Historical and non-invasive samples: A study case of genotyping errors in newly isolated microsatellites for the lesser anteater (Tamandua tetradactyla L., Pilosa)

Molecular Ecology Resources

Volumn 14, Issue 3, 2014, Pages 531-540

  Clozato, Camila L ^a   Moraes Barros, Nadia ^a,b   Santos, Fabrício R ^c   Morgante, João S ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b CENTRO DE INVESTIGAÇÃO EM BIODIVERSIDADE E RECURSOS GENÉTICOS   (Portugal)

^c FEDERAL UNIVERSITY OF MINAS GERAIS   (Brazil)

Author keywords

Genotyping errors; Historical samples; Microsatellite loci; Non invasive samples; Quality index; Tamandua tetradactyla

Indexed keywords

MAMMALIA; MYRMECOPHAGIDAE; TAMANDUA TETRADACTYLA;

MICROSATELLITE DNA;

ANIMAL; CLASSIFICATION; GENETICS; GENOTYPE; MOLECULAR GENETICS; POLYMERASE CHAIN REACTION; PROCEDURES; STANDARDS; XENARTHRA;

ANIMALS; GENOTYPE; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; XENARTHRA;

EID: 84898541239     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12214     Document Type: Article

References (36)

1. Arandjelovic M, Guschanski K, Schubert G et al. (2009) Two-step multiplex polymerase chain reaction improves the speed and accuracy of genotyping using DNA from noninvasive and museum samples. Molecular Ecology Resources, 9, 28-36.
2. Beja-Pereira A, Oliveira R, Alves PC et al. (2009) Advancing ecological understandings through technological transformations in noninvasive genetics. Molecular Ecology Resources, 9, 1279-1301.
3. Billotte N, Lagoda PJL, Risterucci AM et al. (1999) Microsatellite enriched libraries: applied methodology for the development of SSR markers in tropical crops. Fruits, 54, 277-288.
4. Bonin A, Bellemain E, Bronken Eidesen P et al. (2004) How to track and assess genotyping errors in population genetics studies. Molecular Ecology, 13, 3261-3273.
5. Boston ESM, Puechmaille SJ, Scott DD et al. (2012) Empirical assessment of noninvasive population genetics in bats: comparison of dna quality from faecal and tissue samples. Acta Chiropterologica, 14, 45-52.
6. Broquet T, Petit E (2004) Quantifying genotyping errors in noninvasive population genetics. Molecular Ecology, 13, 3601-3608.
7. Broquet T, Ménard N, Petit E (2007) Noninvasive population genetics: a review of sample source, diet, fragment length and microsatellite motif effects on amplification success and genotyping error rates. Conservation Genetics, 8, 249-260.
8. Carlsson J (2008) Effects of microsatellite null alleles on assignment testing. Journal of Heredity, 99, 616-623.
9. Casas-Marce M, Revilla E, Godoy J (2010) Searching for DNA in museum specimens: a comparison of sources in a mammal species. Molecular Ecology Resources, 10, 502-507.
10. Chapuis M-P, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Molecular Biology and Evolution, 24, 621-631.
11. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567.
12. Gardner AL (2005) Order Pilosa. In: Mammal Species of the World: A Taxonomic and Geographic Reference, 3rd edn.(eds Wilson DE, Reeder DM), pp. 98-102. The John Hopkins University Press, Baltimore.
13. Hall ML, Willcox MS, Jones DS (1997) Association of enzyme inhibition with methods of museum skin preparation. BioThecniques, 22, 928-934.
14. Hartl DL, Clark AG (2006) Testing Hardy-Weinberg Equilibrium. Principles of Population Genetics(eds Daniel LH, Andrew GC), pp. 70-82. Sinauer Associates, Massachusetts.
15. Hayssen V (2011) Tamandua tetradactyla (Pilosa: Myrmecophagidae). Mammalian Species, 43, 64-74.
16. Kelly C, Mateus-Pinilla NE, Douglas M et al. (2011) Microsatellites behaving badly: empirical evaluation of genotyping errors and subsequent impacts on population studies. Genetics and Molecular Research, 10, 2534-2553.
17. Kelly MJ, Betsch J, Wultsch C et al. (2012) Noninvasive sampling for carnivores. In: Carnivore Ecology and Conservation, A handbook of Techniques(eds Boitani Luigi, Roger AP), pp. 49-54. Oxford University Press, New York.
18. Luikart G, Zundel S, Rioux D et al. (2008) Low genotyping error rates and non-invasive sampling in bighorn sheep. Journal of Wildlife Management, 72, 299-304.
19. Miquel C, Bellemain E, Poillot C et al. (2006) Quality indexes to assess the reliability of genotypes in studies using noninvasive sampling and multiple-tube approach. Molecular Ecology Notes, 6, 985-988.
20. Mondol S, Karanth KU, Kumar NS et al. (2009) Evaluation of non-invasive genetic sampling methods for estimating tiger population size. Biological Conservation, 142, 2350-2360.
21. Montgomery GG, Lubin YD (1977) Prey influences on movements of neotropical anteaters. In: Proceedings of 1975 Predator Symposium(eds Philips RL, Jonkel C), pp. 103-131. University of Montana, Missoula.
22. de Moraes-Barros N, Morgante JS (2007) A simple protocol for the extraction and sequence analysis of DNA from study skin of museum collections. Genetics and Molecular Biology, 30, 1181-1185.
23. Morin PA, Leduc RG, Archer FI et al. (2009) Significant deviations from Hardy-Weinberg equilibrium caused by low levels of microsatellite genotyping errors. Molecular Ecology Resources, 9, 498-504.
24. Polanc P, Sindičić M, Jelenčič M et al. (2012) Genotyping success of historical Eurasian lynx (Lynx lynx L.) samples. Molecular Ecology Resources, 12, 293-298.
25. Pompanon F, Bonin A, Bellemain E, Taberlet P (2005) Genotyping errors: causes, consequences and solutions. Nature Reviews Genetics, 6, 847-859.
26. R Development Core Team(2008) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org
27. Rohland N, Siedel H, Hofreiter M (2004) Nondestructive DNA extraction method for mitochondrial DNA analyses of museum specimens. BioTechniques, 36, 814-818.
28. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, New York.
29. Shaw PW, Pierce GJ, Boyle PR (1999) Subtle population structure within a highly vagile marine invertebrate, the vained squid Loligo forbesi, demonstrated with microsatellite DNA markers. Molecular Ecology, 8, 407-417.
30. Taberlet P, Griffin S, Goossens B et al. (1996) Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Research, 24, 3189-3194.
31. Taberlet P, Waits LP, Luikart G (1999) Noninvasive genetic sampling: look before you leap. Trends in Ecology and Evolution, 14, 323-327.
32. Van Oosterhout C, Hutchinson WF, Wills DPM et al. (2004) Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes, 4, 535-538.
33. Waits LP, Paetkau D (2005) Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations for accurate data collection. Journal of Wildlife Management, 69, 1419-1433.
34. Wandeler P, Hoeck PE, Keller LF (2007) Back to the future: museum specimens in population genetics. Trends in Ecology and Evolution, 22, 634-642.
35. Ware DH, Jaiswal P, Ni J et al. (2002) Gramene, a tool for grass genomics. Plant Physiology, 130, 1606-1613.
36. Wetzel RM (1975) The species of Tamandua Gray (Edentata, Myrmecophagidae). Proceedings of the Biological Society of Washington, 88, 95-112.