Skip to main content
SpringerLink
Log in

The loach genus Lepidocephalichthys (Teleostei: Cobitidae) in Sri Lanka and peninsular India: multiple colonizations and unexpected species diversity

  • Primary Research Paper
  • Published:
Hydrobiologia Aims and scope Submit manuscript

Abstract

Loaches of the genus Lepidocephalichthys are ubiquitous in Peninsular India and the nearby continental-shelf island of Sri Lanka. Four valid species are reported from this region: L. thermalis, a species reported from across this region; L. jonklaasi, confined to rainforests in southern Sri Lanka; L. coromandelensis, from the Eastern Ghats and L. guntea, from the northern Western Ghats of the Indian peninsula. Here, based on collections from 25 locations in 13 river basins in Sri Lanka and 20 locations across India, including a dataset downloaded from GenBank, we present a molecular phylogeny constructed from the mitochondrial cytochrome b (cytb) and cytochrome c oxidase subunit 1 (cox1) sequences. We show that ancestral Lepidocephalichthys colonized Sri Lanka in the late Miocene. Multiple back-migrations to India, as well as colonizations from the mainland, took place in the Plio-Pleistocene. The persistence on the island of L. jonklaasi, an obligatory rainforest associate, suggests that perhumid refugia existed in Sri Lanka throughout this time. Lepidocephalichthys thermalis appears to have colonized the Sri Lankan highlands as recently as the Pleistocene. The data suggest that Lepidocephalichthys thermalis is a species complex in which multiple species remain to be investigated and described, both in India and Sri Lanka.

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
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Bandelt, H. J., P. Forster & A. Röhl, 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16: 37–48.

    Article  CAS  PubMed  Google Scholar 

  • Berner, D., 2011. Size correction in biology: how reliable are approaches based on (common) principal component analysis? Oecologia 166: 961–971.

    Article  PubMed  ADS  Google Scholar 

  • Blaxter, M., J. Mann, T. Chapman, F. Thomas, C. Whitton, R. Floyd & E. Abebe, 2005. Defining operational taxonomic units using DNA barcode data. Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1935–1943.

    Article  CAS  Google Scholar 

  • Bossuyt, F., M. Meegaskumbura, N. Beenaerts, D. J. Gower, R. Pethiyagoda, K. Roelants, A. Mannaert, M. Wilkinson, M. M. Bahir, K. Manamendra-Arachchi, P. K. L. Ng, C. J. Schneider, O. V. Oommen & M. C. Milinkovitch, 2004. Local endemism within the Western Ghats-Sri Lanka biodiversity hotspot. Science 306: 479–481.

    Article  CAS  PubMed  ADS  Google Scholar 

  • Bouckaert, R., J. Heled, D. Kühnert, T. Vaughan, C.-H. Wu, D. Xie, M. A. Suchard, A. Rambaut & A. J. Drummond, 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10: e1003537.

    Article  PubMed  PubMed Central  Google Scholar 

  • Dahanukar, N., S. Philip, K. Krishnakumar, A. Ali & R. Raghavan, 2013. The phylogenetic position of Lepidopygopsis typus (Teleostei: Cyprinidae), a monotypic freshwater fish endemic to the Western Ghats of India. Zootaxa 3700: 113–139.

    Article  PubMed  Google Scholar 

  • Edgar, R. C., 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792–1797.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fox, J. & S. Weisberg, 2019. An R Companion to Applied Regression. Sage, Thousand Oaks [available on internet at https://socialsciences.mcmaster.ca/jfox/Books/Companion/].

  • Fricke, R., W. N. Eschmeyer & R. Van der Laan, 2023. Eschmeyer’s catalog of fishes: genera, species, references [available on internet at http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp].

  • Fu, Y. X. & W. H. Li, 1993. Statistical tests of neutrality of mutations. Genetics 133: 693–709.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • GEBCO Bathymetric Compilation Group. 2020. The GEBCO_2020 grid - A continuous terrain model of the global oceans and land. British Oceanographic Data Centre, National Oceanography Centre, NERC, UK. https://doi.org/10.5285/a29c5465-b138-234d-e053-6c86abc040b9

  • Havird, J. C. & L. M. Page, 2010. A revision of Lepidocephalichthys (Teleostei: Cobitidae) with descriptions of two new species from Thailand, Laos, Vietnam, and Myanmar. Copeia 2010: 137–159.

    Article  Google Scholar 

  • Hoang, D. T., O. Chernomor, A. von Haeseler, B. Q. Minh & L. S. Vinh, 2018. UFBoot2: improving the ultrafast bootstrap approximation. Molecular Biology and Evolution 35: 518–522.

    Article  CAS  PubMed  Google Scholar 

  • Kalyaanamoorthy, S., B. Q. Minh, T. K. F. Wong, A. von Haeseler & L. S. Jermiin, 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods 14: 587–589.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kapli, P., S. Lutteropp, J. Zhang, K. Kobert, P. Pavlidis, A. Stamatakis & T. Flouri, 2017. Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics 33: 1630–1638.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Keskar, A., R. Raghavan, M. S. Paingankar, P. Kumkar, U. Katwate, S. Jadhav, A. Padhye & N. Dahanukar, 2018. Molecular phylogeny unveils hidden diversity of hillstream loaches (Cypriniformes: Cobitoidea) in the northern Western Ghats of India. Meta Gene 17: 237–248.

    Article  Google Scholar 

  • Kottelat, M., 1990. Indochinese Nemacheilines. A Revision of Nemacheiline Loaches (Pisces: Cypriniformes) of Thailand, Burma, Laos, Cambodia and Southern Viet Nam, Pfeil, München.

    Google Scholar 

  • Kottelat, M., 2012. Conspectus cobitidum: an inventory of the loaches of the world (Teleostei: Cypriniformes: Cobitoidei). The Raffles Bulletin of Zoology 26(Supplement): 1–199.

    Google Scholar 

  • Kottelat, M., 2017. Lepidocephalichthys eleios, a new loach from Lake Indawgyi basin, Kachin State, Myanmar (Teleostei: Cobitidae). Raffles Bulletin of Zoology 65: 707–714.

    Google Scholar 

  • Kumar, S., G. Stecher & K. Tamura, 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33: 1870–1874.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lê, S., J. Josse & F. Husson, 2008. FactoMineR: an R package for multivariate analysis. Journal of Statistical Software 25: 1–18.

    Article  Google Scholar 

  • Leigh, J. W. & D. Bryant, 2015. POPART: full-feature software for haplotype network construction. Methods in Ecology and Evolution 6: 1110–1116.

    Article  Google Scholar 

  • Minh, B. Q., H. A. Schmidt, O. Chernomor, D. Schrempf, M. D. Woodhams, A. von Haeseler & R. Lanfear, 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution 37: 1530–1534.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pethiyagoda, R., 1991. Freshwater Fishes of Sri Lanka, Wildlife Heritage Trust, Colombo.

    Google Scholar 

  • Pethiyagoda, R. & H. Sudasinghe, 2021. The Ecology and Biogeography of Sri Lanka: A Context for Freshwater Fishes, WHT Publications (Private) Limited, Colombo:

    Google Scholar 

  • Puillandre, N., S. Brouillet & G. Achaz, 2021. ASAP: assemble species by automatic partitioning. Molecular Ecology Resources 21: 609–620.

    Article  PubMed  Google Scholar 

  • R Core Team, 2020. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna [available on internet at https://www.R-project.org].

  • Reuter, M., M. Harzhauser & W. E. Piller, 2021. The role of sea-level and climate changes in the assembly of Sri Lankan biodiversity: a perspective from the Miocene Jaffna limestone. Gondwana Research 91: 152–165.

    Article  ADS  Google Scholar 

  • Roberts, P., N. Perera, O. Wedage, S. Deraniyagala, J. Perera, S. Eregama, M. D. Petraglia & J. A. Lee-Thorp, 2017. Fruits of the forest: human stable isotope ecology and rainforest adaptations in Late Pleistocene and Holocene (∼ 36 to 3 ka) Sri Lanka. Journal of Human Evolution 106: 102–118.

    Article  PubMed  Google Scholar 

  • Rozas, J., A. Ferrer-Mata, J. C. Sánchez-DelBarrio, S. Guirao-Rico, P. Librado, S. E. Ramos-Onsins & A. Sánchez-Gracia, 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution 34: 3299–3302.

    Article  CAS  PubMed  Google Scholar 

  • Rüber, L., R. Britz, S. O. Kullander & R. Zardoya, 2004. Evolutionary and biogeographic patterns of the Badidae (Teleostei: Perciformes) inferred from mitochondrial and nuclear DNA sequence data. Molecular Phylogenetics and Evolution 32: 1010–1022.

    Article  PubMed  Google Scholar 

  • Rüber, L., R. Britz & R. Zardoya, 2006. Molecular phylogenetics and evolutionary diversification of labyrinth fishes (Perciformes: Anabantoidei). Systematic Biology 55: 374–397.

    Article  PubMed  Google Scholar 

  • Rüber, L., M. Kottelat, H. Tan, P. K. Ng & R. Britz, 2007. Evolution of miniaturization and the phylogenetic position of Paedocypris, comprising the world’s smallest vertebrate. BMC Evolutionary Biology 7: 38.

    Article  PubMed  PubMed Central  Google Scholar 

  • Sudasinghe, H., R. H. T. Ranasinghe, S. de A. Goonatilake & M. Meegaskumbura, 2018. A review of the genus Labeo (Teleostei: Cyprinidae) in Sri Lanka. Zootaxa 4486: 201–235.

    Article  PubMed  Google Scholar 

  • Sudasinghe, H., R. Pethiyagoda & M. Meegaskumbura, 2020a. Evolution of Sri Lanka’s Giant Danios (Teleostei: Cyprinidae: Devario): teasing apart species in a recent diversification. Molecular Phylogenetics and Evolution 149: 106853.

    Article  PubMed  Google Scholar 

  • Sudasinghe, H., R. Pethiyagoda & M. Meegaskumbura, 2020b. A molecular phylogeny of the genus Laubuka (Teleostei: Cyprinidae) in Sri Lanka reveals multiple origins and a cryptic species. Systematics and Biodiversity 18: 592–613.

    Article  Google Scholar 

  • Sudasinghe, H., R. Pethiyagoda, R. Raghavan, N. Dahanukar, L. Rüber & M. Meegaskumbura, 2020c. Diversity, phylogeny and biogeography of Systomus (Teleostei, Cyprinidae) in Sri Lanka. Zoologica Scripta 49: 710–731.

    Article  Google Scholar 

  • Sudasinghe, H., R. Pethiyagoda, R. H. T. Ranasinghe, R. Raghavan, N. Dahanukar & M. Meegaskumbura, 2020d. A molecular phylogeny of the freshwater-fish genus Rasbora (Teleostei: Cyprinidae) in Sri Lanka reveals a remarkable diversification- and a cryptic species. Journal of Zoological Systematics and Evolutionary Research 58: 1076–1110.

    Article  Google Scholar 

  • Sudasinghe, H., R. H. T. Ranasinghe, R. Pethiyagoda, M. Meegaskumbura & R. Britz, 2020e. Genetic diversity and morphological stasis in the Ceylon Snakehead, Channa orientalis (Teleostei: Channidae). Ichthyological Research 68: 67–80.

    Article  Google Scholar 

  • Sudasinghe, H., N. Dahanukar, R. Raghavan, T. Senavirathna, D. J. Shewale, M. S. Paingankar, A. Amarasinghe, R. Pethiyagoda, L. Rüber & M. Meegaskumbura, 2021a. Island colonization by a ‘rheophilic’ fish: the phylogeography of Garra ceylonensis (Teleostei: Cyprinidae) in Sri Lanka. Biological Journal of the Linnean Society 132: 872–893.

    Article  Google Scholar 

  • Sudasinghe, H., R. Raghavan, N. Dahanukar, R. Pethiyagoda, L. Rüber & M. Meegaskumbura, 2021b. Diversification and biogeography of Dawkinsia (Teleostei: Cyprinidae) in the Western Ghats-Sri Lanka Biodiversity Hotspot. Organisms Diversity & Evolution 21: 795–820.

    Article  Google Scholar 

  • Sudasinghe, H., T. Ranasinghe, J. Herath, K. Wijesooriya, R. Pethiyagoda, L. Rüber & M. Meegaskumbura, 2021c. Molecular phylogeny and phylogeography of the freshwater-fish genus Pethia (Teleostei: Cyprinidae) in Sri Lanka. BMC Ecology and Evolution. https://doi.org/10.1186/s12862-021-01923-5.

    Article  PubMed  PubMed Central  Google Scholar 

  • Tajima, F., 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585–595.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

HS and MM are grateful to the Director General of Wildlife Conservation and the Conservator General of Forests, Sri Lanka, for permits to carry out fieldwork. HS and TR thanks Charana Widuranga, Dhanushka Lakshan and Supun Chandana for assistance in the field. We thank two anonymous referees for reviewing the manuscript.

Author information

Authors and Affiliations

  1. Evolutionary Ecology and Systematics Laboratory, Department of Molecular Biology and Biotechnology, University of Peradeniya, Peradeniya, 20400, Sri Lanka

    Hiranya Sudasinghe

  2. Postgraduate Institute of Science, University of Peradeniya, Peradeniya, 20400, Sri Lanka

    Hiranya Sudasinghe

  3. Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, 3012, Bern, Switzerland

    Hiranya Sudasinghe

  4. Naturhistorisches Museum Bern, Bernastrasse, 15, 3005, Bern, Switzerland

    Hiranya Sudasinghe & Lukas Rüber

  5. Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR, Greater Noida, India

    Neelesh Dahanukar

  6. Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies (KUFOS), Kochi, India

    Rajeev Raghavan

  7. Wild Island Foundation, 6A, Mendis Lane, Moratuwa, 10400, Sri Lanka

    Tharindu Ranasinghe

  8. Department of Zoology, Faculty of Science, University of Peradeniya, Peradeniya, 20400, Sri Lanka

    Kumudu Wijesooriya

  9. Ichthyology Section, Australian Museum, Sydney, NSW, Australia

    Rohan Pethiyagoda

  10. Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012, Bern, Switzerland

    Lukas Rüber

  11. Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, 530004, Guangxi, People’s Republic of China

    Madhava Meegaskumbura

Authors
  1. Hiranya Sudasinghe
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Neelesh Dahanukar
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rajeev Raghavan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Tharindu Ranasinghe
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kumudu Wijesooriya
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Rohan Pethiyagoda
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Lukas Rüber
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Madhava Meegaskumbura
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Madhava Meegaskumbura.

Ethics declarations

Conflict of interest

Partial financial support to carry out the research was received from the Wildlife Heritage Trust of Sri Lanka to HS. The authors have no competing interests to declare that are relevant to the content of this article.

Additional information

Handling editor: Louise Chavarie

Publisher's Note

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

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (JPG 3656 KB)

Figure S1. Diversity of color pattern in Sri Lankan Lepidocephalichthys in preservation. a DZ4060A, L. jonklaasi, 46.1 mm SL, female, Dombagaskanda Forest Reserve, Kalu basin; b DZ4948, L. jonklaasi, 49.4 mm SL, male, Kottawa Forest Reserve, Gin basin; c DZ4054, L. thermalis, L6.IV, 37.7 mm SL, male, Aranyake, Ma Oya basin; d DZ3944A, L. thermalis, L6.IV, 42.0 mm SL, female, Halwala, Kalu basin; e DZ4147, L. thermalis, L6.II, 33.2 mm SL, male, topotypes, Kantale, Mahaweli basin; f DZ3908A, L. thermalis, L6.II, 51.0 mm SL, female, Peradeniya, Mahaweli basin; g DZ4658B, L. cf. thermalis, L5, 49.0 mm SL, female, Badalkumbura, Menik basin; and h DZ4690C, L. cf. thermalis, L5, 42.8 mm SL, male, Buttala, Menik basin.

Supplementary file2 (DOCX 49 KB)

Supplementary file3 (DOCX 12 KB)

Supplementary file4 (DOCX 13 KB)

Supplementary file5 (DOCX 14 KB)

Supplementary file6 (DOCX 16 KB)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sudasinghe, H., Dahanukar, N., Raghavan, R. et al. The loach genus Lepidocephalichthys (Teleostei: Cobitidae) in Sri Lanka and peninsular India: multiple colonizations and unexpected species diversity. Hydrobiologia 851, 1113–1133 (2024). https://doi.org/10.1007/s10750-023-05321-4

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10750-023-05321-4

Keywords

Search

Navigation