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

Hydrobiologia - Tập 851 - Trang 1113-1133 - 2023
Hiranya Sudasinghe1,2,3,4, Neelesh Dahanukar5, Rajeev Raghavan6, Tharindu Ranasinghe7, Kumudu Wijesooriya8, Rohan Pethiyagoda9, Lukas Rüber4,10, Madhava Meegaskumbura11
1Evolutionary Ecology and Systematics Laboratory, Department of Molecular Biology and Biotechnology, University of Peradeniya, Peradeniya, Sri Lanka
2Postgraduate Institute of Science, University of Peradeniya, Peradeniya, Sri Lanka
3Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
4Naturhistorisches Museum Bern, Bern, Switzerland
5Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR, Greater Noida, India
6Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies (KUFOS), Kochi, India
7Wild Island Foundation, Moratuwa, Sri Lanka
8Department of Zoology, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
9Ichthyology Section, Australian Museum, Sydney, Australia
10Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
11Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, People’s Republic of China

Tóm tắt

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.

Tài liệu tham khảo

Bandelt, H. J., P. Forster & A. Röhl, 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16: 37–48. Berner, D., 2011. Size correction in biology: how reliable are approaches based on (common) principal component analysis? Oecologia 166: 961–971. 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. 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. 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. 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. Edgar, R. C., 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792–1797. 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. 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. 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. 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. 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. 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. Kottelat, M., 1990. Indochinese Nemacheilines. A Revision of Nemacheiline Loaches (Pisces: Cypriniformes) of Thailand, Burma, Laos, Cambodia and Southern Viet Nam, Pfeil, München. 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. Kottelat, M., 2017. Lepidocephalichthys eleios, a new loach from Lake Indawgyi basin, Kachin State, Myanmar (Teleostei: Cobitidae). Raffles Bulletin of Zoology 65: 707–714. 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. Lê, S., J. Josse & F. Husson, 2008. FactoMineR: an R package for multivariate analysis. Journal of Statistical Software 25: 1–18. Leigh, J. W. & D. Bryant, 2015. POPART: full-feature software for haplotype network construction. Methods in Ecology and Evolution 6: 1110–1116. 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. Pethiyagoda, R., 1991. Freshwater Fishes of Sri Lanka, Wildlife Heritage Trust, Colombo. Pethiyagoda, R. & H. Sudasinghe, 2021. The Ecology and Biogeography of Sri Lanka: A Context for Freshwater Fishes, WHT Publications (Private) Limited, Colombo: Puillandre, N., S. Brouillet & G. Achaz, 2021. ASAP: assemble species by automatic partitioning. Molecular Ecology Resources 21: 609–620. 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. 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. 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. 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. Rüber, L., R. Britz & R. Zardoya, 2006. Molecular phylogenetics and evolutionary diversification of labyrinth fishes (Perciformes: Anabantoidei). Systematic Biology 55: 374–397. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. Tajima, F., 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585–595.
Thông tin
Thông tin xuất bản

Hydrobiologia

Tập 851

1113-1133

Thông tin tác giả