- Email: [email protected]
Y chromosome STR haplotypes in the Caribbean city of Cartagena (Colombia)
Forensic Science International 167 (2007) 62–69 www.elsevier.com/locate/forsciint
Announcement of Population Data
Y chromosome STR haplotypes in the Caribbean city of Cartagena (Colombia) Juan Jose´ Builes a,b,*, Beatriz Martı´nez c, Alfredo Go´mez b, Luis Caraballo c, Claudia Espinal a, Diana Aguirre a, Alba Montoya b, Manuel Moreno a,b, Anto´nio Amorim d,e, Leonor Gusma˜o d, M Luisa Bravo a a GENES Ltda., Medellı´n, Colombia Instituto de Biologı´a, Universidad de Antioquia, Medellı´n, Colombia c Instituto de Investigaciones Inmunolo´gicas, Universidad de Cartagena, Cartagena, Colombia d IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal e Faculdade de Cieˆncias da Universidade do Porto, Porto, Portugal b
Received 8 November 2005; received in revised form 12 December 2005; accepted 12 December 2005 Available online 7 February 2006
Abstract Haplotype data were obtained from a sample of 173 unrelated male individuals from Cartagena (Colombia), for 16 Y-chromosome STRs (DYS19, DYS385, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460, DYS461, DYS635, GATA H4 and GATA A10). No shared haplotypes were observed, demonstrating the usefulness and informative power of these Y-STRs in male lineage identification in Cartagena. Genetic distances were calculated using previously published haplotype data and the lowest values were found for the comparisons with samples of Iberian origin. # 2006 Elsevier Ireland Ltd. All rights reserved. Keywords: Y-chromosome; STR; Cartagena; Colombia; Haplotype frequency
Population: Blood samples were obtained from 173 unrelated healthy male donors who were born in Cartagena, Bolı´var (Colombia, Fig. 1). DNA extraction: Salting-out [1]. PCR: DNA Amplification and detection of the amplicons were performed according to Builes et al. [2,3]. Alleles were typed by comparison with in-house constructed allelic ladders and the nomenclature follows and ISFG recommendations on Y chromosome STR analysis [4]. Quality control: Proficiency testing has been carried out for the proficiency testing of the GEP-ISFG working group [5] and the Y-STR haplotyping quality assurance exercise 2001 (http:// www.yhrd.org) [6]. Analysis of data: Haplotype frequencies were estimated by gene counting. Haplotype diversities were calculated according
* Corresponding author at: GENES Ltda., Carrera 48 No. 10–45 Cons. 611–612, Medellı´n, Colombia. Tel.: +574 268 4875; fax: +574 318 5270. E-mail address: [email protected] (J.J. Builes). 0379-0738/$ – see front matter # 2006 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2005.12.015
to Nei [7] using the Arlequin software, version 2.000 [8]. Analysis of molecular variance (AMOVA) results were summarized in the form of sum of squared size differences Rst values and assessed for statistical significance using a Monte Carlo test as implemented in the referred software. UPGMA tree was built from the distance matrix (Rst) using the option neighbour and drawtree in the PHYLIP software package [9]. The tree was visualized with the Treeview software [10]. In population comparisons, DYS385 was not considered and the number of repeats in DYS389I was subtracted from DYS389II. Results: Table 1 shows the haplotype distribution in a sample of unrelated males from Cartagena for the 17 Y-chromosome STR loci, DYS19, DYS385, DYS389I and II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460, DYS461, DYS635, GATA H4 and GATA A10. No shared haplotypes were obtained between the 173 individuals studied. The sample yielded an overall haplotype diversity of 1.000 0.0006, demonstrating the usefulness and informative power of these Y-STRs in male lineage identification in
J.J. Builes et al. / Forensic Science International 167 (2007) 62–69
Fig. 1. Map of Colombia showing Cartagena, Bolı´var Department, in black (Colombian Caribbean Coast).
Cartagena, Colombia. Considering the ‘minimal haplotype’ included in the YHRD (Y-STR haplotype reference database; http://www.yhrd.org) [6], the most frequent haplotype observed in Europe (2.72%) and in Latin American population sample (varying from 1.25% in Argentina to 4.47% in Sa˜o Paulo) matches the most frequent haplotype in Cartagena (8.67%). Access to the data: E-mail to [email protected]. Other remarks: Cartagena, a tropical city Caribbean Sea, is the capital of the departament of Bolı´var in Colombia. Current
63
population of Cartagena is an admixture from Caucasians, African and in a less extent, Native American ancestries. Previously, we have evaluated the distribution of some alleles of the HLA complex in this population and found mainly alleles from both Caucasian and African populations [11]. Also, we have compared the distribution of some autosomal STRs between Cartagena and other Colombian and African populations and significant differences were found, except with two Colombian Caribbean Coast subregions [12]. The present haplotype data were compared with the previously published data available for the same set of Y-STR loci in samples from North Portugal [13], Spain [14], Rio de Janeiro [15], Cantabria [16], Mozambique [17] and Equatorial Guinea [18]. Pairwise analysis showed no significant differences (P > 0.05) in the comparison of Cartagena and Rio de Janeiro (Rst = 0.00784). With other Iberian origin samples from northern Portugal, Spain and Cantabria, although significant, low Rst values were obtained (0.013, 0.012 and 0.024, respectively). In the comparison with the remaining populations, highly significant distances were observed (P = 0.000). Considering the ‘minimal haplotype’ loci included in the YHRD [6], data from Cartagena were compared with those previously published Antioquia, Colombia [19], CaucasianMestizo, East-central Andean, Colombia [20], Afro-Colombian, Choco´, Colombia [20], Co´rdoba, Argentina [21], northern Portugal [13], Basque Country, Spain [22], Spain [14], Peru´ [23], Buenos Aires [24], Rio de Janeiro [15], Macau [25] and Equatorial Guinea [18]. The lowest, non-significant (P > 0.05), pairwise differences between the Cartagena and other populations were obtained in the comparison with Rio de Janeiro (Rst = 0.000) and Co´rdoba (Rst = 0.006) samples. With the samples from northern Portugal, Spain and Antioquia, although significant, low Rst values were obtained (0.019; 0.021 and 0.007, respectively). In the comparison with the remaining
Fig. 2. Unrooted NJ tree based on pairwise Rst genetic distances using (A) 16 Y-STR haplotypes and (B) YHRD ‘minimal haplotypes’ data from: CAR: Cartagena (this work), NP: North Portugal [12], SP: Spain [13], RJ: Rio de Janeiro [14], MO: Mozambique [16], EG: Equatorial Guinea [17], AN: Antioquia [18], BG: Colombian Caucasian-Mestizo [19], CH: Choco´ [19], CO: Co´rdoba, Argentina [20], BC: Basque Country [21], PE: Peru´ [22], BA: Buenos Aires [23], MC: Macau [24].
64
Table 1 Y-Chromosome STR haplotypes detected in 173 unrelated males from Cartagena, Bolı´var (Colombia) DYS 19
DYS 389 I
DYS 389 II
DYS 390
DYS 391
DYS 392
DYS 393
DYS 385
DYS 437
DYS 438
DYS 439
DYS 460
DYS 461
GATA A10
DYS 635
GATA H4
n
H1 H2 H3 H4 H5 H6 H7 H8 H9 H10 H11 H12 H13 H14 H15 H16 H17 H18 H19 H20 H21 H22 H23 H24 H25 H26 H27 H28 H29 H30 H31 H32 H33 H34 H35 H36 H37 H38 H39 H40 H41 H42 H43 H44 H45
14 13 14 14 15 15 14 17 15 15 14 16 16 14 16 14 14 14 15 14 14 13 14 15 14 15 16 14 14 14 14 14 14 14 14 14 14 14 13 13 15 15 14 14 14
12 13 13 13 13 13 13 12 12 12 13 14 13 13 13 13 13 14 13 15 12 10 13 12 13 13 13 14 13 13 13 12 14 13 13 13 12 13 14 13 13 12 12 13 13
28 30 29 29 29 29 29 29 29 28 30 31 29 30 29 31 31 30 29 32 28 26 30 30 28 28 29 32 31 31 30 29 30 29 29 30 28 29 31 32 30 28 29 30 30
24 24 24 23 24 24 24 21 21 22 25 21 22 23 24 23 24 24 23 24 24 22 24 22 24 24 24 23 24 23 24 22 24 24 23 24 23 24 23 24 24 24 23 24 24
11 10 11 9 10 12 11 10 11 10 11 10 11 10 11 10 10 10 10 11 11 10 11 10 11 11 10 10 11 11 10 11 12 10 11 10 11 11 11 10 11 11 10 11 11
13 11 13 13 13 13 13 11 14 11 13 11 13 11 13 11 13 11 13 13 14 13 13 11 13 13 12 11 13 11 13 13 14 13 13 13 13 13 11 11 11 11 13 13 13
13 13 13 13 13 13 13 14 13 13 13 15 13 12 13 12 13 12 13 13 13 12 13 14 13 15 14 12 13 12 13 13 13 13 13 12 13 13 13 13 13 13 13 13 13
11/14 16/19 11/14 15/17 11/14 13/16 11/14 16/16 11/14 12/13 11/14 18/18 11/11 15/18 12/16 13/17 11/14 12/13 14/14 10/14 11/14 15/15 11/11 12/16 11/14 13/17 15/15 13/18 12/12 13/19 12/12 11/14 11/14 11/13 10/14 11/14 12/14 11/14 14/18 15/17 11/14 11/14 11/14 10/14 11/13
15 14 15 14 15 14 15 14 14 16 14 14 15 16 15 14 15 15 14 15 14 14 15 16 15 16 14 14 15 14 15 15 14 15 15 15 15 15 15 14 14 15 15 15 14
12 10 12 9 12 12 12 11 12 10 11 11 12 9 12 9 12 9 9 12 12 9 12 11 11 10 10 10 12 10 12 12 11 12 12 12 12 12 9 10 11 12 12 12 12
12 12 12 12 11 11 12 10 12 13 10 12 11 11 12 9 12 11 11 12 12 12 9 12 12 11 12 11 12 11 12 12 11 13 12 12 12 12 11 12 10 12 13 12 11
12 9 11 10 12 11 10 11 11 10 11 10 11 11 11 10 10 11 10 10 11 11 10 11 11 10 11 10 11 11 10 11 11 10 11 10 11 11 11 11 11 11 11 11 10
12 12 12 12 12 12 12 13 12 13 11 13 12 13 12 11 12 12 11 12 12 10 12 11 11 11 12 11 12 12 12 12 12 13 12 12 12 12 12 13 11 12 12 12 12
15 16 14 14 14 14 15 14 15 15 15 13 15 16 15 16 15 14 16 15 14 15 14 15 15 13 14 16 15 14 16 15 15 15 15 15 15 15 15 14 15 15 15 15 15
23 23 23 21 23 23 23 22 23 21 23 22 24 21 23 19 23 22 21 23 23 17 23 22 23 21 21 20 24 20 24 23 23 23 23 23 24 23 21 21 23 23 23 23 23
28 29 29 27 28 27 28 27 28 27 28 28 28 27 29 27 27 27 27 27 27 28 27 28 28 27 27 28 26 27 28 28 27 27 28 29 28 28 27 27 29 28 28 28 28
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
J.J. Builes et al. / Forensic Science International 167 (2007) 62–69
Haplot.
15 15 16 15 14 14 13 16 15 15 14 13 13 13 14 15 14 16 14 14 13 14 15 14 14 13 14 14 16 14 14 16 14 16 16 14 14 16 14 14 15 14 15 15 12 16 13 14 13 14 16
12 14 13 14 13 14 14 14 13 14 13 14 13 12 12 12 13 13 13 13 13 13 14 13 13 13 14 14 12 13 12 13 13 13 13 11 14 12 12 14 14 12 12 12 13 13 12 13 13 13 13
30 30 27 30 28 29 29 30 29 32 30 31 30 29 30 30 29 30 30 29 30 29 30 29 29 31 30 30 29 29 29 29 30 29 29 28 32 29 28 30 30 30 29 28 31 28 28 29 29 29 30
24 24 23 24 24 24 24 24 23 25 22 25 24 23 22 23 24 21 24 24 23 24 23 24 24 24 25 25 21 24 21 24 22 24 24 21 21 21 24 25 24 22 23 24 23 23 23 23 24 24 21
10 10 10 9 10 12 10 10 11 10 10 10 10 10 10 12 11 10 10 10 10 11 10 10 11 10 11 11 10 11 10 10 10 10 10 11 10 10 11 10 11 10 11 10 10 10 10 10 11 11 10
14 11 11 11 12 13 14 11 13 11 11 11 14 11 11 11 13 11 13 13 11 13 11 13 13 11 13 13 11 13 11 12 13 11 11 13 11 11 14 13 13 11 11 11 14 11 11 11 13 13 11
13 13 13 12 12 13 14 13 13 13 12 13 13 13 13 13 14 15 12 13 13 14 12 13 13 13 14 13 14 13 12 14 13 13 13 13 13 15 13 13 13 13 12 12 13 13 13 12 13 13 15
13/16 14/17 11/14 13/14 13/13 11/14 15/17 12/14 12/15 11/14 15/18 15/18 15/17 14/17 12/17 14/15 10/14 13/16 11/14 11/15 15/16 10/14 13/15 12/15 11/13 16/17 11/14 11/14 13/17 11/14 12/15 14/15 11/14 11/13 16/17 11/14 15/18 12/13 11/15 11/14 11/12 12/17 14/17 15/17 14/14 12/17 14/16 12/17 11/14 10/14 16/16
14 14 15 16 16 15 14 15 15 14 16 14 14 14 16 15 15 14 15 15 14 15 15 15 15 14 15 14 16 15 14 14 14 14 15 15 14 17 14 15 15 15 16 16 14 15 15 15 15 15 14
10 11 10 7 10 12 10 10 12 11 9 10 11 10 10 10 12 11 12 12 10 12 9 12 12 10 11 12 10 12 9 10 12 11 12 9 11 10 12 12 12 10 9 9 11 10 10 9 12 12 11
11 12 11 13 12 12 13 11 13 10 11 13 12 10 11 14 12 12 12 12 12 12 10 12 12 12 13 11 11 11 11 11 12 11 13 11 12 12 12 12 12 11 12 12 12 12 12 12 12 13 12
10 10 10 11 11 11 11 10 11 12 11 9 11 10 12 10 10 11 10 10 11 11 10 11 11 9 11 10 10 10 10 11 10 10 10 10 10 11 11 10 12 12 10 11 11 11 10 10 11 11 11
11 13 11 13 12 12 13 11 12 11 13 12 13 13 11 12 13 13 13 13 11 13 13 12 12 12 13 12 11 11 12 12 12 13 12 12 13 12 12 12 13 11 10 10 13 11 12 13 12 12 13
14 13 15 16 15 15 16 16 14 14 16 16 14 15 16 14 15 13 15 15 14 15 15 16 14 15 14 15 13 15 15 14 15 14 15 15 14 14 14 15 16 16 14 14 15 15 14 15 15 14 13
21 21 24 22 21 23 23 22 23 23 21 22 23 22 21 22 24 21 23 25 21 24 20 23 23 22 24 23 21 23 22 22 23 24 23 22 22 20 23 23 23 21 21 21 24 22 21 21 23 23 23
27 28 28 28 28 28 28 28 28 28 27 28 28 27 28 27 28 27 28 27 27 28 27 27 28 28 28 27 27 28 27 27 28 28 28 28 27 27 27 28 28 28 28 27 27 29 27 29 27 27 27
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
J.J. Builes et al. / Forensic Science International 167 (2007) 62–69
H46 H47 H48 H49 H50 H51 H52 H53 H54 H55 H56 H57 H58 H59 H60 H61 H62 H63 H64 H65 H66 H67 H68 H69 H70 H71 H72 H73 H74 H75 H76 H77 H78 H79 H80 H81 H82 H83 H84 H85 H86 H87 H88 H89 H90 H91 H92 H93 H94 H95 H96
65
66
Table 1 (Continued ) DYS 19
DYS 389 I
DYS 389 II
DYS 390
DYS 391
DYS 392
DYS 393
DYS 385
DYS 437
DYS 438
DYS 439
DYS 460
DYS 461
GATA A10
DYS 635
GATA H4
n
H97 H98 H99 H100 H101 H102 H103 H104 H105 H106 H107 H108 H109 H110 H111 H112 H113 H114 H115 H116 H117 H118 H119 H120 H121 H122 H123 H124 H125 H126 H127 H128 H129 H130 H131 H132 H133 H134 H135 H136 H137 H138 H139 H140 H141 H142 H143
14 14 17 13 15 14 14 14 14 14 13 14 14 14 14 13 14 14 14 16 14 15 14 15 14 14 15 17 14 14 14 14 15 14 14 14 15 17 15 15 15 14 15 14 14 14 15
13 13 13 13 14 12 13 13 13 13 13 13 13 13 13 13 13 12 12 13 14 12 12 12 13 14 13 13 13 13 13 13 14 13 13 13 13 14 14 13 13 14 14 12 10 13 12
30 28 29 30 30 28 29 29 29 29 29 29 29 30 29 30 29 28 29 30 30 29 29 30 30 30 30 28 29 29 29 29 32 29 28 30 29 29 30 30 30 30 30 28 26 29 28
24 24 25 24 23 23 27 24 24 24 24 24 24 24 24 24 23 24 23 21 24 21 22 21 24 24 21 23 24 24 24 24 21 26 23 24 24 23 24 21 21 24 24 24 23 23 22
10 10 10 10 11 11 11 10 10 11 9 12 11 11 10 10 11 11 10 10 11 11 10 10 11 11 10 10 11 11 10 11 11 12 11 11 10 9 11 10 10 11 11 11 10 10 10
11 14 11 11 14 11 13 14 13 13 11 13 13 13 14 11 13 13 11 11 13 13 11 11 13 13 11 11 13 13 13 13 11 13 12 13 13 11 13 11 11 13 12 13 13 13 11
12 13 13 13 13 13 13 13 13 14 13 13 13 13 13 13 13 13 13 14 13 15 12 13 12 13 15 14 13 13 13 13 13 13 13 13 13 13 13 14 14 13 13 13 13 13 14
16/18 11/15 11/14 16/16 11/14 11/15 11/13 11/15 11/14 11/14 10/14 11/14 11/14 11/14 11/14 15/18 15/17 11/14 13/14 11/14 11/14 13/17 15/15 17/17 13/15 11/14 14/14 15/18 14/16 12/17 11/14 13/15 16/17 11/14 16/16 12/14 11/14 12/12 13.2/15 11/14 16/17 11/14 11/14 11/15 11/14 11/14 12/15
15 15 14 14 15 15 15 15 14 15 14 15 14 14 15 15 15 15 16 14 14 16 14 14 15 14 16 15 15 15 15 15 14 14 14 14 15 15 14 15 14 14 15 15 15 15 15
9 12 11 10 12 10 12 12 12 12 10 12 12 12 12 10 12 12 10 11 12 10 11 11 12 12 10 10 12 12 12 10 11 12 10 12 12 10 12 12 11 9 12 12 12 13 10
12 12 10 12 12 11 12 12 13 12 12 11 12 12 11 12 13 12 11 10 12 12 12 12 13 12 11 11 12 11 11 12 11 11 11 12 10 12 13 11 11 13 11 12 11 12 11
11 10 11 9 10 10 11 10 10 11 10 11 11 11 10 11 10 11 11 11 11 10 11 10 11 10 11 10 11 11 11 10 10 11 10 13 10 10 12 10 10 11 11 11 11 11 11
13 12 11 12 12 11 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 11 13 13 11 11 11 11 18 12 12 12 13 12 13 13 12 12 12 12 13 12 12 12 12 12 11
16 15 16 15 15 15 15 15 15 15 15 15 15 15 15 14 14 16 14 14 15 13 14 14 14 14 14 14 14 15 15 14 14 15 15 15 15 15 15 15 13 15 16 15 15 14 14
24 25 23 21 23 23 23 23 23 24 22 23 23 23 23 21 23 23 22 23 23 21 21 22 23 23 21 22 23 23 23 22 21 23 21 25 23 21 24 23 23 24 24 23 23 23 21
27 28 28 28 28 28 27 28 28 28 28 28 27 28 28 27 28 28 27 27 28 27 27 27 28 27 27 28 27 28 28 27 29 27 28 28 27 27 27 28 27 27 28 28 28 28 28
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
J.J. Builes et al. / Forensic Science International 167 (2007) 62–69
Haplot.
14 14 15 14 14 14 15 16 14 14 15 15 16 15 14 14 15 13 14 15 16 17 14 13 13 15 14 15 14 15
13 13 14 13 13 13 12 13 14 13 13 14 13 13 13 13 13 13 14 13 11 13 13 12 13 13 13 13 13 13
29 31 31 31 30 29 29 29 30 29 29 30 30 30 29 29 30 29 29 29 28 30 30 28 29 31 29 30 29 29
24 23 23 23 23 25 23 23 23 24 23 23 24 23 24 24 23 24 23 22 21 21 25 25 24 23 24 24 24 22
11 10 11 11 10 10 11 9 11 11 10 11 10 10 11 11 10 10 10 10 10 10 11 11 10 11 11 10 11 10
13 11 11 11 11 13 12 11 13 13 11 13 11 12 13 13 11 11 11 13 11 11 13 11 13 13 13 11 13 13
13 12 13 12 12 12 14 12 13 13 12 13 13 14 14 13 12 13 12 12 13 14 13 13 13 14 13 15 13 12
11/14 13/17 15/16 13/16 13/17 12/14 15/15 13/13 11/14 11/14 12/17 13/15 11/14 15/15 11/13 11/15 13/17 16/17 13/16 11/14 11/15 11/13 12/14 13/14 11/14 12/14 13/17 12/14 11/14 16/17
15 14 14 14 14 15 15 14 14 14 15 14 14 14 15 15 14 14 14 15 14 14 14 15 15 14 15 14 15 15
12 10 11 10 9 11 10 12 12 12 9 12 11 10 12 12 10 10 9 12 11 11 12 11 12 12 12 10 12 12
12 11 13 10 9 11 12 13 13 12 11 12 10 12 11 12 11 13 11 11 11 12 11 11 12 11 12 11 12 11
10 10 10 11 10 10 11 10 11 11 10 12 12 11 11 11 10 10 10 11 10 11 11 10 10 11 10 10 11 11
12 11 13 11 11 12 12 12 12 12 13 12 11 12 13 14 11 11 12 12 13 13 12 12 12 15 12 13 12 12
16 15 14 16 16 14 15 15 15 15 15 16 17 14 15 15 14 14 14 15 14 13 15 14 15 15 15 15 16 15
23 20 21 20 19 23 20 21 23 23 21 23 23 21 23 23 20 22 21 23 24 21 23 23 23 23 23 23 23 23
28 27 28 27 27 27 27 28 27 28 29 28 28 27 28 28 28 27 27 28 28 27 28 27 28 28 28 28 28 28
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
J.J. Builes et al. / Forensic Science International 167 (2007) 62–69
H144 H145 H146 H147 H148 H149 H150 H151 H152 H153 H154 H155 H156 H157 H158 H159 H160 H161 H162 H163 H164 H165 H166 H167 H168 H169 H170 H171 H172 H173
67
68
J.J. Builes et al. / Forensic Science International 167 (2007) 62–69
populations, highly significant distances were observed (P = 0.000). Fig. 2 shows neighbour joining trees built from the Rst distance matrices between the seven (16 Y-STR haplotypes) and 13 (‘minimal haplotype’ loci) populations, respectively, where Cartagena sample clusters with European origin samples and stands far apart of the non-Caucasian samples: a Chinese sample from Macao (Rst = 0.134), two African samples from Mozambique (Rst = 0.343) and Equatorial Guinea (Rst = 0.306), a African origin sample from Choco´ (Rst = 0.162) and Native Americans from Peru´ (Rst = 0.212). These findings suggest a high proportion of male contribution of European origin in the population of Cartagena. Although a high degree of African genetic influence is present in Cartagena population [11], the present work results suggest that Cartagena presents a much higher proportion of European male lineages than those from African or Amerindian origin. This is in accordance with the sex-biased contribution of socially and economically asymmetric gene pools [26]. Nevertheless, the assignment of male lineages to each continent could only be evaluated by SNP analysis. Moreover, since data are only available for two African populations, we cannot discard the hypothesis that lower genetic distances could be obtained between Cartagena and other uncharacterized African populations. In summary, because of the significant genetic distances detected between Cartagena and other populations from Colombia, as well as those from Iberia and Africa, a specific Y STR haplotype database should be used in paternity and forensic cases in Cartagena. This paper follows the guidelines for publication of population data requested by the journal [27]. Acknowledgments This work was partially supported by GENES Ltda., Instituto de Investigaciones Inmunolo´gicas (Universidad de Cartagena, Colombia) and Fundac¸a˜o para a Cieˆncia e a Tecnologia (POCTI, Programa Operacional Cieˆncia, Tecnologia e Inovac¸a˜o).
[5]
[6]
[7] [8]
[9] [10] [11]
[12]
[13]
[14]
[15]
[16]
[17]
[18]
References [19] [1] S.A. Miller, D.D. Dykes, H.F. Polesky, A simple salting-out procedure for extracting DNA from human nucleated cells, Nucleic Acids Res. 16 (1988) 1215. [2] J.J. Builes, M.L.J. Bravo, M. Martı´nez-Pancorbo, M.A. Moreno, C.P. Go´mez, Discrimination index of Y-chromosomal haplotypes in an Antioquia (Colombia) population sample, in: C. Doutreme´puich, N. Morling (Eds.), Progress in Forensic Genetics, vol. 10, Elsevier, Amsterdam, 2004, pp. 275–277. [3] J.J. Builes, M.L.J. Bravo, A. Montoya, L. Caraballo, B. Martı´nez, M. Moreno, Population genetics of eight new Y-chromosomal STR haplotypes in three Colombian populations: Antioquia, Choco´ and Cartagena, in: C. Doutreme´puich, N. Morling (Eds.), Progress in Forensic Genetics, vol. 10, Elsevier, Amsterdam, 2004, pp. 310–312. [4] L. Gusma˜o, J.M. Butler, A. Carracedo, P. Gill, M. Kayser, M.R. Mayr, N. Morling, M. Prinz, L. Roewer, C. Tyler-Smith, P.M. Schneider, DNA Commission of the International Society of Forensic Genetics (ISFG): An
[20]
[21]
[22]
[23]
update of the recommendations on the use of Y-STRs in forensic analysis, Forensic Sci. Int. 21 May 2005; [Epub ahead of print]. J. Go´mez, A. Carracedo, The 1998–1999 collaborative exercises and proficiency testing program on DNA typing of the Spanish and Portuguese Working Group of the International Society for Forensic Genetics (GEPISFG), Forensic Sci. Int. 114 (2000) 21–30. L. Roewer, M. Krawczak, S. Willuweit, M. Nagy, C. Alves, A. Amorim, K. Anslinger, C. Augustin, A. Betz, E. Bosch, A. Caglia`, A. Carracedo, D. Corach, T. Dobosz, B.M. Dupuy, S. Fu¨redi, C. Gehrig, L. Gusma˜o, J. Henke, L. Henke, M. Hidding, C. Hohoff, B. Hoste, M. Jobling, H.J. Ka¨rgel, P. De Knijff, R. Lessig, E. Liebeherr, M. Lorente, B. Martı´nezJarreta, P. Nievas, M. Nowak, W. Parson, V.L. Pascali, G. Penacino, R. Ploski, B. Rolf, A. Sala, U. Schmidt, C. Schmitt, P.M. Schneider, R. Szibor, J. Teifel-Greding, M. Kayser, Online reference database of Ychromosomal short tandem repeat (STR) haplotypes, Forensic Sci. Int. 118 (2001) 103–111. M. Nei, Molecular Evolutionary Genetics, Columbia University Press, New York, USA, 1987. S. Schneider, D. Roessli, L. Excoffier, Arlequin Version 2000: A Software for Population Genetics Data Analysis, Genetics and Biometrics Laboratory, University of Geneva, Switzerland, 2000. J. Felsenstein, PHYLIP: phylogeny inference package (version 3.2), Cladistics 5 (1989) 164–166. R.D.M. Page, Treeview: an application to display phylogenetic trees on personal computers, Comput. Appl. Biosci. 12 (1996) 357–358. L. Caraballo, J. Marrugo, H. Erlich, M. Pastorizo, HLA alleles in the populations of Cartagena (Colombia), Tissue Antigens 39 (1992) 128– 133. B. Martı´nez, L. Caraballo, F. Baro´n, L. Gusma˜o, A. Amorim, A. Carracedo, Analysis of STR loci in Cartagena, a Caribbean city of Colombia, Forensic Sci. Int., 14 July 2005; [Epub ahead of print]. S. Beleza, C. Alves, A. Gonza´lez-Neira, M. Lareu, A. Amorim, A. Carracedo, L. Gusma˜o, Extending STR markers in Y chromosome haplotypes, Int. J. Leg. Med. 117 (2003) 27–33. P. Martı´n, J. Garcı´a-Hirschfeld, O. Garcı´a, L. Gusma˜o, P. Garcı´a, C. Albarra´n, M. Sancho, A. Alonso, A Spanish population study of 17 Ychromosome STR loci, Forensic Sci. Int. 139 (2004) 231–235. A.C.S. Go´es, E.F. Carvalho, I. Gomes, D.A. Silva, E.H.F. Gil, A. Amorim, L. Gusma˜o, Population and mutational analysis in 17 Y-STR loci from Rio de Janeiro (Brazil), Int. J. Legal Med. 119 (2005) 70–76. M.T. Zarrabeitia, J.A. Riancho, L. Gusma˜o, M.V. Lareu, C. San˜udo, A. Amorim, A. Carracedo, Spanish population data and forensic usefulness of a novel Y-STR set (DYS437, DYS438, DYS439, DYS460, DYS461, GATA A10, GATA C4, GATA H4), Int. J. Legal Med. 117 (2003) 306–311. C. Alves, L. Gusma˜o, J. Barbosa, A. Amorim, Evaluating the informative power of Y-STRs: a comparative study using European and new African haplotype data, Forensic Sci. Int. 134 (2003) 126–133. E. Arroyo-Pardo, L. Gusma˜o, A.M. Lo´pez-Parra, C. Baeza, M.S. Mesa, A. Amorim, Genetic variability of 16 Y-chromosome STRs in a sample from Equatorial Guinea (Central Africa), Forensic Sci. Int. 149 (2005) 109– 113. J.J. Builes, M.L. Bravo, C. Go´mez, C. Espinal, D. Aguirre, A. Go´mez, J. Rodrı´guez, P. Castan˜eda, A. Montoya, M. Moreno, A. Amorim, L. Gusma˜o, Y Chromosome STRs in an Antioquian (Colombia) population sample, Forensic Sci. Int., 7 November 2005 [Epub ahead of print]. J.J. Yunis, L.E. Acevedo, D.S. Campo, E.J. Yunis, Population data of YSTR minimal haplotypes in a sample of Caucasian-Mestizo and African descent individuals of Colombia, Forensic Sci. Int. 151 (2005) 307– 313. M. Fondevila, J.C. Jaime, A. Salas, M.V. Lareu, A. Carracedo, Y-chromosome STR haplotypes in Co´rdoba (Argentina), Forensic Sci. Int. 137 (2003) 217–220. O. Garcı´a, P. Martı´n, L. Gusma˜o, C. Albarra´n, S. Alonso, C. de la Rua, C. Flores, N. Izagirre, R. Pen˜a, J.A. Pe´rez, I. Uriarte, I. Yurrebaso, A. Alonso, A Basque Country autochthonous population study of 11 Y-chromosome STR loci, Forensic Sci. Int. 145 (2004) 65–68. G.C. Iannacone, R.Y. Tito, P.W. Lo´pez, M.E. Medina, B. Lizarraga, Y-chromosomal haplotypes for the PowerPlex Y for twelve STRs
J.J. Builes et al. / Forensic Science International 167 (2007) 62–69 in a Peruvian population sample, J. Forensic Sci. 50 (2005) 239– 242. [24] M. Kayser, M. Krawczak, L. Excoffier, P. Dieltjes, D. Corach, V. Pascali, C. Gehrig, L.F. Bernini, J. Jespersen, E. Bakker, L. Roewer, P. de Knijff, An extensive analysis of Y-chromosomal microsatellite haplotypes in globally dispersed human populations, Am. J. Hum. Genet. 68 (2001) 990–1018. [25] L. Gusma˜o, A. Amorim, N. Martins, M.J. Prata, A. Gonzalez-Neira, M.V. Lareu, A. Carracedo, Y chromosome STR haplotypes in Macau (SE
69
China), Progress in Forensic Genetics vol. 8, Elsevier Science, Amsterdam, 2000, pp. 324–326. [26] E.J. Parra, A. Marcini, J. Akey, J. Martinson, M.A. Batzer, R. Cooper, T. Forrester, D.B. Allison, R. Deka, R.E. Ferrell, M.D. Shriver, Estimating African American admixture proportions by use of population-specific alleles, Am. J. Hum. Genet. 63 (1998) 1839–1851. [27] P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.
Announcement of Population Data
Y chromosome STR haplotypes in the Caribbean city of Cartagena (Colombia) Juan Jose´ Builes a,b,*, Beatriz Martı´nez c, Alfredo Go´mez b, Luis Caraballo c, Claudia Espinal a, Diana Aguirre a, Alba Montoya b, Manuel Moreno a,b, Anto´nio Amorim d,e, Leonor Gusma˜o d, M Luisa Bravo a a GENES Ltda., Medellı´n, Colombia Instituto de Biologı´a, Universidad de Antioquia, Medellı´n, Colombia c Instituto de Investigaciones Inmunolo´gicas, Universidad de Cartagena, Cartagena, Colombia d IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal e Faculdade de Cieˆncias da Universidade do Porto, Porto, Portugal b
Received 8 November 2005; received in revised form 12 December 2005; accepted 12 December 2005 Available online 7 February 2006
Abstract Haplotype data were obtained from a sample of 173 unrelated male individuals from Cartagena (Colombia), for 16 Y-chromosome STRs (DYS19, DYS385, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460, DYS461, DYS635, GATA H4 and GATA A10). No shared haplotypes were observed, demonstrating the usefulness and informative power of these Y-STRs in male lineage identification in Cartagena. Genetic distances were calculated using previously published haplotype data and the lowest values were found for the comparisons with samples of Iberian origin. # 2006 Elsevier Ireland Ltd. All rights reserved. Keywords: Y-chromosome; STR; Cartagena; Colombia; Haplotype frequency
Population: Blood samples were obtained from 173 unrelated healthy male donors who were born in Cartagena, Bolı´var (Colombia, Fig. 1). DNA extraction: Salting-out [1]. PCR: DNA Amplification and detection of the amplicons were performed according to Builes et al. [2,3]. Alleles were typed by comparison with in-house constructed allelic ladders and the nomenclature follows and ISFG recommendations on Y chromosome STR analysis [4]. Quality control: Proficiency testing has been carried out for the proficiency testing of the GEP-ISFG working group [5] and the Y-STR haplotyping quality assurance exercise 2001 (http:// www.yhrd.org) [6]. Analysis of data: Haplotype frequencies were estimated by gene counting. Haplotype diversities were calculated according
* Corresponding author at: GENES Ltda., Carrera 48 No. 10–45 Cons. 611–612, Medellı´n, Colombia. Tel.: +574 268 4875; fax: +574 318 5270. E-mail address: [email protected] (J.J. Builes). 0379-0738/$ – see front matter # 2006 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2005.12.015
to Nei [7] using the Arlequin software, version 2.000 [8]. Analysis of molecular variance (AMOVA) results were summarized in the form of sum of squared size differences Rst values and assessed for statistical significance using a Monte Carlo test as implemented in the referred software. UPGMA tree was built from the distance matrix (Rst) using the option neighbour and drawtree in the PHYLIP software package [9]. The tree was visualized with the Treeview software [10]. In population comparisons, DYS385 was not considered and the number of repeats in DYS389I was subtracted from DYS389II. Results: Table 1 shows the haplotype distribution in a sample of unrelated males from Cartagena for the 17 Y-chromosome STR loci, DYS19, DYS385, DYS389I and II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460, DYS461, DYS635, GATA H4 and GATA A10. No shared haplotypes were obtained between the 173 individuals studied. The sample yielded an overall haplotype diversity of 1.000 0.0006, demonstrating the usefulness and informative power of these Y-STRs in male lineage identification in
J.J. Builes et al. / Forensic Science International 167 (2007) 62–69
Fig. 1. Map of Colombia showing Cartagena, Bolı´var Department, in black (Colombian Caribbean Coast).
Cartagena, Colombia. Considering the ‘minimal haplotype’ included in the YHRD (Y-STR haplotype reference database; http://www.yhrd.org) [6], the most frequent haplotype observed in Europe (2.72%) and in Latin American population sample (varying from 1.25% in Argentina to 4.47% in Sa˜o Paulo) matches the most frequent haplotype in Cartagena (8.67%). Access to the data: E-mail to [email protected]. Other remarks: Cartagena, a tropical city Caribbean Sea, is the capital of the departament of Bolı´var in Colombia. Current
63
population of Cartagena is an admixture from Caucasians, African and in a less extent, Native American ancestries. Previously, we have evaluated the distribution of some alleles of the HLA complex in this population and found mainly alleles from both Caucasian and African populations [11]. Also, we have compared the distribution of some autosomal STRs between Cartagena and other Colombian and African populations and significant differences were found, except with two Colombian Caribbean Coast subregions [12]. The present haplotype data were compared with the previously published data available for the same set of Y-STR loci in samples from North Portugal [13], Spain [14], Rio de Janeiro [15], Cantabria [16], Mozambique [17] and Equatorial Guinea [18]. Pairwise analysis showed no significant differences (P > 0.05) in the comparison of Cartagena and Rio de Janeiro (Rst = 0.00784). With other Iberian origin samples from northern Portugal, Spain and Cantabria, although significant, low Rst values were obtained (0.013, 0.012 and 0.024, respectively). In the comparison with the remaining populations, highly significant distances were observed (P = 0.000). Considering the ‘minimal haplotype’ loci included in the YHRD [6], data from Cartagena were compared with those previously published Antioquia, Colombia [19], CaucasianMestizo, East-central Andean, Colombia [20], Afro-Colombian, Choco´, Colombia [20], Co´rdoba, Argentina [21], northern Portugal [13], Basque Country, Spain [22], Spain [14], Peru´ [23], Buenos Aires [24], Rio de Janeiro [15], Macau [25] and Equatorial Guinea [18]. The lowest, non-significant (P > 0.05), pairwise differences between the Cartagena and other populations were obtained in the comparison with Rio de Janeiro (Rst = 0.000) and Co´rdoba (Rst = 0.006) samples. With the samples from northern Portugal, Spain and Antioquia, although significant, low Rst values were obtained (0.019; 0.021 and 0.007, respectively). In the comparison with the remaining
Fig. 2. Unrooted NJ tree based on pairwise Rst genetic distances using (A) 16 Y-STR haplotypes and (B) YHRD ‘minimal haplotypes’ data from: CAR: Cartagena (this work), NP: North Portugal [12], SP: Spain [13], RJ: Rio de Janeiro [14], MO: Mozambique [16], EG: Equatorial Guinea [17], AN: Antioquia [18], BG: Colombian Caucasian-Mestizo [19], CH: Choco´ [19], CO: Co´rdoba, Argentina [20], BC: Basque Country [21], PE: Peru´ [22], BA: Buenos Aires [23], MC: Macau [24].
64
Table 1 Y-Chromosome STR haplotypes detected in 173 unrelated males from Cartagena, Bolı´var (Colombia) DYS 19
DYS 389 I
DYS 389 II
DYS 390
DYS 391
DYS 392
DYS 393
DYS 385
DYS 437
DYS 438
DYS 439
DYS 460
DYS 461
GATA A10
DYS 635
GATA H4
n
H1 H2 H3 H4 H5 H6 H7 H8 H9 H10 H11 H12 H13 H14 H15 H16 H17 H18 H19 H20 H21 H22 H23 H24 H25 H26 H27 H28 H29 H30 H31 H32 H33 H34 H35 H36 H37 H38 H39 H40 H41 H42 H43 H44 H45
14 13 14 14 15 15 14 17 15 15 14 16 16 14 16 14 14 14 15 14 14 13 14 15 14 15 16 14 14 14 14 14 14 14 14 14 14 14 13 13 15 15 14 14 14
12 13 13 13 13 13 13 12 12 12 13 14 13 13 13 13 13 14 13 15 12 10 13 12 13 13 13 14 13 13 13 12 14 13 13 13 12 13 14 13 13 12 12 13 13
28 30 29 29 29 29 29 29 29 28 30 31 29 30 29 31 31 30 29 32 28 26 30 30 28 28 29 32 31 31 30 29 30 29 29 30 28 29 31 32 30 28 29 30 30
24 24 24 23 24 24 24 21 21 22 25 21 22 23 24 23 24 24 23 24 24 22 24 22 24 24 24 23 24 23 24 22 24 24 23 24 23 24 23 24 24 24 23 24 24
11 10 11 9 10 12 11 10 11 10 11 10 11 10 11 10 10 10 10 11 11 10 11 10 11 11 10 10 11 11 10 11 12 10 11 10 11 11 11 10 11 11 10 11 11
13 11 13 13 13 13 13 11 14 11 13 11 13 11 13 11 13 11 13 13 14 13 13 11 13 13 12 11 13 11 13 13 14 13 13 13 13 13 11 11 11 11 13 13 13
13 13 13 13 13 13 13 14 13 13 13 15 13 12 13 12 13 12 13 13 13 12 13 14 13 15 14 12 13 12 13 13 13 13 13 12 13 13 13 13 13 13 13 13 13
11/14 16/19 11/14 15/17 11/14 13/16 11/14 16/16 11/14 12/13 11/14 18/18 11/11 15/18 12/16 13/17 11/14 12/13 14/14 10/14 11/14 15/15 11/11 12/16 11/14 13/17 15/15 13/18 12/12 13/19 12/12 11/14 11/14 11/13 10/14 11/14 12/14 11/14 14/18 15/17 11/14 11/14 11/14 10/14 11/13
15 14 15 14 15 14 15 14 14 16 14 14 15 16 15 14 15 15 14 15 14 14 15 16 15 16 14 14 15 14 15 15 14 15 15 15 15 15 15 14 14 15 15 15 14
12 10 12 9 12 12 12 11 12 10 11 11 12 9 12 9 12 9 9 12 12 9 12 11 11 10 10 10 12 10 12 12 11 12 12 12 12 12 9 10 11 12 12 12 12
12 12 12 12 11 11 12 10 12 13 10 12 11 11 12 9 12 11 11 12 12 12 9 12 12 11 12 11 12 11 12 12 11 13 12 12 12 12 11 12 10 12 13 12 11
12 9 11 10 12 11 10 11 11 10 11 10 11 11 11 10 10 11 10 10 11 11 10 11 11 10 11 10 11 11 10 11 11 10 11 10 11 11 11 11 11 11 11 11 10
12 12 12 12 12 12 12 13 12 13 11 13 12 13 12 11 12 12 11 12 12 10 12 11 11 11 12 11 12 12 12 12 12 13 12 12 12 12 12 13 11 12 12 12 12
15 16 14 14 14 14 15 14 15 15 15 13 15 16 15 16 15 14 16 15 14 15 14 15 15 13 14 16 15 14 16 15 15 15 15 15 15 15 15 14 15 15 15 15 15
23 23 23 21 23 23 23 22 23 21 23 22 24 21 23 19 23 22 21 23 23 17 23 22 23 21 21 20 24 20 24 23 23 23 23 23 24 23 21 21 23 23 23 23 23
28 29 29 27 28 27 28 27 28 27 28 28 28 27 29 27 27 27 27 27 27 28 27 28 28 27 27 28 26 27 28 28 27 27 28 29 28 28 27 27 29 28 28 28 28
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
J.J. Builes et al. / Forensic Science International 167 (2007) 62–69
Haplot.
15 15 16 15 14 14 13 16 15 15 14 13 13 13 14 15 14 16 14 14 13 14 15 14 14 13 14 14 16 14 14 16 14 16 16 14 14 16 14 14 15 14 15 15 12 16 13 14 13 14 16
12 14 13 14 13 14 14 14 13 14 13 14 13 12 12 12 13 13 13 13 13 13 14 13 13 13 14 14 12 13 12 13 13 13 13 11 14 12 12 14 14 12 12 12 13 13 12 13 13 13 13
30 30 27 30 28 29 29 30 29 32 30 31 30 29 30 30 29 30 30 29 30 29 30 29 29 31 30 30 29 29 29 29 30 29 29 28 32 29 28 30 30 30 29 28 31 28 28 29 29 29 30
24 24 23 24 24 24 24 24 23 25 22 25 24 23 22 23 24 21 24 24 23 24 23 24 24 24 25 25 21 24 21 24 22 24 24 21 21 21 24 25 24 22 23 24 23 23 23 23 24 24 21
10 10 10 9 10 12 10 10 11 10 10 10 10 10 10 12 11 10 10 10 10 11 10 10 11 10 11 11 10 11 10 10 10 10 10 11 10 10 11 10 11 10 11 10 10 10 10 10 11 11 10
14 11 11 11 12 13 14 11 13 11 11 11 14 11 11 11 13 11 13 13 11 13 11 13 13 11 13 13 11 13 11 12 13 11 11 13 11 11 14 13 13 11 11 11 14 11 11 11 13 13 11
13 13 13 12 12 13 14 13 13 13 12 13 13 13 13 13 14 15 12 13 13 14 12 13 13 13 14 13 14 13 12 14 13 13 13 13 13 15 13 13 13 13 12 12 13 13 13 12 13 13 15
13/16 14/17 11/14 13/14 13/13 11/14 15/17 12/14 12/15 11/14 15/18 15/18 15/17 14/17 12/17 14/15 10/14 13/16 11/14 11/15 15/16 10/14 13/15 12/15 11/13 16/17 11/14 11/14 13/17 11/14 12/15 14/15 11/14 11/13 16/17 11/14 15/18 12/13 11/15 11/14 11/12 12/17 14/17 15/17 14/14 12/17 14/16 12/17 11/14 10/14 16/16
14 14 15 16 16 15 14 15 15 14 16 14 14 14 16 15 15 14 15 15 14 15 15 15 15 14 15 14 16 15 14 14 14 14 15 15 14 17 14 15 15 15 16 16 14 15 15 15 15 15 14
10 11 10 7 10 12 10 10 12 11 9 10 11 10 10 10 12 11 12 12 10 12 9 12 12 10 11 12 10 12 9 10 12 11 12 9 11 10 12 12 12 10 9 9 11 10 10 9 12 12 11
11 12 11 13 12 12 13 11 13 10 11 13 12 10 11 14 12 12 12 12 12 12 10 12 12 12 13 11 11 11 11 11 12 11 13 11 12 12 12 12 12 11 12 12 12 12 12 12 12 13 12
10 10 10 11 11 11 11 10 11 12 11 9 11 10 12 10 10 11 10 10 11 11 10 11 11 9 11 10 10 10 10 11 10 10 10 10 10 11 11 10 12 12 10 11 11 11 10 10 11 11 11
11 13 11 13 12 12 13 11 12 11 13 12 13 13 11 12 13 13 13 13 11 13 13 12 12 12 13 12 11 11 12 12 12 13 12 12 13 12 12 12 13 11 10 10 13 11 12 13 12 12 13
14 13 15 16 15 15 16 16 14 14 16 16 14 15 16 14 15 13 15 15 14 15 15 16 14 15 14 15 13 15 15 14 15 14 15 15 14 14 14 15 16 16 14 14 15 15 14 15 15 14 13
21 21 24 22 21 23 23 22 23 23 21 22 23 22 21 22 24 21 23 25 21 24 20 23 23 22 24 23 21 23 22 22 23 24 23 22 22 20 23 23 23 21 21 21 24 22 21 21 23 23 23
27 28 28 28 28 28 28 28 28 28 27 28 28 27 28 27 28 27 28 27 27 28 27 27 28 28 28 27 27 28 27 27 28 28 28 28 27 27 27 28 28 28 28 27 27 29 27 29 27 27 27
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
J.J. Builes et al. / Forensic Science International 167 (2007) 62–69
H46 H47 H48 H49 H50 H51 H52 H53 H54 H55 H56 H57 H58 H59 H60 H61 H62 H63 H64 H65 H66 H67 H68 H69 H70 H71 H72 H73 H74 H75 H76 H77 H78 H79 H80 H81 H82 H83 H84 H85 H86 H87 H88 H89 H90 H91 H92 H93 H94 H95 H96
65
66
Table 1 (Continued ) DYS 19
DYS 389 I
DYS 389 II
DYS 390
DYS 391
DYS 392
DYS 393
DYS 385
DYS 437
DYS 438
DYS 439
DYS 460
DYS 461
GATA A10
DYS 635
GATA H4
n
H97 H98 H99 H100 H101 H102 H103 H104 H105 H106 H107 H108 H109 H110 H111 H112 H113 H114 H115 H116 H117 H118 H119 H120 H121 H122 H123 H124 H125 H126 H127 H128 H129 H130 H131 H132 H133 H134 H135 H136 H137 H138 H139 H140 H141 H142 H143
14 14 17 13 15 14 14 14 14 14 13 14 14 14 14 13 14 14 14 16 14 15 14 15 14 14 15 17 14 14 14 14 15 14 14 14 15 17 15 15 15 14 15 14 14 14 15
13 13 13 13 14 12 13 13 13 13 13 13 13 13 13 13 13 12 12 13 14 12 12 12 13 14 13 13 13 13 13 13 14 13 13 13 13 14 14 13 13 14 14 12 10 13 12
30 28 29 30 30 28 29 29 29 29 29 29 29 30 29 30 29 28 29 30 30 29 29 30 30 30 30 28 29 29 29 29 32 29 28 30 29 29 30 30 30 30 30 28 26 29 28
24 24 25 24 23 23 27 24 24 24 24 24 24 24 24 24 23 24 23 21 24 21 22 21 24 24 21 23 24 24 24 24 21 26 23 24 24 23 24 21 21 24 24 24 23 23 22
10 10 10 10 11 11 11 10 10 11 9 12 11 11 10 10 11 11 10 10 11 11 10 10 11 11 10 10 11 11 10 11 11 12 11 11 10 9 11 10 10 11 11 11 10 10 10
11 14 11 11 14 11 13 14 13 13 11 13 13 13 14 11 13 13 11 11 13 13 11 11 13 13 11 11 13 13 13 13 11 13 12 13 13 11 13 11 11 13 12 13 13 13 11
12 13 13 13 13 13 13 13 13 14 13 13 13 13 13 13 13 13 13 14 13 15 12 13 12 13 15 14 13 13 13 13 13 13 13 13 13 13 13 14 14 13 13 13 13 13 14
16/18 11/15 11/14 16/16 11/14 11/15 11/13 11/15 11/14 11/14 10/14 11/14 11/14 11/14 11/14 15/18 15/17 11/14 13/14 11/14 11/14 13/17 15/15 17/17 13/15 11/14 14/14 15/18 14/16 12/17 11/14 13/15 16/17 11/14 16/16 12/14 11/14 12/12 13.2/15 11/14 16/17 11/14 11/14 11/15 11/14 11/14 12/15
15 15 14 14 15 15 15 15 14 15 14 15 14 14 15 15 15 15 16 14 14 16 14 14 15 14 16 15 15 15 15 15 14 14 14 14 15 15 14 15 14 14 15 15 15 15 15
9 12 11 10 12 10 12 12 12 12 10 12 12 12 12 10 12 12 10 11 12 10 11 11 12 12 10 10 12 12 12 10 11 12 10 12 12 10 12 12 11 9 12 12 12 13 10
12 12 10 12 12 11 12 12 13 12 12 11 12 12 11 12 13 12 11 10 12 12 12 12 13 12 11 11 12 11 11 12 11 11 11 12 10 12 13 11 11 13 11 12 11 12 11
11 10 11 9 10 10 11 10 10 11 10 11 11 11 10 11 10 11 11 11 11 10 11 10 11 10 11 10 11 11 11 10 10 11 10 13 10 10 12 10 10 11 11 11 11 11 11
13 12 11 12 12 11 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 11 13 13 11 11 11 11 18 12 12 12 13 12 13 13 12 12 12 12 13 12 12 12 12 12 11
16 15 16 15 15 15 15 15 15 15 15 15 15 15 15 14 14 16 14 14 15 13 14 14 14 14 14 14 14 15 15 14 14 15 15 15 15 15 15 15 13 15 16 15 15 14 14
24 25 23 21 23 23 23 23 23 24 22 23 23 23 23 21 23 23 22 23 23 21 21 22 23 23 21 22 23 23 23 22 21 23 21 25 23 21 24 23 23 24 24 23 23 23 21
27 28 28 28 28 28 27 28 28 28 28 28 27 28 28 27 28 28 27 27 28 27 27 27 28 27 27 28 27 28 28 27 29 27 28 28 27 27 27 28 27 27 28 28 28 28 28
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
J.J. Builes et al. / Forensic Science International 167 (2007) 62–69
Haplot.
14 14 15 14 14 14 15 16 14 14 15 15 16 15 14 14 15 13 14 15 16 17 14 13 13 15 14 15 14 15
13 13 14 13 13 13 12 13 14 13 13 14 13 13 13 13 13 13 14 13 11 13 13 12 13 13 13 13 13 13
29 31 31 31 30 29 29 29 30 29 29 30 30 30 29 29 30 29 29 29 28 30 30 28 29 31 29 30 29 29
24 23 23 23 23 25 23 23 23 24 23 23 24 23 24 24 23 24 23 22 21 21 25 25 24 23 24 24 24 22
11 10 11 11 10 10 11 9 11 11 10 11 10 10 11 11 10 10 10 10 10 10 11 11 10 11 11 10 11 10
13 11 11 11 11 13 12 11 13 13 11 13 11 12 13 13 11 11 11 13 11 11 13 11 13 13 13 11 13 13
13 12 13 12 12 12 14 12 13 13 12 13 13 14 14 13 12 13 12 12 13 14 13 13 13 14 13 15 13 12
11/14 13/17 15/16 13/16 13/17 12/14 15/15 13/13 11/14 11/14 12/17 13/15 11/14 15/15 11/13 11/15 13/17 16/17 13/16 11/14 11/15 11/13 12/14 13/14 11/14 12/14 13/17 12/14 11/14 16/17
15 14 14 14 14 15 15 14 14 14 15 14 14 14 15 15 14 14 14 15 14 14 14 15 15 14 15 14 15 15
12 10 11 10 9 11 10 12 12 12 9 12 11 10 12 12 10 10 9 12 11 11 12 11 12 12 12 10 12 12
12 11 13 10 9 11 12 13 13 12 11 12 10 12 11 12 11 13 11 11 11 12 11 11 12 11 12 11 12 11
10 10 10 11 10 10 11 10 11 11 10 12 12 11 11 11 10 10 10 11 10 11 11 10 10 11 10 10 11 11
12 11 13 11 11 12 12 12 12 12 13 12 11 12 13 14 11 11 12 12 13 13 12 12 12 15 12 13 12 12
16 15 14 16 16 14 15 15 15 15 15 16 17 14 15 15 14 14 14 15 14 13 15 14 15 15 15 15 16 15
23 20 21 20 19 23 20 21 23 23 21 23 23 21 23 23 20 22 21 23 24 21 23 23 23 23 23 23 23 23
28 27 28 27 27 27 27 28 27 28 29 28 28 27 28 28 28 27 27 28 28 27 28 27 28 28 28 28 28 28
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
J.J. Builes et al. / Forensic Science International 167 (2007) 62–69
H144 H145 H146 H147 H148 H149 H150 H151 H152 H153 H154 H155 H156 H157 H158 H159 H160 H161 H162 H163 H164 H165 H166 H167 H168 H169 H170 H171 H172 H173
67
68
J.J. Builes et al. / Forensic Science International 167 (2007) 62–69
populations, highly significant distances were observed (P = 0.000). Fig. 2 shows neighbour joining trees built from the Rst distance matrices between the seven (16 Y-STR haplotypes) and 13 (‘minimal haplotype’ loci) populations, respectively, where Cartagena sample clusters with European origin samples and stands far apart of the non-Caucasian samples: a Chinese sample from Macao (Rst = 0.134), two African samples from Mozambique (Rst = 0.343) and Equatorial Guinea (Rst = 0.306), a African origin sample from Choco´ (Rst = 0.162) and Native Americans from Peru´ (Rst = 0.212). These findings suggest a high proportion of male contribution of European origin in the population of Cartagena. Although a high degree of African genetic influence is present in Cartagena population [11], the present work results suggest that Cartagena presents a much higher proportion of European male lineages than those from African or Amerindian origin. This is in accordance with the sex-biased contribution of socially and economically asymmetric gene pools [26]. Nevertheless, the assignment of male lineages to each continent could only be evaluated by SNP analysis. Moreover, since data are only available for two African populations, we cannot discard the hypothesis that lower genetic distances could be obtained between Cartagena and other uncharacterized African populations. In summary, because of the significant genetic distances detected between Cartagena and other populations from Colombia, as well as those from Iberia and Africa, a specific Y STR haplotype database should be used in paternity and forensic cases in Cartagena. This paper follows the guidelines for publication of population data requested by the journal [27]. Acknowledgments This work was partially supported by GENES Ltda., Instituto de Investigaciones Inmunolo´gicas (Universidad de Cartagena, Colombia) and Fundac¸a˜o para a Cieˆncia e a Tecnologia (POCTI, Programa Operacional Cieˆncia, Tecnologia e Inovac¸a˜o).
[5]
[6]
[7] [8]
[9] [10] [11]
[12]
[13]
[14]
[15]
[16]
[17]
[18]
References [19] [1] S.A. Miller, D.D. Dykes, H.F. Polesky, A simple salting-out procedure for extracting DNA from human nucleated cells, Nucleic Acids Res. 16 (1988) 1215. [2] J.J. Builes, M.L.J. Bravo, M. Martı´nez-Pancorbo, M.A. Moreno, C.P. Go´mez, Discrimination index of Y-chromosomal haplotypes in an Antioquia (Colombia) population sample, in: C. Doutreme´puich, N. Morling (Eds.), Progress in Forensic Genetics, vol. 10, Elsevier, Amsterdam, 2004, pp. 275–277. [3] J.J. Builes, M.L.J. Bravo, A. Montoya, L. Caraballo, B. Martı´nez, M. Moreno, Population genetics of eight new Y-chromosomal STR haplotypes in three Colombian populations: Antioquia, Choco´ and Cartagena, in: C. Doutreme´puich, N. Morling (Eds.), Progress in Forensic Genetics, vol. 10, Elsevier, Amsterdam, 2004, pp. 310–312. [4] L. Gusma˜o, J.M. Butler, A. Carracedo, P. Gill, M. Kayser, M.R. Mayr, N. Morling, M. Prinz, L. Roewer, C. Tyler-Smith, P.M. Schneider, DNA Commission of the International Society of Forensic Genetics (ISFG): An
[20]
[21]
[22]
[23]
update of the recommendations on the use of Y-STRs in forensic analysis, Forensic Sci. Int. 21 May 2005; [Epub ahead of print]. J. Go´mez, A. Carracedo, The 1998–1999 collaborative exercises and proficiency testing program on DNA typing of the Spanish and Portuguese Working Group of the International Society for Forensic Genetics (GEPISFG), Forensic Sci. Int. 114 (2000) 21–30. L. Roewer, M. Krawczak, S. Willuweit, M. Nagy, C. Alves, A. Amorim, K. Anslinger, C. Augustin, A. Betz, E. Bosch, A. Caglia`, A. Carracedo, D. Corach, T. Dobosz, B.M. Dupuy, S. Fu¨redi, C. Gehrig, L. Gusma˜o, J. Henke, L. Henke, M. Hidding, C. Hohoff, B. Hoste, M. Jobling, H.J. Ka¨rgel, P. De Knijff, R. Lessig, E. Liebeherr, M. Lorente, B. Martı´nezJarreta, P. Nievas, M. Nowak, W. Parson, V.L. Pascali, G. Penacino, R. Ploski, B. Rolf, A. Sala, U. Schmidt, C. Schmitt, P.M. Schneider, R. Szibor, J. Teifel-Greding, M. Kayser, Online reference database of Ychromosomal short tandem repeat (STR) haplotypes, Forensic Sci. Int. 118 (2001) 103–111. M. Nei, Molecular Evolutionary Genetics, Columbia University Press, New York, USA, 1987. S. Schneider, D. Roessli, L. Excoffier, Arlequin Version 2000: A Software for Population Genetics Data Analysis, Genetics and Biometrics Laboratory, University of Geneva, Switzerland, 2000. J. Felsenstein, PHYLIP: phylogeny inference package (version 3.2), Cladistics 5 (1989) 164–166. R.D.M. Page, Treeview: an application to display phylogenetic trees on personal computers, Comput. Appl. Biosci. 12 (1996) 357–358. L. Caraballo, J. Marrugo, H. Erlich, M. Pastorizo, HLA alleles in the populations of Cartagena (Colombia), Tissue Antigens 39 (1992) 128– 133. B. Martı´nez, L. Caraballo, F. Baro´n, L. Gusma˜o, A. Amorim, A. Carracedo, Analysis of STR loci in Cartagena, a Caribbean city of Colombia, Forensic Sci. Int., 14 July 2005; [Epub ahead of print]. S. Beleza, C. Alves, A. Gonza´lez-Neira, M. Lareu, A. Amorim, A. Carracedo, L. Gusma˜o, Extending STR markers in Y chromosome haplotypes, Int. J. Leg. Med. 117 (2003) 27–33. P. Martı´n, J. Garcı´a-Hirschfeld, O. Garcı´a, L. Gusma˜o, P. Garcı´a, C. Albarra´n, M. Sancho, A. Alonso, A Spanish population study of 17 Ychromosome STR loci, Forensic Sci. Int. 139 (2004) 231–235. A.C.S. Go´es, E.F. Carvalho, I. Gomes, D.A. Silva, E.H.F. Gil, A. Amorim, L. Gusma˜o, Population and mutational analysis in 17 Y-STR loci from Rio de Janeiro (Brazil), Int. J. Legal Med. 119 (2005) 70–76. M.T. Zarrabeitia, J.A. Riancho, L. Gusma˜o, M.V. Lareu, C. San˜udo, A. Amorim, A. Carracedo, Spanish population data and forensic usefulness of a novel Y-STR set (DYS437, DYS438, DYS439, DYS460, DYS461, GATA A10, GATA C4, GATA H4), Int. J. Legal Med. 117 (2003) 306–311. C. Alves, L. Gusma˜o, J. Barbosa, A. Amorim, Evaluating the informative power of Y-STRs: a comparative study using European and new African haplotype data, Forensic Sci. Int. 134 (2003) 126–133. E. Arroyo-Pardo, L. Gusma˜o, A.M. Lo´pez-Parra, C. Baeza, M.S. Mesa, A. Amorim, Genetic variability of 16 Y-chromosome STRs in a sample from Equatorial Guinea (Central Africa), Forensic Sci. Int. 149 (2005) 109– 113. J.J. Builes, M.L. Bravo, C. Go´mez, C. Espinal, D. Aguirre, A. Go´mez, J. Rodrı´guez, P. Castan˜eda, A. Montoya, M. Moreno, A. Amorim, L. Gusma˜o, Y Chromosome STRs in an Antioquian (Colombia) population sample, Forensic Sci. Int., 7 November 2005 [Epub ahead of print]. J.J. Yunis, L.E. Acevedo, D.S. Campo, E.J. Yunis, Population data of YSTR minimal haplotypes in a sample of Caucasian-Mestizo and African descent individuals of Colombia, Forensic Sci. Int. 151 (2005) 307– 313. M. Fondevila, J.C. Jaime, A. Salas, M.V. Lareu, A. Carracedo, Y-chromosome STR haplotypes in Co´rdoba (Argentina), Forensic Sci. Int. 137 (2003) 217–220. O. Garcı´a, P. Martı´n, L. Gusma˜o, C. Albarra´n, S. Alonso, C. de la Rua, C. Flores, N. Izagirre, R. Pen˜a, J.A. Pe´rez, I. Uriarte, I. Yurrebaso, A. Alonso, A Basque Country autochthonous population study of 11 Y-chromosome STR loci, Forensic Sci. Int. 145 (2004) 65–68. G.C. Iannacone, R.Y. Tito, P.W. Lo´pez, M.E. Medina, B. Lizarraga, Y-chromosomal haplotypes for the PowerPlex Y for twelve STRs
J.J. Builes et al. / Forensic Science International 167 (2007) 62–69 in a Peruvian population sample, J. Forensic Sci. 50 (2005) 239– 242. [24] M. Kayser, M. Krawczak, L. Excoffier, P. Dieltjes, D. Corach, V. Pascali, C. Gehrig, L.F. Bernini, J. Jespersen, E. Bakker, L. Roewer, P. de Knijff, An extensive analysis of Y-chromosomal microsatellite haplotypes in globally dispersed human populations, Am. J. Hum. Genet. 68 (2001) 990–1018. [25] L. Gusma˜o, A. Amorim, N. Martins, M.J. Prata, A. Gonzalez-Neira, M.V. Lareu, A. Carracedo, Y chromosome STR haplotypes in Macau (SE
69
China), Progress in Forensic Genetics vol. 8, Elsevier Science, Amsterdam, 2000, pp. 324–326. [26] E.J. Parra, A. Marcini, J. Akey, J. Martinson, M.A. Batzer, R. Cooper, T. Forrester, D.B. Allison, R. Deka, R.E. Ferrell, M.D. Shriver, Estimating African American admixture proportions by use of population-specific alleles, Am. J. Hum. Genet. 63 (1998) 1839–1851. [27] P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.