Abstract
We compared the population histories of two deep-sea eelpouts, Lycodes japonicus and Lycodes ocellatus, to elucidate the impacts of the last glacial period on deep-sea species in the western North Pacific area. The results of phylogenetic analyses based on the nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I and cytochrome b genes revealed that the two species are closely related to each other. The results of mismatch distribution analyses, Bayesian skyline plots, and a Bayes factor test supported a constant population size of L. ocellatus in the western North Pacific during the last glacial period, but suggested a post-glacial population expansion of L. japonicus.
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Aboim MA, Menezes GM, Schlitt T, Rogers AD (2005) Genetic structure and history of populations of the deep-sea fish Helicolenus dactylopterus (Delaroche, 1809) inferred from mtDNA sequence analysis. Mol Ecol 14:1343–1354
Adachi T, Hagihara S, Itoh M, Shinohara G, Hayashi I, Kojima S (2009) Genetic population structure and morphological characters of Japanese psychrolutids of genus Malacocottus (Scorpaeniformes: Psychrolutidae). Ichthyol Res 56:323–329
Amano K (2004) Biogeography and the Pleistocene extinction of neogastropods in the Japan Sea. Palaeogeogr Palaeoclimatol Palaeoecol 202:245–252
Anderson ME (1994) Systematics and osteology of the Zoarcidae (Teleostei: Perciformes). Ichthyol Bull, J. L. B. Smith Inst Ichthyol 60:1–120
Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge
Balanov A, Badaev O, Napazakov V, Chuchukalo V (2006) Distribution and some biological features of Lycodes raridens (Zoarcidae) in the western part of the Bering Sea. J Ichthyol 46:148–155
Burridge CP, Craw D, Fletcher D, Waters JM (2008) Geological dates and molecular rates: fish DNA sheds light on time dependency. Mol Biol Evol 25:624–633
Clement M, Posada D, Crandall K (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9:1657–1660
Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 22:1185–1192
Drummond AJ, Suchard MA, Xie D, Rambaut A(2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29:1969–1973
Excoffier L, Lischer H (2010) Arlequin suite ver. 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567
Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3:294–299
Harada N, Sato M, Seki O, Timmermann A, Moossen H, Bendle J, Nakamura Y, Kimoto K, Okazaki Y, Nagashima K, Gorbarenko SA, Ijiri A, Nakatsuka T, Menviel L, Chikamoto MO, Abe-Ouchi A, Schouten S (2012) Sea surface temperature changes in the Okhotsk Sea and adjacent North Pacific during the last glacial maximum and deglaciation. Deep-Sea Res Pt II 61–64:93–105
Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J MolEvol 22:160–174
Hebert PDN, Ratnasingham S, DeWaard JR (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc Biol Sci Lond B (Suppl) 270:S96–S99
Hewitt G (2000) The genetic legacy of the Quaternary ice ages. Nature 405:907–913
Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A (2011) Time-dependent rates of molecular evolution. Mol Ecol 20:3087–3101
Ikeda S, Imamura H, Nakaya K. (2008) Redescription of two eelpouts, Lycodes microporus Toyoshima 1983 and Lycodes ocellatus Toyoshima 1985 (Perciformes: Zoarcidae). Ichthyol Res 55:356–366
Itaki T, Ikehara K, Motoyama I, Hasegawa S (2004) Abrupt ventilation changes in the Japan Sea over the last 30 ky: evidence from deep-dwelling radiolarians. Palaeogeogr Palaeoclimatol Palaeoecol 208:263–278
Kodama Y, Yanagimoto T, Shinohara G, Hayashi I, Kojima S (2008) Deviation age of a deep-sea demersal fish, Bothrocara hollandi, between the Japan Sea and the Okhotsk Sea. Mol Phylogenet Evol 49:682–687
Mäkinen HS, Merilä J (2008) Mitochondrial DNA phylogeography of the three-spined stickleback (Gasterosteus aculeatus) in Europe—evidence for multiple glacial refugia. Mol Phylogenet Evol 46:167–182
Matarese A, Kendall A, Blood D, Vinter B (1989) Laboratory guide to early life history stages of northeast Pacific fishes. NOAA Tech Rep 80:490–491
McCusker MR, Bentzen P (2010) Positive relationships between genetic diversity and abundance in fishes. Mol Ecol 19:4852–4862
Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Kawaguchi A, Mabuchi K, Shirai SM, Nishida M (2003) Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol 26:121–138
Møller PR, Gravlund P (2003) Phylogeny of the eelpout genus Lycodes (Pisces, Zoarcidae) as inferred from mitochondrial cytochrome b and 12S rDNA. Mol Phylogenet Evol 26:369–388
Near TJ, Eytan RI, Dornburg A, Kuhn KL, Moore JA, Davis MP, Wainwright PC, Friedman M, Smith WL (2012) Resolution of ray-finned fish phylogeny and timing of diversification. Proc Natl Acad Sci USA 109:13698–13703
Palumbi SR (1996) Nucleic acids II: the polymerase chain reaction. In: Hillis D, Moritz C, Mable B (eds) Molecular Systematics. Sinauer Associates Inc., Sunderland, pp 205–247
Provan J, Bennett KD (2008) Phylogeographic insights into cryptic glacial refugia. Trends Ecol Evol 23:564–571
Rambaut A, Drummond AJ (2009) Tracer v1.5. http://beast.bio.ed.ac.uk/Tracer. Accessed 18 September 2012
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 31:375–382
Suchard MA, Weiss RE, Dorman KS, Sinsheimer JS (2003) Inferring spatial phylogenetic variation along nucleotide sequences. J Am Stat Assoc 98:427–437
Suchard MA, Weiss RE, Sinsheimer JS (2005) Models for estimating Bayes factors with applications to phylogeny and tests of monophyly. Biometrics 61:665–673
Shirai SM, Kuranaga R, Sugiyama H, Higuchi M (2006) Population structure of the sailfin sandfish, Arctoscopus japonicus (Trichodontidae), in the Sea of Japan. Ichthyol Res 53:357–368
Stefanni S, Knutsen H (2007) Phylogeography and demographic history of the deep-sea fish Aphanopus carbo (Lowe, 1839) in the NE Atlantic: vicariance followed by secondary contact or speciation? Mol Phylogenet Evol 42:38–46
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
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
Toyoshima M (1984) Zoarcidae. In: Masuda H, Amaoka K, Araga C, Uyeno T, Yoshino T (eds) The fishes of the Japanese Archipelago. Tokai University Press, Tokyo, pp 305–309
Varela AI, Ritchie PA, Smith PJ (2012) Low levels of global genetic differentiation and population expansion in the deep-sea teleost Hoplostethus atlanticus revealed by mitochondrial DNA sequences. Mar Biol 159:1049–1060
Wang P (1999) Response of Western Pacific marginal seas to glacial cycles: paleoceanographic and sedimentological features. Mar Geol 156:5–39
Acknowledgments
We thank the captains, officers, and crews of the T/S Tanshu-Maru (Kasumi High School, Hyogo Prefecture) and the R/V Wakataka-maru (Tohoku National Fishery Institute, Fisheries Research Agency) for their help with sampling. The samples were collected on behalf of the Fishery Resources Survey contracted by the Ministry of Agriculture, Forestry, and Fisheries of Japan. This study was also supported in part by a grant from the Ministry of Education, Culture, Sports, Science, and Technology of Japan (no. 22370032).
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Sakuma, K., Ueda, Y., Ito, M. et al. Demographic histories of two deep-sea eelpouts, Lycodes japonicus and Lycodes ocellatus: paleoenvironmental implications of the western North Pacific deep waters. Ichthyol Res 62, 363–367 (2015). https://doi.org/10.1007/s10228-014-0441-8
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DOI: https://doi.org/10.1007/s10228-014-0441-8