Skip to main content
Log in

Comparative phylogeography of coastal gobies in the Japanese Archipelago: future perspectives for the study of adaptive divergence and speciation

  • Review
  • Ichthyology 50 years in Japan—Celebrating its history to set the stage for the next generations
  • Published:
Ichthyological Research Aims and scope Submit manuscript

Abstract

Phylogeography infers the demographic history of various species by resolving genetic relationships among populations across a geographic range. Comparison of phylogeographic patterns of multiple species with similar geographic distributions, i.e., comparative phylogeography, allows us to assess the roles of regional historical events and species-specific ecological factors in shaping intraspecific genetic diversity, providing model systems for studying the processes and genetic basis of adaptive evolution and speciation. In addition, these patterns can also be compared among species from different regions to infer the impact of global-scale historical and present events, such as Pleistocene glacial cycles, on current biodiversity. In this review, I summarize and integrate recent findings of phylogeographic studies for two geographic lineages, Pacific Ocean (PO) and Sea of Japan (SJ) lineages, of five coastal gobies distributed around the Japanese Archipelago. Using mitochondrial and nuclear DNA markers, these studies revealed genetic divergences of the PO and SJ lineages in the coastal gobies. However, the two types of markers showed discordant patterns for genetic divergences between the two lineages (mitonuclear discordance), suggesting different coalescent processes between these genetic markers. Ecological features that depend on shallow coastal resources may contribute to restricted gene flow and be responsible for the existence of the two lineages that are predominantly found in the coastal gobies. All coastal gobies shared sharp contrasts in genetic diversity between the two lineages, with the SJ lineages rapidly expanding during Pleistocene interglacial periods. Such rapid population expansions can provide alternative ways to obtain recent calibration points to estimate divergence times of the two lineages. A comparison of the geographic distributions between the two lineages indicated that the centers of their secondary contact zones vary, which may appear to represent the continuous transition process of the two lineage distributions. Compared with results of phylogeographic studies from other oceans, multiple divergence times, sharply contrasting demographic histories, and two independent secondary contact zones are unique characteristics of the divergence between the PO and SJ lineages. These characteristics will allow us to test the continuous processes of genomic divergence during geographical isolation with environmental fluctuations and the consequences of hybridization of divergent lineages in independent secondary contact zones with different environmental settings.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Aboim M, Mavárez J, Bernatchez L, Coelho M (2010) Introgressive hybridization between two Iberian endemic cyprinid fish: a comparison between two independent hybrid zones. J Evol Biol 23:817–828

    Article  CAS  PubMed  Google Scholar 

  • Akihito, Sakamoto K, Ikeda Y, Sugiyama K (2002) Gobioidei. In: Nakabo T (ed) Fishes of Japan with pictorial keys to the species, English edn. Tokai University Press, Tokyo, pp1139–1310, 1596–1619

  • Akihito, Fumihito A, Ikeda Y, Aizawa M, Makino T, Umehara Y, Kai Y, Nishimoto Y, Hasegawa M, Nakabo T, Gojobori T (2008) Evolution of Pacific Ocean and the Sea of Japan populations of the gobiid species, Pterogobius elapoides and Pterogobius zonoleucus, based on molecular and morphological analyses. Gene 427:7–18

    Article  CAS  PubMed  Google Scholar 

  • Akihito, Akishinonomiya F, Ikeda Y, Aizawa M, Nakagawa S, Umehara Y, Yonezawa T, Mano S, Hasegawa M, Nakabo T, Gojobori T (2016) Speciation of two gobioid species, Pterogobius elapoides and Pterogobius zonoleucus revealed by multi-locus nuclear and mitochondrial DNA analyses. Gene 576:593–602

    Article  CAS  PubMed  Google Scholar 

  • April J, Hanner RH, Dion‐Côté AM, Bernatchez L (2013) Glacial cycles as an allopatric speciation pump in north‐eastern American freshwater fishes. Mol Ecol 22:409–422

    Article  CAS  PubMed  Google Scholar 

  • Arnqvist G, Dowling DK, Eady P, Gay L, Tregenza T, Tuda M, Hosken DJ (2010) Genetic architecture of metabolic rate: environment specific epistasis between mitochondrial and nuclear genes in an insect. Evolution 64:3354–3363

    Article  CAS  PubMed  Google Scholar 

  • Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge, MA

    Book  Google Scholar 

  • Avise JC, Neigel JE, Arnold J (1984) Demographic influences on mitochondrial DNA lineage survivorship in animal populations. J Mol Evol 20:99–105

    Article  CAS  PubMed  Google Scholar 

  • Ballard JWO, Whitlock MC (2004) The incomplete natural history of mitochondria. Mol Ecol 13:729–744

    Article  PubMed  Google Scholar 

  • Beheregaray LB (2008) Twenty years of phylogeography: the state of the field and the challenges for the Southern Hemisphere. Mol Ecol 17:3754–3774

    PubMed  Google Scholar 

  • Bernatchez L, Wilson CC (1998) Comparative phylogeography of Nearctic and Palearctic fishes. Mol Ecol 7:431–452

    Article  Google Scholar 

  • Bowen B, Avise J (1990) Genetic structure of Atlantic and Gulf of Mexico populations of sea bass, menhaden, and sturgeon: influence of zoogeographic factors and life-history patterns. Mar Biol 107:371–381

    Article  Google Scholar 

  • Bowen BW, Gaither MR, DiBattista JD, Iacchei M, Andrews KR, Grant WS, Toonen RJ, Briggs JC (2016) Comparative phylogeography of the ocean planet. Proc Natl Acad Sci U S A 113:7962–7969

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carstens BC, Knowles LL (2007) Shifting distributions and speciation: species divergence during rapid climate change. Mol Ecol 16:619–627

    Article  PubMed  Google Scholar 

  • Coyne JA, Orr HA (2004) Speciation. Sinauer Associates, Sunderland, MA

    Google Scholar 

  • Crandall ED, Sbrocco EJ, DeBoer TS, Barber PH, Carpenter KE (2012) Expansion dating: calibrating molecular clocks in marine species from expansions onto the Sunda Shelf following the Last Glacial Maximum. Mol Biol Evol 29:707–719

    Article  CAS  PubMed  Google Scholar 

  • Crusius J, Pedersen TF, Calvert SE, Cowie GL, Oba T (1999) A 36 kyr geochemical record from the Sea of Japan of organic matter flux variations and changes in intermediate water oxygen concentrations. Paleoceanography 14:248–259

    Article  Google Scholar 

  • Cunningham CW, Collins TM (1998) Beyond area relationships: extinction and recolonization in molecular marine biogeography. In: Schierwater B, Streit B, Wagner G, DeSalle R (eds) Molecular ecology and evolution: approaches and applications. Birkhäuser, Basel, pp 297–321

  • Dawson M, Louie K, Barlow M, Jacobs D, Swift C (2002) Comparative phylogeography of sympatric sister species, Clevelandia ios and Eucyclogobius newberryi (Teleostei, Gobiidae), across the California Transition Zone. Mol Ecol 11:1065–1075

    Article  CAS  PubMed  Google Scholar 

  • Degnan SM (1993) The perils of single gene trees—mitochondrial versus single-copy nuclear DNA variation in white-eyes (Aves: Zosteropidae). Mol Ecol 2:219–225

    Article  Google Scholar 

  • Derycke S, Remerie T, Backeljau T, Vierstraete A, Vanfleteren J, Vincx M, Moens T (2008) Phylogeography of the Rhabditis (Pellioditis) marina species complex: evidence for long‐distance dispersal, and for range expansions and restricted gene flow in the northeast Atlantic. Mol Ecol 17:3306–3322

    Article  CAS  PubMed  Google Scholar 

  • Di Rienzo A, Wilson AC (1991) Branching pattern in the evolutionary tree for human mitochondrial DNA. Proc Natl Acad Sci U S A 88:1597–1601

    Article  PubMed  PubMed Central  Google Scholar 

  • Dotsu Y, Mito S (1955) On the breeding-habits, larvae and young of a goby, Acanthogobius flavimanus (Temminck et Schlegel). Jpn J Ichthyol 4:153–161 (in Japanese)

    Google Scholar 

  • Dotsu Y, Tsutsumi T (1959) The reproductive behaviour in the gobiid fish, Pterogobius elapoides (Günther). Bull Fac Fish, Nagasaki Univ 8:186–190 (in Japanese)

    Google Scholar 

  • Edwards SV, Beerli P (2000) Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54:1839–1854

    CAS  PubMed  Google Scholar 

  • Gaither MR, Rocha LA (2013) Origins of species richness in the Indo‐Malay‐Philippine biodiversity hotspot: evidence for the centre of overlap hypothesis. J Biogeogr 40:1638–1648

    Article  Google Scholar 

  • Galtier N, Nabholz B, Glémin S, Hurst G (2009) Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Mol Ecol 18:4541–4550

    Article  CAS  PubMed  Google Scholar 

  • Gissi C, Reyes A, Pesole G, Saccone C (2000) Lineage-specific evolutionary rate in mammalian mtDNA. Mol Biol Evol 17:1022–1031

    Article  CAS  PubMed  Google Scholar 

  • Gorbarenko S, Southon J (2000) Detailed Japan Sea paleoceanography during the last 25 kyr: constraints from AMS dating and \(\delta\)18O of planktonic foraminifera. Palaeogeogr Palaeoclimatol Palaeoecol 156:177–193

    Article  Google Scholar 

  • Grant W, Bowen B (1998) Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J Hered 89:415–426

    Article  Google Scholar 

  • Harada S, Jeon S-R, Kinoshita I, Tanaka M, Nishida M (2002) Phylogenetic relationships of four species of floating gobies (Gymnogobius) as inferred from partial mitochondrial cytochrome b gene sequences. Ichthyol Res 49: 324-332

    Article  Google Scholar 

  • Hendry AP (2009) Ecological speciation! Or the lack thereof? Can J Fish Aquat Sci 66:1383–1398

    Article  Google Scholar 

  • Hewitt G (2004) Genetic consequences of climatic oscillations in the Quaternary. Philos Trans R Soc Lond B Biol Sci 359:183–195

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Higuchi M, Goto A (1996) Genetic evidence supporting the existence of two distinct species in the genus Gasterosteus around Japan. Environ Biol Fishes 47:1–16

    Article  Google Scholar 

  • Higuchi M, Sakai H, Goto A (2014) A new threespine stickleback, Gasterosteus nipponicus sp. nov. (Teleostei: Gasterosteidae), from the Japan Sea region. Ichthyol Res 61:341–351

    Article  Google Scholar 

  • Hill GE (2019) Mitonuclear Ecology. Oxford University Press, Oxford

    Book  Google Scholar 

  • Hillis DM, Moritz C (1994) An overview of applications of molecular systematics. In: Hillis DM, Moritz C (eds) Molecular Systematics. Sinauer, Sunderland, pp 502–515

  • Hirase S, Ikeda M (2014a) Divergence of mitochondrial DNA lineage of the rocky intertidal goby Chaenogobius gulosus around the Japanese Archipelago: reference to multiple Pleistocene isolation events in the Sea of Japan. Mar Biol 161:565–574

  • Hirase S, Ikeda M (2014b) Long-term vicariance and post-glacial expansion in the Japanese rocky intertidal goby Chaenogobius annularis. Mar Ecol Prog Ser 499: 217–231

  • Hirase S, Ikeda M (2015) Hybrid population of highly divergent groups of the intertidal goby Chaenogobius annularis. J Exp Mar Biol Ecol 473:121–128

    Article  Google Scholar 

  • Hirase S, Ikeda M, Kanno M, Kijima A (2012a) Phylogeography of the intertidal goby Chaenogobius annularis associated with paleoenvironmental changes around the Japanese Archipelago. Mar Ecol Prog Ser 450:167–179

  • Hirase S, Kanno M, Ikeda M, Kijima A (2012b) Evidence of the restricted gene flow within a small spatial scale in the Japanese common intertidal goby Chaenogobius annularis. Mar Ecol 33:481–489

  • Hirase S, Ikeda M, Kanno M, Kijima A (2012c) Detection of regional allozyme divergence in the rocky intertidal goby Chaenogobius annularis. Ichthyol Res 59:264–267

  • Hirase S, Takeshima H, Nishida M, Iwasaki W (2016) Parallel mitogenome sequencing alleviates random rooting effect in phylogeography. Genome Biol Evol 8:1267–1278

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hirase S, Chambers S, Hassell K, Carew M, Pettigrove V, Soyano K, Nagae M, Iwasaki W (2017) Phylogeography of the yellowfin goby Acanthogobius flavimanus in native and non-native distributions. Mar Biol 164:106

    Article  Google Scholar 

  • Hirase S, Kokita T, Nagano AJ, Kikuchi K (2020a) Genomic and phenotypic consequences of two independent secondary contact zones between allopatric lineages of the anadromous ice goby Leucopsarion petersii. Heredity 124:223–235

  • Hirase S, Tezuka A, Nagano AJ, Kikuchi K, Iwasaki W (2020b) Genetic isolation by distance in the yellowfin goby populations revealed by RAD sequencing. Ichthyol Res 67:98–104

  • Hirase S, Tezuka A, Nagano AJ, Sato M, Hosoya S, Kikuchi K, Iwasaki W (2020c) Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population. Evolution 75:176–194

  • Ho SY, Phillips MJ, Cooper A, Drummond AJ (2005) Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol 22:1561–1568

    Article  CAS  PubMed  Google Scholar 

  • Hoarau G, Coyer J, Veldsink J, Stam W, Olsen J (2007) Glacial refugia and recolonization pathways in the brown seaweed Fucus serratus. Mol Ecol 16:3606–3616

    Article  CAS  PubMed  Google Scholar 

  • Hobbs J-PA, Frisch AJ, Allen GR, Van Herwerden L (2008) Marine hybrid hotspot at Indo-Pacific biogeographic border. Biol Lett 5:258–261

    Article  PubMed  PubMed Central  Google Scholar 

  • Hosoya S, Hirase S, Kikuchi K, Nanjo K, Nakamura Y, Kohno H, Sano M (2019) Random PCR‐based genotyping by sequencing technology GRAS‐Di (genotyping by random amplicon sequencing, direct) reveals genetic structure of mangrove fishes. Mol Ecol Resour 19:1153–1163

    Article  CAS  PubMed  Google Scholar 

  • Ishikawa A, Kabeya N, Ikeya K, Kakioka R, Cech JN, Osada N, Leal MC, Inoue J, Kume M, Toyoda A, Tezuka A, Nagano AJ, Yamasaki YY, Suzuki Y, Kokita T, Takahashi H, Lucek K, Marques D, Takehana Y, Naruse K, Mori S, Monroig O, Ladd N, Schubert CJ, Matthews B, Peichel CL, Seehausen O, Yoshizaki G, Kitano J (2019) A key metabolic gene for recurrent freshwater colonization and radiation in fishes. Science 364:886–889

    Article  CAS  PubMed  Google Scholar 

  • Ishizu M, Itoh S, Tanaka K, Komatsu K (2017) Influence of the Oyashio Current and Tsugaru Warm Current on the circulation and water properties of Otsuchi Bay, Japan. J Oceanogr 73:115–131

    Article  CAS  Google Scholar 

  • Jacobsen MW, Hansen MM, Orlando L, Bekkevold D, Bernatchez L, Willerslev E, Gilbert MTP (2012) Mitogenome sequencing reveals shallow evolutionary histories and recent divergence time between morphologically and ecologically distinct European whitefish (Coregonus spp.). Mol Ecol 21:2727–2742

    Article  PubMed  Google Scholar 

  • Kanou K, Sano M, Kohno H (2005) Ontogenetic diet shift, feeding rhythm, and daily ration of juvenile yellowfin goby Acanthogobius flavimanus on a tidal mudflat in the Tama River estuary, central Japan. Ichthyol Res 52:319–324

    Article  Google Scholar 

  • Katayama S, Sakai K, Iwata T, Honda H (2000) Life history of Japanese common goby Acanthogobius flavimanus in Hiroura Lagoon of Natori River mouth. Bull Miyagi Pref Fish Res Dev Center 16:93–97

    Google Scholar 

  • Kato S, Arakaki S, Kikuchi K, Hirase S (2021) Complex phylogeographic patterns in the intertidal goby Chaenogobius annularis around Kyushu Island as a boundary zone of three different seas. Ichthyol Res:1–15

  • Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kitamura A, Kimoto K (2006) History of the inflow of the warm Tsushima Current into the Sea of Japan between 3.5 and 0.8 Ma. Palaeogeogr Palaeoclimatol Palaeoecol 236:355–366

    Article  Google Scholar 

  • Kitamura A, Takano O, Takata H, Omote H (2001) Late Pliocene-early Pleistocene paleoceanographic evolution of the Sea of Japan. Palaeogeogr Palaeoclimatol Palaeoecol 172:81–98

    Article  Google Scholar 

  • Kitano J, Ross JA, Mori S, Kume M, Jones FC, Chan YF, Absher DM, Grimwood J, Schmutz J, Myers RM (2009) A role for a neo-sex chromosome in stickleback speciation. Nature 461:1079–1083

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kojima S, Segawa R, Hayashi I (1997) Genetic differentiation among populations of the Japanese turban shell Turbo (Batillus) cornutus corresponding to warm currents. Mar Ecol Prog Ser 150:149–155

    Article  Google Scholar 

  • Kojima S, Hayashi I, Kim D, Iijima A, Furota T (2004) Phylogeography of an intertidal direct-developing gastropod Batillaria cumingi around the Japanese Islands. Mar Ecol Prog Ser 276:161–172

    Article  CAS  Google Scholar 

  • Kokita T, Nohara K (2011) Phylogeography and historical demography of the anadromous fish Leucopsarion petersii in relation to geological history and oceanography around the Japanese Archipelago. Mol Ecol 20:143–164

    Article  PubMed  Google Scholar 

  • Kokita T, Takahashi S, Kumada H (2013) Molecular signatures of lineage‐specific adaptive evolution in a unique sea basin: the example of an anadromous goby Leucopsarion petersii. Mol Ecol 22:1341–1355

    Article  CAS  PubMed  Google Scholar 

  • Kokita T, Takahashi S, Kinoshita M (2017) Evolution of gigantism and size-based female mate choice in ice goby (Leucopsarion petersii) populations in a semi-enclosed sea basin. Biol J Linn Soc 120:563–577

    Google Scholar 

  • Kurogi M, Hasumi H (2019) Tidal control of the flow through long, narrow straits: a modeling study for the Seto Inland Sea. Sci Rep 9:1–9

    Article  CAS  Google Scholar 

  • Laakkonen HM, Lajus DL, Strelkov P, Väinölä R (2013) Phylogeography of amphi-boreal fish: tracing the history of the Pacific herring Clupea pallasii in North-East European seas. BMC Evol Biol 13:67

    Article  PubMed  PubMed Central  Google Scholar 

  • Leigh JW, Bryant D (2015) PopART: full-feature software for haplotype network construction. Methods Ecol Evol 6:1110–1116

    Article  Google Scholar 

  • Lemaire C, Versini JJ, Bonhomme F (2005) Maintenance of genetic differentiation across a transition zone in the sea: discordance between nuclear and cytoplasmic markers. J Evol Biol 18:70–80

    Article  CAS  PubMed  Google Scholar 

  • Lessios HA (2008) The great American schism: divergence of marine organisms after the rise of the Central American Isthmus. Annu Rev Ecol Evol Syst 39:6–91

    Article  Google Scholar 

  • Li H, Durbin R (2011) Inference of human population history from individual whole-genome sequences. Nature 475:493–496

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mandeville EG, Parchman TL, Thompson KG, Compton RI, Gelwicks KR, Song SJ, Buerkle CA (2017) Inconsistent reproductive isolation revealed by interactions between Catostomus fish species. Evol Lett 1:255–268

    Article  PubMed  PubMed Central  Google Scholar 

  • Marko PB (2004) 'What's larvae got to do with it?' Disparate patterns of post-glacial population structure in two benthic marine gastropods with identical dispersal potential. Mol Ecol 13:597–611

    Article  CAS  PubMed  Google Scholar 

  • Marko PB, Hoffman JM, Emme SA, McGovern TM, Keever CC, Nicole Cox L (2010) The ‘Expansion-Contraction’ model of Pleistocene biogeography: rocky shores suffer a sea change? Mol Ecol 19:146–169

    Article  CAS  PubMed  Google Scholar 

  • Matsui S (1986) Studies on the ecology and the propagation of the ice goby, Leucopsarion petersi Hilgendorf. Sci Bull Fac Agr, Kyushu Univ 40:135–174 (in Japanese)

    Google Scholar 

  • McCormack JE, Heled J, Delaney KS, Peterson AT, Knowles LL (2011) Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays. Evolution 65:184–202

    Article  PubMed  Google Scholar 

  • Montanari SR, Hobbs JPA, Pratchett MS, Bay LK, Van Herwerden L (2014) Does genetic distance between parental species influence outcomes of hybridization among coral reef butterflyfishes? Mol Ecol 23:2757–2770

    Article  CAS  PubMed  Google Scholar 

  • Morgan-Richards M, Wallis GP (2003) A comparison of five hybrid zones of the weta Hemideina thoracica (Orthoptera: Anostostomatidae): degree of cytogenetic differentiation fails to predict zone width. Evolution 57:849–861

    PubMed  Google Scholar 

  • Ni G, Li Q, Kong L, Yu H (2014) Comparative phylogeography in marginal seas of the northwestern Pacific. Mol Ecol 23:534–548

    Article  PubMed  Google Scholar 

  • Nolte A, Gompert Z, Buerkle C (2009) Variable patterns of introgression in two sculpin hybrid zones suggest that genomic isolation differs among populations. Mol Ecol 18:2615–2627

    Article  CAS  PubMed  Google Scholar 

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

    Article  Google Scholar 

  • Palumbi SR, Baker CS (1994) Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales. Mol Biol Evol 11:426–435

    CAS  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Pelc R, Warner R, Gaines S (2009) Geographical patterns of genetic structure in marine species with contrasting life histories. J Biogeogr 36:1881–1890

    Article  Google Scholar 

  • Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7:e37135

  • Provan J, Bennett K (2008) Phylogeographic insights into cryptic glacial refugia. Trends Ecol Evol 23:564–571

    Article  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Ravinet M, Yoshida K, Shigenobu S, Toyoda A, Fujiyama A, Kitano J (2018) The genomic landscape at a late stage of stickleback speciation: high genomic divergence interspersed by small localized regions of introgression. PLoS Genet 14:e1007358

  • Sakai K, Katayama S, Iwata T (2000) Life history of the Japanese common goby, Acanthogobius flavimanus in the Matsushima Bay. Bull Miyagi Pref Fish Res Dev Center 16:85–92

    Google Scholar 

  • Sakuma K, Ueda Y, Hamatsu T, Kojima S (2014) Contrasting population histories of the deep-sea demersal fish, Lycodes matsubarai, in the Sea of Japan and the Sea of Okhotsk. Zool Sci 31:375–383

    Article  Google Scholar 

  • Sakuma K, Ishida R, Kodama T, Takada Y (2019) Reconstructing the population history of the sandy beach amphipod Haustorioides japonicus using the calibration of demographic transition (CDT) approach. PLoS One 14:e0223624

  • Sasaki T, Hattori J (1969) Comparative ecology of two closely related sympatric gobiid fishes living in tide pools. Jpn J Ichthyol 15:143–155 (in Japanese)

    Google Scholar 

  • Soltis DE, Morris AB, McLachlan JS, Manos PS, Soltis PS (2006) Comparative phylogeography of unglaciated eastern North America. Mol Ecol 15:4261–4293

    Article  PubMed  Google Scholar 

  • Sota T, Mukai T, Shinozaki T, Sato H, Yodoe Ki (2005) Genetic differentiation of the gobies Gymnogobius castaneus and G. taranetzi in the region surrounding the Sea of Japan as inferred from a mitochondrial gene genealogy. Zool Sci 22:87–93

    Article  CAS  Google Scholar 

  • Suyama Y, Matsuki Y (2015) MIG-seq: an effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform. Sci Repo 5:1–12

    Google Scholar 

  • Suzuki T, Shibukawa K, Yano K (2004) Pterogobius elapoides, Pterogobius zonoleucus. In: Senou H (ed) A photographic guide to the gobioid fishes of Japan. Heibonsha, Tokyo, pp 231, 233 (in Japanese)

  • Tada R (1994) Paleoceanographic evolution of the Japan Sea. Palaeogeogr, Palaeoclimatol, Palaeoecol 108:487–508

    Article  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tamura K, Tao Q, Kumar S (2018) Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates. Mol Biol Evol 35:1770–1782

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Toews DP, Brelsford A (2012) The biogeography of mitochondrial and nuclear discordance in animals. Mol Ecol 21:3907–3930

    Article  CAS  PubMed  Google Scholar 

  • Tringali MD, Bert TM, Seyoum S, Bermingham E, Bartolacci D (1999) Molecular phylogenetics and ecological diversification of the transisthmian fish genus Centropomus (Perciformes: Centropomidae). Mol Phylogenet Evol 13:193–207

    Article  CAS  PubMed  Google Scholar 

  • Tsutsumi T, Dotsu Y (1961) The reproductive behavior in the gobiid fish, Pterogobius zonoleucus Jordan et Snyder. Bull Fac Fish, Nagasaki Univ 10:149–155 (in Japanese)

    Google Scholar 

  • Watanabe K, Mori S, Nishida M (2003) Genetic relationships and origin of two geographic groups of the freshwater threespine stickleback, 'Hariyo'. Zool Sci 20:265–274

    Article  CAS  Google Scholar 

  • Wessel P, Smith WH, Scharroo R, Luis J, Wobbe F (2013) Generic mapping tools: improved version released. Eos Trans A G U 94:409–410

    Article  Google Scholar 

  • Wilson AB, Veraguth EI (2010) The impact of Pleistocene glaciation across the range of a widespread European coastal species. Mol Ecol 19:4535–4553

    Article  CAS  PubMed  Google Scholar 

  • Yamasaki YY, Kakioka R, Takahashi H, Toyoda A, Nagano AJ, Machida Y, Møller PR, Kitano J (2020) Genome-wide patterns of divergence and introgression after secondary contact between Pungitius sticklebacks. Philos Trans R Soc Lond B Biol Sci 375:20190548

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang Y, Ryder O (1995) Different Rates of Mitochondrial DNA Sequence Evolution in Kirk's Dik-dik (Madoqua-kirkii) Populations. Mol Phylogenet Evol 4:291–297

    Article  PubMed  Google Scholar 

  • Zhang C, Montooth KL, Calvi BR (2017) Incompatibility between mitochondrial and nuclear genomes during oogenesis results in ovarian failure and embryonic lethality. Development 144:2490–2503

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

I sincerely thank Seishi Kimura and other organizing committee members of the Commemoration of the 50th Anniversary of the Ichthyological Society of Japan for providing me with an opportunity for writing this review article. I am grateful to Carol A. Stepien and Kiyoshi Kikuchi for their constructive feedback and language improvements. I am grateful to Shuya Kato for providing me with the photos of the five gobies. I would like to thank all my collaborators. This work was supported by the Japan Society for the Promotion of Science (KAKENHI 18H02493). Publication of this article was also supported by the Commemoration of the 50th Anniversary of the Ichthyological Society of Japan Society. I would like to thank the editor and two anonymous reviewers for their helpful comments on earlier versions of this article.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Shotaro Hirase.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Hirase, S. Comparative phylogeography of coastal gobies in the Japanese Archipelago: future perspectives for the study of adaptive divergence and speciation. Ichthyol Res 69, 1–16 (2022). https://doi.org/10.1007/s10228-021-00824-3

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10228-021-00824-3

Keywords

Navigation