Skip to main content
SpringerLink
Log in

A ddRAD-based population genetics and phylogenetics of an endangered freshwater fish from Japan

  • Research Article
  • Published:
Conservation Genetics Aims and scope Submit manuscript

Abstract

Rhodeus ocellatus kurumeus is a small cyprinid fish endemic to the Japanese archipelago. This fish frequently hybridizes with an exotic subspecies Rhodeus ocellatus ocellatus, and non-introgressed populations of R. o. kurumeus have greatly decreased. Previous studies based on mitochondrial and nuclear DNA identified introgressed populations and inferred phylogenetic relationships, but these approaches may lead to underestimates of introgression or ambiguous results owing to the small number of genetic markers used. The present study applied double digest restriction site-associated DNA (ddRAD) sequencing to assignment tests and phylogenetic inferences. Data matrices can vary in size and content depending on the strategies used to process ddRAD sequences; therefore, we prepared 25 data matrices with various processing strategies. The assignment tests based on the 25 data matrices resulted in similar assignment patterns and provided evidence for introgression in some populations that had been identified as non-introgressed populations in previous studies. The maximum-likelihood (ML) phylogenetic trees differed in robustness and topology among the 25 matrices; interestingly, ML trees with low statistical support reflected geographical distributions of fish better than ML trees with high statistical support. These results indicate that ddRAD sequencing can detect introgression with greater sensitivity than conventional DNA markers, that ddRAD sequencing is useful for phylogenetic inference among closely related populations within a subspecies, and that statistically robust ML trees do not necessarily reflect the true phylogeny. Application of ddRAD data to conservation genetics and evolutionary history of this subspecies are also discussed.

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

Access this article

Log in via an institution

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

Similar content being viewed by others

References

  • Abe T, Kobayashi I, Watanabe K (2013) An extant native population of the Japanese rosy bittering, Rhodeus ocellatus kurumeus, in the Sanyo Region, western Japan. Jpn J Ichthyol 60:49–55 (in Japanese with English abstract)

    Google Scholar 

  • Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V, Poz MF (2005) PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Env Microbiol 71:8966–8969

    Article  CAS  Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 30:2114–2120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Buerkle CA (2005) Maximum-likelihood estimation of a hybrid index based on molecular markers. Mol Ecol Notes 5:684–687

    Article  CAS  Google Scholar 

  • Catchen JM, Amores H, Hohenlohe P, Cresko W, Postlethwait JH (2011) Stacks: building and genotyping loci de novo from short-read sequences. Genes Genomes Genet 1:171–182

    CAS  Google Scholar 

  • Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124–3140

    Article  PubMed  PubMed Central  Google Scholar 

  • Dobson M, Kawamura Y (1998) Origin of the Japanese land mammal fauna: allocation of extant species to historically-based categories. Quat Res 37:385–395

    Article  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Res 10:564–567

    Article  Google Scholar 

  • Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 2005:47–50

    Google Scholar 

  • Hosoya K (1982) Freshwater fish fauna of the Yoshii River, Okayama Prefecture. Bull Biogeogr Soc Jpn 7:23–35

    Google Scholar 

  • Ichihara M (2001) Zoku Ohsakasougun, Kosetouchi-kakosuikei. Urban Kubota 39:1–65 (in Japanese)

    Google Scholar 

  • Japan Association for Quaternary Research (1987) Quaternary Maps of Japan. University of Tokyo Press, Tokyo (in Japanese)

    Google Scholar 

  • Japan Ministry of the Environment (2018) Red list of Japanese blackish and freshwater fishes in 2018. https://www.env.go.jp/press/files/jp/109187.pdf. Accessed 22 January 2019 (in Japanese)

  • Kawamura K (2005) Low genetic variation and inbreeding depression in small isolated populations of the Japanese rosy bittering, Rhodeus ocellatus kurumeus. Zool Sci 22:517–524

    Article  CAS  Google Scholar 

  • Kawamura K, Ueda T, Arai R, Nagata Y, Saitoh K, Ohtaka H, Kanoh Y (2001a) Genetic introgression by the rose bitterling, Rhodeus ocellatus ocellatus, into the Japanese rose bitterling, R. o. kurumeus (Teleostei: Cyprinidae). Zool Sci 18:1027–1039

    Article  CAS  Google Scholar 

  • Kawamura K, Nagata Y, Ohtaka H, Kanoh Y, Kitamura J (2001b) Genetic diversity in the Japanese rosy bittering, Rhodeus ocellatus kurumeus (Cyprinidae). Ichthyol Res 48:369–378

    Article  Google Scholar 

  • Kawamura K, Ueda T, Arai R, Smith C (2014) Phylogenetic relationships of bitterling fishes (Teleostei: Cypriniformes: Acheilognathinae), inferred from mitochondrial cytochrome b sequences. Zool Sci 31:321–329

    Article  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 

  • Lam AW, Gueuning M, Kindler C, Van Dam M, Alvarez N, Panjaitan R, Shaverdo H, White LT, Roderick GK, Balke M (2018) Phylogeography and population genomics of a lotic water beetle across a complex tropical landscape. Mol Ecol 27:3346–3356

    Article  Google Scholar 

  • Lee KM, Kivelä SM, Ivanov V, Hausmann A, Kaila L, Wahlberg N, Mutanen M (2018) Information dropout patterns in restriction site associated DNA phylogenomics and a comparison with multilocus Sanger data in a species-rich moth genus. Syst Biol 67:925–939

    Article  CAS  PubMed  Google Scholar 

  • Mikura T, Takamori R, Fujiwara M, Tsuruta T, Kanoh Y, Kawamura K (2014) Genetic characteristics of pond populations of Japanese rosy bittering Rhodeus ocellatus kurumeus in Osaka Prefecture, inferred from microsatellite markers. Nippon Suisan Gakkaishi 80:908–916 (in Japanese with English abstract)

    Article  Google Scholar 

  • Miyake K, Tachida H, Oshima Y, Arai R, Kimura S, Imada N, Honjo T (2001) Genetic variation of the cytochrome b gene in the rosy bitterling, Rhodeus ocellatus (Cyprinidae) in Japan. Ichthyol Res 48:105–110

    Article  Google Scholar 

  • Miyake T, Kawamura K, Hosoya K, Okazaki T, Kitagawa T (2007) Discovery of the Japanese rosy bitterling, Rhodeus ocellatus kurumeus, in Nara Prefecture. Jpn J Ichthyol 54:139–148 (in Japanese with English abstract)

    Google Scholar 

  • Miyake T, Nakajima J, Onikura N, Komaru A, Kawamura K (2008) Present distribution of Japanese rosy bitterling Rhodeus ocellatus kurumeus in Kyushu, inferred from mitochondrial DNA and morphology. Nippon Suisan Gakkaishi 74:1060–1067 (in Japanese with English abstract)

    Article  CAS  Google Scholar 

  • Nagata Y (1997) Rhodeus ocellatus kurumeus. In: Nagata Y, Hosoya K (eds) Circumstances in endangered Japanese freshwater fishes and their protection. Midori Shobo, Tokyo, pp 76–85 (in Japanese)

    Google Scholar 

  • Nagata Y, Fukuhara S (2000) Fish spawning eggs in bivalves. Tonbo Press, Osaka (in Japanese)

    Google Scholar 

  • Nakamura M (1955) On the freshwater fishes introduced and propagated in Kanto Plain. Bull Biogeogr Soc Jpn 16–19:333–337 (in Japanese)

    Google Scholar 

  • Nakamura M (1969) Cyprinid fishes of Japan. Research Institute for Natural Resources, Japan (in Japanese)

    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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rašić G, Filipović I, Weeks AR, Hoffmann AA (2014) Genome-wide SNPs lead to strong signals of geographic structure and relatedness patterns in the major arbovirus vector Aedes aegypti. BMC Genomics 15:275

    Article  PubMed  PubMed Central  Google Scholar 

  • Rhymer JM, Simberloff D (1996) Extinction by hybridization and introgression. Ann Rev Ecol Syst 27:83–109

    Article  Google Scholar 

  • Rubin BER, Ree RH, Moreau CS (2012) Inferring phylogenies from RAD sequence data. PLoS ONE 7:e33394

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sakaguchi S, Sugino T, Tsumura Y, Ito M, Crisp MD, Bowman DMJS, Nagano AJ, Honjo MN, Yasugi M, Kudoh H, Matsuki Y, Suyama Y, Isagi Y (2015) High-throughput linkage mapping of Australian white cypress pine (Callitris glaucophylla) and map transferability to related species. Tree Genet Genomes 11:121

    Article  Google Scholar 

  • Sakai H, Yamamoto C, Iwata A (1998) Genetic divergence, variation and zoogeography of a freshwater goby, Odontobutis obscura. Ichthyol Res 45:363–376

    Article  Google Scholar 

  • Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 57:758–771

    Article  PubMed  Google Scholar 

  • Sze MA, Schloss PD (2019) The impact of DNA polymerase and number of rounds of amplification in PCR on 16S rRNA gene sequence data. mSphere 4:e00163–e00719

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Taool M, Fukuhara S (1997) Rhodeus ocellatus kurumeus, an endangered cyprinid collected in a small pond, Sanda, Hyogo Prefecture, Japan. Hum Nat 8:145–149 (in Japanese with English abstract)

    Google Scholar 

  • Takahashi T, Moreno E (2015) A RAD-based phylogenetics for Orestias fishes from Lake Titicaca. Mol Phylogenet Evol 93:307–317

    Article  PubMed  Google Scholar 

  • Takahashi T, Sota T (2016) A robust phylogeny among major lineages of the East African cichlids. Mol Phylogenet Evol 100:234–242

    Article  PubMed  Google Scholar 

  • Takahashi T, Nagata N, Sota T (2014) Application of RAD-based phylogenetics to complex relationships among variously related taxa in a species flock. Mol Phylogenet Evol 80:137–144

    Article  PubMed  Google Scholar 

  • Takehana Y, Nagai N, Matsuda M, Tsuchiya K, Sakaizumi M (2003) Geographic variation and diversity of the cytochrome b gene in Japanese wild populations of medaka, Oryzias latipes. Zool Sci 20:1279–1291

    Article  CAS  Google Scholar 

  • Tominaga K, Nakajima J, Watanabe K (2016) Cryptic digergence and phylogeography of the pike gudgeon Pseudogobio esocinus (Teleostei: Cyprinidae): a comprehensive case of freshwater phylogeography in Japan. Ichthyol Res 63:79–93

    Article  Google Scholar 

  • Tominaga K, Kawase S (2019) Two new species of Pseudogobio pike gudgeon (Cypriniformes: Cyprinidae: Gobioninae) from Japan, and redescription of P. esocinus (Temminck and Schlegel 1846). Ichthyol Res 66:488–508

    Article  Google Scholar 

  • Tomoda Y (1970) A preliminary study of the freshwater fish fauna in the Iki-Tsushima Islands. Mem Natl Mus Nat Sci 3:199–210 (in Japanese with English summary)

    Google Scholar 

  • Tsao Y-F, Lin W-W, Chang C-H, Ueda T, Jang-Liaw N-H, Zhao Y-H, Kao H-W (2016) Phylogeography, historical demography, and genetic structure of the rose bitterling, Rhodeus ocellatus (Kner, 1866) (Cypriniformes: Acheilognathidae), in East Asia. Zool Stud 55:49

    Google Scholar 

  • Uematsu T, Aki M (1984) Distribution of the Japanese rose bittering, Rhodeus ocellatus smithi in Kagawa Prefecture. Kagawa Seibutsu 12:7–14 (in Japanese with English abstract)

    Google Scholar 

  • Watanabe K, Kawase S, Mukai T, Kakioka R, Miyazaki J-I, 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. Zool Sci 27:647–655

    Article  Google Scholar 

  • Yoshigou H (2003) Inland water fishes of the Tsushima and Iki Islands, Nagasaki Prefecture, Japan Miscellaneous Rep. Hiwa Mus Nat Hist 42:1–29 (in Japanese with English abstract)

    Google Scholar 

Download references

Acknowledgements

We thank K. Watanabe for providing DNA samples from the Okayama population; R. Tabata for advice on experiments; S. Kato for advice on the manuscript; and S. Kondo for assistance in the laboratory. Computations were performed mainly on the NIG supercomputer at ROIS National Institute of Genetics, Japan. This study was partly supported by Grants-in-Aid for Scientific Research (Nos. 26291078, 18H02499) from the Ministry of Education, Culture, Sports, Science and Technology, Japan.

Author information

Authors and Affiliations

  1. Institute of Natural and Environmental Sciences, University of Hyogo, Yayoigaoka, Sanda, Hyogo, 669-1546, Japan

    Tetsumi Takahashi

  2. Museum of Nature and Human Activities, Yayoigaoka, Sanda, Hyogo, 669-1546, Japan

    Tetsumi Takahashi & Takuya Tanimoto

  3. Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan

    Atsushi J. Nagano & Lina Kawaguchi

  4. Fishery Research Laboratory, Kyushu University, Tsuyazaki, Fukutsu, Fukuoka, 811-3304, Japan

    Norio Onikura

  5. Fukuoka Institute of Health and Environmental Sciences, Mukaizano, Dazaifu, Fukuoka, 818-0135, Japan

    Jun Nakajima

  6. Graduate School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan

    Takuya Miyake, Noriyasu Suzuki & Kouichi Kawamura

  7. Nature Conservation Division, Environmental and Community Affairs Department, Chiba Biodiversity Center, Chiba Prefectural Government, Aoba, Chuo, Chiba, 260-8682, Japan

    Noriyasu Suzuki

  8. College of Liberal Arts and Science, Osaka University of Economics and Law, Yao, Osaka, 581-8511, Japan

    Yoshihiko Kanoh

  9. Faculty of Design Technology, Osaka Sangyo University, Nakagaito, Daito, Osaka, 574-8530, Japan

    Tetsuya Tsuruta

  10. Hyogo Aquatic Zone Network, Mikatadai, Nishi, Kobe, Hyogo, 651-2277, Japan

    Yukio Yasui & Noriyuki Oshima

Authors
  1. Tetsumi Takahashi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Atsushi J. Nagano
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lina Kawaguchi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Norio Onikura
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jun Nakajima
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Takuya Miyake
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Noriyasu Suzuki
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Yoshihiko Kanoh
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Tetsuya Tsuruta
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Takuya Tanimoto
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Yukio Yasui
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Noriyuki Oshima
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Kouichi Kawamura
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Tetsumi Takahashi.

Additional information

Publisher's Note

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

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (NEX 269 kb)

Supplementary file2 (PDF 902 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Takahashi, T., Nagano, A.J., Kawaguchi, L. et al. A ddRAD-based population genetics and phylogenetics of an endangered freshwater fish from Japan. Conserv Genet 21, 641–652 (2020). https://doi.org/10.1007/s10592-020-01275-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10592-020-01275-5

Keywords

Search

Navigation