Forensic DNA profiling of tropical timber species in Peninsular Malaysia

Forest Ecology and Management

Volumn 259, Issue 8, 2010, Pages 1436-1446

  Tnah, Lee Hong ^a   Lee, Soon Leong ^a   Ng, Kevin Kit Siong ^a   Faridah, Qamaruz Zaman ^b   Faridah Hanum, Ibrahim ^b  

^a FOREST RESEARCH INSTITUTE MALAYSIA   (Malaysia)

^b UNIVERSITY PUTRA MALAYSIA   (Malaysia)

Author keywords

Dipterocarpaceae; Forestry forensic; Neobalanocarpus heimii; Random match probability; Short tandem repeats (STRs)

Indexed keywords

COURT PROCEEDINGS; DIPTEROCARPACEAE; DNA DATABASE; DNA PROFILING; ILLEGAL LOGGING; INDEPENDENCE TESTS; LOGGED TIMBER; MALAYSIA; NATURAL POPULATION; PRODUCT RULE; SHORT TANDEM REPEATS; TROPICAL FOREST; TROPICAL TIMBER;

CLUSTER ANALYSIS; DATABASE SYSTEMS; DNA; ECOSYSTEMS; FORESTRY; GENES; TIMBER; TIMING CIRCUITS;

PROBABILITY;

CLUSTER ANALYSIS; DATABASE; DNA; ECOLOGICAL IMPACT; FOREST ECOSYSTEM; HUMAN ACTIVITY; INBREEDING; LOGGING (TIMBER); POPULATION STRUCTURE; SUBPOPULATION; SUSTAINABILITY; TROPICAL FOREST;

DATA BASES; ECOSYSTEMS; FORENSICS; FORESTRY; GENES; NUCLEIC ACIDS; PROBABILITY;

MALAYSIA; WEST MALAYSIA;

DIPTEROCARPACEAE; NEOBALANOCARPUS HEIMII;

EID: 77649271064     PISSN: 03781127     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.foreco.2010.01.017     Document Type: Article

References (65)

1. Anon. Information Malaysia 2005 (2005), Berita Publishing, Kuala Lumpur 905 pp
2. Asia Forest Partnership (AFP), 2005. Developing Minimum Standards of Legality, Timber Tracking and Chain of Custody Systems, Verification Systems among Asia Forest Partnership (AFP) Partners. Work Plan on Legality, prepared by The Global Forestry Services (GFS) under the coordination of the Center for International Forestry Research (CIFOR).
3. Ayres K.L., and Overall A.D.J. Allowing for within-subpopulation inbreeding in forensic match probabilities. Forensic Sci. Int. 103 (1999) 207-216
4. 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
5. Balding D.J., and Nichols R.A. A method for quantifying differentiation between populations at a multi-allelic loci and its implications for investigating identity and paternity. Genetica 96 (1995) 3-12
6. Becker J., Vos P., Kuiper M., Salamini F., and Heun M. Combined mapping of AFLP and RFLP markers in barley. Mol. Gen. Genet. 249 (1995) 65-73
7. Bless C., Palmeter H., and Wallance M.M. Identification of Acer rubrum using amplified fragment length polymorphism. J. Forensic Sci. 51 (2006) 31-37
8. Buckleton J.S., Curran J.M., and Walsh S.J. How reliable is the sub-population model in DNA testimony?. Forensic Sci. Int. 157 (2006) 144-148
9. Buckleton J.S., Walsh S.J., and Harbison S.A. The fallacy of independence testing and the use of the product rule. Sci. Just. 41 (2001) 81-84
10. Butler J.M. Forensic DNA Typing: Biology, Technology, and Genetics of STR Marker. second ed. (2005), Elsevier Academic Press, Burlington, MA 660 pp
11. Chakraborty R., and Jin L. Determination of relatedness between individuals by DNA fingerprinting. Hum. Biol. 65 (1993) 875-895
12. Chua, L.S.L., 1998. Neobalanocarpus heimii. In: IUCN 2008, 2008 IUCN Red List of Threatened Species. Available at http://www.iucnredlist.org.
13. Congiu L., Chicca M., Cella R., Rossi R., and Bernacchai G. The use of random amplified polymorphic DNA (RAPD) markers to identify strawberry varieties: a forensic application. Mol. Ecol. 9 (2000) 229-232
14. Craft K.J., Owens J.D., and Ashley M.V. Application of plant DNA markers in forensic botany: genetic comparison of Quercus evidence leaves to crime scene trees using microsatellites. Forensic Sci. Int. 165 (2007) 64-70
15. Curran J.M., Buckleton J.S., and Triggs C.M. What is the magnitude of the subpopulation effect?. Forensic Sci. Int. 135 (2003) 1-8
16. Degen B., Petit R., and Kremer A. Spatial Genetic Software (SGS): a computer program for analysis of spatial genetic and phenotypic structures of individuals and populations. J. Hered. 92 (2001) 447-449
17. Donnelly P. Non-independence of matches at different loci in DNA profiles: quantifying the effect of close relatives on the match probability. Heredity 75 (1995) 26-34
18. Foreman L.A., and Evett I.W. Statistical analyses to support forensic interpretation for a new 10-locus STR profiling system. Int. J. Legal Med. 114 (2001) 147-155
19. Foreman L.A., Lambert J.A., and Evett I.W. Regional genetic variation in Caucasians. Forensic Sci. Int. 95 (1998) 27-37
20. Gill P., Foreman L.A., Buckleton J.S., Triggs C.M., and Allen H. A comparison of adjustment methods to test the robustness of a STR database comprised of 24 European populations. Forensic Sci. Int. 131 (2003) 184-196
21. Gilmore S., Peakall R., and Robertson J. Short tandem repeat (STR) DNA markers are hypervariable and informative in Cannabis sativa: implications for forensic investigations. Forensic Sci. Int. 131 (2003) 65-74
22. Goodwin W., Linacre A., and Hadi S. An Introduction to Forensic Genetics (2007), John Wiley & Sons, England 151 pp
23. Goudet, J., 2000. Fstat (version 2.9.1): a program to estimate and test gene diversities and fixation indices. Available at http://www.unil.ch/izea/softwares/fstat.html.
24. Hamrick J.L., Godt M.J.W., and Sherman-Broyles S.L. Factor influencing levels of genetic diversity in woody plant species. New Forest 6 (1992) 95-124
25. Howard C., Gilmore S., Robertson J., and Peakall R. A Cannabis sativa STR genotype database for Australian seizures: forensic applications and limitations. J. Forensic Sci. 54 (2009) 556-563
26. Iwata H., Konuma A., and Tsumura Y. Development of microsatellite markers in the tropical tree Neobalanocarpus heimii (Dipterocarpaceae). Mol. Ecol. 9 (2000) 1661-1686
27. Jong K., and Lethbridge A. Cytological studies in the Dipterocarpaceae I. Chromosome numbers of certain Malaysian genera. Notes R. Bot. Gard. Edinburgh 27 (1967) 175-184
28. Kalinowski S.T., Wagner A.P., and Taper M. ML-Relate: a computer program for maximum likelihood estimation of relatedness and relationship. Mol. Ecol. Notes 4 (2006) 576-579
29. Kobilinsky L., Liotti T., and Oeser-Sweat J. DNA: Forensic and Legal Applications (2005), John Wiley and Sons, Hoboken, NJ 364 pp
30. Konuma A., Tsumura Y., Lee C.T., Lee S.L., and Okuda T. Estimation of gene flow in the tropical-rainforest tree Neobalanocarpus heimii (Dipterocarpaceae), inferred from paternity analysis. Mol. Ecol. 9 (2000) 1843-1853
31. Lander E.S. DNA fingerprinting on trial. Nature 339 (1989) 501-505
32. Lander E.S. Fight erupts over DNA fingerprinting. Science 254 (1991) 1921-1923
33. Lee S.L. Mating system parameters of Dryobalanopus aromatica Gaertn. F. (Dipterocarpaceae) in three different forest types and a seed orchard. Heredity 85 (2000) 338-345
34. Lee S.L., Ng K.K.S., Saw L.G., Lee C.T., Norwati M., Tani N., Tsumura Y., and Koskela J. Linking the gaps between conservation research and conservation management of rare dipterocarps: a case study of Shorea lumutensis. Biol. Conserv. 131 (2006) 72-92
35. Lee S.L., Tani N., Ng K.K.S., and Tsumura Y. Characterization of 15 polymorphic microsatellite loci in an endangered tropical tree Hopea bilitonensis (Dipterocarpaceae) in Peninsular Malaysia. Mol. Ecol. Notes 4 (2004) 147-149
36. Lee S.L., Tani N., Ng K.K.S., and Tsumura Y. Isolation and characterization of 20 microsatellite loci for an important tropical tree Shorea leprosula (Dipterocarpaceae) and their applicability to S. parvifolia. Mol. Ecol. Notes 4 (2004) 222-225
37. Lee S.L., Wickneswari R., Mahani M.C., and Zakri A.H. Mating system parameters in a tropical tree species, Shorea leprosula Miq. (Dipterocarpaceae) from Malaysian Lowland Dipterocarp Forest. Biotropica 32 (2000) 693-702
38. Lewis, P.O., Zaykin, D., 2001. Genetic Data Analysis (GDA: version 1.0 d16c): a computer program for the analysis of allelic data. Available at http://lewis.eeb.uconn.edu/lewishome/software.html.
39. Liu K., and Muse S.V. PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21 (2005) 2128-2129
40. Manel S., Berthier P., and Luikart G. Detecting wildlife poaching: identifying the origin of individuals with Bayesian assignment test and multilocus genotypes. Conserv. Biol. 16 (2002) 650-659
41. Murawski D.A., Gunatilleke I.A.U.N., and Bawa K.S. The effects of selective logging on inbreeding in Shorea megistophyll (Dipterocarpaceae) from Sri Lanka. Conserv. Biol. 8 (1994) 997-1002
42. Murray M., and Thompson W.F. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8 (1980) 4321-4325
43. Naito Y., Konuma A., Iwata H., Suyama Y., Seiwa K., Okuda T., Lee S.L., Norwati M., and Tsumura Y. Selfing and inbreeding depression in seeds and seedlings of Neobalanocarpus heimii (Dipterocarpaceae). J. Plant Res. 118 (2005) 423-430
44. NRC II (National Research Council Report). The Evaluation of Forensic DNA Evidence (1996), National Academy Press, Washington, DC 254 pp
45. Obayashi K., Tsumura Y., Ujino T., Niiyama K., Tanouchi H., Suyama Y., Washitani I., Lee C.T., Lee S.L., and Norwati M. Genetic diversity and outcrossing rate between undisturbed and selectively logged forests of Shorea curtisii (Dipterocarpaceae) using microsatellite DNA analysis. Int. J. Plant Sci. 163 (2002) 151-158
46. Overall, A.D.J., 1998. The Geographic Scale of Human Genetic Differentiation at Short Tandem Loci. PhD Thesis. University of London, London, 172 pp.
47. Pritchard J.K., Stephens M., and Donnelly P. Inference of population structure using multilocus genotype data. Genetics 155 (2000) 945-959
48. Raymond M., and Rousset F. Genepop (version 3.4): population genetics software for exact tests and ecumenicism. J. Hered. 86 (1995) 248-249
49. Rice W.R. Analysing tables of statistical tests. Evolution 43 (1989) 223-225
50. Saitou N., and Nei M. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 11 (1987) 553-570
51. Siver P.A., Lord W.D., and McCarthy D.J. Forensic limnology: the use of freshwater algal community ecology to link suspects to an aquatic crime scene in southern New England. J. Forensic Sci. 39 (1994) 847-853
52. Sjerps M., and Kloosterman A.D. Statistical aspects of interpreting DNA profiling in legal cases. Stat. Neerl. 57 (2003) 368-389
53. Smith W. Undercutting sustainability: the global problem of illegal logging and trade. In: Ravenel R.M., Granoff I.M.E., and Magee C.A. (Eds). Illegal Logging in the Tropics: Strategies for Cutting Crime (2004), The Haworth Press, New York 7-30
54. Symington C.F. Foresters' Manual of Dipterocarps, Malayan Forest Records 16 (1943), Forest Research Institute Malaysia, Kuala Lumpur 519 pp
55. Thomas A.R. Malayan timber-chengal and balau. Malayan Forester 16 (1953) 103-108
56. Tnah, L.H., Lee, S.L., Ng, K.K.S., Faridah, Q.Z., Faridah-Hanum, I., 2010. Highly variable STR markers of Neobalanocarpus heimii (Dipterocarpaceae) for forensic DNA profiling. J. Trop. Forest Sci. In press.
57. Triggs C.M., and Buckleton J.S. Logical implications of applying the principles of population genetics to the interpretation of DNA profiling evidence. Forensic Sci. Int. 128 (2002) 108-114
58. Ujino T., Kawahara T., Tsumura Y., Nagamitsu T., Yoshimaru H., and Wickneswari R. Development and polymorphism of simple sequence repeat DNA markers for Shorea curtisii and other Dipterocarpaceae species. Heredity 81 (1998) 422-428
59. Waits L.P., Luikart G., and Tarberlet P. Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol. Ecol. 10 (2001) 249-256
60. Weir B.S., and Cockerham C.C. Estimating F statistics for the analysis of population structure. Evolution 38 (1984) 1358-1370
61. Weising K., Nybom H., Wolff K., and Kahl G. DNA Fingerprinting in Plants: Principles, Methods, and Applications. second ed. (2005), Taylor & Francis Group, Boca Raton, FL 444 pp
62. White E., Hunter J., Dubetz C., Brost R., Bratton A., Eded S., and Sahota R. Microsatellite markers for individual tree genotyping: application in forest crime prosecutions. J. Chem. Technol. Biotechnol. 75 (2000) 923-926
63. Withler R.E., Candy J.R., Beacham T.D., and Miller K.M. Forensic DNA analysis of Pacific salmonid samples for species and stock identification. Environ. Biol. Fish. 69 (2004) 275-285
64. Yoon C.K. Botanical witness for the prosecution. Science 260 (1993) 894-895
65. Ziegenhagen B., Liepelt S., Kuhlenkamp V., and Fladung M. Molecular identification of individual oak and fir tree from maternal tissues of their seeds. Trees 17 (2003) 345-350