Take one step backward to move forward: Assessment of genetic diversity and population structure of captive Asian woolly-necked storks (Ciconia episcopus)

Autoři: Kornsuang Jangtarwan aff001;  Tassika Koomgun aff001;  Tulyawat Prasongmaneerut aff001;  Ratchaphol Thongchum aff001;  Worapong Singchat aff001;  Panupong Tawichasri aff001;  Toshiharu Fukayama aff001;  Siwapech Sillapaprayoon aff001;  Ekaphan Kraichak aff003;  Narongrit Muangmai aff004;  Sudarath Baicharoen aff005;  Chainarong Punkong aff006;  Surin Peyachoknagul aff001;  Prateep Duengkae aff002;  Kornsorn Srikulnath aff001
Působiště autorů: Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand aff001;  Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, Thailand aff002;  Department of Botany, Faculty of Science, Kasetsart University, Bangkok, Thailand aff003;  Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand aff004;  Bureau of Research and Conservation, The Zoological Park Organization (ZPO), Bangkok, Thailand aff005;  Khao Kheow Open Zoo, Chonburi, Thailand aff006;  Center for Advanced Studies in Tropical Natural Resources (CASTNAR), National Research University-Kasetsart University (NRU-KU), Kasetsart University, Bangkok, Thailand aff007;  Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, Thailand aff008;  Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand aff009
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article
doi: 10.1371/journal.pone.0223726


The fragmentation of habitats and hunting have impacted the Asian woolly-necked stork (Ciconia episcopus), leading to a serious risk of extinction in Thailand. Programs of active captive breeding, together with careful genetic monitoring, can play an important role in facilitating the creation of source populations with genetic variability to aid the recovery of endangered species. Here, the genetic diversity and population structure of 86 Asian woolly-necked storks from three captive breeding programs [Khao Kheow Open Zoo (KKOZ) comprising 68 individuals, Nakhon Ratchasima Zoo (NRZ) comprising 16 individuals, and Dusit Zoo (DSZ) comprising 2 individuals] were analyzed using 13 microsatellite loci, to aid effective conservation management. Inbreeding and an extremely low effective population size (Ne) were found in the KKOZ population, suggesting that deleterious genetic issues had resulted from multiple generations held in captivity. By contrast, a recent demographic bottleneck was observed in the population at NRZ, where the ratio of Ne to abundance (N) was greater than 1. Clustering analysis also showed that one subdivision of the KKOZ population shared allelic variability with the NRZ population. This suggests that genetic drift, with a possible recent and mixed origin, occurred in the initial NRZ population, indicating historical transfer between captivities. These captive stork populations require improved genetic variability and a greater population size, which could be achieved by choosing low-related individuals for future transfers to increase the adaptive potential of reintroduced populations. Forward-in-time simulations such as those described herein constitute the first step in establishing an appropriate source population using a scientifically managed perspective for an in situ and ex situ conservation program in Thailand.

Klíčová slova:

Conservation genetics – Genetic loci – Genetic polymorphism – Inbreeding – Microsatellite loci – Population genetics – Species diversity – Thailand


1. Bird Life International. Ciconia episcopus (amended version of 2016 assessment). The IUCN Red List of Threatened Species 2017; e.T22727255A110064997. http://dx.doi.org/10.2305/IUCN.UK.2017-1.RLTS.T22727255A110064997.en. Downloaded on 03 April 2019.

2. Choudhary DN, Ghosh TK, Mandal JN, Rohitashwa R, Manda SK. Observations on the breeding of the woolly-necked stork Ciconia episcopus in Bhagalpur, Bihar, India. Indian BIRDS. 2013; 8: 93–94. http://doi.org/10.11609/jott.2904.9.1.9738-9742

3. Vaghela U, Sawant D, Bhagwat V. Woolly-necked storks Ciconia episcopus nesting on mobile-towers in Pune, Maharashtra. Indian BIRDS. 2015; 10: 154–155.

4. Chaipakdee M. Situation and management of wetlands in Thailand. Wildlife Research Division, Department of National Parks, Wildlife and Plant Conservation, Bangkok 2005; 30.

5. Eiamampai K, Pothieng D, Laong S, Thongaree S, Wanghongsa S, Simchareon S, et al. 3 decades tracking the location, spread and population of rare endangered birds in Thailand. Wildlife Conservation Bureau, Thailand. 2007.

6. Ghale TR, Karmacharya DK. A new altitudinal record for Asian woollyneck Ciconia episcopus in South Asia. BirdingASIA. 2018; 29: 96–97

7. Paleeri G, Nair RP, Jayson EA, Karingamadathil M. Breeding of woolly-necked stork Ciconia episcopus in Barathapuzha River basin, Kerala, India. Indian BIRDS. 2018; 14: 86–87.

8. Ghimire P. Status of Asian woolly neck stork Ciconia episcopus in Nepal: A Review. Prabhat, 2017.

9. Xia C, Cao J, Zhang H, Gao X, Yang W, Blank D. Reintroduction of Przewalski’s horse (Equus ferus przewalskii) in Xinjiang, China: the status and experience. Biol. Conserv. 2014; 177: 142–147. https://doi.org/10.1016/j.biocon.2014.06.021

10. Schulte‐Hostedde AI, Mastromonaco GF. Integrating evolution in the management of captive zoo populations. Evol. Appl. 2015; 8: 413–422. https://doi.org/10.1111/eva.12258 26029256

11. Frankham R, Ballou JD, Briscoe DA. Introduction to conservation genetics. 2nd ed. Cambridge: Cambridge University Press; 2010. https://doi.org/10.1017/CBO9780511809002.

12. Harding G, Griffiths RA, Pavajeau L. Developments in amphibian captive breeding and reintroduction programs. Conserv. Biol. 2016; 30: 340–349. https://doi.org/10.1111/cobi.12612 26306460

13. Cheyne SM. Wildlife reintroduction: considerations of habitat quality at the release site. BMC Ecol. 2006; 6: 5. https://doi.org/10.1186/1472-6785-6-5 16611369

14. Robert A. Captive breeding genetics and reintroduction success. Biol. Conserv. 2009; 142: 2915–2922. https://doi.org/10.1016/j.biocon.2009.07.016

15. Witzenberger KA, Hochkirch A. Ex situ conservation genetics: a review of molecular studies on the genetic consequences of captive breeding programmes for endangered animal species. Biodivers. Conserv. 2011; 20: 1843–1861. https://doi.org/10.1007/s10531-011-0074-4

16. Keller LF, Biebach I, Ewing SR, Hoeck PE. The genetics of reintroductions: inbreeding and genetic drift. Reintroduction biology: integrating science and management. (eds J.G. Ewen, D.P. Armstrong, K.A. Parker and P.J. Seddon). 2012. https://doi.org/10.1002/9781444355833.ch11

17. Lapbenjakul S, Thapana W, Twilprawat P, Muangmai N, Kanchanaketu T, Temsiripong Y, et al. High genetic diversity and demographic history of captive Siamese and Saltwater crocodiles suggest the first step toward the establishment of a breeding and reintroduction program in Thailand. PloS One. 2017; 12: e0184526. https://doi.org/10.1371/journal.pone.0184526 28953895

18. Eggert LS, Powell DM, Ballou JD, Malo AF, Turner A, Kumer J, et al. Pedigrees and the study of the wild horse population of Assateague Island National Seashore. J. Wildlife Manage. 2010; 74: 963–973. https://doi.org/10.2193/2009-231

19. Giglio RM, Ivy JA, Jones LC, Latch EK. Evaluation of alternative management strategies for maintenance of genetic variation in wildlife populations. Anim. Conserv. 2016; 19: 380–390. https://doi.org/10.1111/acv.12254

20. Huang Y, Zhou L. Screening and application of microsatellite markers for genetic diversity analysis of oriental white stork (Ciconia boyciana). Chinese Birds. 2011; 2: 33–38. http://doi.org/10.5122/cbirds.2011.0009

21. Yamamoto Y, Murata K, Matsuda H, Hosoda T, Tamura K, Furuyama JI. Determination of the complete nucleotide sequence and haplotypes in the D-loop region of the mitochondrial genome in the oriental white stork, Ciconia boyciana. Genes Genet. Syst. 2000; 75: 25–32. https://doi.org/10.1266/ggs.75.25 10846618

22. Murata K, Satou M, Matsushima K, Satake S, Yamamoto Y. Retrospective estimation of genetic diversity of an extinct oriental white stork (Ciconia boyciana) population in Japan using mounted specimens and implications for reintroduction programs. Conserv. Genet. 2004; 5: 553–560. https://doi.org/10.1023/B:COGE.0000041022.71104.1f

23. Kocherga M, Tyagunin V, Parilov M, Sasin A, Edyta S. Evaluation of genetic diversity of wild oriental white stork (Ciconia boyciana) in Russia and their phylogenetic relationship with extinct populations in Japan. JPN. J. Zoo Wildl. Med. 2011; 16: 139–144. https://doi.org/10.5686/jjzwm.16.139

24. Supikamolseni A, Ngaoburanawit N, Sumontha M, Chanhome L, Suntrarachun S, Peyachoknagul S, et al. Molecular barcoding of venomous snakes and species-specific multiplex PCR assay to identify snake groups for which antivenom is available in Thailand. Genet. Mol. Res. 2015; 14: 13981–13997. https://doi.org/10.1007/s10592-008-9784-x 26535713

25. Fridolfsson AK, Ellegren H. A simple and universal method for molecular sexing of non-ratite birds. J. Avian Biol. 1999; 116–121. https://doi.org/10.2307/3677252

26. Kularatne H, Udagedara S. First record of the woolly-necked stork Ciconia episcopus Boddaert, 1783 (Aves: Ciconiiformes: Ciconiidae) breeding in the lowland wet zone of Sri Lanka. J. Threat. Taxa. 2017; 9: 9738–9742. http://doi.org/10.11609/jott.2904.9.1.9738-9742

27. Shephard JM, Galbusera P, Hellemans B, Jusic A, Akhandaf Y. Isolation and characterization of a new suite of microsatellite markers in the European white stork, Ciconia ciconia. Conserv. Genet. 2009; 10: 1525. https://doi.org/10.1007/s10592-008-9784-x

28. Wang H, Lou X, Zhu Q, Huang Y, Zhou L, Zhang B. Isolation and characterization of microsatellite DNA markers for the oriental white stork, Ciconia boyciana. Zoolog. Sci. 2011; 28: 606–609. https://doi.org/10.2108/zsj.28.606 21801002

29. Huang Y, Zhou L. Screening and application of microsatellite markers for genetic diversity analysis of oriental white stork (Ciconia boyciana). Chinese Birds. 2011; 2: 33–38. https://doi.org/10.5122/cbirds.2011.0009

30. Turjeman SF, Centeno–Cuadros A, Nathan R. Isolation and characterization of novel polymorphic microsatellite markers for the white stork, Ciconia ciconia: applications in individual-based and population genetics. Anim. Biodivers. Conserv. 2016; 39: 11–16. https://doi.org/10.32800/abc.2016.39.0011

31. Excoffier L, Lischer HE. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 2010; 10: 564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x 21565059

32. Guo SW, Thompson EA. Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics. 1992; 361–372. https://doi.org/10.2307/2532296 1637966

33. Raymond M, Rousset F. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity. 1995; 86: 248–249 https://doi.org/10.1093/oxfordjournals.jhered.a111573

34. R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna. 2018

35. Welch BL. The generalization of student’s’ problem when several different population variances are involved. Biometrika. 1947; 34: 28–35. https://doi.org/10.2307/2332510 20287819

36. Goudet JF. FSTAT (version 1.2): a computer program to calculate F-statistics. J. Hered. 1995; 86: 485–486. https://doi.org/10.1093/oxfordjournals.jhered.a111627

37. Peakall R, Smouse PE. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research–an update. Bioinformatics. 2012; 28: 2537–2539. https://doi.org/10.1093/bioinformatics/bts460 22820204

38. Zar JH. Biostatistical Analysis. Englewood Cliffs, New Jersey: Prentice Hall. 1999.

39. Van Oosterhout C, Hutchinson WF, Wills DP, Shipley P. MICRO‐CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Notes. 2004; 4: 535–538. https://doi.org/10.1111/j.1471-8286.2004.00684.x

40. Park SDE. Trypanotolerance in West African cattle and the population genetic effects of selection. PhD thesis. University of Dublin. 2001

41. Do C, Waples RS, Peel D, Macbeth GM, Tillett BJ, Ovenden JR. NeEstimator v2: re‐implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Mol. Ecol. Resour. 2014; 14: 209–214. https://doi.org/10.1111/1755-0998.12157 23992227

42. Præstgaard JT. Permutation and bootstrap Kolmogorov-Smirnov tests for the equality of two distributions. Scand. J. Stat. 1995; 22: 305–322.

43. Lynch M, Ritland K. Estimation of pairwise relatedness with molecular markers. Genetics. 1999; 152: 1753–1766. 10430599

44. Wang J. COANCESTRY: a program for simulating, estimating and analysing relatedness and inbreeding coefficients. Mol. Ecol. Resour. 2011; 11: 141–145. https://doi.org/10.1111/j.1755-0998.2010.02885.x 21429111

45. Wang J. User’s guide for software COLONY Version 2018

46. Valière N. GIMLET: a computer program for analysing genetic individual identification data. Mol. Ecol. Notes. 2002; 2: 377–379. https://doi.org/10.1046/j.1471-8286.2002.00228.x-i2

47. Chapuis MP, Estoup A. Microsatellite null alleles and estimation of population differentiation. Mol. Biol. Evol. 2006; 24: 621–631. https://doi.org/10.1093/molbev/msl191 17150975

48. Nei M. Genetic distance between populations. Am. Nat. 1972; 106: 283–292. https://doi.org/10.1086/282771

49. Piry S, Luikart G, Cornuet JM. BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. J. Hered. 1999; 90: 502–503. https://doi.org/10.1093/jhered/90.4.502

50. Garza JC, Williamson EG. Detection of reduction in population size using data from microsatellite loci. Mol. Ecol. 2001; 10: 305–318. https://doi.org/10.1046/j.1365-294X.2001.01190.x 11298947

51. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000; 155: 945–959. 10835412

52. Earl DA. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 2012; 4: 359–361. https://doi.org/10.1007/s12686-011-9548-7

53. Allendorf FW, Leary RF. Heterozygosity and fitness in natural populations of animals. In: Soulé ME, editor. Conservation biology. Sinauer, Sunderland, Mass. Conservation biology: the science of scarcity and diversity; 1986. pp. 58–72.

54. Lacy RC. Importance of genetic variation to the viability of mammalian populations. J. Mammal. 1997; 78: 320–335. https://doi.org/10.2307/1382885

55. Ralls K, Meadows R. Captive breeding and reintroduction. In Levin S.,ed., Encyclopedia of Biodiversity, Academic Press, San Diego. 2001; 1: 599–607 https://doi.org/10.1016/B978-0-12-384719-5.00268-9

56. Allendorf FW. Genetic drift and the loss of alleles versus heterozygosity. Zoo. Biol. 1986; 5: 181–190. https://doi.org/10.1002/zoo.1430050212

57. Pujolar JM, Maes GE, Vancoillie C, Volckaert FA. Growth rate correlates to individual heterozygosity in the European eel, Anguilla anguilla L. Evolution. 2005; 59: 189–199. https://doi.org/10.1111/j.0014-3820.2005.tb00905.x 15792238

58. Larson S, Jameson R, Bodkin J, Staedler M, Bentzen P. Microsatellite DNA and mitochondrial DNA variation in remnant and translocated sea otter (Enhydra lutris) populations. J. Mammal. 2002; 83: 893–906. https://doi.org/10.1644/1545-1542(2002)083<0893:MDAMDV>2.0.CO;2

59. Leberg PL. Estimating allelic richness: effects of sample size and bottlenecks. Mol. Ecol. 2002; 11: 2445–2449. https://doi.org/10.1046/j.1365-294X.2002.01612.x 12406254

60. Meirmans PG, Hedrick PW. Assessing population structure: FST and related measures. Mol. Ecol. Resour. 2011; 11: 5–18. https://doi.org/10.1111/j.1755-0998.2010.02927.x 21429096

61. Norton JE, Ashley MV. Genetic variability and population differentiation in captive Baird’s tapirs (Tapirus bairdii). Zoo. Biol. 2004; 23: 521–531. https://doi.org/10.1002/zoo.20031

62. Marker L, O’Brien SJ. Captive breeding of the cheetah (Acinonyx jubatus) in North American zoos (1871–1986). Zoo. Biol. 1989; 8: 3–16. https://doi.org/10.1002/zoo.1430080103

63. Palstra FP, Fraser DJ. Effective/census population size ratio estimation: a compendium and appraisal. Ecol. Evol. 2012; 2: 2357–2365. https://doi.org/10.1002/ece3.329 23139893

64. Frankham R. Inbreeding and extinction: a threshold effect. Conserv. Biol. 1995; 9: 792–799. https://doi.org/10.1046/j.1523-1739.1995.09040792.x

65. Athrey G, Faust N, Hieke AS, Brisbin IL. Effective population sizes and adaptive genetic variation in a captive bird population. PeerJ. 2018; 6: e5803.https://doi.org/10.7717/peerj.5803 30356989

66. Karl SA. The effect of multiple paternity on the genetically effective size of a population. Mol. Ecol. 2008; 3973–3977. https://doi.org/10.1111/j.1365-294X.2008.03902.x 19238700

67. Charlesworth B. Effective population size and patterns of molecular evolution and variation. Nat. Rev. Genet. 2009; 195. https://doi.org/10.1038/nrg2526

68. Nussey DH, Clitton-Brock TH, Elston DA, Albon SD, Kruuk LE. Phenotypic plasticity in a maternal trait in red deer. J. Anim. Ecol. 2005; 74: 387–396. https://doi.org/10.1111/j.1365-2656.2005.00941.x

69. DeYoung RW, Demarais S, Gee KL, Honeycutt RL, Hellickson MW, Gonzales RA. Molecular evaluation of the white-tailed deer (Odocoileus virginianus) mating system. J. Mammal. 2009; 90: 946–953. https://doi.org/10.1644/08-MAMM-A-227.1

70. Grueber CE, Jamieson IG. Quantifying and managing the loss of genetic variation in a free-ranging population of takahe through the use of pedigrees. Conserv. Genet. 2008; 9: 645–651. https://doi.org/10.1007/s10592-007-9390-3

71. Wayne RK, Morin PA. Conservation genetics in the new molecular age. Front. Ecol. Environ. 2004; 2: 89–97. https://doi.org/10.2307/3868215

72. Ivy JA, Lacy RC. A comparison of strategies for selecting breeding pairs to maximize genetic diversity retention in managed populations. J. Hered. 2012; 103: 186–196. https://doi.org/10.1093/jhered/esr129 22246407

73. Frankham R, Ballou JD, Briscoe DA. Introduction to Conservation Genetics, 2nd Edition. CUP, Cambridge, 2010. https://doi.org/10.1017/CBO9780511809002

74. Ralls K and Ballou JD. Captive Breeding and Reintroduction. In: Levin S.A., editor. Encyclopedia of Biodiversity, second edition, Academic Press, Waltham, MA. 2013; 1: 662–667. https://doi.org/10.1016/B978-0-12-809633-8.02024-0

75. Kirkwood JK. Welfare, husbandry and veterinary care of wild animals in captivity: changes in attitudes, progress in knowledge and techniques. Int. Zoo Yb. 2003; 38: 124–130. https://doi.org/10.1111/j.1748-1090.2003.tb02072.x

76. Pelletier F, Réale D, Watters J, Boakes EH, Garant D. Value of captive populations for quantitative genetics research. Trends Ecol. Evol. (Amst.). 2009; 24: 263–270. https://doi.org/10.1016/j.tree.2008.11.013 19269058

77. Hedrick PW, Fredrickson RJ. Captive Breeding and the reintroduction of Mexican and red wolves. Mol. Ecol. 2008; 17: 344–350. https://doi.org/10.1111/j.1365-294X.2007.03400.x 18173506

Článek vyšel v časopise


2019 Číslo 10