Conservation Genetics Resources

, Volume 2, Issue 1, pp 181–184 | Cite as

Microsatellite markers for mating system and population analyses of the spectacled caiman Caiman crocodilus (Linnaeus 1758)

  • Deyla Paula de Oliveira
  • Izeni Pires Farias
  • Boris Marioni
  • Zilca Campos
  • Tomas Hrbek
Technical Note


We used a microsatellite enriched library to isolate and characterize 12 di-nucleotide microsatellite loci of Caiman crocodilus. Microsatellites were characterized in populations of C. c. crocodilus from Piagaçu-Purus, Amazonas, Brazil and C. c. yacare from Cáceres, Mato Grosso, Brazil. Results of characterization were comparable between the two subspecies, with number of alleles varying from three to 20 and one to 14 per locus in C. c. crocodilus and C. c. yacare, respectively. Observed heterozygosities ranged from 0.088 to 0.816 and 0.115 to 0.833, respectively. Joint paternity exclusion (QC) was >0.999 in both subspecies, and probability of genetic identity varied from 4.631 × 10−13 in C. c. crocodilus to 2.233 × 10−8 in C. c. yacare. All loci are unlinked, and with the exception of three loci in C. c. crocodilus all loci were at Hardy–Weinberg equilibrium. The characteristics of these loci makes them an excellent tool set for the study of mating systems, and fine-scaled population structuring in the Caiman crocodilus species complex.


Caiman crocodilus System of mating analysis Population analysis Microsatellite loci Spectacled caiman 



The development of the markers was supported by PROCAD-Amazônia—INPA/UNICAMP/UFRGS/CAPES (023/2006) grant to Miriam da Silva, CNPq/PPG7 557090/2005-9 and CNPq/CT-Amazônia 575603/2008-9 grants to IPF, and an NSF HRD-0931659 grant to TH. The authors thank the faculty and RAs of the PROCAD-funded course and Silvia Planas for discussion and technical help. Permission to collect tissue samples was granted by RAN/IBAMA no. 18187-1 and SDS/CEUC. This study forms a portion of a Masters Thesis of DPO at the Genética, Conservação e Biologia Evolutiva graduate program of INPA/UFAM. DPO was supported by a fellowship from CNPq, with fieldwork supported by WCS and Instituto Piagaçu.


  1. Billotte N, Lagoda PLJ, Risterucci AM, Baurens FC (1999) Microsatellite-enriched libraries: applied methodology for the development of SSR markers in tropical crops. Fruits 54:277–288Google Scholar
  2. Brazaitis P, Rebêlo GH, Yamashita C (1996) The status of Caiman crocodilus crocodilus and Melanosuchus niger populations in the Amazonian regions of Brazil. Amph-Rept 17:377–385CrossRefGoogle Scholar
  3. Busack SD, Pandya S (2001) Geographic variation in Caiman crocodilus and Caiman yacare (Crocodylia: Alligatoridae): Systematics and legal implications. Herpetologica 57:294–312Google Scholar
  4. Dever JA, Densmore LD III (2001) Microsatellites in Morelet’s crocodile (Crocodylus moreletii) and their utility in addressing crocodilian population genetics. J Herpetol 35:541–544CrossRefGoogle Scholar
  5. DeWoody JA, Schupp J, Kenefic L, Busch J, Murfitt L, Keim P (2004) Universal method for producing ROX-labeled size standards suitable for automated genotyping. Biotechniques 37:348–352PubMedGoogle Scholar
  6. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15Google Scholar
  7. Fitzsimmons NN, Tanksley SD, Forstner MRJ (2001) Microsatellite markers for Crocodylus: new genetic tools for population genetics, mating system studies and forensics. In: Grigg J, Seebacher F, Franlin C (eds) Crocodilian biology, evolution. Surrey Beatty and Sons, Chipping Norton, Australia, pp 51–57Google Scholar
  8. Glenn TC, Dessauer HC, Braun MJ (1998) Characterization of microsatellite DNA loci in American alligators. Copeia 1998:591–601CrossRefGoogle Scholar
  9. Goudet J (1995) Fstat version 1.2: a computer program to calculate F statistics. J Hered 86:485–486Google Scholar
  10. Hrbek T, Vasconcelos WR, Rebêlo GH, Farias IP (2008) Phylogenetic relationships of South American alligatorids and the Caiman of Madeira River. J Exp Zool 309A:588–599CrossRefGoogle Scholar
  11. Jing W, Wang X-L, Lan H, Fang S-G (2009) Eleven novel microsatellite markers for the Chinese alligator (Alligator sinensis). Conserv Genet 10:543–546Google Scholar
  12. Miles LG, Isberg SR, Moran C, Hagen C, Glenn TC (2009) 253 Novel polymorphic microsatellites for the saltwater crocodile (Crocodylus porosus). Conserv Genet 10:963–980CrossRefGoogle Scholar
  13. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295CrossRefGoogle Scholar
  14. Ross JP (1998) Crocodiles. Status survey and conservation action plan, 2nd edn. IUCN–SSC. Crocodile Specialist Group, Gland, SwitzerlandGoogle Scholar
  15. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, NJ, pp 465–486Google Scholar
  16. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nature Biotech. 18:233–234CrossRefGoogle Scholar
  17. Smith NJH (1980) Caimans, capybaras, otters, manatees, and man in Amazônia. Biol Conserv 19:177–187CrossRefGoogle Scholar
  18. 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 4:535–538CrossRefGoogle Scholar
  19. Venegas-Anaya M, Crawford AJ, Escobedo Galván AH, Sanjur OI, Densmore LD III, Bermingham E (2008) Mitochondrial DNA phylogeography of Caiman crocodilus in Mesoamerica and South America. J Exp Zool 309A:614–627CrossRefGoogle Scholar
  20. Villela PMS (2008) Caracterização genética de crocodilianos brasileiros e desenvolvimento de marcadores microssatélites para Paleosuchus trigonatus. In: Ecologia Aplicada, p 130. Universidade de São Paulo (USP), Escola Superior de Agricultura Luiz de Queiroz (ELSAQ), Centro de Energia Nuclear na Agricultura, Piracicaba, SP, BrazilGoogle Scholar
  21. Zhu H, Wu X, Xue H, Wei L, Hu Y (2009) Isolation of polymorphic microsatellite loci from the Chinese alligator (Alligator sinensis). Mol Ecol Res 9:892–894CrossRefGoogle Scholar
  22. Zucoloto RB, Verdade LM, Coutinho LL (2002) Microsatellite DNA library for Caiman latirostris. J Exp Zool (Mol Dev Evol) 294:346–351CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Deyla Paula de Oliveira
    • 1
  • Izeni Pires Farias
    • 1
  • Boris Marioni
    • 2
  • Zilca Campos
    • 3
  • Tomas Hrbek
    • 1
    • 4
  1. 1.Laboratório de Evolução e Genética Animal, Departamento de BiologiaUniversidade Federal do AmazonasManausBrazil
  2. 2.Instituto Piagaçu, Rua UZManausBrazil
  3. 3.EMBRAPA-PantanalCorumbáBrazil
  4. 4.Biology DepartmentUniversity of Puerto RicoRio Piedras, San JuanPuerto Rico

Personalised recommendations