The genetic diversity, individual relatedness and possible mating system of an isolated population of the Cyprinid species <i>Megalobrama pellgrini</i> in upper reaches of the Changjiang (Yangtze) River, China -- Journal of Oceanology and Limnology,2019,37(3):1042-1050

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	WANG Huanshan, WANG Teng, LI Wenjing, LIU Huanzhang. The genetic diversity, individual relatedness and possible mating system of an isolated population of the Cyprinid species Megalobrama pellgrini in upper reaches of the Changjiang (Yangtze) River, China[J]. Journal of Oceanology and Limnology, 2019, 37(3): 1042-1050

The genetic diversity, individual relatedness and possible mating system of an isolated population of the Cyprinid species Megalobrama pellgrini in upper reaches of the Changjiang (Yangtze) River, China

WANG Huanshan^1,2, WANG Teng^1,2, LI Wenjing^1,2, LIU Huanzhang^1,2

1 The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
2 University of Chinese Academy of Sciences, Beijing 100049, China

Abstract:

Megalobrama pellegrini is a cyprinid fish endemic to upper reaches of the Changjiang (Yangtze) River, China, which is also an important economic species in the local area. In recent years, resources of this species have decreased sharply and its conservation has drawn great attention. In the present study, we collected 120 individuals from the Longxi River, a tributary isolated from the main channel of the Changjiang River, where M. pellegrini is still relatively abundant. Using two different molecular markers, mitochondrial cytochrome b (cyt b) gene, and nuclear microsatellite (simple sequence repeat, SSR), we analyzed the genetic diversity of this isolated population. The results show that sequence genetic diversity was low (H_d:0.290 and P_i:0.000 77 for cyt b gene), while the SSR genetic diversity was high (H_o:0.824 4±0.147 2, H_e:0.823 5±0.145 1). Analysis indicated that this population had experienced a bottleneck, with inbreeding and small effective population size (around 50). Based on SSR data, relatedness analyzing revealed that the 120 samples were grouped into 10 completely independent clusters. It was inferred that the mating system of M. pellegrini was polygamy. We suggested that the low genetic diversity could be induced by the overfishing and inbreeding depression. Therefore, we suggested that the urgent conservation measures should be taken to control the overfishing and give better conditions for the fish to grow and spawn, then to restore population size.

Key words: isolated population|genetic diversity|individual relatedness|mating system|conservation

Received: 2018-05-11 Revised: 2018-06-19

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References:
Aljanabi S M, Martinez I. 1997. Universal and rapid saltextraction of high-quality genomic DNA for PCR-based techniques. Nucleic. Acids. Res., 25(22):4 692-4 693.
Allendorf F W, Luikart G H. 2007. Conservation and the Genetics of Populations. Blackwell Publishing, Malden, MA, USA; Oxford, UK; and Carlton, Victoria, Australia.
Bateman A J. 1948. lntra-sexual selection in Drosophila.Heredity, 2(3):349-368.
Bendjilali N, Hsueh W C, He Q M, Willcox D C, Nievergelt C M, Donlon T A, Kwok P Y, Suzuki M, Willcox B J. 2014.
Who are the Okinawans? Ancestry, genome diversity, and implications for the genetic study of human longevity from a geographically isolated population. J. Gerontol.:Ser. A, 69(12):1 474-1 484.
Bonnen P E, Pe'er I, Plenge R M, Salit J, Lowe J K, Shapero M H, Lifton R P, Breslow J L, Daly M J, Reich D E, Jones K W, Stoffel M, Altshuler D, Friedman J M. 2006.Evaluating potential for whole-genome studies in Kosrae, an isolated population in Micronesia. Nat. Genetics, 38(2):214-217.
Brook B W, Tonkyn D W, Q'Grady J J, Frankham R. 2002.Contribution of inbreeding to extinction risk in threatened species. Conserv. Ecol., 6(1):16.
Chen Y Y. 1998. Fauna Sinica, Osteichthyes Cypriniformes Ⅱ.Science Press, Beijing. (in Chinese)
Cornuet J M, Luikart G. 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics, 144(4):2 001-2 014.
Daniels S J, Priddy J A, Walters J R. 2000. Inbreeding in small populations of red-cockaded woodpeckers:insights from a spatially explicit individual-based model. Genetics, Demography and Viability of Fragmented Populations, 4:129-147.
Do C, Waples R S, Peel D, Macbeth G M, Tillett B J, Ovenden J R. 2014. NeEstimator v2:re-implementation of software for the estimation of contemporary effective population size (N_e) from genetic data. Mol. Ecol. Resour., 14(1):209-214.
Emlen S T, Oring L W. 1977. Ecology, sexual selection, and the evolution of mating systems. Science, 197(4300):215-223.
Excoffier L, Lischer H E. 2010.Arlequin suite ver 3.5:a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour., 10(3):564-567.
Frankham R, Ralls K. 1998. Conservation biology:inbreeding leads to extinction. Nature, 392(6675):441-442.
Franklin I R. 1980. Evolutionary change in small populations.In:Soule M E, Wilcox B A eds. Conservation Biology-An Evolutionary-Ecological Perspective. Sinauer Associates, Sunderland, Massachusetts, USA. p.135-149.
Galtier N, Gouy M, Gautier C. 1996. SEAVIEW and PHYLO_WIN:two graphic tools for sequence alignment and molecular phylogeny. Bioinformatics, 12(6):543-548.
Gao X, Tan D Q, Liu H Z, Wang J W. 2009. Exploitation status and conservation of a population of Megalobrama pellegrini in Longxi River in the Upper Yangtze River basin. Sichuan J. Zool., 28(3):329-333. (in Chinese with English abstract)
Gilpin M E. 1986. Minimum viable populations:processes of species extinction. In:Soulé M E ed. Conservation Biology:The Science of Scarcity and Diversity. Sinauer Associates, Sunderland, Massachusetts. p.19-34.
Grant W, Bowen B W. 1998. Shallow population histories in deep evolutionary lineages of marine fishes:insights from sardines and anchovies and lessons for conservation. J.Heredity, 89(5):415-426.
Grayson K L, Mitchell N J, Monks J M, Keall S N, Wilson J N, Nelson N J. 2014. Sex ratio bias and extinction risk in an isolated population of tuatara (Sphenodon punctatus).PLoS One, 9(4):e94214.
Hauser L, Adcock G J, Smith P J, Ramírez J H B, Carvalho G R. 2002. Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). Proc. Natl. Acad. Sci.U.S.A., 99(18):11 742-11 747.
Huxley J. 1940. The New Systematics. Clarendon Press, Oxford. 596p.
Jones O R, Wang J L. 2010.COLONY:a program for parentage and sibship inference from multilocus genotype data.Mol. Ecol. Resour., 10(3):551-555.
Kalinowski S T, Wagner A P, Taper M L. 2006. ML-RELATE:a computer program for maximum likelihood estimation of relatedness and relationship. Mol. Ecol. Notes, 6(2):576-579.
Keller L F, Arcese P, Smith J N M, Hochachka W M, Stearns S C. 1994. Selection against inbred song sparrows during a natural population bottleneck. Nature, 372(6504):356-357.
Klug H. 2011. Animal Mating Systems. In:eLS. John Wiley& Sons, Ltd., Chichester. https://doi.org/10.1002/9780470015902.a0022553.
Langella O. 2000. POPULATIONS 1.2:population genetic software, individuals or population distance, phylogenetic trees. http://bioinformatics.org/~tryphon/populations/.
Larkin M A, Blackshields G, Brown N P, Chenna R, McGettigan P A, McWilliam H, Valentin F, Wallace I M, Wilm A, Lopez R, Thompson J D, Gibson T J, Higgins D.G. 2007. Clustal W and Clustal X version 2.0.Bioinformatics, 23(21):2 947-2 948.
Lee S L, Ng K K S, Saw L G, Lee C T, Muhammad N, Tani N, Tsumura Y, Koskela J. 2006. Linking the gaps between conservation research and conservation management of rare dipterocarps:a case study of Shorea lumutensis. Biol.Conserv., 131(1):72-92.
Li W J, Wang J W, Xie C X, Tan D Q. 2007a. Age structure and growth characteristics of Megalobrama pellegrini-an endemic fish living only in upper reaches of Yangtze River. J. Fish. Sci. China, 14(2):215-222. (in Chinese with English abstract)
Li W J, Wang J W, Xie C X, Tan D Q. 2007b. Reproductive biology and spawning habitats of Megalobrama pellegrini, an endemic fish in upper-reaches of Yangtze River basin. Acta Ecol. Sin., 27(5):1 917-1 925. (in Chinese with English abstract)
Librado P, Rozas J. 2009. DnaSP v5:a software for comprehensive analysis of DNA polymorphism data.Bioinformatics, 25(11):1 451-1 452.
Lindenmayer D B, Peakall R. 2000. The Tumut experimentintegrating demographic and genetic studies to unravel fragmentation effects:a case study of the native Bush Rat.In:Young A G, Clarke G M eds. Genetics, Demography, and Viability of Fragmented Populations. Cambridge University Press, Cambridge, UK. p.173-201.
Luikart G, Allendorf F W, Cornuet J M, Sherwin W B. 1998.Distortion of allele frequency distributions provides a test for recent population bottlenecks. J. Heredity, 89(3):238-247.
Luo Y L. 1990. A revision of fishes of the cyprinid genus Megalobrama. Acta Hydrobiol. Sin., 14(2):160-165. (in Chinese with English abstract)
Madsen T, Stille B, Shine R. 1996. Inbreeding depression in an isolated population of adders Vipera berus. Biol. Conserv., 75(2):113-118.
Mayr E. 1963. Animal Species and Evolution. Harvard University Press, Cambridge, Massachusetts. 797p.
Pardo L M, MacKay I, Oostra B, van Duijn C M, Aulchenko Y S. 2005. The effect of genetic drift in a young genetically isolated population. Ann. Human Genetics, 69(3):288-295.
Service S, DeYoung J, Karayiorgou M, Roos J L, Pretorious H, Bedoya G, Ospina J, Ruiz-Linares A, Macedo A, Palha J A, Heutink P, Aulchenko Y, Oostra B, van Duijn C, Jarvelin M-R, Varilo T, Peddle L, Rahman P, Piras G, Monne M, Murray S, Galver L, Peltonen L, Sabatti C, Collins A, Freimer N. 2006. Magnitude and distribution of linkage disequilibrium in population isolates and implications for genome-wide association studies. Nat.Genetics, 38(5):556-560.
Shriver M D, Jin L, Chakraborty R, Boerwinkle E. 1993.VNTR allele frequency distributions under the stepwise mutation model:a computer simulation approach.Genetics, 134(3):983-993.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013.MEGA6:molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol., 30(12):2 725-2 729.
Valdes A M, Slatkin M, Freimer N B. 1993. Allele frequencies at microsatellite loci:the stepwise mutation model revisited. Genetics, 133(3):737-749.
van Oosterhout C, Hutchinson W F, Wills D P M, Shipley P. 2004. Micro-checker:software for identifying and correcting genotyping errors in microsatellite data. Mol.Ecol. Notes, 4(3):535-538.
Wang J J, Tong J G, Zhang Y G, Peng Z G. 2014. Study on the genetic diversity of two wild populations of Megalobrama pellegrini (Teleostei, Cyprinidae). Acta Hydrobiol. Sin., 38(5):975-979. (in Chinese with English abstract)
Westemeier R L, Brawn J D, Simpson S A, Esker T L, Jansen R W, Walk J W, Kershner E L, Bouzat J L, Paige K N. 1998. Tracking the long-term decline and recovery of an isolated population. Science, 282(5394):1 695-1 698.
Xiao W H, Zhang Y P, Liu H Z. 2001. Molecular systematics of Xenocyprinae (Teleostei:Cyprinidae):taxonomy, biogeography, and coevolution of a special group restricted in East Asia. Mol. Phylogenet. Evol., 18(2):163-173.
Yeh F C, Yang R C, Boyle T, Ye Z H, Mao J. 1997. PopGene Version 1.31, Microsoft Window-based Freeware for Population Genetic Analysis. Quick User Guide.
Edmonton, Biology and Biotechnology Center, University of Alberta, Canada. https://sites.ualberta.ca/~fyeh/popgene.pdf.