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Population data from sub-populations of the Northern Territory of Australia for 15 autosomal short tandem repeat (STR) loci
Forensic Science International 171 (2007) 237–249 www.elsevier.com/locate/forsciint
Announcement of population data
Population data from sub-populations of the Northern Territory of Australia for 15 autosomal short tandem repeat (STR) loci Carmen Eckhoff a,1, Simon J. Walsh b,c,*, John S. Buckleton d b
a Northern Territory Police, Fire and Emergency Services, PO Box 39764, Winnellie, NT 0821, Australia Centre for Forensic Science, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia c Science & Justice Consulting, PO Box 83, Surry Hills, NSW 2010, Australia d ESR Ltd., Private Bag 92-021, Auckland, New Zealand
Received 2 May 2005; received in revised form 5 March 2006; accepted 8 June 2006 Available online 1 August 2006
Abstract It is a requirement that forensic DNA profiling evidence be accompanied by an estimation of its weight, in order that the court can assign an appropriate probative value to the evidence during legal proceedings. There are various models by which this estimation can be made, but each relies on approximations of the allele frequencies in the relevant population. It is also important to assess relevant population genetic features of the available data. This report provides allele frequencies and estimates of common population genetic parameters for the major sub-populations of the Northern Territory of Australia genotyped at 15 autosomal short tandem repeat (STR) loci. # 2006 Elsevier Ireland Ltd. All rights reserved. Keywords: DNA profiling; Autosomal microsatellites; Population data; Allele frequencies; Profiler plus; Identifiler; Independence testing; Northern Territory
Population: Forensic biology personnel from the Northern Territory Police, Fire and Emergency Services (NTPFES) have compiled sub-population datasets from five major subpopulation groups of Northern Australia (Table 1). The subpopulation of origin of each donor was assigned by a combination of self-declaration or assignment by a third party. Extraction: DNA was extracted from blood stain cards and buccal swabs. The reference samples were air-dried before being stored at 20 8C. A small portion was removed from the reference sample and DNA was extracted using the Chelex method as described by Walsh et al. [1]. Amplification: The NTPFES Forensic Biology Laboratory uses both the Applied Biosystems AMPFlSTR1 Profiler PlusTM kit and AMPFlSTR1 IdentifilerTM kit for routine casework and database samples. In a single PCR reaction the kits amplify 9 and 15 tetranucleotide loci, respectively, as well
* Corresponding author. Tel.: +61 2 9514 4064; fax: +61 2 9514 8206. E-mail addresses: [email protected] (C. Eckhoff), [email protected] (S.J. Walsh). 1 Tel.: +61 8 8922 1324; fax: +61 8 8922 1326. 0379-0738/$ – see front matter # 2006 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2006.06.009
as a gender identification marker. The procedures used by the NTPFES Biology Laboratory are proportionate to the manufacture’s protocols for both kits, using a total amplification volume of 20 ml, not 50 ml as recommended. The samples were amplified on the Applied Biosystems GeneAmp1 PCR System 9700 thermal cycler in accordance to the respective Applied Biosystems protocol for each kit. Detection: Aliquots of 1–2 ml of the amplified product were combined with 24 ml of HiDi Formamide containing 0.4 ml GeneScanTM 500RoxTM (Profiler PlusTM) or 0.4 ml GeneScanTM 500LizTM (IdentifilerTM) and analysed using an automated sequencer, the ABI PrismTM 310 Genetic Analyzer, as per the Applied Biosystems protocols. GeneScanTM and Genotyper software were used to verify the fragment size of the alleles and thus determine the DNA profile for each of the reference samples. All DNA results were independently verified by a second reader. Results:The allele frequencies for the 15 STR loci have been tabulated within each of the five sub-population categories listed in Table 1. The data are represented in Tables 2–6. Estimates of observed and expected heterozygosity (HO and HE, respectively; Tables 2–6) and Fisher’s exact test [2] for allelic association was undertaken with 10,000 shuffles using the Genetic Data Analysis [3] software provided courtesy of Paul
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C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
Table 1 Description of sub-population categories for the NT Sub-population
Description
NT Caucasian NT Declared Aboriginal NT Pure Aboriginal NT Asian NT East Timorese
Data Data Data Data Data
compiled compiled compiled compiled compiled
from from from from from
individuals individuals individuals individuals individuals
who who who who who
have self-declared their ethnicity as Caucasian have self-declared their ethnicity as Aboriginal (or Indigenous Australian) are known to be Indigenous Australian and who are resident of remote tribal communities have self-declared their ethnicity as Asian have self-declared their ethnicity as East Timorese
Lewis (Department of Ecology and Evolutionary Biology, The University of Connecticut). Departures from Hardy–Weinberg equilibrium ( p < 0.05) were detected at some loci (Table 7). However, in this dataset we have what is termed the ‘multi-testing problem’ as we have undertaken 15 Hardy–Weinberg and 105 linkage-equilibrium tests per ethnic group. In addition, some of these comparisons were based on small datasets. Hypothesis testing on very small datasets is ineffective [4,5]. Accordingly the results from tests on datasets of less than 200 profiles were not considered. This meant that six loci (TH01, TPOX, CSF, D16, D2 and D19) from the Asian sub-population dataset were excluded from consideration. There are various ways offered to deal with the multitesting problem. These include the Bonferonni correction, a simple graphical examination (including p–p plots) or the truncated product method. The Bonferonni correction suffers from the handicap that it lowers the power of an already weak test [6]. For these reasons we prefer the other two methods. Graphical representations of these data are given in Fig. 1. If the hypotheses of Hardy–Weinberg and linkage equilibrium are true then the p-values should be distributed uniformly between 0 and 1; p U[0,1]. As an example, the x = y trend-line in the p–p plots (Fig. 1) represents equilibrium and deviations from that trend-line can be seen as mild departures from equilibrium. The 95% confidence limit is also displayed on the p–p plots as the region within the two curved lines. The p–p plot for the Caucasian dataset (Fig. 1) shows evidence of mild departure. The values are plotting away from the linear trend-line (which represents a state of Hardy– Weinberg and linkage equilibrium) although remain within the 95% confidence limit envelope. The p–p plots for both the Declared and Pure Aboriginal (Fig. 1) datasets show evidence of departure from independence as values plot away from the linear trend-line (which represents a state of Hardy– Weinberg and linkage equilibrium) and occur mostly outside the 95% confidence limit envelope. The shape of the curve is more pronounced in the Declared Aboriginal dataset, than in the Pure Aboriginal dataset, however, the difference in the sizes of these datasets limits our ability to compare these outcomes. The p–p plots for both the Asian and East Timorese (Fig. 1) sub-populations do not show any evidence of departure. The truncated product method gives the test statistics provided in Table 8. This elegant method was described by Zaykin et al. [7]. This method involves forming the sum of 2 ln( p) across, say, x independent tests. This sum is expected
to have a chi-square distribution with 2x degrees of freedom and a p-value is estimated (Table 8). It is important to note that these tests are not independent and hence the truncated product method can only be used as a guide. The truncated product test statistics do not suggest any strong evidence for departure from independence for the Asian or East Timorese datasets ( p > 0.05) but do give such an indication for the Caucasian, Declared and Pure Aboriginal datasets ( p < 0.05). Discussion: Due to the range of loci analysed in the Northern Territory sub-population datasets, their sizes vary widely for different loci and different sub-population categories. The Caucasian and Aboriginal datasets are large by world standards for 9 of the 15 loci analysed (corresponding with the loci of the Profiler PlusTM system), and moderately sized for the remaining six loci. The Asian and East Timorese datasets are small by comparison, but of suitable size for allele frequency estimation at 9 of the 15 loci (again corresponding with the loci of the Profiler PlusTM system). Caution must be exercised when interpreting data from small datasets. We have advised in the past, and re-iterate here, the need for adequate correction for sampling error when using allele frequency data from moderate to small datasets [8]. A discussion of approaches has been given by Curran and colleagues [9,10]. Caucasian populations worldwide are believed to be very close to equilibrium and previously when we have analysed datasets of this size we have found little or no evidence for departure [11–14]. However, some evidence of departure was observed in the NT Caucasian sub-population dataset (Fig. 1, Table 8). This mild departure is not grossly beyond expectation. The size of the dataset is approaching a level that permits the detection of small-scale departures. Aboriginal populations are believed to be sub-structured with complex patterns of relatedness within and between communities and/or tribal groups. Additionally, certain Aboriginal populations of Australia have undergone admixture with other non-indigenous sub-populations. Hence, the expectation for Aboriginal datasets is moderate disequilibrium. The combined Aboriginal dataset analysed here is extensive. It has also been partitioned into declared and pure categories. Testing these sub-sets revealed a greater extent of disequilibrium in the Declared Aboriginal dataset. This may be indicative of more extensive admixture, or may also be related to the increased power of the tests to find departures, due to the greater size of the Declared Aboriginal dataset relative to the Pure Aboriginal dataset.
Table 2 Allele frequencies for the 15 IdentifilerTM loci for the NT Caucasian sub-population Allele
D3 TM
– – – – – – – – – 0.0001 – 0.0004 – – – 0.0011 – – 0.1063 – – 0.0975 – 0.2223 – 0.2671 – 0.2001 – 0.0886 – 0.0152 – 0.0011 – – 0.0001 – – – – – – – – – –
– – – – – – – – – – – – – – – – – – – – – 0.0001 – 0.0003 – 0.0009 – 0.0144 0.0001 0.0591 0.0002 0.1370 0.0021 0.1791 – 0.0028 0.1799 0.0090 0.0001 0.1467 0.0045 0.1390 0.0007 0.0817 0.0004 0.0317 0.0001
D8
D21 – – – – 0.0210 – 0.0131 – 0.0887 0.0785 – 0.1423 0.0001 – – 0.3215 – – 0.1919 – – 0.1076 – 0.0313 – 0.0037 – 0.0003 – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.0010 – 0.0009 0.0019 –
D18 – – – – – – 0.0004 – 0.0078 0.0147 0.0001 0.1443 – – – 0.1260 – 0.0001 0.1643 0.0001 0.0001 0.1491 – 0.1375 – 0.1070 0.0001 0.0711 – 0.0436 – 0.0180 0.0002 0.0081 – – 0.0049 – – 0.0015 – 0.0004 – 0.0003 – 0.0001 –
D5
D13 – 0.0002 0.0007 – 0.0024 – 0.0369 – 0.0704 0.3632 – 0.3588 – – – 0.1541 – – 0.0106 – – 0.0026 – – – – – – – – – – – – – – – – – – – – – – – – –
– – 0.0003 – 0.1342 – 0.0773 – 0.0654 0.3058 – 0.2801 – – – 0.0936 – – 0.0429 – – 0.0005 – – – – – – – – – – – – – – – – – – – – – – – – –
D7
TH01 – – 0.0234 0.0001 0.1587 – 0.1588 – 0.2665 0.2086 – 0.1459 – – – 0.0307 0.0001 – 0.0067 – – 0.0006 – – – – – – – – – – – – – – – – – – – – – – – – –
0.0016 0.2322 0.1885 – 0.1328 0.0005 0.1525 0.2814 0.0093 0.0011 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
TPOX – 0.0012 – – 0.5125 – 0.1241 – 0.0546 0.2696 – 0.0374 – – – – – – – – – 0.0006 – – – – – – – – – – – – – – – – – – – – – – – – –
CSF – – 0.0018 – 0.0072 – 0.0235 – 0.2398 0.3060 – 0.3325 – – – 0.0759 – – 0.0120 – – 0.0012 – – – – – – – – – – – – – – – – – – – – – – – – –
D16 – – – – 0.0088 – 0.1103 – 0.0574 0.2926 – 0.3309 – – – 0.1721 – – 0.0265 – – 0.0015 – – – – – – – – – – – – – – – – – – – – – – – – –
D2 – – – – – – – – – – – – – – 0.0015 – – – – – – 0.0030 – 0.0519 – 0.1840 – 0.0801 – 0.1039 – 0.1350 – 0.0282 – – 0.0341 – – 0.1068 – 0.1187 – 0.1276 – 0.0223 –
D19 – – – – – – – – 0.0015 0.0044 – 0.0746 0.0015 – – 0.2515 – 0.0058 0.3480 – 0.0190 0.1725 0.0570 0.0512 0.0073 0.0044 – – 0.0015 – – – – – – – – – – – – – – – – – –
239
loci – – – – – – – – – 0.0010 – 0.0004 – – – 0.0029 – – 0.1175 – – 0.2745 – 0.2505 – 0.2014 – 0.1373 0.0001 0.0134 – 0.0008 – 0.0001 0.0001 – – – – – – – – – – – –
FGA
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
Identifiler 5 6 7 7.3 8 8.3 9 9.3 10 11 11.2 12 12.1 12.2 12.3 13 13.1 13.2 14 14.1 14.2 15 15.2 16 16.2 17 17.1 18 18.2 19 19.2 20 20.2 21 21.1 21.2 22 22.2 22.3 23 23.2 24 24.2 25 25.2 26 26.1
vWA
240
Table 2 (Continued ) Allele
vWA
FGA
D8
D21
D18
D5
D13
D7
TH01
TPOX
CSF
D16
D2
D19
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.789 0.789 9702
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.810 0.808 9684
– 0.0079 0.0014 – 0.0004 – – – 0.0001 – – – – – – – – – – – – – – – – – – 0.864 0.861 9692
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.812 0.806 9696
0.0002 0.0356 0.1519 0.0001 0.2159 0.0001 0.0010 0.0001 0.2409 0.0335 0.0719 0.1058 0.0148 0.0845 0.0009 0.0299 0.0003 0.0002 0.0039 0.0010 0.0011 0.0001 0.0005 0.0007 0.0007 0.0004 0.0001 0.845 0.846 9686
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.876 0.881 9588
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.709 0.707 9696
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.789 0.779 9668
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.812 0.813 9574
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.791 0.785 1830
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.645 0.639 1684
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.732 0.745 1660
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.760 0.776 680
– 0.0015 0.0015 – – – – – – – – – – – – – – – – – – – – – – – – 0.885 0.896 674
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.775 0.807 684
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
26.2 27 28 28.2 29 29.1 29.2 29.3 30 30.2 31 31.2 32 32.2 33 33.2 34 34.1 34.2 35 35.2 36 36.2 37.2 38.2 39.2 40.2 HE HO n
D3
Table 3 Allele frequencies for the 15 IdentifilerTM loci from the NT Declared Aboriginal sub-population Allele
D3 TM
– – – – – – – – – – – – – 0.0001 – 0.0356 – – 0.0702 – – 0.2427 – 0.2701 0.2181 – 0.1398 – – 0.0219 – – 0.0014 0.0001 – – – – – – – – – – – – –
D8 – – – – – – – – – – – – – 0.0001 – – – – – – – 0.0017 – 0.0052 0.0258 – 0.0729 0.0001 0.0001 0.1050 0.0001 0.0011 0.1087 – 0.0037 – 0.1671 0.0056 0.1639 0.0034 0.1642 0.0037 0.1139 0.0001 0.0002 0.0403 0.0118
D21 – – – 0.0028 – 0.0025 – – – 0.0313 0.0889 0.1531 – 0.2372 – 0.1812 – – 0.1907 – 0.0033 0.0813 – 0.0233 0.0041 – 0.0002 – – – – – – – – – – – – – – – – – – – –
D18 – – – – – – – – – – – 0.0001 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.0003 – – 0.0022 0.0065 0.0106
D5 – – – – – – – – – 0.0028 0.0585 0.0471 0.0002 0.2038 0.0001 0.1694 0.0001 – 0.1216 – – 0.1297 – 0.0737 0.0781 0.0001 0.0619 0.0001 0.0001 0.0257 0.0001 – 0.0175 – – 0.0001 0.0080 – 0.0010 – 0.0001 – – – – – –
D13 – 0.0007 – 0.0006 – 0.0771 – – – 0.2201 0.2772 0.2822 – 0.1273 – 0.0137 – – 0.0011 – – – – – – – – – – – – – – – – – – – – – – – – – – – –
D7 0.0007 0.0028 – 0.3074 – 0.0513 – – – 0.0376 0.3184 0.2120 – 0.0517 – 0.0182 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
TH01 0.0003 0.0085 0.0040 0.3697 0.0001 0.0847 0.0001 – – 0.1987 0.2261 0.0909 – 0.0160 – 0.0008 – – 0.0001 – – – – – – – – – – – – – – – – – – – – – – – – – – – –
0.3615 0.2559 – 0.1227 – 0.1925 – – 0.0599 0.0065 0.0012 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
TPOX 0.0006 0.0006 – 0.2239 – 0.4325 – – – 0.0486 0.2790 0.0142 – 0.0006 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
CSF – 0.0012 – 0.0090 – 0.0127 – 0.0006 – 0.2398 0.2795 0.3560 – 0.0886 – 0.0114 – – 0.0012 – – – – – – – – – – – – – – – – – – – – – – – – – – – –
D16 – 0.0009 – 0.0091 – 0.0356 – – – 0.1005 0.3958 0.2331 – 0.1764 – 0.0439 – – 0.0046 – – – – – – – – – – – – – – – – – – – – – – – – – – – –
D2
D19 – – – – – – – – – – – – – – – – – – – – – 0.0064 – 0.0681 0.1031 – 0.2320 – – 0.0958 – – 0.0617 – – – 0.0773 – 0.1510 – 0.1197 – 0.0672 – – 0.0175 –
– – – – – – – – – – 0.0027 0.0605 – 0.3484 0.0045 0.4161 – 0.0045 0.1227 0.0054 – 0.0289 0.0027 0.0027 0.0009 – – – – – – – – – – – – – – – – – – – – – –
241
loci – – – – – – – – – – 0.0013 0.0004 – 0.0028 – 0.0444 – – 0.3773 – – 0.2448 – 0.2158 0.0967 – 0.0131 – – 0.0023 0.0003 – 0.0002 0.0007 – – – – – – – – – – – – –
FGA
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
Identifiler 6 7 7.3 8 8.3 9 9.1 9.2 9.3 10 11 12 12.2 13 13.2 14 14.1 14.2 15 15.2 15.3 16 16.2 17 18 18.2 19 19.1 19.2 20 20.1 20.2 21 21.1 21.2 21.3 22 22.2 23 23.2 24 24.2 25 25.1 25.2 26 27
vWA
242
Table 3 (Continued ) Allele
D3
FGA
D8
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.794 0.783 10744
0.0001 – 0.0011 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.875 0.835 0.853 0.833 10732 10750
D21
D18
– – 0.1131 – 0.0001 – 0.2258 – 0.0003 – 0.0018 – 0.0001 – 0.1948 – 0.0386 – 0.0413 – 0.1142 – 0.0135 – 0.0909 – 0.0014 – 0.0468 – 0.0001 – 0.0005 – 0.0076 – 0.0237 – 0.0001 – 0.0203 – 0.0001 – 0.0174 – 0.0155 – 0.0078 – 0.0034 – 0.0010 – 0.870 0.876 0.845 0.849 10714 10564
D5
D13
D7
TH01
TPOX
CSF
D16
D2
D19
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.773 0.746 10746
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.752 0.735 10710
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.757 0.746 10530
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.749 0.725 1704
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.683 0.635 1688
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.730 0.728 1660
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.745 0.697 1094
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.871 0.856 1086
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.686 0.713 1108
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
27.1 – 28 – 28.2 – 29 – 29.1 – 29.2 – 29.3 – 30 – 30.2 – 31 – 31.2 – 32 – 32.2 – 33 – 33.2 – 34 – 34.1 – 34.2 – 35.2 – 36 – 36.2 – 37 – 37.2 – 38.2 – 39.2 – 40.2 – 41.2 – HE 0.740 0.721 HO n 10756
vWA
Table 4 Allele frequencies for the 15 IdentifilerTM loci from the NT Pure Aboriginal sub-population Allele
D3 TM
– – – – – – – – – – – 0.0350 – 0.0650 – – 0.2359 – 0.2906 0.2222 0.1274 – 0.0231 – 0.0009 – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – – – 0.0017 – 0.0017 0.0299 0.0589 – 0.1032 0.0017 0.1101 – 0.0034 0.1894 0.0051 0.1613 0.0034 0.1596 0.0034 0.1135 – 0.0418 0.0119 – – – – – – – – – –
D8
D21 – – – 0.0026 0.0026 – 0.0274 0.0915 0.1641 0.2248 – 0.1615 – 0.2145 – 0.0017 0.0846 – 0.0222 0.0026 – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – 0.0009 – – – – – – – – – – – – – – – – – – – – – – – – – 0.0034 0.0043 0.0094 0.1026 0.2291 0.0034 0.2077 0.0385 0.0376 0.1179 0.0094 0.0778 0.0009
D18 – – – – – – 0.0009 0.0575 0.0334 0.2144 – 0.1801 – 0.1184 – – 0.1407 – 0.0540 0.0780 0.0635 0.0009 0.0309 – 0.0197 – – 0.0069 – 0.0009 – – – – – – – – – – – – – – – – –
D5
D13 – 0.0009 – – 0.0701 – 0.2598 0.2427 0.2667 0.1385 – 0.0162 – 0.0051 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– 0.0060 – 0.3353 0.0350 – 0.0512 0.3106 0.2022 0.0410 – 0.0188 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
D7
TH01 – 0.0111 0.0077 0.3699 0.0616 – 0.1978 0.2568 0.0796 0.0137 – 0.0017 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
0.3808 0.2598 – 0.1379 0.1842 0.0329 0.0036 0.0009 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
TPOX – 0.0028 – 0.1955 0.4609 0.0475 0.2812 0.0121 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
CSF – – – 0.0123 0.0113 – 0.2155 0.3299 0.3393 0.0870 – 0.0038 – 0.0009 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
D16 – – – 0.0084 0.0253 – 0.1132 0.3632 0.2736 0.1841 – 0.0321 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
D2 – – – – – – – – – – – – – – – – 0.0098 – 0.0623 0.0574 0.3049 – 0.0918 – 0.0656 – – 0.0689 – 0.1361 – 0.1262 – 0.0623 – 0.0148 – – – – – – – – – – –
D19 – – – – – – – – 0.0984 0.3419 0.0048 0.4081 0.0032 0.0952 0.0048 – 0.0371 0.0016 0.0016 0.0032 – – – – – – – – – – – – – – – – – – – – – – – – – – –
243
loci – – – – – – – – – 0.0026 – 0.0401 – 0.3942 – – 0.2278 – 0.2099 0.1024 0.0205 – 0.0017 – – 0.0009 – – – – – – – – – – – – – – – – – – – – –
FGA
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
Identifiler 6 7 7.3 8 9 9.3 10 11 12 13 13.2 14 14.2 15 15.2 15.3 16 16.2 17 18 19 19.1 20 20.2 21 21.1 21.2 22 22.2 23 23.2 24 24.2 25 25.2 26 27 28 29 29.2 30 30.2 31 31.2 32 32.2 33
vWA
244
Table 4 (Continued ) Allele
D3
vWA
FGA
D8
D21
D18
D5
D13
D7
TH01
TPOX
CSF
D16
D2
D19
– – – – – – – – – – 0.737 0.700 1172
– – – – – – – – – – 0.789 0.761 1170
– – – – – – – – – – 0.871 0.858 1172
– – – – – – – – – – 0.834 0.800 1170
0.0487 0.0009 0.0060 0.0222 0.0214 0.0179 0.0009 0.0214 0.0094 0.0085 0.867 0.834 1170
– – – – – – – – – – 0.870 0.852 1166
– – – – – – – – – – 0.779 0.749 1170
– – – – – – – – – – 0.745 0.746 1172
– – – – – – – – – – 0.748 0.728 1168
– – – – – – – – – – 0.734 0.740 1124
– – – – – – – – – – 0.670 0.649 1074
– – – – – – – – – – 0.722 0.677 1058
– – – – – – – – – – 0.746 0.770 592
– – – – – – – – – – 0.845 0.816 610
– – – – – – – – – – 0.698 0.645 620
TH01
TPOX
Table 5 Allele frequencies for the 15 IdentifilerTM loci from the NT Asian sub-population Allele
D3 TM
Identifiler 6 7 8 9 9.3 10 11 12 12.2 13 13.2 14 14.2 15 15.2 16 16.2 17 18 18.2
loci – – – – – – – – – 0.0044 – 0.0267 – 0.3178 – 0.3489 – 0.2178 0.0800 –
vWA – – – – – – – – – – – 0.1733 – 0.0511 – 0.1667 – 0.2844 0.2289 –
FGA – – – – – – – – – – – – – – – 0.0044 – 0.0022 0.0222 0.0022
D8 – – 0.0022 0.0044 – 0.1222 0.1222 0.0889 – 0.2311 – 0.2044 – 0.1356 – 0.0667 – 0.0178 0.0044 –
D21 – – – – – – – – – – – – – – – – – – – –
D18 – – – – – 0.0022 0.0089 0.0578 – 0.1067 – 0.2244 – 0.1956 – 0.1489 – 0.1089 0.0667 –
D5 – 0.0156 – 0.0600 – 0.2178 0.2911 0.2467 – 0.1533 – 0.0156 – – – – – – – –
D13 – 0.0022 0.2701 0.1339 – 0.1027 0.2589 0.1496 – 0.0625 – 0.0201 – – – – – – – –
D7 – 0.0045 0.1875 0.0670 – 0.1763 0.3304 0.1808 – 0.0513 – 0.0022 – – – – – – – –
0.1613 0.3226 0.0726 0.3145 0.0726 0.0484 0.0081 – – – – – – – – – – – – –
– – 0.4919 0.1129 – 0.0645 0.3145 0.0161 – – – – – – – – – – – –
CSF – – 0.0081 0.0242 – 0.1935 0.2339 0.4435 – 0.0726 – 0.0161 – 0.0081 – – – – – –
D16 – – 0.0250 0.2250 – 0.1500 0.3500 0.2000 – 0.0250 – 0.0250 – – – – – – – –
D2 – – – – – – – – – – – – – – – 0.0750 – 0.0750 0.0500 –
D19 – – – – – 0.0250 0.0500 0.0500 0.0250 0.2250 0.0250 0.2750 0.0750 0.0750 0.0500 0.0250 0.0750 0.0250 – –
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
33.2 34.1 34.2 35.2 36.2 37.2 38 38.2 39.2 40.2 HE HO n
0.0044 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.724 0.702 450
0.0822 0.0133 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.801 0.804 450
0.0822 0.0600 0.0022 0.1267 0.0111 0.1867 0.0111 0.1600 0.0044 0.1711 0.0044 0.0778 0.0067 0.0578 0.0044 0.0022 – – – – – – – – – – – – – – – – 0.876 0.858 450
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.846 0.836 450
– – – – – – – – – – – – – – 0.0133 0.0756 0.0044 0.2467 0.0022 0.2133 0.0244 0.1000 0.0800 0.0222 0.1444 0.0022 0.0600 0.0022 0.0022 0.0022 0.0022 0.0022 0.848 0.862 450
0.0200 0.0200 – 0.0267 – 0.0111 – – – – – – – 0.0022 – – – – – – – – – – – – – – – – – – 0.858 0.831 450
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.781 0.738 450
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.807 0.817 448
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.787 0.777 448
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.764 0.806 124
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.647 0.597 124
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.711 0.742 124
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.782 0.700 40
0.2000 0.2000 – 0.0250 – 0.0250 – 0.0750 – 0.2250 – 0.0250 – 0.0250 – – – – – – – – – – – – – – – – – – 0.869 0.850 40
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.868 0.900 40
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
19 20 20.2 21 21.2 22 22.2 23 23.2 24 24.2 25 25.2 26 27 28 28.2 29 29.2 30 30.2 31 31.2 32 32.2 33 33.2 34 34.2 36.2 38.2 39.2 HE HO n
245
246
Table 6 Allele frequencies for the 15 IdentifilerTM loci from the NT East-Timorese sub-population Allele
D3
vWA
FGA
D8
D21
D18
D5
D13
D7
TH01
TPOX
CSF
D16
D2
D19
– – – – – – – – – – – – 0.0922 – 0.0461 – 0.1986 – 0.2376 – 0.3156 0.0816 0.0248 0.0035 – – – – – – – – – – – – – – – – – – – – 0.789 0.745 282
– – – – – – – – – – – – – – – – – – – – – 0.0714 0.0821 0.1143 0.1643 0.2107 0.1214 0.1107 0.0893 0.0214 0.0107 0.0036 – – – – – – – – – – – – 0.871 0.850 280
– – – 0.0072 – 0.0435 0.0978 – 0.0797 – 0.2246 – 0.2572 – 0.1630 – 0.0833 – 0.0435 – – – – – – – – – – – – – – – – – – – – – – – – – 0.833 0.746 276
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.0179 0.0964 0.2679 0.0036 0.1821 0.0071 0.1071 0.1214 0.0107 0.1214 0.0036 0.0536 0.0036 0.0036 0.844 0.886 280
– – – – – – 0.0250 0.0036 0.0571 – 0.0607 – 0.2321 – 0.1286 – 0.1500 – 0.1179 – 0.0821 0.0643 0.0250 0.0214 0.0107 0.0071 0.0071 – 0.0036 – 0.0036 – – – – – – – – – – – – – 0.877 0.850 280
– 0.0036 – 0.0288 – 0.2986 0.1727 – 0.3309 – 0.1511 – 0.0108 – 0.0036 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.750 0.741 278
– – 0.2163 0.0816 – 0.0993 0.2695 – 0.2447 – 0.0603 – 0.0284 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.803 0.816 282
– 0.0252 0.2338 0.0432 – 0.1763 0.3165 – 0.1835 – 0.0216 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.780 0.813 278
0.1168 0.1729 0.3271 0.3084 0.0187 0.0561 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.754 0.738 214
– 0.0047 0.3679 0.3443 – 0.0330 0.2217 – 0.0283 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.698 0.726 212
– – 0.0100 0.0400 – 0.2350 0.2550 – 0.3650 – 0.0750 – 0.0200 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.743 0.780 200
– – 0.0381 0.1619 – 0.1810 0.2952 – 0.2381 – 0.0667 – 0.0190 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.795 0.848 210
– – – – – – – – – – – – – – – – – – 0.0446 – 0.0347 0.1386 0.0891 0.0248 0.1337 0.2426 0.2178 0.0743 – – – – – – – – – – – – – – – – 0.844 0.802 202
– – – – – – – – 0.0421 0.0047 0.2383 0.0093 0.2850 0.0561 0.0794 0.2009 0.0421 0.0374 – 0.0047 – – – – – – – – – – – – – – – – – – – – – – – – 0.811 0.813 214
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
IdentifilerTM loci 6 – 7 – 8 – 9 – 9.3 – 10 – 11 – 11.2 – 12 0.0035 12.2 – 13 0.0142 13.2 – 14 0.0213 14.2 – 15 0.2660 15.2 – 16 0.3582 16.2 – 17 0.2979 17.2 – 18 0.0390 19 – 20 – 21 – 22 – 23 – 24 – 25 – 26 – 26.1 – 27 – 28 – 29 – 29.2 – 30 – 30.2 – 31 – 31.2 – 32 – 32.2 – 33 – 33.2 – 35.2 – 36.2 – 0.713 HE 0.730 HO n 282
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
247
Fig. 1. p–p Plots for each of the five population groups. The two curves on the Aboriginal plot represent the Pure (filled points) and Declared (unfilled points) Aboriginal datasets.
Variant alleles at the HumD21S11 locus were observed in the Caucasian and Aboriginal datasets (notably 37.2, 38.2, 39.2, 40.2 and 41.2). These off-ladder incomplete alleles in the upper range of the repeat region have been observed in other Australian populations [11,14]. Further molecular analysis of these variant alleles [15] observed in the Western Australian Aboriginal dataset revealed a structural conformation (allele type V) that had previously only been observed in samples from a Papuan population [16,17]. A recent publication reports the observation of a HumD21S11 37.2 allele in a population from East Timor [18]. The findings of similar alleles at the HumD21S11 locus in the Northern Territory Aboriginal Australian datasets implies these variant alleles appear related to peoples of the Australasian region. The structural confirmation of these variant alleles also provides support for an ancestral
link between the Australian Aborigine and the Papuan people. Asian and East Timorese populations in Australia are expected to be both sub-structured and undergoing admixture. There is little evidence of that here, although the data are uninformative in this respect due to the limited size of the datasets. In summary, population data from the major sub-populations of the Northern Territory of Australia at the 15 STR loci of the AMPFlSTR1 IdentifilerTM STR multiplex system has been statistically examined to the level required by the international forensic community. We consider these databases suitable for use in matters of disputed paternity or DNA-based forensic evidence. This paper follows the specified approach outlined by Lincoln and Carracedo [19].
Table 8 Truncated product method statistics for examining p-values from the results of Fisher’s exact test on NT sub-populations Caucasian
HWE
2 ln( p) p(sum)
41.335 0.081
LE
2 ln( p) p(sum)
260.753 0.010
0.556 0.013 0.761 – 0.856
0.885 0.624 0.028 – 0.697
Test statistic
0.029 0.005 0.397 – 0.967
Asian
East Timorese
120.469 0.000
79.528 0.000
15.477 0.629
35.684 0.219
526.518 0.000
310.543 0.000
87.984 0.097
218.399 0.331
References
0.388 0.071 0.753 0.715 0.903
0.551 0.032 0.048 0.147 0.389
Pure Aboriginal
The authors wish to acknowledge the cooperation of management of the Northern Territory Police, Fire and Emergency Services Forensic Services Branch, and the contribution of staff of the forensic biology section. We also thank ESR internal reviewers Catherine McGovern and Dr. SallyAnn Harbison whose comments greatly improved this manuscript.
Some loci in the Asian dataset were not analysed due to the small sample size (indicated by a dash).
0.008 0.002 0.395 0.274 0.398 0.593 0.000 0.132 0.529 0.555 0.091 0.000 0.058 0.080 0.627 0.540 0.336 0.023 0.960 0.275 0.679 0.016 0.222 0.777 0.000 0.012 0.199 0.001 0.732 0.157 0.719 0.393 0.116 0.654 0.118 Caucasian Declared Aboriginal Pure Aboriginal Asian East Timorese
Declared Aboriginal
Acknowledgements
0.437 0.030 0.003 – 0.623
0.806 0.521 0.045 – 0.597
D2 D16 CSF TPOX TH01 D7 D13 D5 D18 D21 D8 FGA vWA D3
Table 7 Results of Fisher’s exact test for allelic association within loci (Hardy–Weinberg equilibrium) in the five major categories of sub-populations of the Northern Territory
0.723 0.003 0.061 – 0.841
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[1] P.S. Walsh, D.A. Metzger, R. Higuchi, Chelex1 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material, BioTechniques 10 (1991) 506–513. [2] S.W. Guo, E.A. Thompson, Performing the exact tests of Hardy–Weinberg proportion for multiple alleles, Biometrics 48 (1992) 361–372. [3] P.O. Lewis, D. Zaykin. Genetic Data Analysis: computer program for the analysis of allelic data. Version 1.0 (d16c), 2001. Free program distributed by the authors over the internet from http://lewis.eeb.uconn.edu/ lewishome/software.html. [4] B. Law, J.S. Buckleton, C.M. Triggs, B.S. Weir, Effects of population structure and admixture on exact tests for association between loci, Genetics 164 (2003) 381–387. [5] J.S. Buckleton, J.M. Curran, S.J. Walsh, R v Bropho: the need for careful interpretation of independence testing in courtroom decision-making, Aust. Law J. 79 (2005) 709–721. [6] J.S. Buckleton, S.J. Walsh, S.A. Harbison, The fallacy of independence testing and the use of the product rule, Sci. Justice 41 (2001) 81–84. [7] D. Zaykin, L.A. Zhivotovsky, B.S. Weir, Truncated product method for combining p-values, Genet. Epidemiol. 22 (2002) 170–185. [8] J.S. Buckleton, Validating databases, in: J.S. Buckleton, C.M. Triggs, S.J. Walsh (Eds.), Forensic DNA Evidence Interpretation, CRC Press LLC, Boca Raton, FL, 2005, pp. 149–196. [9] J.M. Curran, J.S. Buckleton, C.M. Triggs, B.S. Weir, Assessing uncertainty in DNA evidence caused by sampling effects, Sci. Justice 42 (2002) 29–37. [10] J.S. Buckleton, J.M. Curran, Sampling effects, in: J.S. Buckleton, C.M. Triggs, S.J. Walsh (Eds.), Forensic DNA Evidence Interpretation, CRC Press LLC, Boca Raton, FL, 2005, pp. 195–215. [11] A. Bagdonavicius, G.R. Turbett, J.S. Buckleton, S.J. Walsh, Western Australian sub-population data for the thirteen AMPFlSTR Profiler PlusTM and COfilerTM STR loci, J. Forensic Sci. 47 (2002) 1149– 1153. [12] S.J. Walsh, J.R. Cullen, S.A. Harbison, Allele frequencies for the four major sub-populations of New Zealand at the 10 AMPFlSTR1 SGM PlusTM loci, Forensic Sci. Int. 122 (2001) 189–195. [13] J. Lee, S.J. Walsh, Population data for the AMPFlSTR Profiler PlusTM STR loci from residents of the Australian Capital Territory (ACT), J. Forensic Sci. 50 (2005) 984–985. [14] V. Ientile, B. Blair, P. Clausen, M. Hadfield, J.S. Buckleton, S.J. Walsh, Population data for the AMPFlSTR Profiler PlusTM STR loci for Queensland
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249 Caucasian, Aboriginal Australian and Asian sub-populations. Journal of Forensic Sciences, submitted for publication. [15] S.J. Walsh, G.R. Turbett, S.L. Robinson, N.P. Davies, A.N. Wilton, Characterisation of variant alleles at the HumD21S11 locus implies unique Australasian genotypes and re-classification of nomenclature guidelines, Forensic Sci. Int. 135 (2003) 35–41. [16] B. Brinkmann, E. Meyer, A. Junge, Complex mutational events at the HumD21S11 locus, Human Genet. 98 (1996) 60–64.
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[17] B. Brinkmann, A. Junge, E. Meyer, P. Wiegand, Population genetic diversity in relation to microsatellite heterogeneity, Human Mutat. 11 (1998) 135–144. [18] L. Souto, C. Alves, L. Gusmao, E. Ferreira, A. Amorim, F. Corte-Real, D.N. Vieira, Population data on 15 autosomal STRs in a sample from East Timor, Forensic Sci. Int. 155 (2005) 77–80. [19] P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.
Announcement of population data
Population data from sub-populations of the Northern Territory of Australia for 15 autosomal short tandem repeat (STR) loci Carmen Eckhoff a,1, Simon J. Walsh b,c,*, John S. Buckleton d b
a Northern Territory Police, Fire and Emergency Services, PO Box 39764, Winnellie, NT 0821, Australia Centre for Forensic Science, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia c Science & Justice Consulting, PO Box 83, Surry Hills, NSW 2010, Australia d ESR Ltd., Private Bag 92-021, Auckland, New Zealand
Received 2 May 2005; received in revised form 5 March 2006; accepted 8 June 2006 Available online 1 August 2006
Abstract It is a requirement that forensic DNA profiling evidence be accompanied by an estimation of its weight, in order that the court can assign an appropriate probative value to the evidence during legal proceedings. There are various models by which this estimation can be made, but each relies on approximations of the allele frequencies in the relevant population. It is also important to assess relevant population genetic features of the available data. This report provides allele frequencies and estimates of common population genetic parameters for the major sub-populations of the Northern Territory of Australia genotyped at 15 autosomal short tandem repeat (STR) loci. # 2006 Elsevier Ireland Ltd. All rights reserved. Keywords: DNA profiling; Autosomal microsatellites; Population data; Allele frequencies; Profiler plus; Identifiler; Independence testing; Northern Territory
Population: Forensic biology personnel from the Northern Territory Police, Fire and Emergency Services (NTPFES) have compiled sub-population datasets from five major subpopulation groups of Northern Australia (Table 1). The subpopulation of origin of each donor was assigned by a combination of self-declaration or assignment by a third party. Extraction: DNA was extracted from blood stain cards and buccal swabs. The reference samples were air-dried before being stored at 20 8C. A small portion was removed from the reference sample and DNA was extracted using the Chelex method as described by Walsh et al. [1]. Amplification: The NTPFES Forensic Biology Laboratory uses both the Applied Biosystems AMPFlSTR1 Profiler PlusTM kit and AMPFlSTR1 IdentifilerTM kit for routine casework and database samples. In a single PCR reaction the kits amplify 9 and 15 tetranucleotide loci, respectively, as well
* Corresponding author. Tel.: +61 2 9514 4064; fax: +61 2 9514 8206. E-mail addresses: [email protected] (C. Eckhoff), [email protected] (S.J. Walsh). 1 Tel.: +61 8 8922 1324; fax: +61 8 8922 1326. 0379-0738/$ – see front matter # 2006 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2006.06.009
as a gender identification marker. The procedures used by the NTPFES Biology Laboratory are proportionate to the manufacture’s protocols for both kits, using a total amplification volume of 20 ml, not 50 ml as recommended. The samples were amplified on the Applied Biosystems GeneAmp1 PCR System 9700 thermal cycler in accordance to the respective Applied Biosystems protocol for each kit. Detection: Aliquots of 1–2 ml of the amplified product were combined with 24 ml of HiDi Formamide containing 0.4 ml GeneScanTM 500RoxTM (Profiler PlusTM) or 0.4 ml GeneScanTM 500LizTM (IdentifilerTM) and analysed using an automated sequencer, the ABI PrismTM 310 Genetic Analyzer, as per the Applied Biosystems protocols. GeneScanTM and Genotyper software were used to verify the fragment size of the alleles and thus determine the DNA profile for each of the reference samples. All DNA results were independently verified by a second reader. Results:The allele frequencies for the 15 STR loci have been tabulated within each of the five sub-population categories listed in Table 1. The data are represented in Tables 2–6. Estimates of observed and expected heterozygosity (HO and HE, respectively; Tables 2–6) and Fisher’s exact test [2] for allelic association was undertaken with 10,000 shuffles using the Genetic Data Analysis [3] software provided courtesy of Paul
238
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
Table 1 Description of sub-population categories for the NT Sub-population
Description
NT Caucasian NT Declared Aboriginal NT Pure Aboriginal NT Asian NT East Timorese
Data Data Data Data Data
compiled compiled compiled compiled compiled
from from from from from
individuals individuals individuals individuals individuals
who who who who who
have self-declared their ethnicity as Caucasian have self-declared their ethnicity as Aboriginal (or Indigenous Australian) are known to be Indigenous Australian and who are resident of remote tribal communities have self-declared their ethnicity as Asian have self-declared their ethnicity as East Timorese
Lewis (Department of Ecology and Evolutionary Biology, The University of Connecticut). Departures from Hardy–Weinberg equilibrium ( p < 0.05) were detected at some loci (Table 7). However, in this dataset we have what is termed the ‘multi-testing problem’ as we have undertaken 15 Hardy–Weinberg and 105 linkage-equilibrium tests per ethnic group. In addition, some of these comparisons were based on small datasets. Hypothesis testing on very small datasets is ineffective [4,5]. Accordingly the results from tests on datasets of less than 200 profiles were not considered. This meant that six loci (TH01, TPOX, CSF, D16, D2 and D19) from the Asian sub-population dataset were excluded from consideration. There are various ways offered to deal with the multitesting problem. These include the Bonferonni correction, a simple graphical examination (including p–p plots) or the truncated product method. The Bonferonni correction suffers from the handicap that it lowers the power of an already weak test [6]. For these reasons we prefer the other two methods. Graphical representations of these data are given in Fig. 1. If the hypotheses of Hardy–Weinberg and linkage equilibrium are true then the p-values should be distributed uniformly between 0 and 1; p U[0,1]. As an example, the x = y trend-line in the p–p plots (Fig. 1) represents equilibrium and deviations from that trend-line can be seen as mild departures from equilibrium. The 95% confidence limit is also displayed on the p–p plots as the region within the two curved lines. The p–p plot for the Caucasian dataset (Fig. 1) shows evidence of mild departure. The values are plotting away from the linear trend-line (which represents a state of Hardy– Weinberg and linkage equilibrium) although remain within the 95% confidence limit envelope. The p–p plots for both the Declared and Pure Aboriginal (Fig. 1) datasets show evidence of departure from independence as values plot away from the linear trend-line (which represents a state of Hardy– Weinberg and linkage equilibrium) and occur mostly outside the 95% confidence limit envelope. The shape of the curve is more pronounced in the Declared Aboriginal dataset, than in the Pure Aboriginal dataset, however, the difference in the sizes of these datasets limits our ability to compare these outcomes. The p–p plots for both the Asian and East Timorese (Fig. 1) sub-populations do not show any evidence of departure. The truncated product method gives the test statistics provided in Table 8. This elegant method was described by Zaykin et al. [7]. This method involves forming the sum of 2 ln( p) across, say, x independent tests. This sum is expected
to have a chi-square distribution with 2x degrees of freedom and a p-value is estimated (Table 8). It is important to note that these tests are not independent and hence the truncated product method can only be used as a guide. The truncated product test statistics do not suggest any strong evidence for departure from independence for the Asian or East Timorese datasets ( p > 0.05) but do give such an indication for the Caucasian, Declared and Pure Aboriginal datasets ( p < 0.05). Discussion: Due to the range of loci analysed in the Northern Territory sub-population datasets, their sizes vary widely for different loci and different sub-population categories. The Caucasian and Aboriginal datasets are large by world standards for 9 of the 15 loci analysed (corresponding with the loci of the Profiler PlusTM system), and moderately sized for the remaining six loci. The Asian and East Timorese datasets are small by comparison, but of suitable size for allele frequency estimation at 9 of the 15 loci (again corresponding with the loci of the Profiler PlusTM system). Caution must be exercised when interpreting data from small datasets. We have advised in the past, and re-iterate here, the need for adequate correction for sampling error when using allele frequency data from moderate to small datasets [8]. A discussion of approaches has been given by Curran and colleagues [9,10]. Caucasian populations worldwide are believed to be very close to equilibrium and previously when we have analysed datasets of this size we have found little or no evidence for departure [11–14]. However, some evidence of departure was observed in the NT Caucasian sub-population dataset (Fig. 1, Table 8). This mild departure is not grossly beyond expectation. The size of the dataset is approaching a level that permits the detection of small-scale departures. Aboriginal populations are believed to be sub-structured with complex patterns of relatedness within and between communities and/or tribal groups. Additionally, certain Aboriginal populations of Australia have undergone admixture with other non-indigenous sub-populations. Hence, the expectation for Aboriginal datasets is moderate disequilibrium. The combined Aboriginal dataset analysed here is extensive. It has also been partitioned into declared and pure categories. Testing these sub-sets revealed a greater extent of disequilibrium in the Declared Aboriginal dataset. This may be indicative of more extensive admixture, or may also be related to the increased power of the tests to find departures, due to the greater size of the Declared Aboriginal dataset relative to the Pure Aboriginal dataset.
Table 2 Allele frequencies for the 15 IdentifilerTM loci for the NT Caucasian sub-population Allele
D3 TM
– – – – – – – – – 0.0001 – 0.0004 – – – 0.0011 – – 0.1063 – – 0.0975 – 0.2223 – 0.2671 – 0.2001 – 0.0886 – 0.0152 – 0.0011 – – 0.0001 – – – – – – – – – –
– – – – – – – – – – – – – – – – – – – – – 0.0001 – 0.0003 – 0.0009 – 0.0144 0.0001 0.0591 0.0002 0.1370 0.0021 0.1791 – 0.0028 0.1799 0.0090 0.0001 0.1467 0.0045 0.1390 0.0007 0.0817 0.0004 0.0317 0.0001
D8
D21 – – – – 0.0210 – 0.0131 – 0.0887 0.0785 – 0.1423 0.0001 – – 0.3215 – – 0.1919 – – 0.1076 – 0.0313 – 0.0037 – 0.0003 – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.0010 – 0.0009 0.0019 –
D18 – – – – – – 0.0004 – 0.0078 0.0147 0.0001 0.1443 – – – 0.1260 – 0.0001 0.1643 0.0001 0.0001 0.1491 – 0.1375 – 0.1070 0.0001 0.0711 – 0.0436 – 0.0180 0.0002 0.0081 – – 0.0049 – – 0.0015 – 0.0004 – 0.0003 – 0.0001 –
D5
D13 – 0.0002 0.0007 – 0.0024 – 0.0369 – 0.0704 0.3632 – 0.3588 – – – 0.1541 – – 0.0106 – – 0.0026 – – – – – – – – – – – – – – – – – – – – – – – – –
– – 0.0003 – 0.1342 – 0.0773 – 0.0654 0.3058 – 0.2801 – – – 0.0936 – – 0.0429 – – 0.0005 – – – – – – – – – – – – – – – – – – – – – – – – –
D7
TH01 – – 0.0234 0.0001 0.1587 – 0.1588 – 0.2665 0.2086 – 0.1459 – – – 0.0307 0.0001 – 0.0067 – – 0.0006 – – – – – – – – – – – – – – – – – – – – – – – – –
0.0016 0.2322 0.1885 – 0.1328 0.0005 0.1525 0.2814 0.0093 0.0011 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
TPOX – 0.0012 – – 0.5125 – 0.1241 – 0.0546 0.2696 – 0.0374 – – – – – – – – – 0.0006 – – – – – – – – – – – – – – – – – – – – – – – – –
CSF – – 0.0018 – 0.0072 – 0.0235 – 0.2398 0.3060 – 0.3325 – – – 0.0759 – – 0.0120 – – 0.0012 – – – – – – – – – – – – – – – – – – – – – – – – –
D16 – – – – 0.0088 – 0.1103 – 0.0574 0.2926 – 0.3309 – – – 0.1721 – – 0.0265 – – 0.0015 – – – – – – – – – – – – – – – – – – – – – – – – –
D2 – – – – – – – – – – – – – – 0.0015 – – – – – – 0.0030 – 0.0519 – 0.1840 – 0.0801 – 0.1039 – 0.1350 – 0.0282 – – 0.0341 – – 0.1068 – 0.1187 – 0.1276 – 0.0223 –
D19 – – – – – – – – 0.0015 0.0044 – 0.0746 0.0015 – – 0.2515 – 0.0058 0.3480 – 0.0190 0.1725 0.0570 0.0512 0.0073 0.0044 – – 0.0015 – – – – – – – – – – – – – – – – – –
239
loci – – – – – – – – – 0.0010 – 0.0004 – – – 0.0029 – – 0.1175 – – 0.2745 – 0.2505 – 0.2014 – 0.1373 0.0001 0.0134 – 0.0008 – 0.0001 0.0001 – – – – – – – – – – – –
FGA
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
Identifiler 5 6 7 7.3 8 8.3 9 9.3 10 11 11.2 12 12.1 12.2 12.3 13 13.1 13.2 14 14.1 14.2 15 15.2 16 16.2 17 17.1 18 18.2 19 19.2 20 20.2 21 21.1 21.2 22 22.2 22.3 23 23.2 24 24.2 25 25.2 26 26.1
vWA
240
Table 2 (Continued ) Allele
vWA
FGA
D8
D21
D18
D5
D13
D7
TH01
TPOX
CSF
D16
D2
D19
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.789 0.789 9702
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.810 0.808 9684
– 0.0079 0.0014 – 0.0004 – – – 0.0001 – – – – – – – – – – – – – – – – – – 0.864 0.861 9692
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.812 0.806 9696
0.0002 0.0356 0.1519 0.0001 0.2159 0.0001 0.0010 0.0001 0.2409 0.0335 0.0719 0.1058 0.0148 0.0845 0.0009 0.0299 0.0003 0.0002 0.0039 0.0010 0.0011 0.0001 0.0005 0.0007 0.0007 0.0004 0.0001 0.845 0.846 9686
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.876 0.881 9588
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.709 0.707 9696
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.789 0.779 9668
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.812 0.813 9574
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.791 0.785 1830
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.645 0.639 1684
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.732 0.745 1660
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.760 0.776 680
– 0.0015 0.0015 – – – – – – – – – – – – – – – – – – – – – – – – 0.885 0.896 674
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.775 0.807 684
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
26.2 27 28 28.2 29 29.1 29.2 29.3 30 30.2 31 31.2 32 32.2 33 33.2 34 34.1 34.2 35 35.2 36 36.2 37.2 38.2 39.2 40.2 HE HO n
D3
Table 3 Allele frequencies for the 15 IdentifilerTM loci from the NT Declared Aboriginal sub-population Allele
D3 TM
– – – – – – – – – – – – – 0.0001 – 0.0356 – – 0.0702 – – 0.2427 – 0.2701 0.2181 – 0.1398 – – 0.0219 – – 0.0014 0.0001 – – – – – – – – – – – – –
D8 – – – – – – – – – – – – – 0.0001 – – – – – – – 0.0017 – 0.0052 0.0258 – 0.0729 0.0001 0.0001 0.1050 0.0001 0.0011 0.1087 – 0.0037 – 0.1671 0.0056 0.1639 0.0034 0.1642 0.0037 0.1139 0.0001 0.0002 0.0403 0.0118
D21 – – – 0.0028 – 0.0025 – – – 0.0313 0.0889 0.1531 – 0.2372 – 0.1812 – – 0.1907 – 0.0033 0.0813 – 0.0233 0.0041 – 0.0002 – – – – – – – – – – – – – – – – – – – –
D18 – – – – – – – – – – – 0.0001 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.0003 – – 0.0022 0.0065 0.0106
D5 – – – – – – – – – 0.0028 0.0585 0.0471 0.0002 0.2038 0.0001 0.1694 0.0001 – 0.1216 – – 0.1297 – 0.0737 0.0781 0.0001 0.0619 0.0001 0.0001 0.0257 0.0001 – 0.0175 – – 0.0001 0.0080 – 0.0010 – 0.0001 – – – – – –
D13 – 0.0007 – 0.0006 – 0.0771 – – – 0.2201 0.2772 0.2822 – 0.1273 – 0.0137 – – 0.0011 – – – – – – – – – – – – – – – – – – – – – – – – – – – –
D7 0.0007 0.0028 – 0.3074 – 0.0513 – – – 0.0376 0.3184 0.2120 – 0.0517 – 0.0182 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
TH01 0.0003 0.0085 0.0040 0.3697 0.0001 0.0847 0.0001 – – 0.1987 0.2261 0.0909 – 0.0160 – 0.0008 – – 0.0001 – – – – – – – – – – – – – – – – – – – – – – – – – – – –
0.3615 0.2559 – 0.1227 – 0.1925 – – 0.0599 0.0065 0.0012 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
TPOX 0.0006 0.0006 – 0.2239 – 0.4325 – – – 0.0486 0.2790 0.0142 – 0.0006 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
CSF – 0.0012 – 0.0090 – 0.0127 – 0.0006 – 0.2398 0.2795 0.3560 – 0.0886 – 0.0114 – – 0.0012 – – – – – – – – – – – – – – – – – – – – – – – – – – – –
D16 – 0.0009 – 0.0091 – 0.0356 – – – 0.1005 0.3958 0.2331 – 0.1764 – 0.0439 – – 0.0046 – – – – – – – – – – – – – – – – – – – – – – – – – – – –
D2
D19 – – – – – – – – – – – – – – – – – – – – – 0.0064 – 0.0681 0.1031 – 0.2320 – – 0.0958 – – 0.0617 – – – 0.0773 – 0.1510 – 0.1197 – 0.0672 – – 0.0175 –
– – – – – – – – – – 0.0027 0.0605 – 0.3484 0.0045 0.4161 – 0.0045 0.1227 0.0054 – 0.0289 0.0027 0.0027 0.0009 – – – – – – – – – – – – – – – – – – – – – –
241
loci – – – – – – – – – – 0.0013 0.0004 – 0.0028 – 0.0444 – – 0.3773 – – 0.2448 – 0.2158 0.0967 – 0.0131 – – 0.0023 0.0003 – 0.0002 0.0007 – – – – – – – – – – – – –
FGA
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
Identifiler 6 7 7.3 8 8.3 9 9.1 9.2 9.3 10 11 12 12.2 13 13.2 14 14.1 14.2 15 15.2 15.3 16 16.2 17 18 18.2 19 19.1 19.2 20 20.1 20.2 21 21.1 21.2 21.3 22 22.2 23 23.2 24 24.2 25 25.1 25.2 26 27
vWA
242
Table 3 (Continued ) Allele
D3
FGA
D8
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.794 0.783 10744
0.0001 – 0.0011 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.875 0.835 0.853 0.833 10732 10750
D21
D18
– – 0.1131 – 0.0001 – 0.2258 – 0.0003 – 0.0018 – 0.0001 – 0.1948 – 0.0386 – 0.0413 – 0.1142 – 0.0135 – 0.0909 – 0.0014 – 0.0468 – 0.0001 – 0.0005 – 0.0076 – 0.0237 – 0.0001 – 0.0203 – 0.0001 – 0.0174 – 0.0155 – 0.0078 – 0.0034 – 0.0010 – 0.870 0.876 0.845 0.849 10714 10564
D5
D13
D7
TH01
TPOX
CSF
D16
D2
D19
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.773 0.746 10746
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.752 0.735 10710
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.757 0.746 10530
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.749 0.725 1704
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.683 0.635 1688
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.730 0.728 1660
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.745 0.697 1094
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.871 0.856 1086
– – – – – – – – – – – – – – – – – – – – – – – – – – – 0.686 0.713 1108
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
27.1 – 28 – 28.2 – 29 – 29.1 – 29.2 – 29.3 – 30 – 30.2 – 31 – 31.2 – 32 – 32.2 – 33 – 33.2 – 34 – 34.1 – 34.2 – 35.2 – 36 – 36.2 – 37 – 37.2 – 38.2 – 39.2 – 40.2 – 41.2 – HE 0.740 0.721 HO n 10756
vWA
Table 4 Allele frequencies for the 15 IdentifilerTM loci from the NT Pure Aboriginal sub-population Allele
D3 TM
– – – – – – – – – – – 0.0350 – 0.0650 – – 0.2359 – 0.2906 0.2222 0.1274 – 0.0231 – 0.0009 – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – – – 0.0017 – 0.0017 0.0299 0.0589 – 0.1032 0.0017 0.1101 – 0.0034 0.1894 0.0051 0.1613 0.0034 0.1596 0.0034 0.1135 – 0.0418 0.0119 – – – – – – – – – –
D8
D21 – – – 0.0026 0.0026 – 0.0274 0.0915 0.1641 0.2248 – 0.1615 – 0.2145 – 0.0017 0.0846 – 0.0222 0.0026 – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – 0.0009 – – – – – – – – – – – – – – – – – – – – – – – – – 0.0034 0.0043 0.0094 0.1026 0.2291 0.0034 0.2077 0.0385 0.0376 0.1179 0.0094 0.0778 0.0009
D18 – – – – – – 0.0009 0.0575 0.0334 0.2144 – 0.1801 – 0.1184 – – 0.1407 – 0.0540 0.0780 0.0635 0.0009 0.0309 – 0.0197 – – 0.0069 – 0.0009 – – – – – – – – – – – – – – – – –
D5
D13 – 0.0009 – – 0.0701 – 0.2598 0.2427 0.2667 0.1385 – 0.0162 – 0.0051 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– 0.0060 – 0.3353 0.0350 – 0.0512 0.3106 0.2022 0.0410 – 0.0188 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
D7
TH01 – 0.0111 0.0077 0.3699 0.0616 – 0.1978 0.2568 0.0796 0.0137 – 0.0017 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
0.3808 0.2598 – 0.1379 0.1842 0.0329 0.0036 0.0009 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
TPOX – 0.0028 – 0.1955 0.4609 0.0475 0.2812 0.0121 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
CSF – – – 0.0123 0.0113 – 0.2155 0.3299 0.3393 0.0870 – 0.0038 – 0.0009 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
D16 – – – 0.0084 0.0253 – 0.1132 0.3632 0.2736 0.1841 – 0.0321 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
D2 – – – – – – – – – – – – – – – – 0.0098 – 0.0623 0.0574 0.3049 – 0.0918 – 0.0656 – – 0.0689 – 0.1361 – 0.1262 – 0.0623 – 0.0148 – – – – – – – – – – –
D19 – – – – – – – – 0.0984 0.3419 0.0048 0.4081 0.0032 0.0952 0.0048 – 0.0371 0.0016 0.0016 0.0032 – – – – – – – – – – – – – – – – – – – – – – – – – – –
243
loci – – – – – – – – – 0.0026 – 0.0401 – 0.3942 – – 0.2278 – 0.2099 0.1024 0.0205 – 0.0017 – – 0.0009 – – – – – – – – – – – – – – – – – – – – –
FGA
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
Identifiler 6 7 7.3 8 9 9.3 10 11 12 13 13.2 14 14.2 15 15.2 15.3 16 16.2 17 18 19 19.1 20 20.2 21 21.1 21.2 22 22.2 23 23.2 24 24.2 25 25.2 26 27 28 29 29.2 30 30.2 31 31.2 32 32.2 33
vWA
244
Table 4 (Continued ) Allele
D3
vWA
FGA
D8
D21
D18
D5
D13
D7
TH01
TPOX
CSF
D16
D2
D19
– – – – – – – – – – 0.737 0.700 1172
– – – – – – – – – – 0.789 0.761 1170
– – – – – – – – – – 0.871 0.858 1172
– – – – – – – – – – 0.834 0.800 1170
0.0487 0.0009 0.0060 0.0222 0.0214 0.0179 0.0009 0.0214 0.0094 0.0085 0.867 0.834 1170
– – – – – – – – – – 0.870 0.852 1166
– – – – – – – – – – 0.779 0.749 1170
– – – – – – – – – – 0.745 0.746 1172
– – – – – – – – – – 0.748 0.728 1168
– – – – – – – – – – 0.734 0.740 1124
– – – – – – – – – – 0.670 0.649 1074
– – – – – – – – – – 0.722 0.677 1058
– – – – – – – – – – 0.746 0.770 592
– – – – – – – – – – 0.845 0.816 610
– – – – – – – – – – 0.698 0.645 620
TH01
TPOX
Table 5 Allele frequencies for the 15 IdentifilerTM loci from the NT Asian sub-population Allele
D3 TM
Identifiler 6 7 8 9 9.3 10 11 12 12.2 13 13.2 14 14.2 15 15.2 16 16.2 17 18 18.2
loci – – – – – – – – – 0.0044 – 0.0267 – 0.3178 – 0.3489 – 0.2178 0.0800 –
vWA – – – – – – – – – – – 0.1733 – 0.0511 – 0.1667 – 0.2844 0.2289 –
FGA – – – – – – – – – – – – – – – 0.0044 – 0.0022 0.0222 0.0022
D8 – – 0.0022 0.0044 – 0.1222 0.1222 0.0889 – 0.2311 – 0.2044 – 0.1356 – 0.0667 – 0.0178 0.0044 –
D21 – – – – – – – – – – – – – – – – – – – –
D18 – – – – – 0.0022 0.0089 0.0578 – 0.1067 – 0.2244 – 0.1956 – 0.1489 – 0.1089 0.0667 –
D5 – 0.0156 – 0.0600 – 0.2178 0.2911 0.2467 – 0.1533 – 0.0156 – – – – – – – –
D13 – 0.0022 0.2701 0.1339 – 0.1027 0.2589 0.1496 – 0.0625 – 0.0201 – – – – – – – –
D7 – 0.0045 0.1875 0.0670 – 0.1763 0.3304 0.1808 – 0.0513 – 0.0022 – – – – – – – –
0.1613 0.3226 0.0726 0.3145 0.0726 0.0484 0.0081 – – – – – – – – – – – – –
– – 0.4919 0.1129 – 0.0645 0.3145 0.0161 – – – – – – – – – – – –
CSF – – 0.0081 0.0242 – 0.1935 0.2339 0.4435 – 0.0726 – 0.0161 – 0.0081 – – – – – –
D16 – – 0.0250 0.2250 – 0.1500 0.3500 0.2000 – 0.0250 – 0.0250 – – – – – – – –
D2 – – – – – – – – – – – – – – – 0.0750 – 0.0750 0.0500 –
D19 – – – – – 0.0250 0.0500 0.0500 0.0250 0.2250 0.0250 0.2750 0.0750 0.0750 0.0500 0.0250 0.0750 0.0250 – –
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
33.2 34.1 34.2 35.2 36.2 37.2 38 38.2 39.2 40.2 HE HO n
0.0044 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.724 0.702 450
0.0822 0.0133 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.801 0.804 450
0.0822 0.0600 0.0022 0.1267 0.0111 0.1867 0.0111 0.1600 0.0044 0.1711 0.0044 0.0778 0.0067 0.0578 0.0044 0.0022 – – – – – – – – – – – – – – – – 0.876 0.858 450
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.846 0.836 450
– – – – – – – – – – – – – – 0.0133 0.0756 0.0044 0.2467 0.0022 0.2133 0.0244 0.1000 0.0800 0.0222 0.1444 0.0022 0.0600 0.0022 0.0022 0.0022 0.0022 0.0022 0.848 0.862 450
0.0200 0.0200 – 0.0267 – 0.0111 – – – – – – – 0.0022 – – – – – – – – – – – – – – – – – – 0.858 0.831 450
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.781 0.738 450
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.807 0.817 448
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.787 0.777 448
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.764 0.806 124
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.647 0.597 124
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.711 0.742 124
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.782 0.700 40
0.2000 0.2000 – 0.0250 – 0.0250 – 0.0750 – 0.2250 – 0.0250 – 0.0250 – – – – – – – – – – – – – – – – – – 0.869 0.850 40
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.868 0.900 40
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
19 20 20.2 21 21.2 22 22.2 23 23.2 24 24.2 25 25.2 26 27 28 28.2 29 29.2 30 30.2 31 31.2 32 32.2 33 33.2 34 34.2 36.2 38.2 39.2 HE HO n
245
246
Table 6 Allele frequencies for the 15 IdentifilerTM loci from the NT East-Timorese sub-population Allele
D3
vWA
FGA
D8
D21
D18
D5
D13
D7
TH01
TPOX
CSF
D16
D2
D19
– – – – – – – – – – – – 0.0922 – 0.0461 – 0.1986 – 0.2376 – 0.3156 0.0816 0.0248 0.0035 – – – – – – – – – – – – – – – – – – – – 0.789 0.745 282
– – – – – – – – – – – – – – – – – – – – – 0.0714 0.0821 0.1143 0.1643 0.2107 0.1214 0.1107 0.0893 0.0214 0.0107 0.0036 – – – – – – – – – – – – 0.871 0.850 280
– – – 0.0072 – 0.0435 0.0978 – 0.0797 – 0.2246 – 0.2572 – 0.1630 – 0.0833 – 0.0435 – – – – – – – – – – – – – – – – – – – – – – – – – 0.833 0.746 276
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.0179 0.0964 0.2679 0.0036 0.1821 0.0071 0.1071 0.1214 0.0107 0.1214 0.0036 0.0536 0.0036 0.0036 0.844 0.886 280
– – – – – – 0.0250 0.0036 0.0571 – 0.0607 – 0.2321 – 0.1286 – 0.1500 – 0.1179 – 0.0821 0.0643 0.0250 0.0214 0.0107 0.0071 0.0071 – 0.0036 – 0.0036 – – – – – – – – – – – – – 0.877 0.850 280
– 0.0036 – 0.0288 – 0.2986 0.1727 – 0.3309 – 0.1511 – 0.0108 – 0.0036 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.750 0.741 278
– – 0.2163 0.0816 – 0.0993 0.2695 – 0.2447 – 0.0603 – 0.0284 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.803 0.816 282
– 0.0252 0.2338 0.0432 – 0.1763 0.3165 – 0.1835 – 0.0216 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.780 0.813 278
0.1168 0.1729 0.3271 0.3084 0.0187 0.0561 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.754 0.738 214
– 0.0047 0.3679 0.3443 – 0.0330 0.2217 – 0.0283 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.698 0.726 212
– – 0.0100 0.0400 – 0.2350 0.2550 – 0.3650 – 0.0750 – 0.0200 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.743 0.780 200
– – 0.0381 0.1619 – 0.1810 0.2952 – 0.2381 – 0.0667 – 0.0190 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.795 0.848 210
– – – – – – – – – – – – – – – – – – 0.0446 – 0.0347 0.1386 0.0891 0.0248 0.1337 0.2426 0.2178 0.0743 – – – – – – – – – – – – – – – – 0.844 0.802 202
– – – – – – – – 0.0421 0.0047 0.2383 0.0093 0.2850 0.0561 0.0794 0.2009 0.0421 0.0374 – 0.0047 – – – – – – – – – – – – – – – – – – – – – – – – 0.811 0.813 214
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
IdentifilerTM loci 6 – 7 – 8 – 9 – 9.3 – 10 – 11 – 11.2 – 12 0.0035 12.2 – 13 0.0142 13.2 – 14 0.0213 14.2 – 15 0.2660 15.2 – 16 0.3582 16.2 – 17 0.2979 17.2 – 18 0.0390 19 – 20 – 21 – 22 – 23 – 24 – 25 – 26 – 26.1 – 27 – 28 – 29 – 29.2 – 30 – 30.2 – 31 – 31.2 – 32 – 32.2 – 33 – 33.2 – 35.2 – 36.2 – 0.713 HE 0.730 HO n 282
C. Eckhoff et al. / Forensic Science International 171 (2007) 237–249
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Fig. 1. p–p Plots for each of the five population groups. The two curves on the Aboriginal plot represent the Pure (filled points) and Declared (unfilled points) Aboriginal datasets.
Variant alleles at the HumD21S11 locus were observed in the Caucasian and Aboriginal datasets (notably 37.2, 38.2, 39.2, 40.2 and 41.2). These off-ladder incomplete alleles in the upper range of the repeat region have been observed in other Australian populations [11,14]. Further molecular analysis of these variant alleles [15] observed in the Western Australian Aboriginal dataset revealed a structural conformation (allele type V) that had previously only been observed in samples from a Papuan population [16,17]. A recent publication reports the observation of a HumD21S11 37.2 allele in a population from East Timor [18]. The findings of similar alleles at the HumD21S11 locus in the Northern Territory Aboriginal Australian datasets implies these variant alleles appear related to peoples of the Australasian region. The structural confirmation of these variant alleles also provides support for an ancestral
link between the Australian Aborigine and the Papuan people. Asian and East Timorese populations in Australia are expected to be both sub-structured and undergoing admixture. There is little evidence of that here, although the data are uninformative in this respect due to the limited size of the datasets. In summary, population data from the major sub-populations of the Northern Territory of Australia at the 15 STR loci of the AMPFlSTR1 IdentifilerTM STR multiplex system has been statistically examined to the level required by the international forensic community. We consider these databases suitable for use in matters of disputed paternity or DNA-based forensic evidence. This paper follows the specified approach outlined by Lincoln and Carracedo [19].
Table 8 Truncated product method statistics for examining p-values from the results of Fisher’s exact test on NT sub-populations Caucasian
HWE
2 ln( p) p(sum)
41.335 0.081
LE
2 ln( p) p(sum)
260.753 0.010
0.556 0.013 0.761 – 0.856
0.885 0.624 0.028 – 0.697
Test statistic
0.029 0.005 0.397 – 0.967
Asian
East Timorese
120.469 0.000
79.528 0.000
15.477 0.629
35.684 0.219
526.518 0.000
310.543 0.000
87.984 0.097
218.399 0.331
References
0.388 0.071 0.753 0.715 0.903
0.551 0.032 0.048 0.147 0.389
Pure Aboriginal
The authors wish to acknowledge the cooperation of management of the Northern Territory Police, Fire and Emergency Services Forensic Services Branch, and the contribution of staff of the forensic biology section. We also thank ESR internal reviewers Catherine McGovern and Dr. SallyAnn Harbison whose comments greatly improved this manuscript.
Some loci in the Asian dataset were not analysed due to the small sample size (indicated by a dash).
0.008 0.002 0.395 0.274 0.398 0.593 0.000 0.132 0.529 0.555 0.091 0.000 0.058 0.080 0.627 0.540 0.336 0.023 0.960 0.275 0.679 0.016 0.222 0.777 0.000 0.012 0.199 0.001 0.732 0.157 0.719 0.393 0.116 0.654 0.118 Caucasian Declared Aboriginal Pure Aboriginal Asian East Timorese
Declared Aboriginal
Acknowledgements
0.437 0.030 0.003 – 0.623
0.806 0.521 0.045 – 0.597
D2 D16 CSF TPOX TH01 D7 D13 D5 D18 D21 D8 FGA vWA D3
Table 7 Results of Fisher’s exact test for allelic association within loci (Hardy–Weinberg equilibrium) in the five major categories of sub-populations of the Northern Territory
0.723 0.003 0.061 – 0.841
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