Molecular mechanisms of genomic incompatibility and reproductive isolation in sticklebacks

• Project Area: Correlative gene system: establishing next-generation genetics
• Project/Area Number: 23113007
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: National Institute of Genetics
• Principal Investigator: Kitano Jun 国立遺伝学研究所, 集団遺伝研究系, 教授 (80346105)
• Co-Investigator(Renkei-kenkyūsha): MAKINO Takashi 東北大学, 大学院生命科学研究科, 准教授 (20443442)
• Project Period (FY): 2011-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥99,190,000 (Direct Cost: ¥76,300,000、Indirect Cost: ¥22,890,000); Fiscal Year 2015: ¥16,120,000 (Direct Cost: ¥12,400,000、Indirect Cost: ¥3,720,000); Fiscal Year 2014: ¥16,120,000 (Direct Cost: ¥12,400,000、Indirect Cost: ¥3,720,000); Fiscal Year 2013: ¥17,030,000 (Direct Cost: ¥13,100,000、Indirect Cost: ¥3,930,000); Fiscal Year 2012: ¥16,900,000 (Direct Cost: ¥13,000,000、Indirect Cost: ¥3,900,000); Fiscal Year 2011: ¥33,020,000 (Direct Cost: ¥25,400,000、Indirect Cost: ¥7,620,000)
• Keywords: 種分化 / 性染色体 / トゲウオ / 魚 / 生殖隔離 / クロマチン / 雑種異常 / ゲノム / 雑種 / 多様性 / 進化 / イトヨ / トミヨ

Outline of Final Research Achievements

To characterize the net-sex chromosomes, we conducted whole genome sequencing of the Japan Sea and Pacific Ocean sticklebacks. We also identified a candidate gene encoding a TRIM gene within the QTL causing hybrid male sterility. To investigate the patterns of sex chromosome-autosome fusions, we made a database and analyzed the patterns. To explain the observed patterns, we proposed that female meiotic drive, genetic drift and sexually antagonistic selection may drive the fusions.

Research Products

• [Journal Article] Whole-genome sequencing reveals small genomic regions of introgression in an introduced crater lake population of threespine stickleback. (2016)
  • Author(s): Yoshida, K., Miyagi, R., Mori, S., Takahashi, A., Makino, T., Toyoda, A., Fujiyama, A., and Kitano, J.
  • Journal Title: Ecology and Evolution Volume: 65 Issue: 7 Pages: 2190-2204
  • DOI: 10.1002/ece3.2047
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Comparison of freshwater tolerance during spawning migration between two sympatric Japanese marine threespine stickleback species (2016)
  • Author(s): Ishikawa, A., Kusakabe, M., Kume, M., and Kitano, J.
  • Journal Title: Evolutionary Ecology Research Volume: in press
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Trophic niche differentiation and phenotypic divergence among cryptic species of Japanese ninespine stickleback (2016)
  • Author(s): Ravinet, M., Ishikawa, A., and Kitano, J.
  • Journal Title: Evolutionary Ecology Research Volume: in press
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Toward conservation of genetic and phenotypic diversity in Japanese sticklebacks (2016)
  • Author(s): Kitano, J., Moris, S.
  • Journal Title: Genes and Genetic Systems Volume: in press
  • NAID: 130005421206
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Purifying selection maintains dosage-sensitive genes during degeneration of the threespine stickleback Y chromosome. (2015)
  • Author(s): White, M. A., Kitano, J., and Peichel, C. L.
  • Journal Title: Molecular Biology and Evolution Volume: in press
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Tree of Sex: A database of sexual systems. (2014)
  • Author(s): Ashman, T. L., Bachtrog, D., Blackmon, H., Goldberg, E., Hahn, M., Kirkpatrick, M., Kitano, J., Mank, J., Mayrose, I., Ming, R., Otto, S. P., Peichel, C. L., Pennell, M. W., Perrin, N., Ross, L., Valenzuela, N., and Vamosi, J. C.
  • Journal Title: Scientific Data Volume: 1 Issue: 1 Pages: 140015-140015
  • DOI: 10.1038/sdata.2014.15
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Relaxin-related gene expression differs between anadromous and stream-resident stickleback (Gasterosteus aculeatus) following seawater transfer. (2014)
  • Author(s): Kusakabe, M., Ishikawa, A., and Kitano, J.
  • Journal Title: General and Comparative Endocrinology Volume: 205 Pages: 197-206
  • DOI: 10.1016/j.ygcen.2014.06.017
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Female Mate Preference for Longer Fins in Medaka (2014)
  • Author(s): Shingo Fujimoto, Maiko Kawajiri, Jun Kitano and Kazunori Yamahira
  • Journal Title: Zoological Science Volume: 31 Issue: 11 Pages: 703-708
  • DOI: 10.2108/zs140102
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Ontogenetic stage-specific quantitative trait loci contribute to divergence in developmental trajectories of sexually dimorphic fins between medaka populations (2014)
  • Author(s): Maiko Kawajiri, Kohta Yoshida, Shingo Fujimoto, Daniel Frikli Mokodongan, Mark Ravinet, Mark Kirkpatrick, Kazunori Yamahira, Jun Kitano
  • Journal Title: Molecular Ecology Volume: 23 Issue: 21 Pages: 5129-5391
  • DOI: 10.1111/mec.12933
  • Peer Reviewed
• [Journal Article] Comparative Analysis of Japanese Three-Spined Stickleback Clades Reveals the Pacific Ocean Lineage Has Adapted to Freshwater Environments while the Japan Sea Has Not (2014)
  • Author(s): Ravinet M, Takeuchi N, Kume M, Mori S, Kitano J
  • Journal Title: PLoS ONE Volume: 9 Issue: 12 Pages: e112404-e112404
  • DOI: 10.1371/journal.pone.0112404
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Sex chromosome turnover contributes to genomic divergence between incipient stickleback species. (2014)
  • Author(s): Yoshida, K., Makino, T., Yamaguchi, K., Shigenobu, S., Hasebe, M., Kawata, M., Kume, M., Mori, S., Peichel, C.L., Toyoda, A., et al.
  • Journal Title: PLoS genetics Volume: 10 Issue: 3 Pages: e1004223-e1004223
  • DOI: 10.1371/journal.pgen.1004223
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Speciation in ninespine stickleback : reproductive isolation and phenotypic divergence among cryptic species of Japanese nine stickleback. (2013)
  • Author(s): Ishikawa A, Takeuchi N, Kusakabe M, Kume M, Mori S, Takahashi H, Kitano J.
  • Journal Title: Journal of Evolutionary Biology Volume: (In press) Issue: 7 Pages: 1417-1430
  • DOI: 10.1111/jeb.12146
  • Peer Reviewed
• [Journal Article] Divergence in thyroid hormone levels between juveniles of marine and stream ecotypes of the threespine stickleback (Gasterosteus aculeatus). (2013)
  • Author(s): Kitano, J., and Lema, S. C.
  • Journal Title: Evolutionary Ecology Research Volume: 15 Pages: 143-153
  • Peer Reviewed
• [Journal Article] Are Japanese freshwater populations of threespine stickleback derived from the Pacific Ocean lineage? (2013)
  • Author(s): Cassidy, L. M., Ravinet, M., Mori, S., and Kitano, J.
  • Journal Title: Evolutionary Ecology Research Volume: 15 Pages: 295-311
  • Peer Reviewed
• [Journal Article] RNA sequencing reveals small RNAs differentially expressed between incipient Japanese threespine sticklebacks (2013)
  • Author(s): Kitano, J., Yoshida, K., and Suzuki, Y.
  • Journal Title: BMC Genomics Volume: 14 Issue: 1 Pages: 214-214
  • DOI: 10.1186/1471-2164-14-214
  • Peer Reviewed
• [Journal Article] Are Japanese freshwater populations of threespine stickleback derived from the Pacific Ocean lineage? (2013)
  • Author(s): Cassidy, L. M.
  • Journal Title: Evolutionary Ecology Research Volume: in press
  • Peer Reviewed
• [Journal Article] Divergence in thyroid hormone levels between juveniles of marine and stream ecotypes of the threespine stickleback (Gasterosteus aculeatus) (2013)
  • Author(s): Kitano, J.
  • Journal Title: Evolutionary Ecology Research Volume: in press
  • Peer Reviewed
• [Journal Article] Speciation in ninespine sticklebacks: reproductive isolation and phenotypic divergence among cryptic species of Japanese ninespine stickleback (2013)
  • Author(s): Ishikawa, A.
  • Journal Title: Journal of Evolutionary Biology Volume: in press
  • Peer Reviewed
• [Journal Article] Shifts in morphology and diet of non-native sticklebacks introduced into Japanese crater lakes (2012)
  • Author(s): Adachi T, Ishikawa A, Mori S, Makino W, Kume M, Kawata M, Kitano J
  • Journal Title: Ecology and Evolution Volume: (In press) Issue: 6 Pages: 1083-1098
  • DOI: 10.1002/ece3.234
  • Peer Reviewed
• [Journal Article] The contribution of female meiotic drive to the evolution of neo-sex chromosomes (2012)
  • Author(s): Yoshida. K.
  • Journal Title: Evolution Volume: 66 Pages: 3198-3208
  • Peer Reviewed
• [Journal Article] Physiological and genetic basis for variation in migratory behavior in the three-spined stickleback, Gasterosteus aculeatus. (2012)
  • Author(s): Kitano, J.
  • Journal Title: Ichthyological Research Volume: 59 Issue: 4 Pages: 293-303
  • DOI: 10.1007/s10228-012-0289-8
  • NAID: 10031126621
  • Peer Reviewed
• [Journal Article] The contribution of female meiotic drive to the evolution of neo-sex chromosomes (2012)
  • Author(s): Yoshida, K., J.Kitano
  • Journal Title: Evolution Volume: (in press) Issue: 10 Pages: 3198-3208
  • DOI: 10.1111/j.1558-5646.2012.01681.x
  • Peer Reviewed
• [Journal Article] Shifts in morphology and diet of non-native sticklebacks introduced into Japanese crater lakes (2012)
  • Author(s): Adachi, T., A.Ishikawa, S.Mori, W.Makino, M.Kume, M.Kawata, J.Kitano
  • Journal Title: Ecology and Evolution Volume: (in press) Issue: 6 Pages: 1099-1112
  • DOI: 10.1002/ece3.235
  • Peer Reviewed
• [Journal Article] Turnover of sex chromosomes and speciation in fishes (2012)
  • Author(s): Kitano, J., C.L.Peichel
  • Journal Title: Environmental Biology of Fishes Volume: (in press) Issue: 3 Pages: 131-146
  • DOI: 10.1007/s10641-011-9853-8
  • Peer Reviewed
• [Presentation] Genetic mechanisms of colonization of new niches in sticklebacks (2015)
  • Author(s): Jun Kitano
  • Organizer: Lecture Series in Ecology and Evolution
  • Place of Presentation: University of Bern, Switzerland
  • Year and Date: 2015-10-11
  • Invited
• [Presentation] Drivers of sex chromosome-autosome fusions and their roles in speciation (2015)
  • Author(s): Jun Kitano
  • Organizer: AGA Presidents Symposium, Chromosome Evolution: Molecular Mechanisms and Evolutionary Consequences
  • Place of Presentation: Bainbridge Island, USA
  • Year and Date: 2015-08-17
  • Int'l Joint Research / Invited
• [Presentation] Why are there so many species with Y- autosome fusions? (2015)
  • Author(s): Kitano J. Pennell M., Kirkpatrick M., Otto S., Vamosi J., Peichel C.
  • Organizer: ESEB 2015
  • Place of Presentation: Lausanne, Switzerland
  • Year and Date: 2015-08-10
  • Int'l Joint Research
• [Presentation] Genome-wide expression QTL (eQTL) analysis reveals trans-acting eQTL hotspots underlying transcriptome divergence between Threespine Stickleback ecotypes. (2015)
  • Author(s): Asano Ishikawa, Makoto Kusakabe, Kohta Yoshida, Takashi Makino, Atsushi Toyoda, Asao Fujiyama, and Jun Kitano
  • Organizer: Stickleback Conference 2015
  • Place of Presentation: New York Stony Brook, USA
  • Year and Date: 2015-07-26
  • Int'l Joint Research
• [Presentation] 性染色体進化がトゲウオ適応放散に果たす役割 (2014)
  • Author(s): 北野潤
  • Organizer: 日本分子生物学会
  • Place of Presentation: パシフィコ横浜（横浜市）
  • Year and Date: 2014-11-25 – 2014-11-27
• [Presentation] 野外魚類の遺伝学は何を目指す？ (2014)
  • Author(s): 北野潤
  • Organizer: 日本魚類学会
  • Place of Presentation: 生命の星・地球博物館（小田原市）
  • Year and Date: 2014-11-14 – 2014-11-17
• [Presentation] 繁殖システムの多様性の概観と趣旨説明 (2014)
  • Author(s): 北野潤
  • Organizer: 日本動物学会
  • Place of Presentation: 東北大学（仙台市）
  • Year and Date: 2014-09-11 – 2014-09-13
• [Presentation] 性的二型進化の遺伝理論とトゲウオの性的二型 (2013)
  • Author(s): 北野 潤
  • Organizer: 日本動物学会大会
  • Place of Presentation: 岡山大学
• [Presentation] ゲウオにおけるミクロレベルでの表現型多様化とマクロレベルでの種分化の遺伝機構 (2013)
  • Author(s): 北野 潤
  • Organizer: 日本遺伝学会大会
  • Place of Presentation: 慶応大学
• [Presentation] A young neo-sex chromosome is the site of divergence between incipient stickleback species (2013)
  • Author(s): Kitano J, Yoshida K
  • Organizer: ESEB2013
  • Place of Presentation: Lisbon Portugal
• [Presentation] Physiological genomics of speciation and adaptation in the Japanese stickleback species (2012)
  • Author(s): Kitano, J.
  • Organizer: Stickleback 2012 Seventh International Conference on Stickleback Behavior and Evolution
  • Place of Presentation: Seattle, WA, USA
  • Year and Date: 2012-07-29
• [Presentation] Neo-Sex Chromosome Formation and Speciation in the Japanese Sticklebacks (2012)
  • Author(s): Yoshida K, Makino T, Yamaguchi K, Shigenobu S, Hasebe M, Mori S, Peichel K, Kawata M, Toyoda A, Fujiyama A, Kitano J
  • Organizer: OBC Symposium : Speciation and Adaptation II
  • Place of Presentation: 岡崎国際会議場(招待講演)
  • Year and Date: 2012-03-21
• [Presentation] Physiological genomics of speciation in sticklebacks (2011)
  • Author(s): Kitano J, Kusakabe, M
  • Organizer: 日本動物学会
  • Place of Presentation: 旭川クリスタルホール
  • Year and Date: 2011-09-23
• [Presentation] エソロジーの新展開:トゲウオをモデルに (2011)
  • Author(s): 北野潤、森誠一
  • Organizer: 日本動物行動学会
  • Place of Presentation: 慶応大学
  • Year and Date: 2011-09-10
• [Presentation] Genetic basis for invasive colonization in sticklebacks (2011)
  • Author(s): Kitano J
  • Organizer: Annual Meeting for the American Fisheries Society
  • Place of Presentation: Washington State Convention Center
  • Year and Date: 2011-09-07
• [Presentation] Genomic and functional characterization of a neo-sex chromosome important for stickleback speciation (2011)
  • Author(s): Kitano J, Makino T, Yamaguchi K, Shigenobu S, Hasebe M, Peichel K, Mori S, Kawata M
  • Organizer: Annual Meeting of the Society for Molecular Biology and Evolution
  • Place of Presentation: 京都大学(招待講演)
  • Year and Date: 2011-07-27
• [Book] 遺伝子が語る生命38億年の謎 (2014)
  • Author(s): 高野敏行・角谷徹仁・清水裕・嶋本伸雄・北野潤・斎藤成也・高橋文・隅山健太・荒木弘之・伊藤啓・小出剛・小林武彦・深川竜郎・前島一博・木村暁・榎本和生・岩里啄治・相賀裕美子・酒井則良
  • Publisher: 悠書館
• [Book] Thyroid Hormones (2012)
  • Author(s): Ishikawa, A.
  • Publisher: InTech
• [Remarks] 日本メダカ雌雄差の地理的変異の遺伝基盤
  • URL: http://www.nig.ac.jp/Research-Highlights/1468/1568.html
• [Remarks] 動植物の性決定システムは実に多様
  • URL: http://www.nig.ac.jp/Research-Highlights/1468/1541.html
• [Remarks] 動植物の性決定システムの多様性の総説がPLOS Biologyに掲載
  • URL: http://www.ige.tohoku.ac.jp/prg/genetics/study_report/2014/07/plos-biology.html
• [Remarks] 研究成果がMolecular Ecologyに掲載されました
  • URL: http://www.ige.tohoku.ac.jp/prg/genetics/study_report/2014/09/molecular-ecology-1.html
• [Remarks] 特殊な性染色体を持つ日本海イトヨのゲノムを解読
  • URL: http://www.ige.tohoku.ac.jp/prg/genetics/study_report/kitano/
• [Remarks] 特殊な性染色体を持つ日本海イトヨのゲノムを解読
  • URL: http://www.nig.ac.jp/Research-Highlights/1468/1473.html
• [Remarks] NIGINTERN生が日本の淡水イトヨの起源を確認
  • URL: http://www.nig.ac.jp/Research-Highlights/1170/1182.html
• [Remarks] 性染色体の進化と常染色体の形に強い相関を発見
  • URL: http://www.nig.ac.jp/Research-Highlights/992/1066.html
• [Remarks] トゲウオ近縁種間での低分子RNA分化の論文がBMC Genomicsに出版されました
  • URL: http://www.ige.tohoku.ac.jp/prg/genetics/study_report/2013/04/rnabmc-genomics.html
• [Remarks] 淡水イトヨが幼弱期より甲状腺機能低下であることを発見
  • URL: http://www.ige.tohoku.ac.jp/prg/genetics/study_report/2013/03/post-49.html
• [Remarks] 日本産淡水イトヨの起源を確認
  • URL: http://www.ige.tohoku.ac.jp/prg/genetics/study_report/2013/03/post-48.html
• [Remarks]
  • URL: http://www.nig.ac.jp/labs/EcoGene/
• [Remarks]
  • URL: http://www.nig.ac.jp/Research-Highlights/992/1055.html