Skip to main content
SpringerLink
Log in

Discovery of a genetically distinct lineage in medaka species within Lake Towuti in central Sulawesi

  • Short Report
  • Published:
Ichthyological Research Aims and scope Submit manuscript

Abstract

Oryzias marmoratus and Oryzias profundicola in Lake Towuti in Sulawesi are considered to have experienced ancient admixture with a lineage phylogenetically close to the extant O. marmoratus in Lake Lantoa. However, the admixture may be ongoing because these lakes are currently connected to each other by rivers. In this study, we examined population genetic structures of O. marmoratus and O. profundicola in Lake Towuti and adjacent lakes. Mitochondrial and microsatellite analyses revealed that O. marmoratus and O. profundicola in Lake Towuti are generally clearly separated from O. marmoratus in Lake Lantoa. However, we found one O. marmoratus individual in Lake Towuti shared a mitochondrial haplotype and a large fraction of ancestry with the Lantoa O. marmoratus. The discovery of this Lantoa-type individual in Lake Towuti suggests that either dispersal of individuals from Lake Lantoa to Lake Towuti is ongoing, or that there is another unknown population within Lake Towuti that originated from ancient admixture.

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

Similar content being viewed by others

References

  • Ahmad W (1978) Proceedings: geology along the Matano fault zone, East Sulawesi, Indonesia. In: Wiryosujono S, Sudrajat A (eds) Proceedings: regional conference on the geology and mineral resources of Southeast Asia, Jakarta, 4–7 August 1975. Indonesian Association of Geologists, Jakarta, pp 143–150

  • Ansai S, Mochida K, Fujimoto S, Mokodongan DF, Sumarto BKA, Masengi KWA, Hadiaty RK, Nagano AJ, Toyoda A, Naruse K, Yamahira K, Kitano J (2021) Genome editing reveals fitness effects of a gene for sexual dichromatism in Sulawesian fishes. Nat Commun 12:1350

    Article  CAS  Google Scholar 

  • Brooks JL (1950) Speciation in ancient lakes. Q Rev Biol 25:131–176

    Article  CAS  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  Google Scholar 

  • Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587

    Article  CAS  Google Scholar 

  • Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7:574–578

    Article  CAS  Google Scholar 

  • Francis RM (2017) pophelper: an R package and web app to analyse and visualize population structure. Mol Ecol Resour 17:27–32

    Article  CAS  Google Scholar 

  • Goudet J (2005) Hierfstat, a package for R to compute and test hierarchical F-statistics. Mol Ecol Notes 5:184–186

    Article  Google Scholar 

  • Herder F, Chapuis S (2010) Oryzias hadiatyae, a new species of ricefish (Atherinomorpha: Beloniformes: Adrianichthyidae) endemic to Lake Masapi, Central Sulawesi, Indonesia. Raffles Bull Zool 58:269–280

    Google Scholar 

  • Hilgers L, Schwarzer J (2019) The untapped potential of medaka and its wild relatives. eLife 8:e46994

  • Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 9:1322–1332

    Article  Google Scholar 

  • Inomata N, Hironaka K, Sawada K, Kuriwada T, Yamahira K (2015) Discrepancy in the degree of population differentiation between color-morph frequencies and neutral genetic loci in the damselfly Ischnura senegalensis in Okinawa Island, Japan. Genetica 143:271–277

    Article  Google Scholar 

  • Kottelat M (1990) The ricefishes (Oryziidae) of the Malili Lakes, Sulawesi, Indonesia, with description of a new species. Ichthyol Explor Freshw 1:151–166

    Google Scholar 

  • Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A (2019) RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35:4453–4455

    Article  CAS  Google Scholar 

  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 35:1547–1549

    Article  CAS  Google Scholar 

  • 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. J Evol Biol 34:1767–1780

    Article  CAS  Google Scholar 

  • Mokodongan DF, Yamahira K (2015) Origin and intra-island diversification of Sulawesi endemic Adrianichthyidae. Mol Phylogenet Evol 93:150–160

    Article  Google Scholar 

  • Parenti LR (2008) A phylogenetic analyses and taxonomic revision of ricefishes, Oryzias and relatives (Beloniformes, Adrianichthyidae). Zool J Linn Soc 154:494–610

    Article  Google Scholar 

  • Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537–2539

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249

    Article  Google Scholar 

  • Russell JM, Vogelb H, Bijaksanac S, Mellesd M, Deinoe A, Hafidzc A, Haffnerf D, Hasbergd AKM, Morlockb M, von Rinteleng T, Shepparda R, Stelbrinkh B, Stevensoni J (2020) The late quaternary tectonic, biogeochemical, and environmental evolution of ferruginous Lake Towuti, Indonesia. Paleogeogr Paleoclimatol Paleoecol 556:109905

  • Wilson ME, Moss SJ (1999) Cenozoic paleogeographic evolution of Sulawesi and Borneo. Paleogeogr Paleoclimatol Paleoecol 145:303–337

    Article  Google Scholar 

Download references

Acknowledgments

We thank the Ministry of Research, Technology, and Higher Education, Republic of Indonesia (RISTEKDIKTI), Indonesian Institute of Science (LIPI), and the Faculty of Fisheries and Marine Science, Sam Ratulangi University for the permit to conduct research in Sulawesi (research permit numbers 394/SIP/FRP/SM/XI/2014). We thank Marianne Fish, PhD, from Edanz (http://jp.edanz.com/ac) for editing a draft of this manuscript. This study was supported by the Collaborative Research of Tropical Biosphere Research Center, University of the Ryukyus, to JK and JSPS KAKENHI Grant Number 26291093 to KY.

Author information

Authors and Affiliations

  1. Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, 903-0213, Japan

    Kazunori Yamahira

  2. Museum Zoologicum Bogoriense, Research Center for Biology, National Research and Innovation Agency, Cibinong, 16911, Indonesia

    Daniel F. Mokodongan

  3. Department of Environmental Science, Fukuoka Women’s University, Fukuoka, 813-8529, Japan

    Maki Konishi & Nobuyuki Inomata

  4. Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado, 95115, Indonesia

    Ixchel F. Mandagi & Kawilarang W. A. Masengi

  5. Faculty of Fisheries and Marine Science, Halu Oleo University, Kendari, 93232, Indonesia

    Sjamsu A. Lawelle

  6. Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, 819-0395, Japan

    Junko Kusumi

Authors
  1. Kazunori Yamahira
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Daniel F. Mokodongan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Maki Konishi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ixchel F. Mandagi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kawilarang W. A. Masengi
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Sjamsu A. Lawelle
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Junko Kusumi
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Nobuyuki Inomata
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Kazunori Yamahira or Nobuyuki Inomata.

Additional information

Publisher's Note

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

Supplementary Information

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yamahira, K., Mokodongan, D.F., Konishi, M. et al. Discovery of a genetically distinct lineage in medaka species within Lake Towuti in central Sulawesi. Ichthyol Res 70, 185–189 (2023). https://doi.org/10.1007/s10228-021-00856-9

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10228-021-00856-9

Keywords

Search

Navigation