011;47:440–50.

    Article  Google Scholar 

  • Krueger-Hadfield SA, Roze D, Mauger S, Valero M. Intergametophytic selfing and microgeographic genetic structure shape populations of the intertidal red seaweed Chondrus crispus. Mol Ecol. 2013;22:3242–60.

    Article  CAS  PubMed  Google Scholar 

  • Kuroiwa T, Hori T. Preferential digestion of male chloroplast nuclei and mitochondrial nuclei during gametogenesis of Bryopsis maxima Okamura. Protoplasma. 1986;133:86–7.

    Article  Google Scholar 

  • Kusumo HT, Pfister CA, Wootton JT. Small-scale genetic structure in the sea palm Postelsia palmaeformis Ruprecht (Phaeophyceae). Mar Biol. 2006;149:731–42.

    Article  CAS  Google Scholar 

  • Lee RW, Lemieux C. Biparental inheritance of non-Mendelian gene markers in Chlamydomonas moewusii. Genetics. 1986;113:589–600.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lee KM, Yang EC, Coyer JA, Zuccarello GC, Wang WL, Choi CG, Boo SM. Phylogeography of the seaweed Ishige okamurae (Phaeophysceae): evidence for glacial refugia in the northwest Pacific region. Mar Biol. 2012;159:1021–8.

    Article  Google Scholar 

  • Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinform. 2009;25:1451–2.

    Article  CAS  Google Scholar 

  • Liggins L, Treml EA, Riginos C. Taking the plunge: an introduction to undertaking seascape genetic studies and using biophysical models. Geogr Compass. 2013;7:173–96.

    Article  Google Scholar 

  • Lin SM, Yang WC, Huisman J, de Clerck O, Lee WJ. Molecular phylogeny of the widespread Martensia fragilis complex (Delesseriaceae, Rhodophyta) from the Indo-Pacific region reveals three new species of Martensia from Taiwan. Eur J Phycol. 2013;48:173–87.

    Article  Google Scholar 

  • Lindstrom SC, Hughey JR, Martone PT. New, resurrected and redefined species of Mastocarpus (Phllophoraceae, Rhodophyta) from the northeast Pacific. Phycologia. 2011;50:661–83.

    Article  Google Scholar 

  • Ling S, Johnson CR, Ridgway K, Hobday AJ, Haddon M. Climate-driven range extnsion of sea urchin: inferring future trends by analysis of recent population dynamics. Glob Change Biol. 2009;15:719–31.

    Article  Google Scholar 

  • Lisiecki LE, Raymo ME. A Pliocene-Pleistocene stack of 57 globally distributed benthic δ18 O records. Paleoceanography. 2005;20:PA1003.

    Google Scholar 

  • Lourie SA, Green DM, Vincent ACJ. Dispersal, habitat differences, and comparative phylogeography of Southeast Asian seahorses (Syngnathidae: Hippocampus). Mol Ecol. 2005;14:1073–94.

    Article  CAS  PubMed  Google Scholar 

  • Ludt WB, Bernal M, Bowen BW, Rocha LA. Living in the past: phylogeography and population histories of Indo-Pacific wrasses (Genus Halichoeres) in shallow lagoons versus outer reef slopes. PLoS ONE. 2012;7:e38042.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Maggs CA, Castilho R, Foltz D, Henzler C, Jolly MT, Kelly J, Olsen J, Perez KE, Stam W, Väinölä R, Viard F, Wares J. Evaluating signatures of glacial refugia for North Atlantic Benthic marine taxa. Ecology. 2008;89:S108–22.

    Article  PubMed  Google Scholar 

  • Mann ME, Zhang Z, Rutherford S, Bradley RS, Hughes MK, Shindell D, Ammann C, Faluvegi G, Ni F. Global signatures and dynamical origins of the Little Ice Age and Medieval Climate Anomaly. Science. 2009;326:1256–60.

    Article  CAS  PubMed  Google Scholar 

  • Mantua NJ, Hare SR. The Pacific decadal oscillation. J Oceanogr. 2002;58:35–44.

    Article  Google Scholar 

  • Mantua NJ, Hare SR, Zhang Y, Wallace JM, Francis RC. A Pacific interdecadal climate oscillations with impacts on salmon production. Bull Am Meteorol Soc. 1997;78:1069–79.

    Article  Google Scholar 

  • Marino IA, Pujolar JM, Zane L. Reconciling deep calibration and demographic history: Bayesian inference of post glacial colonization patterns in Carcinus aestuarii (Nardo, 1847) and C. maenas (Linnaeus, 1758). PLoS ONE. 2011;6:e28567.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marins BV, Amado-Filho GM, Barreto MBB, Longo LL. Taxonomy of the southwestern Atlantic endemic kelp: Laminaria abyssalis and Laminaria brasiliensis (Phaeophyeae, Laminariales) are not different species. Phycol Res. 2012;60:51–60.

    Article  CAS  Google Scholar 

  • Marko PB. Fossil calibration of molecular clocks and the divergence times of geminate species pairs separated by the Isthmus of Panama. Mol Biol Evol. 2002;19:2005–21.

    Article  CAS  PubMed  Google Scholar 

  • Marske KA, Rahbek C, Nogués-Bravo D. Phylogeography: spanning the ecology-evolution continuum. Ecography. 2013;36:1169–81.

    Article  Google Scholar 

  • Mathieson AC, Burns RL. Ecological studies of economic red algae. V. Growth and reproduction of natural and harvested populations of Chondrus crispus Stackhouse in New Hampshire. J Mar Exp Mar Biol Ecol. 1975;17:137–56.

    Article  Google Scholar 

  • Mayr E. Cause and effect in biology. Science. 1961;134:1501–6.

    Article  CAS  PubMed  Google Scholar 

  • McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT. Applications of next-generation sequencing to phylogeography and phylogenetics. Mol Phylogenet Evol. 2013;66:526–38.

    Article  CAS  PubMed  Google Scholar 

  • McCulloch RD, Bentley MJ, Purves RS, Hulton NRJ, Sugden DE, Clapperton CM. Climatic inferences from glacial and palaeoecological evidence at the last glacial termination, southern South America. J Quat Sci. 2000;15:409–17.

    Article  Google Scholar 

  • McDevit DC, Saunders GW. A DNA barcode examination of the Laminariaceae (Phaeophyceae) in Canada reveals novel biogeographical and evolutionary insights. Phycologia. 2010;49:235–48.

    Article  CAS  Google Scholar 

  • McKenzie PF, Bellgrove A. Dispersal of Hormosira banksii (Phaeophyceae) via detached fragments: reproductive viability and longevity. J Phycol. 2008;44:1108–15.

    Article  Google Scholar 

  • Meirmans PG. Seven common mistakes in population genetics and how to avoid them. Mol Ecol. 2015;24:3223–31.

    Article  PubMed  Google Scholar 

  • Metzker ML. Sequencing technologies–the next generation. Nat Rev Genet. 2010;11:31–46.

    Article  CAS  PubMed  Google Scholar 

  • Miller KG, Kominz MA, Browning JV, Wright JD, Mountain GS, Katz ME, Sugarman PJ, Cramer BS, Cristie-Blick N, Pekar SF. The Phanerozoic record of global sea-level change. Science. 2005;310:1293–8.

    Article  CAS  PubMed  Google Scholar 

  • Mishmar D, Ruiz-Pesin E, Golik P, Macaulay V, Clark AG, Hosseini S, Brandon M, Easley K, Chen E, Brown MD, Sukerni RI, Olckers A, Wallace DC. Natural selection shaped regional mtDNA variation in humans. Proc Nat Acad Sci USA. 2003;100:171–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miyamura S. Cytoplasmic inheritance in green algae: patterns, mechanisms and relation to sex type. J Plant Res. 2010;123:171–84.

    Article  PubMed  Google Scholar 

  • Miyamura S, Nagumo T. Inheritance pattern of chloroplast DNA is correlated with gamete types based on sex-specific arrangement of the cell fusion site in Caulerpa (Ulvophyceae, Chlorophyta). Phycol Res. 2007;55:47–57.

    Article  CAS  Google Scholar 

  • Mohring MB, Wernberg T, Wright JT, Connell SD, Russell BD. Biogeographic variation in temperature drives performance of kelp gametophytes during warming. Mar Ecol Prog Ser. 2014;513:85–96.

    Article  Google Scholar 

  • Montecinos A, Broitman BR, Faugeron S, Haye PA, Tellier F, Guillemin M-L. Species replacement along a linear coastal habitat: phylogeography and speciation in the red alga Mazzaella laminarioides along the south east Pacific. BMC Evol Biol. 2012;12:97.

    Article  PubMed  PubMed Central  Google Scholar 

  • Motomura T. Ultrastructure of fertilization in Laminaria angustata (Phaeophyta, Laminariales) with emphasis on the behavior of centrioles, mitochondria and chloroplasts of sperm. J Phycol. 1990;26:80–9.

    Article  Google Scholar 

  • Motomura T, Nagasato C, Kimura K. Cytoplasmic inheritance of organelles in brown algae. J Plant Res. 2010;123:185–92.

    Article  PubMed  Google Scholar 

  • Muhlin JF, Engel CR, Stessel R, Weatherbee RA, Brawley SH. The influence of coastal topography, circulation patterns, and rafting in structuring populations of an intertidal alga. Mol Ecol. 2008;17:1198–210.

    Article  CAS  PubMed  Google Scholar 

  • Nagasato C, Motomura T, Ichimura T. Spindle formation in karyogamy-blocked zygotes of the isogamous brown alga Scytosiphon lomentaria (Scytosiponales, Phaeophyceae). Eur J Phycol. 2000;35:339–47.

    Article  Google Scholar 

  • Nagasato C, Inoue A, Mizuno M, Kanazawa K, Ojima T, Okuda K, Motomura T. Membran fusion process and assembly of cell wall during cytokinesis in the brown alga, Silvetia babingtonii (Fucales, Phaeophyceae). Planta. 2010;232:287–298.

    Google Scholar 

  • Nakagawa S, Cuthill IC. Effect size, confidence interval and statistical significance: a practical guide for biologists. Biol Rev. 2007;82:591–605.

    Article  PubMed  Google Scholar 

  • Nei M, Maruyama T, Chakraborty R. The bottleneck effect and genetic variability in populations. Evolution. 1975;29:1–10.

    Article  Google Scholar 

  • Nielsen R, Paul JS, Albrechtsen A, Song YS. Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet. 2011;12:443–51.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Oba T, Kato M, Kitazato H, Koizumi I, Omura A, Sakai T, Takayama T. Paleoenvironmental changes in the Japan Sea during the last 85,000 years. Paleoceanogaphy. 1991;6:499–518.

    Article  Google Scholar 

  • Ogawa S. Disappearance of chloroplast nucleoids during male gamete formation in Bryopsis plumosa (Hudson) C. Ag. (Chlorophyceae). Bot Gaz. 1988;149:25–9.

    Article  Google Scholar 

  • Patel RK, Jain M. NGS QC toolkit: a toolkit for quality control of next generation sequencing data. PLoS ONE. 2012;7:e30619.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pearson GA, Brawley SH. Reproductive ecology of Fucus distichus (Phaeophyceae): an intertidal alga with successful external fertilization. Mar Ecol Prog Ser. 1996;143:211–23.

    Article  Google Scholar 

  • Pearson GA, Serrão EA. Revisiting synchronous gamete release by fucoid algae in the intertidal zone: fertilization success and beyond? Integr Compar Biol. 2006;46:587–97.

    Article  Google Scholar 

  • Pearson GA, Serrão EA, Brawley SH. Control of gamete release in fucoid algae: sensing hydrodynamic conditions via carbon acquisition. Ecology. 1998;79:1725–39.

    Article  Google Scholar 

  • Peck JR, Yearsley JM, Waxman D. Explaining the geographic distributions of sexual and asexual populations. Nature. 1998;391:889–92.

    Article  CAS  Google Scholar 

  • Perrin C, Daguin C, van de Sleit M, Engel CR, Pearson GA, Serrão EA. Implications of mating system for genetic diversity of sister algal species: Fucus spiralis and Fucus vesiculosus (Heterokontophyta, Phaeophyceae). Eur J Phycol. 2007;42:219–30.

    Article  CAS  Google Scholar 

  • Peters AF, Scornet D, Müller DG, Kloareg B, Cock JM. Inheritance of organelles in artificial hybrids of the isogamous multicellular chromist alga Ectocarpus siliculosus (Phaeophyceae). Eur J Phycol. 2004;39:235–42.

    Article  Google Scholar 

  • Philander SGH. El Niño southern oscillation phenomena. Nature. 1983;302:295–301.

    Article  Google Scholar 

  • Prince JS, Kingsbury JM. The ecology of Chondrus crispus at Plymouth, Massachusetts. I. Ontogeny, vegetative anatomy, reproduction and life cycle. Am J Bot. 1973;60:956–63.

    Article  Google Scholar 

  • Prost S, Smirnov N, Fedorov VB, Sommer RS, Stiller M, Nagel D, Knapp M, Hofreiter M. Influence of climate warming on Arctic mammals? New insights from ancient DNA studies of the collared lemming Dicrostonyx torquatus. PLoS ONE. 2010;5:e10447.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Provan J, Bennett KD. Phylogeographic insights into cryptic glacial refugia. Trends Ecol Evol. 2008;23:564–71.

    Article  PubMed  Google Scholar 

  • Provan J, Wattier RA, Maggs CA. Phylogeographic analysis of the red seaweed Palmaria palmata reveals a Pleistocene marine glacial refugium in the English Channel. Mol Ecol. 2005;14:793–803.

    Article  CAS  PubMed  Google Scholar 

  • Provan J, Glendinning K, Kelly R, Maggs CA. Levels and patterns of population genetic diversity in the red seaweed Chondrus crispus (Florideophyceae): a direct comparison of single nucleotide polymorphisms and microsatellites. Biol J Linn Soc. 2013;108:251–62.

    Article  Google Scholar 

  • Qu Y, Luo X, Zhang R, Song G, Zou F, Lei F. Lineage diversification and historical demography of a montane bird Garrulax elliotii–implications for the Pleistocene evolutionary history of the eastern Himalayas. BMC Evol Biol. 2011;11:174.

    Article  PubMed  PubMed Central  Google Scholar 

  • Rainmondi PT, Reed DC, Gaylord B, Washburn L. Effects of self-fertilization of the giant kelp Macrocystis pyrifera. Ecology. 2004;85:3267–76.

    Article  Google Scholar 

  • Reed DC, Amsler CD, Ebeling AW. Dispersal in kelps: factors affecting spore swimming and competency. Ecology. 1992;73:1577–85.

    Article  Google Scholar 

  • Reed DC, Rainmondi PT, Carr MH, Goldwasser L. The role of dispersal and disturbance in determining spatial heterogeneity in sedentary organisms. Ecology. 2000;81:2011–26.

    Article  Google Scholar 

  • Reed DC, Schroeter SC, Raimondi PT. Spore supply and habitat availability as sources of recruitment limitation in the giant kelp Macrocystis pyrifera (Phaeophyceae). J Phycol. 2004;40:275–84.

    Article  Google Scholar 

  • Rogers AR, Harpending H. Population growth makes waves in the distribution of pairwise differences. Mol Biol Evol. 1992;9:552–69.

    CAS  PubMed  Google Scholar 

  • Rosenberg NA, Nordborg M. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat Rev Genet. 2002;3:380–90.

    Article  CAS  PubMed  Google Scholar 

  • Rubinsztein DC, Amos B, Cooper G. Microsatellite and trinucleotide-repeat evolution: evidence for mutational bias and different rates of evolution in different lineages. Philos Trans R Soc B. 1999;354:1095–9.

    Article  CAS  Google Scholar 

  • Russell FS, Southward AJ, Boalch GT, Butler EI. Changes in biological conditions in the English Channel off Plymouth during the last half century. Nature. 1971;234:468–70.

    Article  Google Scholar 

  • Ryman N, Palm S. POWSIM: a computer program for assessing statistical power when testing for genetic differentiation. Mol Ecol Notes. 2006;6:600–2.

    Article  Google Scholar 

  • Ryman N, Palm S, André C, Carvalho G, Dahlgren TG, Jorde PE, Lairkre L, Larsson LC, Palmé A, Ruzzante DE. Power for detecting divergence: differences between statistical methods and marker loci. Mol Ecol. 2006;15:2031–45.

    Article  CAS  PubMed  Google Scholar 

  • Santelices B. Patterns of reproduction, dispersal and recruitment in seaweeds. Oceanogr Mar Biol Ann Rev. 1990;28:177–276.

    Google Scholar 

  • Santos C, Moneiel R, Sierra B, Betencourt C, Fernandez E, Alvarez L, Lima M, Abada A, Aluja MP. Understanding differences between phylogenetic and pedigree-derived mtDNA mutation rate: a model using families from the Azores Islands (Portugal). Mol Biol Evol. 2005;22:1490–505.

    Article  CAS  PubMed  Google Scholar 

  • Saunders GW. Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. Phil Trans R Soc B. 2005;260:1879–88.

    Article  CAS  Google Scholar 

  • Saunders GW, Kucera H. An evaluation of rbcL, tufA, UPA, LSU and ITS as DNA barcode markers for the marine green macroalgae. Cryptogam Algol. 2010;31:487–528.

    Google Scholar 

  • Saunders GW, Chiovitti A, Kraft GT. Small-subunit rNA sequences from representatives of selected families of the Gigartinales and Rhodymeniales (Rhodophyta). 3. Delineating the Gigartinales sensu stricto. Can J Bot. 2004;82:43–74.

    Article  CAS  Google Scholar 

  • Scheet P, Stephens M. A fast and flexible statistical model for large-scale population genotype data: application to inferring missing genotypes and haplotypic phase. Am J Hum Genet. 2006;78:629–44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schiel DR, Foster MS. The population biology of large brown seaweeds: ecological consequnces of multiphase life histories in dynamic coastal environments. Annu Rev Ecol Evol Syst. 2006;37:343–72.

    Article  Google Scholar 

  • Sears BB, Vanwinkle-Swift K. The salvage-turnover-repare (STOR) model for uniparental inheritance in Chlamydomonas: DNA as a source of sustenance. J Hered. 1994;85:366–76.

    CAS  PubMed  Google Scholar 

  • Selkoe KA, Henzler CM, Gaines SD. Seascape genetics and the spatial ecology of marine populations. Fish Fish. 2008;9:363–77.

    Article  Google Scholar 

  • Serrão EA, Pearson GA, Kautsky L, Brawley SH. Successful external fertilization in turbulent environments. Proc Nat Acad Sci USA. 1996a;93:5286–90.

    Article  PubMed  PubMed Central  Google Scholar 

  • Serrão EA, Kautsky L, Brawley SH. Distributional success of the marine seaweed Fucus vesiculosus L. in the brachish Baltic Sea correlates with osmotic capabilities of Baltic gametes. Oecologia. 1996b;107:1–12.

    Article  Google Scholar 

  • Serrão EA, Brawley SH, Hedman J, Kautsky L, Samuelsson G. Reproductive success of Fucus vesiculosus (Phaeophyceae) in the Baltic Sea. J Phycol. 1999;35:254–69.

    Article  Google Scholar 

  • Shaughnessy FJ, De Wreede RE. Reliability of the resorcinol method for identifying isomorphic phases in the Gigartinaceae (Rhodophyta). J Appl Phycol. 1991;3:121–7.

    Article  Google Scholar 

  • Silva G, Lima FP, Martel P, Castilho R. Thermal adaptation and clinal mitochondrial DNA variation of European anchovy. Proc R Soc B. 2014;281:20141093.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Smith GM. The Fresh-water algae of the United States. New York: McGraw-Hill; 1950.

    Google Scholar 

  • Smith JM, Haigh J. The hitch-hiking effect of a favourable gene. Genet Res. 1974;23:23–35.

    Article  CAS  PubMed  Google Scholar 

  • Sork VL, Nason J, Campbell DR, Fernandez JF. Landscape approaches to historical and contemporary gene flow in plants. Trends Ecol Evol. 1999;14:219–23.

    Article  PubMed  Google Scholar 

  • Städler T, Haubold B, Merino C, Stephan W, Pfaffelhuber P. The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. Genetics. 2009;182:205–16.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Staubwasser M, Sirocko F, Grootes PM, Seg M. Climate change at the 4.2 ka BP termination of the Indus valley civilization and Holocene south Asian monsoon variability. Geophys Res Letts. 2003;30:1425.

    Google Scholar 

  • Stebbing ARD, Turk SMT, Wheeler A, Clarke KR. Immigration of southern fish species to south-west England linked to warming of the North Atlantic (1960–2001). J Mar Biol Assoc UK. 2002;82:177–80.

    Article  Google Scholar 

  • Stenseth NC, Ottersen G, Hurrell JW, Mysterud A, Lima M, Chan K-S, Yoccoz NG, Ã…dlandsvik B. Studying climate effects on ecology through the use of climate indices: the North Atlantic Oscillation, El Niño southern oscillation and beyond. Proc R Soc B. 2003;270:2087–96.

    Article  PubMed  PubMed Central  Google Scholar 

  • Stephens M, Donnelly P. A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet. 2003;73:1162–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stephens M, Smith NJ, Donnelly P. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet. 2001;68:978–89.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sunnucks P. Efficient genetic markers for population biology. Trends Ecol Evol. 2000;15:199–203.

    Article  PubMed  Google Scholar 

  • Sutherland JE, Lindstrom SC, Nelson WA, Brodie J, Lynch MDJ, Hwang MS, Choi HG, Miyata M, Kikuchi N, Oliveira MC, Farr T, Neefus C, Mols-Mortensen A, Milstein D, Müller KM. A new look at ancient order: generic revision of the Bangiales (Rhodophyta). J Phycol. 2011;47:1131–51.

    Article  Google Scholar 

  • Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123:585–95.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tatarenkov A, Berström L, Jönsson RB, Serrão EA, Kautsky L, Johannesson K. Intriguing asexual life in marginal populations of the brown seaweed Fucus vesiculosus. Mol Ecol. 2005;14:647–51.

    Article  CAS  PubMed  Google Scholar 

  • Teasdale BW, Klein AS. Genetic variation and biogeographical boundaries within the red alga Porphyra umbilicalis (Bangiales, Rhodyphyta). Bot Mar. 2010;53:417–31.

    Article  CAS  Google Scholar 

  • Tellier F, Meynard AP, Correa JA, Faugeron S, Valero M. Phylogeographic analyses of the 30°S south-east Pacific biogeographic transition zone establish the occurrence of a sharp genetic discontinuity in the kelp Lessonia nigrescens: vicariance or parapatry? Mol Phylogenet Evol. 2009;53:679–93.

    Article  CAS  PubMed  Google Scholar 

  • Thornber CS, Gaines SD. Population demographics in species with biphasic life cycles. Ecology. 2004;85:1661–74.

    Article  Google Scholar 

  • Tinbergen N. On aims and methods of ethology. Z Tier Psychol. 1963;20:410–33.

    Google Scholar 

  • Toonen RJ, Puritz JB, Forsman ZH, Whitney JL, Fernandez-Silva I, Andrews KR, Bird CE. ezRAD: a simplified method for genomic genotyping in non-model organisms. PeerJ. 2013;1:e203.

    Article  PubMed  PubMed Central  Google Scholar 

  • Turmel M, Lemieux C, Burger G, Lang F, Otc C, Plate I, Gray MW. The complete mitochondrial DNA sequences of Nephroselmis olivacea and Pedinomonas minor: two radically different evolutionary patterns within green algae. Plant Cell. 1999;11:1717–29.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Uwai S, Kogame K, Yoshida G, Kawai H, Ajisaka T. Geographical genetic structure and phylogeography of the Sargassum horneri/filicinum complex in Japan, based on the mitochondrial cox3 haplotype. Mar Biol. 2009;156:901–11.

    Article  Google Scholar 

  • van der Strate HJ, van de Zande L, Stam WT, Olsen JL. The contribution of haploids, diploids and clones to fine-scale population structure in the seaweed Cladophoropsis membranacea (Chlorophyta). Mol Ecol. 2002;11:329–45.

    Article  PubMed  Google Scholar 

  • Verbruggen H, Maggs CA, Saunders GW, Le Gall L, Yoon HS, De Clerck O. Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life. BMC Evol Biol. 2010;10:16.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Villalba R. Tree-ring and glacial evidence for the medieval warm epoch and the Little Ice Age in southern South America. Clim Chang. 1994;26:183–97.

    Article  Google Scholar 

  • Voris HK. Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations. J Biogeogr. 2000;27:1153–67.

    Article  Google Scholar 

  • Wahl M, Molis M, Hobday AJ, Dudgeon S, Neumann R, Steinberg P, Campbell AH, Marzinelli E, Connell S. The responses of brown macroalgae to environmental change from local to global scales: direct versus ecologically mediated effects. Perspect Phycol. 2015. doi:10.1127/pip/2015/0019.

    Google Scholar 

  • Wang PX. Response of the Western Pacific marginal seas to glacial cycles: paleoceanographic and sedimentological features. Mar Geol. 1999;165:5–39.

    Article  Google Scholar 

  • Wang XL, Zhao FJ, Hu ZM, Critchley AT, Morrell SL, Duan DL. Inter-simple sequence repeat (ISSR) analysis of genetic variation of Chondrus crispus populations from North Atlantic. Aquat Bot. 2008;88:154–9.

    Article  CAS  Google Scholar 

  • Waters JM. Driven by the West Wind Drift? A synthesis of southern temperate marine biogeography, with new directions for dispersalism. J Biogeogr. 2008;35:417–27.

    Article  Google Scholar 

  • Waters JM, Fraser CI, Hewitt GM. Founder takes all: density-dependent processes structure biodiversity. Trends Ecol Evol. 2013;28:78–85.

    Article  PubMed  Google Scholar 

  • Wattier R, Engel CR, Saumitou-Laprade P, Valero M. Short allele dominance as a source of heterozygote deficiency at microsatellite loci: experimental evidence at the dinucleotide locus Gv1CT in Gracilaria gracilis (Rhodophyta). Mol Eol. 1998;7:1569–73.

    CAS  Google Scholar 

  • Wernberg T, Russell BD, Thomsen MS, Gurgel CFD, Bradshaww CJ, Poloczanska ES, Connell SD. Seaweed communities in retreat from ocean warming. Curr Biol. 2011;21:1828–32.

    Article  CAS  PubMed  Google Scholar 

  • White C, Selkoe KA, Watson J, Siegel DA, Zacherl DC, Toonen RJ. Ocean currents help explain population genetic structure. Proc R Soc B. 2010;277:1658–94.

    Article  Google Scholar 

  • Williams SL, Di Fiori RE. Genetic diversity and structure in Pelvetia fastigiata (Phaeophyta: Fucales): does a small effective neighborhood size explain fine-scale genetic structure? Mar Biol. 1996;126:371–82.

    Article  CAS  Google Scholar 

  • Wolfe KH, Li WH, Sharp PM. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Nat Acad Sci USA. 1987;84:9054–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yesson C, Bush LE, Davies AJ, Maggs CA, Brodie J. Large brown seaweeds of the British Isles: evidence of changes in abundance over four decades. Estu Coast Shelf Sci. 2015;155:167–75.

    Article  Google Scholar 

  • Yotsukura N, Shimizu T, Katayama T, Druehl LD. Mitochondrial DNA sequence variation of four Saccharina species (Laminariales, Phaeophyceae) growing in Japan. J Appl Phycol. 2010;22:243–51.

    Article  CAS  Google Scholar 

  • Zechman FW, Mathieson AC. The distribution of seaweed propagules in estuarine, coastal and offshore waters of New Hampshire, U.S.A. Bot Mar. 1985;28:283–294.

    Google Scholar 

  • Zhang DX, Hewitt GM. Nuclear DNA and analyses in genetic studies of populations: practice, problems and prospects. Mol Ecol. 2003;12:563–84.

    Article  CAS  PubMed  Google Scholar 

  • Zuccarello GC, West JA, Kamiya M, King RJ. A rapid method to score plastid haplotypes in red seaweeds and it use in determining parental inheritance of plastids in the red alga (Ceramiales). Hydrobiologia. 1999a;401:207–14.

    Article  CAS  Google Scholar 

  • Zuccarello GC, Burger G, West JA, King RJ. A mitochondrial marker for red algal intraspecific relationships. Mol Ecol. 1999b;8:1443–7.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

Dr. Sandra Lindstrom kindly commented on an early draft of the manuscript. Drs. Zi-Min Hu and Ceridwen Fraser and an anonymous reviewer provided insightful comments. Thanks to Dr. Zi-Min Hu for the opportunity to articulate my perspective on seaweed phylogeography . The writing of this manuscript was supported by the general funds of the Alaska Department of Fish and Game. This is Professional Publication number PP-280 of the Commercial Fisheries Division of the Alaska Department of Fish and Game, Anchorage Alaska.

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  1. Alaska Department of Fish and Game Commercial Fisheries Division, 333 Raspberry Road, Anchorage, AK, 99518, USA

    W. Stewart Grant

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Correspondence to W. Stewart Grant .

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  1. Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China

    Zi-Min Hu

  2. Fenner School of Environment and Society, Australian National University, Canberra, Aust Capital Terr, Australia

    Ceridwen Fraser

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Grant, W.S. (2016). Paradigm Shifts in the Phylogeographic Analysis of Seaweeds. In: Hu, ZM., Fraser, C. (eds) Seaweed Phylogeography. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-7534-2_2

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