A forensic STR profiling system for the Eurasian badger: A framework for developing profiling systems for wildlife species

Forensic Science International: Genetics

Volumn 2, Issue 1, 2008, Pages 47-53

  Dawnay, Nick ^a   Ogden, Rob ^b   Thorpe, Roger S ^a   Pope, Lisa C ^c   Dawson, Deborah A ^c   McEwing, Ross ^b  

^a BANGOR UNIVERSITY   (United Kingdom)

^b Wildlife DNA Services   (United Kingdom)

^c UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

Badger; DNA; Individual identification; Validation; Wildlife forensics

Indexed keywords

DNA;

ARTICLE; DATA ANALYSIS; DNA TEMPLATE; ENVIRONMENTAL EXPOSURE; ENVIRONMENTAL PROTECTION; FORENSIC IDENTIFICATION; FORENSIC SCIENCE; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENE FREQUENCY; GENE LOCUS; GENETIC POLYMORPHISM; INBREEDING; INHERITANCE; MARKER CHROMOSOME; METHODOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; POPULATION STRUCTURE; PRIORITY JOURNAL; PROBABILITY; RELIABILITY; REPRODUCIBILITY; SHORT TANDEM REPEAT; SPECIES DIFFERENCE; UNITED KINGDOM; VALIDATION STUDY; WILDLIFE;

ALLELES; ANIMALS; ANIMALS, WILD; DNA; DNA FINGERPRINTING; ENGLAND; FORENSIC SCIENCES; GENE FREQUENCY; GENOTYPE; MICROSATELLITE REPEATS; MUSTELIDAE; NUCLEIC ACID AMPLIFICATION TECHNIQUES; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; REFERENCE STANDARDS; REPRODUCIBILITY OF RESULTS; SPECIES SPECIFICITY; WALES;

EID: 36048931112     PISSN: 18724973     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fsigen.2007.08.006     Document Type: Article

References (56)

1. Manel S., Berthier P., and Luikart G. Detecting wildlife poaching: Identifying the origin of individuals with Bayesian assignment tests and multilocus genotypes. Conserv. Biol. 16 (2002) 650-659
2. Verma S.K., and Singh L. Novel universal primers establish identity of an enormous number of animal species for forensic application. Mol. Ecol. Notes 3 (2003) 28-31
3. Cassidy B.G., and Gonzales R.A. DNA testing in animal forensics. J. Wildl. Manage. 69 (2005) 1454-1462
4. Cronin M.A., Palmisciano D.A., Vyse E.R., and Cameron D.G. Mitochondrial-DNA in wildlife forensic-science-species identification of tissues. Wildl. Soc. Bull. 19 (1991) 94-105
5. Parson W., Pegoraro K., Niederstatter H., Foger M., and Steinlechner M. Species identification by means of the cytochrome b gene. Int. J. Legal Med. 114 (2000) 23-28
6. Branicki W., Kupiec T., and Pawlowski R. Validation of cytochrome b sequence analysis as a method of species identification. J. Forensic Sci. 48 (2003) 83-87
7. N. Dawnay, R. Ogden, R. McEwing, G.R. Carvalho, R.S. Thorpe, Validation of the Barcoding gene COI for use in forensic genetic species identification. Forensic Sci. Int., in press.
8. Wong K.L., Wang J., But P.P.H., and Shaw P.C. Application of cytochrome b DNA sequences for the authentication of endangered snake species. Forensic Sci. Int. 139 (2004) 49-55
9. Wu H., Wan Q.H., Fang S.G., and Zhang S.Y. Application of mitochondrial DNA sequence analysis in the forensic identification of Chinese sika deer subspecies. Forensic Sci. Int. 148 (2005) 101-105
10. National Research Council. The Evaluation of Forensic DNA Evidence (1996), National Academy Press, Washington, DC
11. Evett I.W., and Weir B.S. Interpreting DNA Evidence: Statistical Genetics for Forensic Scientists (1998), Sinauer Associates Inc., Sunderland, Massachusetts
12. Balding D.J. Weight of Evidence for DNA Profiles (2005), John Wiley & Sons Inc., Great Britain
13. Lincoln P.J., and Thomson J. Methods in Molecular Biology, vol. 98: Forensic DNA Profiling Protocols (1998), Humana Press, Totowa, New Jersey
14. Lincoln P., and Carracedo A. Publication of population data of human polymorphisms. Forensic Sci. Int. 110 (2000) 3-5
15. Budowle B., Garofano P., Hellman A., Ketchum M., Kanthaswamy S., Parson W., van Haeringen W., Fain S., and Broad T. Recommendations for animal DNA forensic and identity testing. Int. J. Legal Med. 119 (2005) 295-302
16. Butler J.M., David V.A., O'Brian S.J., and Menotti-Raymond M. The MeowPlex: a new DNA test kit using tetranucleotide STR markers for the domestic cat. Profiles DNA 5 (2002) 7-10
17. Halverson J., and Basten C. A PCR multiplex and database for forensic DNA identification of dogs. J. Forensic Sci. 50 (2005) 352-363
18. Putnova L., Knoll A., Dvorak V., and Dvorak J. A novel porcine microsatellite panel for the identification of individuals and parentage control in the Czech Republic. Czech J. Anim. Sci. 48 (2003) 307-314
19. Menotti-Raymond M.A., David V.A., and O'Brien S.J. Pet cat hair implicates murder suspect. Nature 386 (1997) 774-1774
20. Savolainen P., and Lundeberg J. Forensic evidence based on mtDNA from dog and wolf hairs. J. Forensic Sci. 44 (1999) 77-81
21. Poetsch M., Seefeldt S., Maschke M., and Lignitz E. Analysis of microsatellite polymorphism in red deer, roe deer, and fallow deer-possible employment in forensic applications. Forensic Sci. Int. 116 (2001) 1-8
22. Xu Y.C., Li B., Li W.S., Bai S.Y., Jin Y., Li X.P., Gu M.B., Jing S.Y., and Zhang W. Individualization of tiger by using microsatellites. Forensic Sci. Int. 151 (2005) 45-51
23. Lorenzini R. DNA forensics and the poaching of wildlife in Italy: a case study. Forensic Sci. Int. 153 (2005) 218-221
24. Jones K.C., Levine K.F., and Banks J.D. DNA-based genetic markers in black-tailed and mule deer for forensic applications. Calif. Fish Game 86 (2000) 115-126
25. Jones K.C., Levine K.F., and Banks J.D. Characterization of 11 polymorphic tetranucleotide microsatellites for forensic applications in California elk (Cervus elaphus canadensis). Mol. Ecol. Notes 2 (2002) 425-427
26. Meredith E.P., Rodzen J.A., Levine K.F., and Banks J.D. Characterization of an additional 14 microsatellite loci in California Elk (Cervus elaphus) for use in forensic and population applications. Conserv. Genet. 6 (2005) 151-153
27. DeNise S., Johnston E., Halverson J., Marshal K., Rosenfeld D., McKenna S., Sharp T., and Edwards J. Power of exclusion for parentage verification and probability of match for identity in American kennel club breeds using 17 canine microsatellite markers. Anim. Genet. 35 (2004) 14-17
28. Marino M., Sala A., and Corach D. Genetic analysis of the populations from Northern and Mesopotamian provinces of Argentina by means of 15 autosomal STRs. Forensic Sci. Int. 160 (2006) 224-230
29. MacDonald D.W., and Newman C. Population dynamics of badgers (Meles meles) in Oxfordshire, UK: numbers, density and cohort life histories, and a possible role of climate change in population growth. J. Zool. 256 (2002) 121-138
30. Carpenter P.J., Dawson D.A., Greig C., Parham A., Cheeseman C.L., and Burke T. Isolation of 39 polymorphic microsatellite loci and the development of a fluorescently labelled marker set for the Eurasian badger (Meles meles) (Carnivora: Mustelidae). Mol. Ecol. Notes 3 (2003) 610-615
31. Saiki R.K., Scharf S., Faloona F., Mullis K.B., Horn G.T., Erlich H.A., and Arnheim N. Enzymatic amplification of beta-globin genomic sequences and restriction site analyses for diagnosis of sickle-cell anemia. Science 230 (1985) 1350-1354
32. Bär W., Brinkmann B., Budowle B., Carracedo A., Gill P., Lincoln P., Mayr W., and Olaisen B. Further report of the DNA Commission of the ISFH regarding the use of short tandem repeat systems. Int. J. Legal Med. 110 (1997) 175-176
33. Hellmann A.P., Rohleder U., Eichmann C., Pfeiffer I., Parson W., and Schleenbecker U. A proposal for standardization in forensic canine DNA typing: allele nomenclature of six canine-specific STR loci. J. Forensic. Sci. 51 (2006) 274-281
34. Dieringer D., and Schlötterer C. Microsatellite analyzer (MSA) a platform independent analysis tool for large microsatellite data sets. Mol. Ecol. Notes 3 (2003) 167-169
35. Raymond M., and Rousset F. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Heredity 86 (1995) 248-249
36. Goudet J. FSTAT (Version 1.2): a computer program to calculate F-statistics. J. Heridity 86 (1995) 485-486
37. Ayres K.L., and Overall A.D.J. API-CALC 1.0: a computer program for calculating the average probability of identity allowing for substructure, inbreeding and the presence of close relatives. Mol. Ecol. Notes 4 (2004) 315-318
38. Balding D.J. Likelihood-based inference for genetic correlation coefficients. Theo. Pop. Biol. 63 (2003) 221-230
39. N.G. Best, M.K. Cowles, K. Vines, CODA: Convergence Diagnosis and Output Analysis Software for Gibbs Sampling Output, Version 0.30, Technical Report, MRC Biostatistics Unit, University of Cambridge, 1995.
40. Carpenter P.J., Pope L.C., Greig C., Dawson D.A., Rogers L.M., Erven K., Wilson G.J., Delahay R.J., Cheeseman C.L., and Burke T. Mating system of the Eurasian badger, Meles meles, in a high density population. Mol. Ecol. 14 (2005) 273-284
41. Smith P.F., DenDanto D., Smith K.T., Palman D., and Kornfield I. Allele frequencies for three STR loci RT24, RT09, and BM1225 in northern New England white-tailed deer. J. Forensic Sci. 47 (2002) 673-675
42. Dawson D.A., Burke T., Hansson B., Pandhal J., Hale M.C., Hinten G.N., and Slate J. A predicted microsatellite map of the passerine genome based on chicken-passerine sequence similarity. Mol. Ecol. 15 (2006) 1299-1320
43. Demars J., Riquet J., Feve K., Gautier M., Morisson M., Demeure O., Renard C., Chardon P., and Milan D. High resolution physical map of porcine chromosome 7 QTL region and comparative mapping of this region among vertebrate genomes. BMC Genomics 7 (2006) Art. No. 13
44. Gusmão L., Butler J.M., Carracedo A., Gill P., Kayser M., Mayr W.R., Morling N., Prinz M., Roewer L., Tyler-Smith C., and Schneider P.M. DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis. Forensic Sci. Int. 157 (2006) 187-197
45. Goldstein D.B., and Schlötterer C. Microsatellites: Evolution and Applications (1999), Oxford University Press, Inc., New York
46. Eichmann C., Berger B., and Parson W. A proposed nomenclature for 15 canine-specific polymorphic STR loci for forensic purposes. Int. J. Legal Med. 118 (2004) 249-266
47. Anderson J.F., Greenhalgh M.J., Butler H.R., Kilpatrick S.R., Piercy R.C., Way K.A., Myhill H.S., Wright J.C., Hallett R., and Parkin B.H. Further validation of a multiplex STR system for use in routine forensic identity testing. Forensic Sci. Int. 78 (1996) 47-64
48. Shutler G.G., Gagnon P., Verret G., Kalyn H., Korkosh S., Johnston E., and Halverson J. Removal of a PCR inhibitor and resolution of DNA STR types in mixed human-canine stains from a five year old case. J. Forensic Sci. 44 (1999) 623-626
49. Hoff-Olsen P., Jacobsen S., Mevag B., and Olaisen B. Microsatellite stability in human post-mortem tissues. Forensic Sci. Int. 119 (2001) 273-278
50. Frantz A.C., Pope L.C., Carpenter P.J., Roper T.J., Wilson G.J., Delahay R.J., and Burke T. Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA. Mol. Ecol. 12 (2003) 1649-1661
51. Waits L.P., Luikart G., and Taberlet P. Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol. Ecol. 10 (2001) 249-256
52. Wright S. Genetical structure of populations. Nature 166 4215 (1950) 247-249
53. Balding D.J., and Nichols R.A. DNA profile match probability calculation: how to allow for population stratification, relatedness, database selection and single bands. Forensic Sci. Int. 64 (1994) 125-140
54. Randi E., Davoli F., Pierpaoli M., Pertoldi C., Madsen A.B., and Loeschcke V. Genetic structure in otter (Lutra lutra) populations in Europe: implications for conservation. Anim. Conserv. 6 (2003) 93-100
55. Pope L.C., Domingo-Roura X., Erven K., and Burke T. Isolation by distance and gene flow in the Eurasian badger (Meles meles) at both a local and broad scale. Mol. Ecol. 15 (2006) 371-386
56. Ayres K.L., and Overall A.D.J. Allowing for within-subpopulation inbreeding in forensic match probabilities. Forensic Sci. Int. 103 (1999) 207-216