[1].Genetic Bottlenecks of the Wild Chinese Giant Salamander in Karst Caves[J].Asian Herpetological Research,2017,8(3):174-183.[doi:10.16373/j.cnki.ahr.170038]
 Jie WANG*,Hongxing ZHANG,Feng XIE,et al.Genetic Bottlenecks of the Wild Chinese Giant Salamander in Karst Caves[J].Asian Herpetological Reserch(AHR),2017,8(3):174-183.[doi:10.16373/j.cnki.ahr.170038]

Genetic Bottlenecks of the Wild Chinese Giant Salamander in Karst Caves()

Asian Herpetological Research[ISSN:2095-0357/CN:51-1735/Q]



Genetic Bottlenecks of the Wild Chinese Giant Salamander in Karst Caves
Jie WANG1* Hongxing ZHANG2 Feng XIE1 Gang WEI3 and Jianping JIANG1*
1 Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China
2 Shaanxi Institute of Zoology, Xi’an 710032, Shaanxi, China
3 GuiyangUniversity, Guiyang 550005, Guizhou, China
limestone cave small population genetic drift Andrias davidianus subterranean habitat
The rarity of limestone cave species due to habitat degradation makes them of special interest in conservation biology. The wild Chinese Giant Salamander Andrias davidianus, an evolutionarily distinct and globally endangered species, are nearly all obligate into living in inaccessible mountain caves now. We detected that only 14–29 breeders, with the effective population size of 9–25 (5–44 of 95% confidence interval), were in each of three caves, through genotyping 20 microsatellite loci on larvae that were flushed out of caves. Both heterzygosity excess and M (ratios of allele number to allele size range) tests indicated severe genetic bottlenecks among populations. Both mitochondrial, with only one or two haplotypes of D-loop region (770–771bp) in each population, and nuclear genetic structure showed clear divergence between populations. Considering the long life history, small population size, and genetic differentiation of the Chinese Giant Salamander, putting an end to poaching and recovering the karst ecosystem instead of releasing may be the sole measures to save this severely threated species.


Cosentino B. J., Phillips C. A., Schooley R. L., Lowe W. H., Douglas M. R. 2012. Linking extinction-colonization dynamics to genetic structure in a salamander metapopulation. Proc R Soc B, 279(1733):1575–1582
Culver D. C., Deharveng L., Bedos A., Lewis J. J., Madden M., Reddell J. R., Sket B., Trontelj P., White D. 2006. The mid-latitude biodiversity ridge in terrestrial cave fauna. Ecography, 29(97333):120–128
Culver D. C., Pipan T. 2009. The Biology of Caves and Other Subterranean Habitats. Oxford: Oxford University Press
Evanno G., Regnaut S., Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol Ecol, 14(8): 2611–2620
Fang Y., Zhang Y., Xiao H., Yang Y. 2008. Genetic diversity analysis of wild Chinese giant salamander (Andrias davidianus) and their artificially propagated progenies. Acta Hydrobiologica Sinica, 32(5): 783–786
Frankham R. 2005. Genetics and extinction. Biol Conserv, 126(2): 131–140
Garza J. C., Williamson E. G. 2001. Detection of reduction in population size using data from microsatellite loci. Mol Ecol, 10(2): 305–318
Goricki S., Niemiller M. L., Fenolio D. B. 2012. Salamanders. 665–676. In: White W.H., Culver D.C. (Eds), Encyclopedia of Caves, 2nd Edition. Elsevier
Guindon S., Dufayard J. F., Lefort V., Anisimova M., Hordijk W., Gascuel O. 2010. New Algorithms and methods to estimate maximum-likelihood phylogenies: accessing the performance of PhyML 3.0. Syst Biol, 59(3): 307–321
Guo S. W., Thomson E. A. 1992. Performing the exact test of Hardy-Weinberg proportions for multiple alleles. Biometrics, 48(2): 361–372
Hoban S. M., Gaggiotti O. E., Bertorelle G. 2013. The number of markers and samples needed for detecting bottlenecks under realistic scenarios, with and without recovery: a simulation-based study. Mol Ecol, 22(13): 3444–3450
Isaac N. J. B., Redding D. W., Meredith H. M., Safi K. 2012. Phylogenetically-informed priorities for amphibian conservation. PLoS ONE, 7(8), e43912
Jamieson I. G., Allendorf F. W. 2012. How does the 50/500 rule apply to MVPs? Trends Ecol Evol, 27(10): 578–584
Jones O. R., Wang J. 2010. COLONY: A program for parentage and sibship inference from multilocus genotype data. Mol Ecol Resour, 10(3): 551–555
K?hler J., Vences M., D’Cruze N., Glaw F. 2010. Giant dwarfs: discovery of a radiation of large-bodied ‘stump-toed frogs’ from karstic cave environments of northern Madagascar. J Zool, 282(1): 21–38
Kuhner?M. K. 2006.?LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters.?Bioinformatics,?22(6): 768–770
Liang G., Geng B., Zhao E. 2004. Andrias davidianus. The IUCN Red List of Threatened Species. Version 2014. 2
Librado P., Rozas J. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25(11): 1451–1452
Liu J., Zhang Z., Zhang Z., Liu X., Zhang L., Zhang J. 2009. A critically endangered cave-dwelling frog—the habitat, status and conservation of Odorrana wuchuanensis in Guizhou, China. Bulletin of Biology, 44(5): 14–16 (in Chinese)
Liu J. 2010. Preliminary study on the development and ecology of Red-spotted toothed toad (Oreolalax rhodostigmatus). Bulletin of Biology, 45(1): 50–52 (in Chinese)
Luikart G., Sherwin W. B., Steele B. M., Allendorf F. W. 1998. Usefulness of molecular markers for detecting population bottlenecks via monitoring genetic change. Mol Ecol, 7(8): 963–974
Luo Q., Liu Y., Zhang L., Chen G., Kang L. 2009. Investigation on resources of Chinese giant salamanders in Zhangjiajie City. Sichuan J Zool, 28(3): 422–436 (in Chinese)
Matsui M., Tominaga A., Liu W.Z., Tanaka-Ueno T. 2008. Reduced genetic variation in the Japanese giant salamander, Andrias japonicus (Amphibia: Caudata). Mol Phylogenet Evol, 49(1): 318-326
Meng Y., Yang Y., Zhang Y., Xiao H. 2008. A comparison of genetic diversity between wild and cultured populations of the Chinese giant salamander, Andrias davidianus, based on microsatellite analyses. Biodiv Sci, 16(6): 533–538 (in Chinese)
Murphy R.W., Fu J.Z., Upton D.E., Lema T.D., Zhao E.M. 2000. Genetic variability among endangered Chinese giant salamanders, Andrias davidianus. Mol Ecol, 9(10): 1539–1547
Niemiller M. L., Miller B. T. 2009. A survey of the cave-associated amphibians of the eastern United States with an emphasis on salamanders. Proceedings of the 15th International Congress of Speleology, Kerrville, Texas, 15: 249–256
Peery M. Z., Kirby R., Reid B.N., Stoelting R., Doucet-B?er E.,?Robinson S.,?Vásquez-Carrillo C.,?Pauli J.N.,?Palsb?ll P. J. 2012. Reliability of genetic bottleneck tests for detecting recent population declines. Mol Ecol, 21(14): 3403–3418
Peterman W. E., Anderson T. L., Drake D. L., Ousterhout B. H., Semlitsch R. D. 2014. Maximizing pond biodiversity across the landscape: a case study of larvae ambystomatid salamanders. Anim Conserv, 17(3): 275–285
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(4): 502–503
Poschadel J.R., M?ller D. 2004. A versatile field method for tissue sampling on small reptiles and amphibians, applied to pond turtles, newts, frogs and toads. Conserv Genet, 5(6): 865-867
Pritchard J.K., Stephens M., Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155(2): 945-959
Radwan J.,?Biedrzycka A., Babik W.?2010.?Does reduced MHC diversity decrease viability of vertebrate populations??Biol Conserv,?143(3): 537–544
Rice W. R. 1989. Analyzing tables of statistical tests. Evolution, 43(2): 223–225
Rodrigá?ez J., Barragán C., Alves E., Gortázar C., Toro M. A., Silió L. 2008. Genetic diversity and allelic richness in Spanish wild and domestic population estimated from microsatellite markers. Span J Agric Res, 6 (Special Issue): 107–115
Rousset F. 2008. GENEPOP’007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Resour 8(1): 103–106
Sabatino S. J., Routman E. J. 2009. Phylogeography and conservation genetics of the hellbender salamander (Cyptobranchus alleganiensis). Conserv Genet, 10(5): 1235–1246
Schwartz M. K., Luikart G., Waples R. S. 2007. Genetic monitoring as a promising tool for conservation and management. Trends Ecol Evol, 22(1): 25–33
Sket B. 1997. Distribution of Proteus (Amphibia: Urodela: Proteidae) and its possible explanation. J Biogeogr, 24(3): 263–280
Storfer A., Mech S.G., Reudink M. W., Lew K. 2014. Inbreeding and strong population subdivision in an endangered salamander. Conserv Genet, 15(1): 137–151
Su H., Yu L., Ma J. 2009. Population status and history dynamics of wild Chinese giant salamander (Andrias davidianus) in Yanxia Natural Reserve in Guizhou province, China. Resources and Environment in the Yangtze Basin, 18(7): 652–657. (in Chinese)
Sutton J. T.,?Nakagawa S.,? Robertson B. C., Jamieson I. G.?2011.?Disentangling the roles of natural selection and genetic drift in shaping variation at MHC immunity genes.?Mol Ecol,?20(21): 4408–4420
Suzuki N., Kuwabara K., Ashikaga K., Nakanishi M., Minamigata N., Morimoto H. 2000. Breeding of the Japanese giant salamander, Andrias japonicus, in a portable artificial nest. J Jpn Assoc Zool Gardens Aquarium, 41: 83–87 (in Japanese)
Tajima F. 1989. The effect of change in population size on DNA polymorphism. Genetics, 123(3): 597–601
Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol, 30(12): 2725–2729
Tao F., Wang X., Zheng H., Fang S. 2005. Genetic structure and geographic subdivision of four populations of the Chinese giant salamander (Andrias davidianus). Zool Res, 26(2):162–167 (in Chinese)
Tao F., Wang X., Zheng H. 2006. Analysis of complete cytochrome b sequences and genetic relationship among Chinese giant salamanders (Andrias davidianus) from different areas. Acta Hydrobiologica Sinica, 30(5): 625–628 (in Chinese)
Tracy L. N., Wallis G. P.,?Efford M. G., Jamieson J. G.?2011.?Preserving genetic diversity in threatened species reintroductions: How many individuals should be released??Anim Conserv,?14(4): 439–446
van Beynen P., Brinkmann R., van Beynen K. 2012. A sustainability index for karst environments. J Cave Karst Stud, 74(2): 221–234
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 X., Zhang K., Wang Z., Ding Y., Wu W., Huang S. 2004. The decline of the Chinese giant salamander Andrias davidianus and implication for its conservation. Oryx 38(2):197–202
Wang W., Jiang F., Wang B. 2000. Survey the reproductive habits of Chinese giant salamander. Res Fish, 20(6):12–13 (in Chinese)
Wang J., Zhang H.X. 2012. An ill-fated life of the larvae of Chinese giant salamander. China Nature, 168:72-73. (in Chinese)
Wang J., Zhang J., Li X., Jiang J. 2014. Isolation and characterization of 16 microsatellite loci for the giant salamander Andrias davidianus. Conserv Genet Resour, 6(2): 367–368
Weir B. S., Cockerham C. C. 1984. Estimating F-statistics for the analysis of population structure. Evolution, 38(6): 1358–1370
Weiser E. L., Grueber C. E., Jamieson I. G. 2013. Simulating retention of rare alleles in small populations to assess management options for species with different life histories. Conserv Biol, 27(2): 335-344
Wilson?I. J.,?Weale?M. E.,?Balding?D. J. 2003.?Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities.?J R Statist Soc A, 166(2): 155–201
Yang L., Meng Z., Liu X., Zhang Y., Huang J., Huang J., Lin H. 2011. AFLP analysis of five natural populations of Andrias davidianus. Acta Sci Nat Univ Sunyatseni, 50(2): 99–104
Zhang P., Wake D. B. 2009. High-level salamander relationships and divergence dates inferred from complete mitochondrial genomes. Mol Phylogenet Evol, 53(2): 492–508

更新日期/Last Update: 2017-09-25