The genomic basis of adaptive evolution in threespine sticklebacks

被引：1315

作者：

Jones, Felicity C. ^{[2
]}

Grabherr, Manfred G. ^{[1
,3
]}

Chan, Yingguang Frank ^{[2
]}

Russell, Pamela ^{[1
]}

Mauceli, Evan ^{[1
]}

Johnson, Jeremy ^{[1
]}

Swofford, Ross ^{[1
]}

Pirun, Mono ^{[1
]}

Zody, Michael C. ^{[1
]}

White, Simon ^{[4
]}

Birney, Ewan ^{[5
]}

Searle, Stephen ^{[4
]}

Schmutz, Jeremy ^{[6
]}

Grimwood, Jane ^{[6
]}

Dickson, Mark C. ^{[6
]}

Myers, Richard M. ^{[6
]}

Miller, Craig T. ^{[2
]}

Summers, Brian R. ^{[2
]}

Knecht, Anne K. ^{[2
]}

Brady, Shannon D. ^{[2
]}

Zhang, Haili ^{[2
]}

Pollen, Alex A. ^{[2
]}

Howes, Timothy ^{[2
]}

Amemiya, Chris ^{[7
]}

Lander, Eric S. ^{[1
]}

Di Palma, Federica ^{[1
]}

Lindblad-Toh, Kerstin ^{[1
,3
]}

Kingsley, David M. ^{[2
,8
]}

机构：

[1] Broad Inst MIT & Harvard, Cambridge Ctr 7, Cambridge, MA 02142 USA

[2] Stanford Univ, Sch Med, Dept Dev Biol, Beckman Ctr B300, Stanford, CA 94305 USA

[3] Uppsala Univ, Dept Med Biochem & Microbiol, Sci Life Lab Uppsala, S-75123 Uppsala, Sweden

[4] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[5] European Bioinformat Inst, Cambridge CB10 1SA, England

[6] HudsonAlpha Inst Biotechnol, Huntsville, AL 35806 USA

[7] Benaroya Res Inst Virginia Mason, Dept Mol Genet, Seattle, WA 98101 USA

[8] Stanford Univ, Howard Hughes Med Inst, Stanford, CA 94305 USA

来源：

NATURE | 2012年 / 484卷 / 7392期

关键词：

GENETIC ARCHITECTURE; PARALLEL EVOLUTION; REGULATORY CHANGES; SIGNALING PATHWAY; PELVIC REDUCTION; EVO-DEVO; VERTEBRATE; DUPLICATION; ADAPTATION; INVERSIONS;

D O I：

10.1038/nature10944

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.

引用

页码：55 / 61

页数：7

共 52 条

[21] Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype [J].

Jaillon, O ;

Aury, JM ;

Brunet, F ;

Petit, JL ;

Stange-Thomann, N ;

Mauceli, E ;

Bouneau, L ;

Fischer, C ;

Ozouf-Costaz, C ;

Bernot, A ;

Nicaud, S ;

Jaffe, D ;

Fisher, S ;

Lutfalla, G ;

Dossat, C ;

Segurens, B ;

Dasilva, C ;

Salanoubat, M ;

Levy, M ;

Boudet, N ;

Castellano, S ;

Anthouard, R ;

Jubin, C ;

Castelli, V ;

Katinka, M ;

Vacherie, B ;

Biémont, C ;

Skalli, Z ;

Cattolico, L ;

Poulain, J ;

de Berardinis, V ;

Cruaud, C ;

Duprat, S ;

Brottier, P ;

Coutanceau, JP ;

Gouzy, J ;

Parra, G ;

Lardier, G ;

Chapple, C ;

McKernan, KJ ;

McEwan, P ;

Bosak, S ;

Kellis, M ;

Volff, JN ;

Guigó, R ;

Zody, MC ;

Mesirov, J ;

Lindblad-Toh, K ;

Birren, B ;

Nusbaum, C .

NATURE, 2004, 431 (7011) :946-957

[22] Reproductive isolation in a threespine stickleback hybrid zone [J].

Jones, F. C. ;

Brown, C. ;

Pemberton, J. M. ;

Braithwaite, V. A. .

JOURNAL OF EVOLUTIONARY BIOLOGY, 2006, 19 (05) :1531-1544

[23] Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry [J].

Joron, Mathieu ;

Frezal, Lise ;

Jones, Robert T. ;

Chamberlain, Nicola L. ;

Lee, Siu F. ;

Haag, Christoph R. ;

Whibley, Annabel ;

Becuwe, Michel ;

Baxter, Simon W. ;

Ferguson, Laura ;

Wilkinson, Paul A. ;

Salazar, Camilo ;

Davidson, Claire ;

Clark, Richard ;

Quail, Michael A. ;

Beasley, Helen ;

Glithero, Rebecca ;

Lloyd, Christine ;

Sims, Sarah ;

Jones, Matthew C. ;

Rogers, Jane ;

Jiggins, Chris D. ;

Ffrench-Constant, Richard H. .

NATURE, 2011, 477 (7363) :203-U102

[24] The medaka draft genome and insights into vertebrate genome evolution [J].

Kasahara, Masahiro ;

Naruse, Kiyoshi ;

Sasaki, Shin ;

Nakatani, Yoichiro ;

Qu, Wei ;

Ahsan, Budrul ;

Yamada, Tomoyuki ;

Nagayasu, Yukinobu ;

Doi, Koichiro ;

Kasai, Yasuhiro ;

Jindo, Tomoko ;

Kobayashi, Daisuke ;

Shimada, Atsuko ;

Toyoda, Atsushi ;

Kuroki, Yoko ;

Fujiyama, Asao ;

Sasaki, Takashi ;

Shimizu, Atsushi ;

Asakawa, Shuichi ;

Shimizu, Nobuyoshi ;

Hashimoto, Shin-ichi ;

Yang, Jun ;

Lee, Yongjun ;

Matsushima, Kouji ;

Sugano, Sumio ;

Sakaizumi, Mitsuru ;

Narita, Takanori ;

Ohishi, Kazuko ;

Haga, Shinobu ;

Ohta, Fumiko ;

Nomoto, Hisayo ;

Nogata, Keiko ;

Morishita, Tomomi ;

Endo, Tomoko ;

Shin-, Tadasu, I ;

Takeda, Hiroyuki ;

Morishita, Shinichi ;

Kohara, Yuji .

NATURE, 2007, 447 (7145) :714-719

[25] Extensive lineage-specific gene duplication and evolution of the spiggin multi-gene family in stickleback [J].

Kawahara, Ryouka ;

Nishida, Mutsumi .

BMC EVOLUTIONARY BIOLOGY, 2007, 7

[26] Evolution and development of facial bone morphology in threespine sticklebacks [J].

Kimmel, CB ;

Ullmann, B ;

Walker, C ;

Wilson, C ;

Currey, M ;

Phillips, PC ;

Bell, MA ;

Postlethwait, JH ;

Cresko, WA .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (16) :5791-5796

[27]

Kingsley David M., 2007, P41

[28] New genomic tools for molecular studies of evolutionary change in threespine sticklebacks [J].

Kingsley, DM ;

Zhu, BL ;

Osoegawa, K ;

De Jong, PJ ;

Schein, J ;

Marra, M ;

Peichel, C ;

Amamiya, C ;

Schluter, D ;

Balabhadra, S ;

Friedlander, B ;

Cha, YM ;

Dickson, M ;

Grimwood, J ;

Schmutz, J ;

Talbot, WS ;

Myers, R .

BEHAVIOUR, 2004, 141 :1331-1344

[29] Chromosome inversions, local adaptation and speciation [J].

Kirkpatrick, Mark ;

Barton, Nick .

GENETICS, 2006, 173 (01) :419-434

[30] Adaptive Divergence in the Thyroid Hormone Signaling Pathway in the Stickleback Radiation [J].

Kitano, Jun ;

Lema, Sean C. ;

Luckenbach, J. Adam ;

Mori, Seiichi ;

Kawagishi, Yui ;

Kusakabe, Makoto ;

Swanson, Penny ;

Peichel, Catherine L. .

CURRENT BIOLOGY, 2010, 20 (23) :2124-2130

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