Population data for 12 Y-chromosome STR loci in a sample from Honduras

Legal Medicine 11 (2009) 251–255

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Population data for 12 Y-chromosome STR loci in a sample from Honduras Mireya Matamoros a, Iñaki Yurrebaso b, Leonor Gusmão c, Oscar García b,* a b c

Dirección de Medicina Forense, Ministerio Público, Tegucigalpa, Honduras Basque Country Forensic Genetics Laboratory, Larrauri Mendotxe 18, 48950 Erandio, Bizkaia, Spain IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal

a r t i c l e

i n f o

Article history: Received 25 February 2009 Received in revised form 28 April 2009 Accepted 9 June 2009 Available online 22 July 2009 Keywords: Y-chromosome STR Honduras Population data

a b s t r a c t Haplotype, allele frequencies and population data of 12 Y-chromosome STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 were determined from a sample of 128 unrelated male individuals from Honduras, Central America. A total of 112 haplotypes were identified by the 12 Y-STR loci of which 98 were unique. The haplotype diversity (98.99%) and the proportion of different haplotypes (87.50%) were estimated. Genetic distances were calculated between Honduras and other populations from Southern and Central America, Europe and Africa. The analysis of a Multi Dimensional Scaling (MDS) plot, based on pairwise RST genetic distances, allowed to conclude that Honduras is highly differentiated from the African samples (0.343 6 RST 6 0.620; P = 0.000) and from a Native American sample from Argentina, Tobas (RST = 0.210, P = 0.000). Honduras showed a lower genetic distance to the European cluster (composed by European and South American general population samples from Brazil, Argentina, Colombia and Venezuela) than to the Central American cluster (Mexico and El Salvador). Ó 2009 Elsevier Ireland Ltd. All rights reserved.

Population: Samples in this study were collected from 128 unrelated healthy male individuals from the Honduras general population. Extraction: DNA was extracted by the Chelex method [1]. PCR: PCR amplifications were performed using the PowerPlex Y System (Promega Corporation) according to the manufacturers’ recommendations. Typing: Amplified products were analyzed using an ABI 310 DNA sequencer (PE-Biosystems, Foster City, CA). Allele designations were made using the allelic ladders provided with the PowerPlex Y System kit, and following the recommendations of the DNA Commission of the ISFG on Y-STR analysis [2,3]. Quality control: Proficiency testing of the GITAD (http://gitad.ugr.es/principal.htm). Results: Allele frequencies and gene diversity values are shown in Table 1 and haplotype distribution is presented in Table 2. Analysis of data: Haplotype and allele frequencies were estimated by gene counting. Gene and haplotype diversities were calculated according to Nei [4] using the ARLEQUIN ver 3.0 software [5]. Genetic distances were also computed using the same software [5], without considering DYS385 and by subtracting the number of repeats in DYS389I from DYS389II. RST genetic distances were visualized in two-dimensional space using the Multi Dimensional Scaling (MDS) method included in the StatSoft, Inc. (2007), STATISTICA (data analysis software system), ver 8.0 (www.statsoft.com). * Corresponding author. Tel.: +34 94 6079533; fax: +34 94 6079500. E-mail address: [email protected] (O. García). 1344-6223/$ - see front matter Ó 2009 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.legalmed.2009.06.001

Access of data: Available upon request to mireyam556 @yahoo.com. Other remarks: A high proportion of different haplotypes (87.50%) was observed in our sample, with a total of 112 haplotypes which 98 were unique. These 12 markers set present a high discrimination capacity of 98.99% (calculated based on the haplotype diversity). Genetic distances were calculated between Honduras and other populations from Southern and Central America, Europe and Africa to which data was available for the same set of 12 Y-STRs (Table 3). The highest RST values were found in the comparison with the African populations, and significant differences were also found with European populations. An RST P value above 5% was only observed in the comparison with a sample from Colla, a Native American community from Argentina known to have a significant influx of European male lineages [11]. Nevertheless, the RST between Honduras and Colla is higher than 2% and, therefore, the non-significant differentiation can be attributed to a low sample size of the Colla sample. For a significant level of 0.26% (after applying Bonferroni’s correction for multiple tests), Honduras could not be differentiated from the general population samples from Buenos Aires (Argentina), Rio de Janeiro (Brazil), Porto Alegre (Brazil) and Venezuela (Table 3). In the MDS plot (Fig. 1), based on pairwise RST genetic distances, Honduras stands between two groups. The first group include the European samples from Italy and Portugal, as well as Brazilian, Argentinean, Colombian and Venezuelan populations. The second group is formed by more heterogeneous samples, harbouring a higher Native American ancestry male component.

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M. Matamoros et al. / Legal Medicine 11 (2009) 251–255

Table 1 Allele frequencies and gene diversities at 12 Y-STRs in a Honduran population sample (128 individuals). Allele 9 10 11 12 13 14 15 16 17 19 21 22 23 24 25 26 28 29 30 31 32 33 NA GD (%)

DYS19

0.0089 0.0089 0.2500 0.5000 0.1429 0.0536 0.0268 0.0089

DYS389 I

DYS389 II

DYS390

DYS391 0.0714 0.5268 0.3929 0.0089

0.0890 0.1429 0.6339 0.2143

DYS392

DYS393

0.0179 0.2589 0.0179 0.4643 0.1607 0.0625 0.0179

0.1518 0.7054 0.1429

7 68.67

3 45.90

DYS437

0.0179 0.5357 0.3750 0.0536 0.0179

DYS438 0.0893 0.1518 0.2857 0.4464 0.0268

DYS439 0.0446 0.3661 0.4464 0.1339 0.0089

0.0625 0.0446 0.3125 0.4821 0.0893 0.0089

8 66.33

4 53.17

0.0804 0.3929 0.3482 0.1607 0.0089 0.0089 6 69.20

6 65.59

4 56.30

5 56.89

5 68.73

Allelic class

DYS385

Allelic class

DYS385

8/15 10/14 11/11 11/13 11/14 11/15 12/14 12/15 12/17 12/18 12/19 13/14 13/15 13/16 13/17 13/18 13/19 14/14 14/15 14/16 14/17 14/18

0.0089 0.0268 0.0089 0.0357 0.3214 0.0446 0.0179 0.0089 0.0089 0.0089 0.0089 0.0357 0.0179 0.0268 0.0179 0.0089 0.0089 0.0089 0.0446 0.0357 0.0446 0.0268

14/19 15/16 15/17 15/18 15/19 16/16 16/17 16/18 16/19 17/17

0.0089 0.0357 0.0089 0.0089 0.0089 0.0268 0.0357 0.0714 0.0089 0.0089

5 64.67

32 87.42

NA, number of alleles/allele classes; GD, Gene Diversity estimated according to Nei [4].

Table 2 List of 112 haplotypes detected in 128 unrelated males from Honduras. Haplotypes

DYS19

DYS385

DYS389I

DYS389II

DYS390

DYS391

DYS392

DYS393

DYS437

DYS438

DYS439

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

11 12 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 14 14 14 14 14 14 14 14 14 14

15/16 16/18 12/18 13/14 13/14 13/14 13/15 13/17 14/15 14/16 14/16 14/16 14/17 14/17 14/17 14/18 14/18 14/18 14/19 15/17 15/18 16/16 16/17 16/17 16/17 16/18 16/18 16/18 16/18 16/19 8/15 10/14 10/14 10/14 11/11 11/13 11/13 11/13 11/13 11/14

13 13 13 13 13 14 14 14 14 13 13 14 13 14 14 13 13 14 13 13 13 13 13 13 14 12 13 13 14 13 13 12 12 13 13 12 13 13 13 12

30 30 30 29 31 30 30 30 30 30 30 31 31 30 31 29 30 30 29 29 30 30 30 31 31 29 30 32 33 30 30 28 29 29 29 29 29 29 29 28

23 24 24 24 24 24 23 23 25 23 24 24 24 23 23 23 25 23 25 22 23 24 24 24 24 24 24 24 24 24 23 24 24 24 23 25 24 25 26 24

10 10 10 9 10 9 9 10 10 11 11 9 10 10 10 11 9 10 10 11 10 10 10 10 9 10 10 10 10 10 11 11 11 11 10 11 11 10 11 11

14 16 15 11 15 11 11 14 14 14 14 15 15 14 13 14 15 14 15 14 14 11 15 14 11 11 11 14 14 11 13 13 13 13 13 14 13 13 13 13

13 13 13 13 14 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 14 14 14 13 13 13 13 13 13 13 13 13 13 13 13 12 13 13

14 14 14 14 14 14 14 14 14 14 15 14 13 15 14 14 14 14 13 15 14 14 14 14 14 14 14 14 14 14 15 15 15 14 15 15 15 15 15 15

11 11 11 10 11 12 10 11 11 11 11 11 11 11 11 11 11 11 11 9 11 10 11 11 9 10 10 11 11 10 12 12 12 12 12 12 12 12 12 12

12 11 11 10 13 10 10 13 11 11 11 11 12 11 13 12 12 13 12 12 12 11 11 12 11 12 12 12 12 12 12 12 12 11 13 12 12 13 12 10

1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 2

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M. Matamoros et al. / Legal Medicine 11 (2009) 251–255 Table 2 (continued) Haplotypes

DYS19

DYS385

DYS389I

DYS389II

DYS390

DYS391

DYS392

DYS393

DYS437

DYS438

DYS439

N

H41 H42 H43 H44 H45 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 H97 H98 H99 H100 H101 H102 H103 H104 H105 H106 H107 H108 H109 H110 H111 H112

14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 16 16 16 16 16 16 17 17 17 19

11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/14 11/15 11/15 11/15 11/15 12/14 12/14 12/15 12/19 13/14 13/16 13/16 13/17 13/18 13/19 14/14 14/17 15/16 16/17 11/14 11/14 11/14 11/14 11/14 11/15 12/17 13/15 13/16 14/15 14/15 14/17 15/16 15/19 16/18 17/17 11/14 11/14 14/15 15/16 16/16 16/18 14/16 16/16 16/18 14/15

13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 14 14 14 14 14 14 13 14 14 14 13 14 13 13 12 12 13 13 13 13 13 13 13 14 12 13 13 13 14 14 12 13 12 12 13 13 13 12 13 13 12 13 12 12 11 13 12 13 13 14

28 29 29 29 29 29 29 29 29 29 29 29 29 29 29 29 29 29 30 31 31 31 29 30 30 30 30 30 28 30 31 31 29 31 30 29 28 29 31 30 30 29 29 31 31 30 28 29 29 30 30 30 30 30 29 29 30 29 30 28 31 30 28 29 29 29 28 30 29 30 31 31

24 23 23 23 23 23 23 24 24 24 24 24 24 24 24 24 24 25 24 24 24 25 23 23 23 24 24 25 24 25 24 24 25 24 22 23 23 24 24 23 23 23 23 24 24 23 24 23 24 24 23 24 23 23 23 23 22 24 21 24 21 21 24 24 23 22 21 21 22 21 21 23

11 10 10 10 11 11 11 10 10 11 11 11 11 11 11 11 11 10 11 10 11 11 11 10 10 11 12 11 10 11 11 11 10 10 10 10 10 10 10 10 10 10 10 10 10 10 11 11 11 11 11 11 10 11 10 10 9 10 10 10 10 11 11 10 11 9 10 10 10 10 11 10

13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 12 13 13 13 14 13 13 13 13 13 13 14 13 13 13 13 13 11 11 11 14 13 11 11 11 11 11 13 14 13 13 13 13 13 13 11 11 11 11 11 11 11 11 10 11 13 13 12 11 16 11 11 11 10 13

13 12 13 14 13 13 13 12 13 13 13 13 13 13 14 14 14 13 13 14 13 13 13 13 13 13 13 13 12 13 13 13 14 13 12 12 13 13 12 12 12 13 13 12 13 12 13 13 12 13 13 13 12 12 12 14 13 13 14 12 13 13 13 13 12 13 13 14 14 14 14 13

15 15 16 15 14 15 15 15 15 14 14 15 15 15 14 15 15 15 15 14 14 15 14 14 15 14 15 14 15 15 14 15 14 14 15 14 16 14 14 14 14 14 16 14 14 16 15 15 15 14 15 14 15 14 15 16 14 14 14 16 14 14 15 15 14 17 15 14 17 14 14 14

12 12 12 12 12 12 12 12 13 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 9 10 10 11 12 10 9 10 10 10 11 10 12 12 12 11 12 13 9 9 9 10 10 11 11 9 11 11 12 12 10 9 11 11 10 11 11 9

12 11 12 14 12 11 12 11 13 12 13 11 12 12 13 11 12 13 11 12 12 11 11 11 13 11 12 12 13 12 12 11 11 12 11 13 11 12 12 11 11 12 12 11 12 11 11 12 12 11 11 12 11 11 10 12 11 11 12 12 13 11 12 12 12 13 11 12 12 11 11 11

1 1 1 1 1 2 2 1 1 2 1 2 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 2 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

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Table 3 Genetic distances (RST) between Honduras and other population samples from Europe, America and Africa. Honduras versus

N

Reference

Rst

P value

Italy – Northeast Austria Portugal Spain – Basque Country Argentina – Buenos Aires Argentina – Colla (Amerindian) Argentina – Tobas (Amerindian) Brazil – Rio de Janeiro Brazil Brazil – Porto Alegre Brazil – Rio de Janeiro (African descendents) Colombia – Cartagena Venezuela Bolivia – El Beni (Amerindian) El Salvador Mexico – Mexico City (Mestizo) Equatorial Guinea Mozambique Angola – Cabinda

155 134 617 168 98 29 49 167 98 99 135 173 173 87 63 357 99 112 72

Turrina et al. [6] Berger et al. [7] Alves et al. [8]; Sánchez-Diz et al. [9] García et al. [10] Sánchez-Diz et al. [9] Toscanini et al. [11] Toscanini et al. [11] Góes et al. [12]; Sánchez-Diz et al. [9] Sánchez-Diz et al. [9] Sánchez-Diz et al. [9] Domingues et al. [13] Builes et al. [14] Borjas et al. [15] Tirado et al. [16] Lovo-Gómez et al. [17] Luna-Vázquez et al. [18] Arroyo-Pardo et al. [19] Alves et al. [20] Alves et al. [20]

0.0521 0.1041 0.0249 0.0549 0.0149 0.0214 0.2099 0.0181 0.0306 0.0167 0.0774 0.0315 0.0184 0.1083 0.0336 0.0272 0.3430 0.6201 0.3835

0.0000 ± 0.0000 0.0000 ± 0.0000 0.0000 ± 0.0000 0.0000 ± 0.0000 0.0183 ± 0.0013* 0.0584 ± 0.0024* 0.0000 ± 0.0000 0.0030 ± 0.0006* 0.0000 ± 0.0000 0.0122 ± 0.0011* 0.0000 ± 0.0000 0.0000 ± 0.0000 0.0031 ± 0.0005* 0.0000 ± 0.0000 0.0000 ± 0.0000 0.0000 ± 0.0000 0.0000 ± 0.0000 0.0000 ± 0.0000 0.0000 ± 0.0000

*

Non-significant (P P 0.0026).

0.8

Austria

Angola

0.6

Italy 0.4 0.2

Portugal Brazil-RJ Brazil Argentina-BA Colombia-Ca Brazil-PA Brazil-ARJ Venezuela

0.0

Dimension 2

Equatorial Guinea

Spain-Basques

Honduras

-0.2

Mexico -0.4 -0.6

Argentina-Colla

El Salvador Bolivia

-0.8 -1.0

Mozambique

-1.2

Argentina-Tobas -1.4 -1.6 -1.5

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

2.5

3.0

Dimension 1 Fig. 1. MDS plot based on population pairwise RST values from haplotype data from Honduras (present study) and from all populations included in Table 3 (Refs. [6–20]).

From this study results, we can conclude that, from the male background perspective, Honduras population is significantly different from other Latin American populations due to its Native American genetic ancestry: (i) lower in comparison to other Central American populations (namely, Mexico and El Salvador) (ii) but higher in comparison to non-Native South American populations (namely, general populations from Buenos Aires, Rio de Janeiro, Porto Alegre, Venezuela and Cartagena). This Y-STR database has complemented previous autosomal STR markers information [21] and is very useful, particular in rape and mixed samples cases. References [1] Walsh PS, Metzger DA, Higuchi R. ChelexÒ 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 1991;10:506–13. [2] Gill P, Brenner C, Brinkmann B, Budowle B, Carracedo A, Jobling MA, et al. DNA Commission of the International Society of Forensic Genetics: recommendations on forensic analysis using Y-chromosome STRs. Int J Legal Med 2001;114:305–9.

[3] Gusmão L, Butler JM, Carracedo A, Gill P, Kayser M, Mayr WR, et al. DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis. Forensic Sci Int 2006;157:187–97. [4] Nei M. Molecular evolutionary genetics. New York, USA: Columbia University Press; 1987. [5] Excoffier L, Laval G, Schneider S. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 2005;1:47–50. [6] Turrina S, Atzei R, De Leo D. Y-chromosomal STR haplotypes in a Northeast Italian population sample using 17plex loci PCR assay. Int J Legal Med 2006;120:56–9. [7] Berger B, Lindinger A, Niederstätter H, Grubwieser P, Parson W. Y-STR typing of an Austrian population sample using a 17-loci multiplex PCR assay. Int J Legal Med 2005;119:241–6. [8] Alves C, Gomes V, Prata MJ, Amorim A, Gusmão L. Population data for Ychromosome haplotypes defined by 17 STRs (AmpFlSTR YFiler) in Portugal. Forensic Sci Int 2007;171:250–5. [9] Sánchez-Diz P, Alves C, Carvalho E, Carvalho M, Espinheira R, Garcia O, et al. Population and segregation data on 17 Y-STRs: results of a GEP-ISFG collaborative study. Int J Legal Med 2008;122:529–33. [10] García O, Martín P, Gusmão L, Albarrán C, Alonso S, De la Rua C, et al. A Basque Country autochthonous population study of 11 Y-chromosome STR loci. Forensic Sci Int 2004;145:65–8. [11] Toscanini U, Gusmão L, Berardi G, Amorim A, Carracedo A, Salas A, et al. Y chromosome microsatellite genetic variation in two Native American

M. Matamoros et al. / Legal Medicine 11 (2009) 251–255

[12]

[13]

[14]

[15]

[16]

populations from Argentina: population stratification and mutation data. Forensic Sci Int Genet 2008;2:274–80. Góes ACS, Carvalho EF, Gomes I, Silva DA, Gil EHF, Amorim A, et al. Population and mutational analysis in 17 Y-STR loci from Rio de Janeiro (Brazil). Int J Legal Med 2005;119:70–6. Domingues PM, Gusmão L, Aparecida da Silva D, Amorim A, Pereira RW, Carvalho EF. Sub-Saharan Africa descendents in Rio de Janeiro (Brazil): population and mutational data for 12 Y-STR loci. Int J Legal Med 2007;121:238–41. Builes JJ, Martínez B, Gómez A, Caraballo L, Espinal C, Aguirre D, et al. Y Chromosome STR haplotypes in the Caribbean city of Cartagena (Colombia). Forensic Sci Int 2007;167:62–9. Borjas L, Bernal LP, Chiurillo MA, Tovar F, Zabala W, Lander N, et al. Usefulness of 12 Y-STRs for forensic genetics evaluation in two populations from Venezuela. Legal Med 2008;10:107–12. Tirado M, López-Parra AM, Baeza C, Bert F, Corella A, Pérez-Pérez A, et al. Ychromosome haplotypes defined by 17 STRs included in AmpFlSTR Yfiler PCR

[17] [18]

[19]

[20]

[21]

255

Amplification Kit in a multi ethnical population from El Beni Department (North Bolivia). Legal Med 2009;11:101–3. Lovo-Gómez J, Blanco-Verea A, Lareu MV, Brión M, Carracedo A. The genetic male legacy from El Salvador. Forensic Sci Int 2007;171:198–203. Luna-Vázquez A, Vilchis-Dorantes G, Aguilar-Ruiz MO, Bautista-Rivas A, PérezGarcía A, Orea-Ochoa R, et al. Haplotype frequencies of the PowerPlex Y system in a Mexican-Mestizo population sample from Mexico City. Forensic Sci Int Genet 2008;2:e11–13. Arroyo-Pardo E, Gusmão L, López-Parra AM, Baeza C, Mesa MS, Amorim A. Genetic variability of 16 Y-chromosome STRs in a sample from Equatorial Guinea (Central Africa). Forensic Sci Int 2005;149:109–13. Alves C, Gusmão L, Barbosa J, Amorim A. Evaluating the informative power of Y-STRs: a comparative study using European and new African haplotype data. Forensic Sci Int 2003;134:126–33. Matamoros M, Silva S, García O. Population data on nine short tandem repeat loci and D1S80 in a sample from Honduras. Forensic Sci Int 2004;141:39–40.