Yamahira K, Kobayashi H, Kakioka R, Montenegro J, Masengi KWA, Okuda N, Nagano AJ, Tanaka R, Naruse K, Tatsumoto S, Go Y, Ansai S, Kusumi J Ghost introgression in ricefishes of the genus Adrianichthys in an ancient Wallacean lake. Journal of Evolutionary Biology. doi: 10.1111/jeb.14223
Takahashi H, Kakioka R, Nagano AJ (2023) Development and validation of novel SNP markers for the rapid identification of natural hybrids of the 11 closely related pufferfish species (Takifugu spp.) distributed in Japan. Aquaculture Reports, 31, 101650. doi: 10.1016/j.aqrep.2023.101650
Mandagi IF, Sumarto BKA, Nuryadi H, Mokodongan DF, Lawelle SA, Masengi KWA, Nagano AJ, Kakioka R, Kitano J, Ansai S, Kusumi J, Yamahira K (2023) Multiple colonizations and hybridization of a freshwater fish group on a satellite island of Sulawesi. Molecular Phylogenetics and Evolution, 184, 107804. doi:10.1016/j.ympev.2023.107804
Muto N, Kawasaki T, Kakioka R, Nagano AJ, Shimizu Y, Inose S, Shimizu Y, Takahashi H (2023) Genetic architectures of postmating isolation and morphology of two highly diverged rockfishes (genus Sebastes). Journal of Heredity, 114, 231–245. doi:10.1093/jhered/esad007
Kitano J., Ansai S, Fujimoto S, Kakioka R, Sato M, Mandagi IF, Sumarto BKA, Yamahira K (2023) A cryptic sex-linked locus revealed by the elimination of a master sex-determining locus in medaka fish. The American Naturalist, 202, 231–240. doi:10.1086/724840
Li Q, Lindtke D., Rodríguez-Ramírez C, Kakioka R, Takahashi H, Toyoda A, Kitano J, Ehrlich RL, Chang Mell J, Yeaman S (2022) Local adaptation and the evolution of genome architecture in threespine stickleback. Genome Biology and Evolution, 14, evac075. doi:10.1093/gbe/evac075
Nofrianto AB, Lawelle SA, Mokodongan, DF, Masengi KWA, Inomata N, Hashiguchi Y, Kitano J, Sumarto BKA, Kakioka R, Yamahira K (2022) Ancient admixture in freshwater halfbeaks of the genus Nomorhamphus in Southeast Sulawesi. Zoological Science, 39, 453–458. doi:10.2108/zs220023.
Kakioka R, Sutra N, Kobayashi H, Ansai S, Masengi KWA, Nagano AJ, Okuda N, Tanaka R, Sato M, Yamahira K (2021) Resource partitioning is not coupled with assortative mating in sympatrically divergent ricefish in a Wallacean ancient lake. Journal of Evolutionary Biology 34, 1133–1143. doi:10.1111/jeb.13874
Kakioka R, Kume M, Ishikawa A, Ansai S, Hosoki TK, Yamasaki YY, Nagano AJ, Toyoda A, Kitano J (2021) Genetic basis for variation in the number of cephalic pores in a hybrid zone between closely related species of goby, Gymnogobius breunigii and Gymnogobius castaneus. Biological Journal of the Linnean Society 133, 143–154. doi:10.1093/biolinnean/blab033 （遺伝研のプレスリリース「ハゼの分類と形態分化の遺伝基盤にゲノムで迫る」）
Muto N, Kakioka R, Ghaffar MA, Quan NV, Vilasri V, Traifalgar RFM, Babaran RP, Muto F, Takeshima H, Motomura H, Ishikawa S (2021) Fine‐scale phylogeography of coastal fishes in the South China Sea: Possible roles of biological traits and geography. Journal of Biogeography 48, 2785–2800. doi:10.1111/jbi.14239
Mandagi IF, Kakioka R, Montenegro J, Kobayashi H, Masengi KWA, Inomata N, Nagano AJ, Toyoda A, Ansai S, Matsunami M, Kimura R, Kitano J, Kusumi J, Yamahira K (2021) Species divergence and repeated ancient hybridization in a Sulawesian lake system. Journal of Evolutionary Biology 34, 1767–1780. doi:10.1111/jeb.13932
Yamahira K, Ansai S, Kakioka R, Yaguchi H, Kon T, Montenegro J, Kobayashi H, Fujimoto S, Kimura R, Takehana Y, Setiamarga DHE, Takami Y, Tanaka R, Maeda K, Tran HD, Koizumi N, Morioka S, Bounsong V, Watanabe K, Musikasinthorn P, Tun S, Yun LKC, Masengi KWA, Anoop VK, Raghavan R, & Kitano J (2021) Mesozoic origin and ‘out-of-India’ radiation of ricefishes (Adrianichthyidae). Biology Letters 17, 20210212. doi:10.1098/rsbl.2021.0212 （琉球大のプレスリリース「メダカはインド亜大陸に乗ってやって来た～メダカ科魚類の網羅的系統解析～ 」）
Kakioka R, Mori S, Kokita T, Hosoki TK, Nagano AJ, Ishikawa A, Kume M, Toyoda A, Kitano J (2020) Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago. BMC Evolutionary Biology 20, 143. doi:10.1186/s12862-020-01713-5 [PDF | Supplementary materials]
Sumarto BKA, Kobayashi H, Kakioka R, Tanaka R, Maeda K, Tran HD, Koizumi N, Morioka S, Bounsong V, Watanabe K, Musikasinthorn P, Tun S, Yun LKC, Anoop VK, Raghavan R, Masengi KWA, Fujimoto S, Yamahira K (2020) Latitudinal variation in sexual dimorphism in a freshwater fish group. Biological Journal of the Linnean Society 131, 898–908. doi:10.1093/biolinnean/blaa166
Kitano J, Kakioka R, Ishikawa A, Toyoda A, Kusakabe M (2020) Differences in the contributions of sex linkage and androgen regulation to sex-biased gene expression in juvenile and adult sticklebacks. Journal of Evolutionary Biology 33, 1129-1138. doi:10.1111/jeb.13662
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. Philosophical Transactions of the Royal Society B: Biological Sciences 375, 20190548. doi:10.1098/rstb.2019.0548
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. doi:10.1126/science.aau5656 （遺伝研のプレスリリース「海から川や湖へ！魚の淡水進出を支えた鍵遺伝子の発見 ― DHAを自分で合成すれば、海から離れても生きられる ―」）
Kakioka R, Muto N, Takeshima H, Gaje AC, Cruz RS, Alama UB, Guzman AMT, Traifalgar RFM, Babaran RP, Muda O, Arshaad WM, Arnupapboon S, Phuttharaksa K, Nguyen QV, Pham TT, Motomura H, Muto F, Ishikawa S (2018) Cryptic genetic divergence in Scolopsis taenioptera (Perciformes: Nemipteridae) in the western Pacific Ocean. Ichthyological Research 65, 92–100. doi:10.1007/s10228-017-0596-1 [Author manuscript PDF | supplementary materials]
Mokodongan DF, Montenegro J, Mochida K, Fujimoto S, Ishikawa A, Kakioka R, Yong L, Mulis, Hadiaty RK, Mandagi IF, Masengi KWA, Wachi N, Hashiguchi Y, Kitano J, Yamahira K (2018) Phylogenomics reveals habitat-associated body shape divergence in Oryzias woworae species group. Molecular Phylogenetics and Evolution 118, 194–203. doi:10.1016/j.ympev.2017.10.005
Muto N, Alama UB, Kakioka R, Babaran RP, Motomura H (2017) First record of Lutjanus madras (Perciformes: Lutjanidae) from the Pacific Ocean, with comments on its intraspecific morphological variation. Cybium 41:295–298. doi:10.26028/cybium/2017-413-008
Tabata R, Kakioka R, Tominaga K, Komiya T, Watanabe K (2016) Phylogeny and historical demography of endemic fishes in Lake Biwa: the ancient lake as a promoter of evolution and diversification of freshwater fishes in western Japan. Ecology and Evolution 6, 2601–2623. doi:10.1002/ece3.2070
Muto N, Takeshima H, Kakioka R, Alama UB, Guzman AMT, Cruz RS, Gaje AC, Traifalgar RFM, Motomura H, Muto F, Babaran RP, Ishikawa S (2016) Rapid and cost-effective molecular identification of the three mackerel species of the genus Rastrelliger (Perciformes: Scombridae) using PCR-RFLP analysis. Marine Biodiversity, doi:10.1007/s12526-016-0537-7
Muto N, Alama UB, Hata H, Guzman AMT, Cruz R, Gaje A, Traifalgar RFM, Kakioka R, Takeshima H, Motomura H, Muto F, Babaran RP, Ishikawa S (2016) Genetic and morphological differences among the three species of the genus Rastrelliger (Perciformes: Scombridae). Ichthyological Research 63, 275–287. doi:10.1007/s10228-015-0498-z
Kakioka R, Kokita T, Kumada H, Watanabe K, Okuda N (2015) Genomic architecture of habitat-related divergence and signature of directional selection in the body shapes of Gnathopogon fishes. Molecular Ecology 24, 4159–4174. doi:10.1111/mec.13309 [Author manuscript PDF | supplementary materials]
Watanabe K, Mori S, Tanaka T, Kanagawa N, Itai T, Kitamura J, Suzuki N, Tominaga K, Kakioka R, Tabata R, Abe T, Tashiro Y, Hashimoto Y, Nakajima J, Onikura N (2014) Genetic population structure of Hemigrammocypris rasborella (Cyprinidae) inferred from mtDNA sequences. Ichthyological Research 61, 352–360. doi:10.1007/s10228-014-0406-y
Kakioka R, Kokita T, Kumada H, Watanabe K, Okuda N (2013) A RAD-based inkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae). BMC Genomics 14, 32. doi:10.1186/1471-2164-14-32 [PDF | supplementary materials]
Kakioka R, Kokita T, Tabata R, Mori S, Watanabe K (2013) The origins of limnetic forms and cryptic divergence in Gnathopogon fishes (Cyprinidae) in Japan. Environmental Biology of Fishes 96, 631–644. doi:10.1007/s10641-012-0054-x [Author manuscript PDF]
Watanabe K, S Kawase, Mukai T, Kakioka R, Miyazaki JI, Hosoya K (2010) Population divergence of Biwia zezera (Cyprinidae: Gobioninae) and the discovery of a cryptic species, based on mitochondrial and nuclear DNA sequence analyses. Zoologocal Science 27, 647–655. doi:10.2108/zsj.27.647
Watanabe K, Kano Y, Takahashi H, Mukai T, Kakioka R, Tominaga K (2010) GEDIMAP: a database of genetic diversity for Japanese freshwater fishes. Ichthyological Research 57, 107–109. doi:10.1007/s10228-009-0129-7
Watanabe K, Kanagawa N, Kakioka R, Itai T, Mori S (2009) Genetic diversity and conservation units in wild and captive populations of endangered freshwater fishes: a case of Hemigrammocypris rasborella in Shizuoka, Japan. Ichthyological Research 56, 411–416. doi:10.1007/s10228-009-0107-0
Kakioka R, Watanabe K, Takeshima H, Nishida M (2009) Isolation and characterization of 12 microsatellite loci for cross-species amplification in the cyprinid gudgeons Squalidus chankaensis and S. japonicus. Molecular Ecology Resources 9, 1141–1144. doi:10.1111/j.1755-0998.2009.02584.x
Tominaga K, Watanabe K, Kakioka R, Mori S, Jeon SR (2009) Two highly divergent mitochondrial DNA lineages within Pseudogobio esocinus populations in central Honshu, Japan. Ichthyological Research 56, 195–199. doi:10.1007/s10228-008-0071-0
Watanabe K, Takeshima H, Iwata A, Abe T, Uehara K, Kakioka R, Kihira D, Nishida M (2008) Isolation and characterization of 39 microsatellite loci in the endangered Japanese loach Leptobotia curta. Molecular Ecology Resources 8, 145–148. doi:10.1111/j.1471-8286.2007.01902.x
柿岡諒（2013）生態・進化ゲノミクスのためのRADシーケンシング．生物科学，64(3)，168–176．総説．[著者原稿PDF]
Watanabe K, Tominaga K, Nakajima J, Kakioka R, Tabata R (2017) Japanese freshwater fishes: biogeography and cryptic diversity. In: Motokawa M, Kajihara H (eds) Species Diversity of Animals in Japan. Springer, Tokyo, pp 183–227. doi:10.1007/978-4-431-56432-4_7
柿岡諒（2024）スゴモロコ．藤岡康弘・川瀬成吾・田畑諒一 編『琵琶湖の魚類図鑑』．サンライズ出版，彦根．pp. 92–93．
柿岡諒（2024）デメモロコ．藤岡康弘・川瀬成吾・田畑諒一 編『琵琶湖の魚類図鑑』．サンライズ出版，彦根．p. 94．
柿岡諒（2024）タモロコ．藤岡康弘・川瀬成吾・田畑諒一 編『琵琶湖の魚類図鑑』．サンライズ出版，彦根．p. 106．
柿岡諒（2018）分断と分散―淡水魚．日本魚類学会 編『魚類学の百科事典』．丸善出版，東京．pp. 172–173．
柿岡諒（2018）系統地理学．日本魚類学会 編『魚類学の百科事典』．丸善出版，東京．pp. 180–181．
柿岡諒（2014）非モデル生物のSNPを探索する：RAD-seq．二階堂愛 編『次世代シークエンシング解析スタンダード』．羊土社，東京．pp. 303–310．
一部の論文はPDFファイルがResearchGateにもあります．