Phenotypic and genotypic variability in the Snowtrout Schizothorax richardsonii (Cypriniformes: Cyprinidae) wild populations from central Himalayan tributaries of the Ganga River basin
DOI:
https://doi.org/10.11609/jott.9541.17.11.27874-27888Keywords:
Schizothorax richardsonii, Phenotypic plasticity, Genetic diversity, COX1 gene, Indian HimalayasAbstract
Schizothorax richardsonii (Gray, 1832), commonly known as Snowtrout, is widely distributed in the Himalayan region of India, particularly in the Ganga River basin tributaries, including Mandakini, Nandakini Pindar, and Alaknanda. Habitat isolation among river ecosystems often drives phenotypic and genotypic differences, leading to changes in fish population structure. In the present study, intraspecific phenotypic and genetic variation in Snowtrout populations from tributaries of the Ganga River basin was assessed to understand their diversity and evolutionary dynamics. Phenotypic and genotypic data were analyzed using a geometric morphometrics approach and the mitochondrial COX1 gene marker. One-hundred-and-ninety specimens were collected from four tributaries of the Ganga River basin. The canonical variates analysis (CVA) confirmed the existence of four phenotypically distinct populations within the Ganga River basin. Principal component one (PC1) based shape wireframe revealed the positions of the pelvic fin, caudal peduncle, and anal fin origin to be important parameters in differentiating these phenotypes. The COX1 sequences revealed three polymorphic sites and five haplotypes overall, including the highest genetic diversity in the Mandakini population (h = 0.67 & л = 0.001). Phylogenetic analysis and Fst-based heatmap showed clear genetic differentiation among the four populations. The distinct phenotypic and genotypic patterns observed among S. richardsonii populations may reflect the combined effects of ecological adaptation and restricted gene flow resulting from anthropogenic barriers, such as dams and altered flow regimes. This study represents the first effort to examine the phenotypic and genotypic variability of Schizothorax richardsonii using an integrated approach that combines geometric morphometrics with the mitochondrial COX1 gene marker, focusing on populations from the Ganga River basin. The observed variations among S. richardsonii populations highlight the importance of maintaining genetic diversity in future management and conservation planning.
References
Anvarifar, H., A. Khyabani, H. Farahmand, S. Vatandoust, H. Anvarifar & S. Jahageerdar (2011). Detection of morphometric differentiation between isolated up-and downstream populations of Siah Mahi (Capoeta capoeta gracilis) (Pisces: Cyprinidae) in the Tajan River (Iran). Hydrobiologia 673: 41–52. https://doi.org/10.1007/s10750-011-0748-7
Begg, G.A., K.D. Friedland & J.B. Pearce (1999). Stock identification and its role in stock assessment and fisheries management: an overview. Fisheries Research 43(1–3): 1–8. https://doi.org/10.1016/S0165-7836(99)00062-4
Bookstein, F.L. (1991). Morphometric Tools for Landmark Data: Geometry and Biology. Cambridge University Press, New York, 435 pp.
Cadrin, S.X., K.D. Friedland & J.R. Waldman (2005). Stock Identification Methods. Elsevier Academic Press, Amsterdam, 153–172 pp. https://doi.org/10.1016/B978-012154351-8/50008-3
Cadrin, S.X. & V.M. Silva (2005). Morphometric variation of yellowtail flounder. ICES Journal of Marine Science 62(4): 683–694. https://doi.org/10.1016/j.icesjms.2005. 02.006
Day, F. (1878). Fishes of India (Vol. 1 and Vol. 2). William Dawson and Sons Ltd., London, 1686 pp.
Devlin, R.H. & Y. Nagahama (2002). Sex determination and sex differentiation in fish: an overview of genetic, physiological, and environmental influences. Aquaculture 208(3–4): 191–364. https://doi.org/10.1016/S0044-8486(02) 00057-1
Daniels, R.R. (2001). Endemic fishes of the Western Ghats and the Satpura hypothesis. Current Science 81(3): 240–244.
Dwivedi, A.K. (2022). Detection of body shape variations in vulnerable snow trout, Schizothorax richardsonii (Gray, 1832) from rivers of the Indian Himalayan Region. Limnologica 97: 126025. https://doi.org/10.1016/j.limno.2022.126025
Excoffier, L. & H.E. Lischer (2010). Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10(3): 564–567. http://doi.org/10.1111/j.1755-0998.2010.02847.x
FAO (2022). The State of World Fisheries and Aquaculture: Towards Blue Transformation. Food and Agriculture Organization, Italy, Rome, 264 pp.
Harris, J.E. (1936). The role of the fins in the equilibrium of the swimming fish: I. Wind-tunnel tests on a model of Mustelus canis (Mitchill). Journal of Experimental Biology 13(4): 476–493. https://doi.org/10.1242/jeb.13.4.476
Hebert, P.D., A. Cywinska, S.L. Ball & J.R. DeWaard (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B: Biological Sciences 270(1512): 313–321. https://doi.org/10.1098/rspb. 2002.2218
Ingram, T. (2015). Diversification of body shape in Sebastes rockfishes of the north-east Pacific. Biological Journal of the Linnean Society 116(4): 805–818. https://doi.org/10.1111/bij.12635
Johns, G.C. & J.C. Avise (1998). A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Molecular Biology and Evolution 15(11): 1481–1490. https://doi.org/10.1093/oxfordjournals.molbev.a025875
Karakousis, Y., C. Triantaphyllidis & P.S. Economidis (1991). Morphological variability among seven populations of brown trout, Salmon trutta L., in Greece. Journal of Fish Biology 38(6): 807–817. https://doi.org/10.1111/j.1095-8649. 1991.tb03620.x
Klingenberg, C.P. (2011). MorphoJ: an integrated software package for geometric morphometrics. Molecular Ecology Resources 11: 353–357. https://doi.org/10.1111/ j.1755-0998.2010.02924.x
Kousar, Y., M. Singh & D. Singh (2025). Stock assessment of Schizothorax richardsonii (Gray, 1832) using geometric morphometrics and mitochondrial marker COX1 from tributaries of the Chenab River, India. Journal of Applied & Natural Science 17(2): 600–613. https://doi.org/10.31018/jans.v17i2.6535
Lakra, W.S., M.S. Verma, M. Goswami, K.K. Lal, V. Mohindra, P. Punia & P.J.M.E.R. Hebert (2011). DNA barcoding Indian marine fishes. Molecular Ecology Resources 11(1): 60–71. https://doi.org/10.1111/j.1755-0998.2010.02894.x
Librado, P. & J. Rozas (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11): 1451–1452. https://doi.org/10.1093/bioinformatics/btp187
Maderbacher, M., C. Bauer, J. Herler, L. Postl, L. Makasa & C. Sturmbauer (2008). Assessment of traditional versus geometric morphometrics for discriminating populations of the Tropheus moorii species complex (Teleostei: Cichlidae), a Lake Tanganyika model for allopatric speciation. Journal of Zoological Systematics and Evolutionary Research 46(2): 153–161. https://doi.org/10.1111/j.1439-0469.2007.00447.x
Mandal, S., A. Singh, P. Sah, R.K. Singh, R. Kumar, K.K. Lal & V. Mohindra (2021). Genetic and morphological assessment of a vulnerable large catfish, Silonia silondia (Hamilton, 1822), in natural populations from India. Journal of Fish Biology 98(2): 430–444. https://doi.org/10.1111/jfb.14590
Mejia, E. & R.E. Reis (2024). Molecular and morphometric data provide evidence of intra specific variation in shape and pigmentation pattern in Otocinclus cocama (Siluriformes: Loricariidae) across major river drainages. Journal of Fish Biology 104(4): 1042–1053. https://doi.org/10.1111/jfb.15639
Min, X.J. & D.A. Hickey (2007). DNA barcodes provide a quick preview of mitochondrial genome composition. PLOS One 2(3): e325. https://doi.org/10.1371/journal.pone.0000325
Mir, F.A., J.I. Mir & S. Chandra (2013). Phenotypic variation in the Snowtrout Schizothorax richardsonii (Gray, 1832) (Actinopterygii: Cypriniformes: Cyprinidae) from the Indian Himalayas. Contributions to Zoology 82(3): 115–122. https://doi.org/10.1163/18759866-08203001
Mirza, M.R. (1991). A contribution to the systematics of the Schizothoracine fishes (Pisces: Cyprinidae) with the description of three new tribes. Pakistan Journal of Zoology 23(4): 339–341.
Murta, A.G., P. Abaunza, F. Cardador & F. Sánchez (2008). Ontogenic migrations of horse mackerel along the Iberian coast. Fisheries Research 89(2): 186–195. https://doi.org/10.1016/j.fishres.2007.09.016
Negi, R.K. & T. Negi (2010). Analysis of morphometric characters of Schizothorax richardsonii (Gray, 1832) from the Uttarkashi District of Uttarakhand State, India. Indian Journal of Biological Science 10(6): 536–540. https://doi.org/10.3923/jbs.2010.536.540
Osburn, R.C. (1906). The functions of the fins of fishes. Science 23(589): 585–587. https://doi.org/10.1126/science.23.589.585
Pandit, M.K. & R.E. Grumbiene (2012). Potential effects of ongoing and proposed hydropower development on terrestrial biological diversity in the Indian Himalaya. Conservation Biology 26(6): 1061–1071. https://doi.org/10.1111/j.1523-1739.2012.01918.x
Qi, D., Y. Chao, S. Guo, L. Zhao, T. Li, F. Wei & X. Zhao (2012). Convergent, parallel, and correlated evolution of trophic morphologies in the subfamily schizothoracinae from the Qinghai-Tibetan plateau. PLoS One 7(3): e34070. https://doi.org/0.1371/journal.pone.0034070
Rabosky, D.L. (2013). Diversity-dependence, ecological speciation, and the role of competition in macroevolution. Annual Review of Ecology, Evolution, and Systematics 44(1): 481–502. https://doi.org/10.1146/annurev-ecolsys-110512-135800
Rajput, V., J.A. Johnson & K. Sivakumar (2013). Environmental effects on the morphology of the Snow Trout Schizothorax richardsonii (Gray, 1832). TAPROBANICA: The Journal of Asian Biodiversity 5(2): 102–110. https://doi.org/10.4038/tapro.v512.6283
Reiss, P. & T.M. Grothues (2015). Geometric morphometric analysis of cyclical body shape changes in color pattern variants of Cichla temensis Humboldt, 1821 (Perciformes: Cichlidae) demonstrates reproductive energy allocation. Neotropical Ichthyology 13(1): 103–112. https://doi.org/10.1590/1982-0224-20140030
Rohlf, F.J. (2008a). tpsUtil (version 1.40). Department of Ecology and Evolution. State University of New York, Stony Brook.
Rohlf, F.J. (2008b). tpsDig (version 2.12). Department of Ecology and Evolution. State University of New York, Stony Brook.
Rohlf, F.J. & D. Slice (1990). Extensions of the Procrustes method for the optimal superimposition of landmarks. Systematic Zoology 39(1): 40–59. https://doi.org/10.2307/2992207
Sanger, F., S. Nicklen & A.R. Coulson (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences 74(12): 5463–5467. https://doi.org/10.1073/pnas.74.12.5463
Sarkar, U.K., A.K. Pathak, R.K. Sinha, K. Sivakumar, A.K. Pandian, A. Pandey & W.S. Lakra (2012). Freshwater fish biodiversity in the River Ganga (India): changing pattern, threats and conservation perspectives. Reviews in Fish Biology and Fisheries 22: 251–272.
Sharma, A., V.K. Dubey, J.A. Johnson, Y.K. Rawal & K. Sivakumar (2021). Is there always space at the top? Ensemble modeling reveals climate-driven high-altitude squeeze for the vulnerable snow trout Schizothorax richardsonii in Himalaya. Ecological Indicators 120: 106900. https://doi.org/10.1016/j.ecolind.2020.106900
Sharma, I. & H.S. Mehta (2010). Studies on Snow Trout Schizothorax richardsonii (Gray) in River Beas and its Tributaries (Himachal Pradesh), India. Zoological Survey of India, 323 pp.
Stange, M., R.D. Barrett & A.P. Hendry (2021). The importance of genomic variation for biodiversity, ecosystems and people. Nature Reviews Genetics 22(2): 89–105. https://doi.org/10.1038/s41576-020-00288-7
Talwar, P.K. & A.G. Jhingran (1991). Inland Fishes of India and Adjacent Countries (Vol. I & II). New Delhi: Oxford and IBH Publishing Company Pvt. Limited, 1158 pp.
Tamura, K., G. Stecher, D. Peterson, A. Filipski & S. Kumar (2021). MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution 38(7): 3022–3027. https://doi.org/10.1093/molbev/msab120
Tickner, D., J.J. Opperman, R. Abell, M. Acreman, A.H. Arthington, S.E. Bunn & L. Young (2020). Bending the curve of global freshwater biodiversity loss: an emergency recovery plan. Bio Science 70(4): 330–342. https://doi.org/10.1093/biosci/biaa002
Turan, C., D. Ergüden, M. Gürlek, N. Başusta & F. Turan (2004). Morphometric structuring of the anchovy (Engraulis encrasicolus L.) in the Black, Aegean and Northeastern Mediterranean Seas. Turkish Journal of Veterinary & Animal Sciences 28(5): 865–871.
Turak, E., I. Harrison, D. Dudgeon, R. Abell, A. Bush, W. Darwall, C.M. Finlayson, S. Ferrier, J. Freyhof, V. Hermoso, D. Juffe-Bignoli, S. Linke, J. Nel, H.C. Patricio, J. Pittock, R. Raghavan, C. Revenga, J.P. Simaika & A. de Wever (2017). Essential biodiversity variables for measuring change in global freshwater biodiversity. Biological Conservation 213: 272–279. https://doi.org/10.1016/j.biocon.2016.09.005
Veasey, E.A., E. A. Schammass, R. Vencovsky, P.S. Martins & G. Bandel (2001). Germplasm characterization of Sesbania accessions based on multivariate analyses. Genetic Resources and Crop Evolution 48(1): 79–91. https://doi.org/10.1023/A:1011238320630
Vishwanath, W. (2010). Schizothorax richardsonii (errata version published in 2020). The IUCN Red List of Threatened Species 2010. Downloaded on 13.vi.2020. https://doi.org/10.2305/IUCN.UK.2010–4.RLTS.T166525A174786567.en
Ward, R.D., T.S. Zemlak, B.H. Innes, P.R. Last & P.D. Hebert (2005). DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society B: Biological Sciences 360(1462): 1847–1857. https://doi.org/10.1098/rstb.2005.1716
Xiao, S., Z. Mou, D. Fan, H. Zhou, M. Zou, Y. Zou & H. Liu (2020). Genome of tetraploid fish Schizothorax o’connori provides insights into early re-diploidization and high-altitude adaptation. Science 23(9): 101497. https://doi.org/10.1016/j.isci.2020.101497
Published
Versions
- 27-11-2025 (2)
- 26-11-2025 (1)
Issue
Section
License
Copyright (c) 2025 Yasmeen Kousar, Mahender Singh, Deepak Singh
This work is licensed under a Creative Commons Attribution 4.0 International License.
Authors own the copyright to the articles published in JoTT. This is indicated explicitly in each publication. The authors grant permission to the publisher Wildlife Information Liaison Development (WILD) Society to publish the article in the Journal of Threatened Taxa. The authors recognize WILD as the original publisher, and to sell hard copies of the Journal and article to any buyer. JoTT is registered under the Creative Commons Attribution 4.0 International License (CC BY), which allows authors to retain copyright ownership. Under this license the authors allow anyone to download, cite, use the data, modify, reprint, copy and distribute provided the authors and source of publication are credited through appropriate citations (e.g., Son et al. (2016). Bats (Mammalia: Chiroptera) of the southeastern Truong Son Mountains, Quang Ngai Province, Vietnam. Journal of Threatened Taxa 8(7): 8953–8969. https://doi.org/10.11609/jott.2785.8.7.8953-8969). Users of the data do not require specific permission from the authors or the publisher.
