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Microsatellite analysis of genetic diversity in the Chinese alligator (Alligator sinensis) Changxing captive population

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Abstract

Chinese alligator (Alligator sinensis) is a critically endangered species endemic to China. In this study, the extent of genetic variation in the captive alligators of the Changxing Reserve Center was investigated using microsatellite markers derived from American alligators. Out of 22 loci employed, 21 were successfully amplified in the Chinese alligator. Sequence analysis showed loci in American alligators had a bigger average size than that of the Chinese alligators and the longest allele of an individual locus almost always existed in the species with longer stretch of repeat units. Eight of the 22 loci were found to be polymorphic with a total of 26 alleles present among 32 animals scored, yielding an average of 3.25 alleles per polymorphic locus. The expected heterozygosity (H E) ranged at a moderate level from 0.4385 to 0.7163 in this population. Compared to that in the American alligators, a lower level of microsatellite diversity existed in the Changxing population as revealed by about 46% fewer alleles per locus and smaller H E at the homologous loci. The average exclusion power and the ability to detect shared genotypes and multiple paternity were evaluated for those markers. Results suggested that when the polymorphic loci were combined, they could be sensitive markers in genetic diversity study and relatedness inference within the Chinese alligator populations. The level of genetic diversity present in the current Changxing population indicated an important resource to complement reintroductions based on the individuals from the other population. In addition, the microsatellite markers and their associated diversity characterized in this population could be utilized to further investigate the genetic status of this species.

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References

  • Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet., 32, 314–331.

    PubMed  CAS  Google Scholar 

  • Chakravarti A, Li CC (1983) The probability of exclusion based on the HLA locus. Am. J. Hum. Genet., 35, 1048–1052.

    PubMed  CAS  Google Scholar 

  • Chen B, Hua Z, Li B (1985) Chinese Alligator. Anhui Science and Technology Press, Hefei, Anhui, China (in Chinese).

    Google Scholar 

  • Chen BH (1990) The past and present situation of the Chinese alligator. Asiat. Herpetol. Res., 3, 129–136.

    Google Scholar 

  • Davis LM, Glenn TC, Elsey RM, Brisbin Jr IL, Rhodes WE, Dessauer HC, Sawyer RH (2001a) Genetic structure of six populations of American alligators: a microsatellite analysis. In: Crocodilian Biology and Evolution (eds. Grigg GC, Seebacher F, Franklin CE), pp. 38–50. Surrey Beatty and Sons, Chipping Norton

    Google Scholar 

  • Davis LM, Glenn TC, Elsey RM, Dessauer HC, Sawyer RH (2001b) Multiple paternity and mating patterns in the American alligator, Alligator mississippiensis. Mol. Ecol., 10, 1011–1024.

    Article  CAS  Google Scholar 

  • Davis LM, Glenn TC, Strickland DC, Guillette Jr LJ, Elsey RM, Rhodes WE, Dessauer HC, Sawyer RH (2002) Microsatellite DNA analyses support an east–west phylogeographic split of America alligator populations. J. Exper. Zool. (Mol. Dev. Evol.), 294, 352–372.

    Article  CAS  Google Scholar 

  • Ellegren H, Primmer CR, Sheldon BC (1995) Microsatellite ‘evolution’: directionality or bias? Nat. Genet., 11, 360–362.

    Article  PubMed  CAS  Google Scholar 

  • Ellsworth DL, Rittenhouse D, Honeycutt RL (1993) Artifactual variation in randomly amplified polymorphic DNA banding patters. Biotechniques, 14, 214–217.

    PubMed  CAS  Google Scholar 

  • Fitzsimmons NN, Moritz C, Moore SS (1995) Conservationand dynamics of microsatellite loci over 300 million years of marine turtle evolution. Mol. Biol. Evol., 12, 432–440.

    PubMed  CAS  Google Scholar 

  • Fitzsimmons NN (1998) Single paternity of clutches and sperm storage in the promiscuous green turtle (Chelonia mydas). Mol. Ecol., 7, 575–584.

    Article  PubMed  CAS  Google Scholar 

  • Forbes SH, Hogg JT, Buchanan FC, Crawford AM, Allendorf FW (1995) Microsatellite evolution incongeneric mammals: domestic and bighorn sheep. Mol. Bio. Evol., 12, 1106–1113.

    PubMed  CAS  Google Scholar 

  • Glenn TC, Stephan W, Dessauer HD, Braun MJ (1996) Allelic diversity in alligator microsatellite loci is negatively correlated with GC content of flanking sequences and evolutionary conservation of PCR amplifiability. Mol. Biol. Evol., 13, 1151–1154.

    PubMed  CAS  Google Scholar 

  • Glenn TC, Dessauer HC, Braun MJ (1998) Characterization of microsatellite DNA loci in American alligators. Copeia, 3, 591–601.

    Article  Google Scholar 

  • Glenn TC, Staton JL, Vu A, Davis LM, Alvardo Bremer JR, Rhodes WH, Brisbin Jr. IL, Sawyer RH (2002) Low mitochondrial DNA variation among American alligators and a novel non-coding region in crocodilians. J. Exper. Zool. (Mol. Dev. Evol.), 394, 312–324.

    Article  CAS  Google Scholar 

  • Huang Z (1981) The Chinese alligator. Oryx, 16, 139–140.

    Google Scholar 

  • Hutter CM, Schug MD, Aquadro CF (1998) Molecularvariation in Drosophila melanogaster and Drosophila simulans: a reciprocal test of the ascertainment bias hypothesis. Mol. Biol. Evol., 15, 1620–1636.

    PubMed  CAS  Google Scholar 

  • Jarne P, Lagoda PJL (1996) Microsatellites, from molecules to populations and back. Tree 11, 424–429.

    Google Scholar 

  • Maruyama T, Fuerst PA (1985) Population bottlenecks and nonequilibrium models in population genetics. II. Number of alleles in a small population that was formed by a recent bottleneck. Genetics 111: 675–689

    PubMed  CAS  Google Scholar 

  • Marshall TC, Slate J, Kruuk LEB, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Mol. Ecol. 7: 639–655.

    Article  PubMed  CAS  Google Scholar 

  • Queller DC, Goodnight KF (1989) Estimating relatedness using genetic markers. Evolution 43: 258–275

    Article  Google Scholar 

  • Queller DC, Strassmann JE, Hughes CR (1993) Microsatellites and kinship. Trends Ecol. Evol. 8: 285–288

    Article  Google Scholar 

  • Raymond M, Rousset F (1995) GENEPOP (Version 1.2): Population genetics software for exact tests and ecumenicism. J. Hered. 86: 248–249

    Google Scholar 

  • Rice WR (1989) Analyzing tables of statistical tests. Evolution 43: 223–225

    Article  Google Scholar 

  • Richards RI, Sutherland GR (1994) Simple repeat DNA is not replicated simply. Nat. Genet. 6: 114–116

    Article  PubMed  CAS  Google Scholar 

  • Rico C, Rico I, Hewitt G (1996) 470 million years of conservation of microsatellite loci among fish species. Proc. R. Soc. Lond. B Biol. Sci. 263: 549–557

    Article  CAS  Google Scholar 

  • Rubinsztein DC, Amos W, Leggo J, Goodburn S, Jain S, Li SH, Margolis RL, Ross CA, Ferguson-Smith MA (1995a) Microsatellite evolution—evidence for directionality and variation in rate between species. Nat. Genet. 10: 337–343

    Article  CAS  Google Scholar 

  • Rubinsztein DC, Leggo J, Amos W (1995b) Microsatellites evolve more rapidly in humans than in chimpanzees. Genomics 30: 610–612

    Article  PubMed  CAS  Google Scholar 

  • Sambrook J, Fritsh EF, Maniatis T (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  • Schweder MEE, Shatters Jr RG, West SH, Smith RL (1995) Effect of transition interval between melting and annealing temperature on RAPD analyses. Biotechniques 38: 40–42

    Google Scholar 

  • Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 17: 6463–6470

    Article  PubMed  CAS  Google Scholar 

  • Tautz D, Schlotterer C (1994) Simple sequences. Curr. Opin. Genet. Dev. 4: 832–837

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Higgins DG, Gibson JJ (1994) Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673–4680

    Article  PubMed  CAS  Google Scholar 

  • Thorbjarnarson J, Wang XM (1999). The conservation status of the Chinese alligator FFI. Oryx 33: 152–159

    Article  Google Scholar 

  • Thorbjarnarson J, Wang XM, Ming S (2002) Wild Populations of the Chinese alligator approach extinction. Biol. Conserv. 103: 93–102

    Article  Google Scholar 

  • Wang YQ, Zhu WQ, Wang CL (2003) D-loop sequence variation of mitochondrial DNA in captive Chinese alligator. Acta Genet. Sin. 30: 425–430 (in Chinese).

    PubMed  CAS  Google Scholar 

  • Watanabe M (1982). The Chinese alligator: is farming the last hope? Oryx 17: 176–181

    Article  Google Scholar 

  • Wu XB, Wang YQ, Zhou KY, Zhu WQ, Nie JS, Wang CL, Xie WS (2002) Genetic variation in captive population of Chinese alligator, Alligator sinensis, revealed by random amplified polymorphic DNA (RAPD). Biol. Conserv. 106: 435–441

    Article  Google Scholar 

  • Zhou YJ (1997) Analysis of the decline of the wild Alligator sinensis population. Sichuan J. Zool. 16: 137 (in Chinese).

    Google Scholar 

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Acknowledgements

We thank the Changxing Nature Reserve and Breeding Research Center for providing all the Chinese alligator samples used in this study. We are also indebted to the people who helped in the sample collection: they are Changjun Zeng and Yunfei Hao. Thanks also go to Dr. Qiuhong Wan for valuable discussions of the manuscript. This work was supported in part by a grant from the Department of Wildlife Conservation, State Forestry Administration of P.R. of China.

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Authors and Affiliations

  1. College of Life Sciences, Zhejiang University, No. 268 Kaixuan Road, Hangzhou, 310029, Zhejiang, P.R. China

    Qianghua Xu & Shengguo Fang

  2. State Conservation Center for Gene Resources of Endangered Wildlife, The Key Laboratory of Conservation Genetics and Reproductive Biology for Endangered Wild Animals of the Ministry of Education, Hangzhou, P.R. China

    Qianghua Xu & Shengguo Fang

  3. Changxing Nature Reserve and Breeding Research Chinese Alligator, Changxing, Zhejiang, P.R. China

    Zhiping Wang & Zhenwei Wang

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  1. Qianghua Xu
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  2. Shengguo Fang
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  3. Zhiping Wang
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  4. Zhenwei Wang
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Correspondence to Shengguo Fang.

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Xu, Q., Fang, S., Wang, Z. et al. Microsatellite analysis of genetic diversity in the Chinese alligator (Alligator sinensis) Changxing captive population. Conserv Genet 6, 941–951 (2005). https://doi.org/10.1007/s10592-005-9081-x

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  • DOI: https://doi.org/10.1007/s10592-005-9081-x

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