Abstract
The tire track eel, Mastacembelus favus, is an economically important freshwater fish in mainland Southeast Asia. Understanding the spatial population structure is important to design an effective and efficient management of the species. The aim of this study was to investigate the genetic diversity and structure of M. favus populations. In total, 519 individuals from 30 locations across its distribution range were genotyped using a set of eight polymorphic microsatellite loci. Results showed that populations in Mekong and Chao Phraya exhibited higher genetic variability than those from Gulf of Thailand and Malay–Thai Peninsula. Clustering results revealed two evolutionarily isolated groups geographically separated at Northeastern Cambodia; the more widespread group was further divided into two subclusters. The spatial genetic variation and structure of its populations are attributed to the evolutionary history and population dynamics of the species. The study provides important information for the management and conservation of M. favus in Southeast Asia.
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References
Adamson EAS (2010) Influence of historical landscapes, drainage evolution and ecological traits on patterns of genetic diversity in Southeast Asian freshwater snakehead fishes. Unpublished D. Phil. Thesis, Queensland University of Technology, Brisbane
Adamson EAS, Hurwood DA, Mather PA (2012) Insights into historical drainage evolution based on the phylogeography of the chevron snakehead fish (Channa striata) in the Mekong Basin. Freshw Biol 57:2211–2229
Beck SV, Carvalho GR, Barlow A, Rüber L, Hui Tan H, Nugroho E, Wowor D, Mohd Nor SA, Herder F, Muchlisin ZA, de Bruyn M (2017) Plio-Pleistocene phylogeography of the Southeast Asian Blue Panchax killifish, Aplocheilus panchax. PLoS ONE 12:e0179557
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol 57:289–300
Bernatchez L (2016) On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes. J Fish Biol 89:2519–2556
Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001–2014
de Bruyn M, Rüber L, Nylinder S, Stelbrink B, Lovejoy NR, Lavoué S, Tan HH, Nugroho E, Wowor D, Ng PK, Siti Azizah MN, von Rintelen T, Hall R, Carvalho GR (2013) Paleo-drainage basin connectivity predicts evolutionary relationships across three Southeast Asian biodiversity hotspots. Syst Biol 62:398–410
DeWoody JA, Avise JC (2000) Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. J Fish Biol 56:461–473
di Rienzo A, Peterson AC, Garza JC, Valdes AM, Freimer NB (1994) Mutational processes of simple-sequence repeat loci in human populations. Proc Natl Acad Sci U S A 91:3166–3170
Dodson JJ, Colombani F, Ng PKL (1995) Phylogeographic structure in the mitochondrial DNA of a South-east Asian freshwater fish, Hemibagrus nemurus (Siluroidei; Bagridae) and Pleistocene sea-level changes on the Sunda shelf. Mol Ecol 4:331–346
Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361
Emerson BC, Hewitt GM (2005) Phylogeography. Curr Biol 15:R367–R371
Esa Y, Abdul Rahim KA (2013) Genetic structure and preliminary findings of cryptic diversity of the Malaysian Mahseer (Tor tambroides Valenciennes: Cyprinidae) inferred from mitochondrial DNA and microsatellite analyses. Biomed Res Int 2013:170980
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
Excoffier L, Lischer HE (2010) Arlequin suite ver. 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567
Faulks LK, Gilligan DM, Beheregaray LB (2011) The role of anthropogenic vs. natural in-stream structures in determining connectivity and genetic diversity in an endangered freshwater fish, Macquarie perch (Macquaria australasica). Evol Appl 4:589–601
Ferreira DG, Galindo BA, Frantine-Silva W, Almeida FS, Sofia SH (2015) Genetic structure of a Neotropical sedentary fish revealed by AFLP, microsatellite and mtDNA markers: a case study. Conserv Genet 16:151–166
Fluker BL, Kuhajda BR, Harris PM (2014) The effects of riverine impoundment on genetic structure and gene flow in two stream fishes in the Mobile River basin. Freshw Biol 59:526–543
Frankham R (1996) Relationship of genetic variation to population size in wildlife. Conserv Biol 10:1500–1508
Frankham R (2009) Genetic architecture of reproductive fitness and its consequences. In: van der Werf J, Graser H-U, Frankham R, Gondro C (eds) Adaptation and fitness in animal populations: evolutionary and breeding perspectives on genetic resource management. Springer, Dordrecht, the Netherlands, pp 15–39
Frankham R, Ballou JD, Briscoe DA (2002) Introduction to conservation genetics. Cambridge University Press, Cambridge
Froese R, Pauly D (eds) (2016) FishBase. World Wide Web electronic publication. http://www.fishbase.org. Accessed 24 January 2016
Goudet J (1995) FSTAT (Version 1.2): a computer program to calculate F statistics. J Hered 86:485–486
Hale ML, Burg TM, Steeves TE (2012) Sampling for microsatellite-based population genetic studies: 25 to 30 individuals per population is enough to accurately estimate allele frequencies. PLoS ONE 7:e45170
Halls A (2010) Estimation of annual yield of fish by guild in the lower Mekong Basin: report for the NIES/the WorldFish Center project: scenario‐based assessment of the potential effects of alternative dam construction schemes on freshwater fish diversity in the Lower Mekong Basin. WorldFish Center, Phnom Penh
Haque AKMA, Middendorp HAJ, Hasan MR (1999) Impact of carp stocking on the abundance and biodiversity of non-stocked indigenous fish species in culture based fisheries in oxbow lakes. In: Middendorp HAJ, Thompson PM, Pomeroy RS (eds) Sustainable inland fisheries management in Bangladesh. NHBS Ltd, Devon, pp 141–148
Hartl DL, Clark AG (1997) Principles of Population Genetics, third edition. Sinauer Associates Inc, Sunderland, Massachusetts
Hewitt G (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biol J Linn Soc 58:247–276
Hurwood DA, Adamson EAS, Mather PB (2008) Evidence for strong genetic structure in a regionally important, highly vagile cyprinid (Henicorhynchus lobatus) in the Mekong river basin. Ecol Freshw Fish 17:273–283
Hurwood DA, Dammannagoda S, Krosch MN, Salin KR, Youssef A-BH, de Bruyn M, Mather PB (2014) Impacts of climatic factors on evolution of molecular diversity and the natural distribution of wild stocks of the giant freshwater prawn (Macrobrachium rosenbergii). Freshw Sci 33:217–231
Jaisuk C, Senanan W (2018) Effects of landscape features on population genetic variation of a tropical stream fish, Stone lapping minnow, Garra cambodgiensis, in the upper Nan River drainage basin, northern Thailand. PeerJ 6:e4487
Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806
Jamaluddin JAF, So N, Bui MT, Amiruddin A, Chaiwut G, Page LM, Khaironizam MZ, Siti Azizah MN (2019) Genetic variation, demographic history and phylogeography of tire track eel, Mastacembelus favus (Synbranchiformes: mastacembelidae) in Southeast Asia. Hydrobiologia 838:163–182
Jamsari AFJ, So N, Tam BM, Siti-Azizah MN (2014) Isolation and characterisation of microsatellite loci in the tire track eel, Mastacembelus favus and cross-species amplification. Conserv Genet Resour 6:477–479
Krützen M, Beasley I, Ackermann CY, Lieckfeldt D, Ludwig A, Ryan GE, Bejder L, Parra GJ, Wolfensberger R, Spencer PBS (2018) Demographic collapse and low genetic diversity of the Irrawaddy dolphin population inhabiting the Mekong River. PLoS ONE 13:e0189200
Lacy RC (1997) Importance of genetic variation to the viability of mammalian populations. J Mammal 78:320–335
Lemopoulos A, Prokkola JM, Uusi-Heikkilä S, Vasemägi A, Huusko A, Hyvärinen P, Koljonen ML, Koskiniemi J, Vainikka A (2019) Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation. Ecol Evol 9:2106–2120
Lukoschek V, Osterhage JL, Karns DR, Murphy JC, Voris HK (2011) Phylogeography of the Mekong mud snake (Enhydris subtaeniata): the biogeographic importance of dynamic river drainages and fluctuating sea levels for semiaquatic taxa in Indochina. Ecol Evol 1:330–342
McConnell SKJ (2004) Mapping aquatic faunal exchanges across the Sunda shelf, South-east Asia, using distributional and genetic data sets from the cyprinid fish Barbodes gonionotus (Bleeker, 1858). J Nat Hist 38:651–670
MRC (Mekong River Commission) (2015) Fisheries research and development in the Mekong Region. Catch and Culture 21:1–48
Na-Nakorn U, Kamonrat W, Ngamsiri T (2004) Genetic diversity of walking catfish, Clarias macrocephalus, in Thailand and evidence of genetic introgression from introduced farmed C. gariepinus. Aquaculture 240:145–163
Nazia AK (2014) Phylogeography and genetic variation of the bighead catfish, Clarias macrocephalus (Günther, 1864) from Peninsular Malaysia and Mekong river basin based on mitochondrial and microsatellite markers. Unpublished D. Phil. Thesis, Universiti Sains Malaysia, Penang
Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York
Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 19:153–170
Ngamsiri T, Nakajima M, Sukmanomon S, Sukumasavin N, Kamonrat W, Na-Nakorn K, Taniguchi N (2007) Genetic diversity of wild Mekong giant catfish Pangasianodon gigas collected from Thailand and Cambodia. Fish Sci 73:792–799
Nguyen TT, Sunnucks P (2012) Strong population genetic structure and its management implications in the mud carp Cirrhinus molitorella, an indigenous freshwater species subject to an aquaculture and culture-based fishery. J Fish Biol 80:651–668
Petit RJ, El Mousadik AE, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12:844–855
Piry S, Luikart G, Cornuet J-M (1999) BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. J Hered 90:502–503
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Rainboth WJ (1996) Fishes of the Cambodian Mekong. Food and Agricultural Organisation of the United Nations, Rome
Reed DH, Frankham R (2003) Correlation between fitness and genetic diversity. Conserv Biol 17:230–237
Roberts TR (1986) Systematic review of the Mastacembelidae or spiny eels of Burma and Thailand, with description of two new species of Macrognathus. Jpn J Ichthyol 33:95–109
Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138
Shen Y, Wang L, Fu J, Xu X, Yue GH, Li J (2019) Population structure, demographic history and local adaptation of the grass carp. BMC Genomics 20:467
So N, van Houdt JK, Volckaert FA (2006) Genetic diversity and population history of the migratory catfishes Pangasianodon hypophthalmus and Pangasius bocourti in the Cambodian Mekong River. Fish Sci 72:469–476
Sokheng C, Chhea CK, Valbo-Jørgensen J (2000) Lateral fish migrations between Tonle Sap River and its flood plain. In: Matics KI (ed) Proceedings of the third technical symposium on Mekong Fisheries. Mekong River Commission, Phnom Penh, pp 102–114
Song N, Yin L, Sun D, Zhao L, Gao TX (2019) Fine‐scale population structure of Collichthys lucidus populations inferred from microsatellite markers. J Appl Ichthyol 35:709–718
Takezaki N, Nei M, Tamura K (2010) POPTREE2: software for constructing population trees from allele frequency data and computing other population statistics with windows interface. Mol Biol Evol 27:747–752
Tan MP, Jamsari AFJ, Siti Azizah MN (2016) Genotyping of microsatellite markers to study genetic structure of the wild striped snakehead Channa striata in Malaysia. J Fish Biol 88:1932–1948
Tian C‐X, He Y-H, Liang X‐F, Guo W‐J, Sun L‐F, Lv L‐Y, He S (2017) Population genetics of wild Siniperca knerii Garman, 1912 in China as evaluated by microsatellites. J Appl Ichthyol 33:991–997
Toews DP, Brelsford A (2012) The biogeography of mitochondrial and nuclear discordance in animals. Mol Ecol 21:3907–3930
van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538
Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370
Whitney KD, Mudge J, Natvig DO, Sundararajan A, Pockman WT, Bell J, Collins SL, Rudgers, JA (2019) Experimental drought reduces genetic diversity in the grassland foundation species Bouteloua eriopoda. Oecologia, 189:1107–1120
Woodruff DS (2010) Biogeography and conservation in Southeast Asia: how 2.7 million years of repeated environmental fluctuations affect today’s patterns and the future of the remaining refugial-phase biodiversity. Biodivers Conserv 19:919–941
Wright S (1978) Evolution and the genetics of populations. Volume 4. Variability within and among natural populations. University of Chicago Press, Chicago
Acknowledgements
We would like to acknowledge Universiti Sains Malaysia for research funding (Research University Grant-1001/PBIOLOGI/815061) and for Vice Chancellor’s Scholarship Award (May 2013 to June 2016) to J.A.F.J. for his Ph.D. program. Fieldwork in Peninsular Malaysia was conducted under permissions issued by the Department of Fisheries Malaysia (Freshwater Fisheries Research Division) [Prk.ML(Peny.)GL01/59JLD2(25)] and Forestry Department of Peninsular Malaysia [PHNT100/22/16/Bhg5(91), PHNKN130/1/9(94) and PHN.NS.&M156/01/377KLT3]. We would like to thank Phanara Thach, Nguyen Hong Quyet Thang, Dang Quang Hieu, Preeda Phumee, Tinnapop Kuanwilai, Muhammad Fahmi Ahmad, Wan Mohd Amzar Wan Zainuddin, Muhammad Izzat Husna, Syed Ahmad Rizal, Haslawati Baharuddin, Mustafa Asmuni and Abdul Ghani Hassan, for their assistance in collecting and providing the samples. We also wish to thank the following collaborating institutions through the loan of tissue and fin samples: Kyushu University, Nagao Natural Environment Foundation and Fisheries Research Institute Malaysia. No potential conflict of interest is reported by the authors.
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Jamaluddin, J.A.F., So, N., Tam, B.M. et al. Genetic diversity of the tire track eel Mastacembelus favus in Southeast Asia inferred from microsatellite markers. Ichthyol Res 68, 529–540 (2021). https://doi.org/10.1007/s10228-021-00807-4
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DOI: https://doi.org/10.1007/s10228-021-00807-4