Announcement of population data

Y-chromosome STR haplotypes in theAcores Archipelago (Portugal)

Ana Fernandes, Antonio Brehm*

Human Genetics Laboratory, Centre of Macaronesian Studies, University of Madeira,

Campus of Penteada, 9000-390 Funchal, Portugal

Received 10 April 2003; received in revised form 30 April 2003; accepted 6 May 2003

Abstract

Allele and haplotype frequencies of 10 Y-chromosome STR loci were co-amplified in a sample from the Acores Islands

(Portugal). We found high haplotype diversity in the Acores sample (0.998). The genetic profile of this population revealed to be

statistically different from that of Madeira Island and from North Portugal, two related populations with already a fairly amount

of published data. This result stresses the importance of using local databases in forensic genetics.

# 2003 Elsevier Ireland Ltd. All rights reserved.

Keywords: STR; Population data; Y chromosome; Acores Islands

Population: 100 unrelated army volunteer donors from

the Acores Archipelago. The subjects were interviewed in

order to select those whose ancestors from the paternal

lineage back to the third generation were known to be

originally from the same island. This way we can be confident

that this sample represents a fraction of the autochthonous

population.

Extraction: Chelex method.

PCR: Co-amplification of Y chromosome STR markers

was done with Y-Plex kits from Reliagene Corp., following

the manufacturer instructions.

Typing: Typing was achieved using an ABI Prism 310

automatic sequencer (PE Biosystems).

Results: Tables 1 and 2.

Quality control: Proficiency testing of the GEP-ISFG

WG; http://www.gep.usc.es.

Analysis of data: Allele frequencies determined by direct

gene counting. Gene and haplotype diversities estimated

with GENEPOP [7] and Arlequin v.2000 [8]. Published

pertinent data was used for comparisons (Madeira Island

[2], Portugal [5], Europe database [9]).

Access to the data: brehm@uma.pt.

Other remarks: Data on Y-chromosome STRs from

Iberian and Iberian-related populations started recently to

appear in the literature [1–6]. These works serve not only as

databases for forensics purposes but in many instances they

have uncovered important differences in the genetic compo-

sition of populations that otherwise one would expect them to

be identical [1]. We have analysed Y-data from the Acores

and compare it with those populations one would assume

to be the closest: Portugal and Madeira. Three loci showed

significant differences between populations of Acores

and Madeira (DYS390, P < 0:04; DYS391, P < 0:0001;

DYS392, P < 0:02). The Acores also show significant dif-

ferences with the North of Portugal at DYS391 and DYS393

(P < 0:001). The 100 individuals wielded 92 unique haplo-

types, five found twice and one was found in four individuals.

This is the reason for the high haplotype diversity observed

(0.998). If one uses only seven loci (those common to

Madeira [1] and Portugal [2] DYS19, DYS389I, DYS389II,

DYS390, DYS391, DYS392 and DYS393), the haplotype

diversity decreases to just 0.991, recovering 71 unique hap-

lotypes. This indicates that the use of both Y-PLEXTM5 and

Y-PLEXTM6 may indeed be redundant for forensic purposes,

at least in these populations. In fact the population from

Madeira was typed for seven markers with an average

diversity of 0.975. Comparing the haplotype frequencies

from the Acores and either Madeira or Portugal we obtain

Forensic Science International 135 (2003) 239–242

* Corresponding author. Tel.: þ351-1291-705383;

fax: þ351-291-705399.

E-mail address: brehm@uma.pt (A. Brehm).

0379-0738/$ – see front matter # 2003 Elsevier Ireland Ltd. All rights reserved.

doi:10.1016/S0379-0738(03)00202-0

Table 1

Allele frequencies and gene diversity value at 10 Y-chromosome STR loci in the Acores Archipelago population

Allele DYS19 DYS389I DYS389II DYS390 DYS391 DYS392 DYS393 DYS438 DYS439 Haplotype DYS385

8 8/11 0.01

9 0.040 0.160 0.010 10/14 0.01

10 0.220 0.040 0.220 0.040 11/11 0.01

11 0.740 0.330 0.030 0.090 0.460 11/13 0.03

12 0.200 0.060 0.290 0.520 0.400 11/14 0.39

13 0.140 0.590 0.540 0.560 0.010 0.090 11/15 0.01

14 0.590 0.210 0.030 0.100 11/16 0.01

15 0.220 0.070 0.020 12/12 0.01

16 0.040 0.590 12/13 0.02

17 0.010 0.250 12/14 0.08

18 0.080 12/15 0.02

19 0.010 12/17 0.01

21 0.070 12/19 0.02

22 0.080 13/13 0.05

23 0.250 13/14 0.04

24 0.440 13/15 0.07

25 0.140 13/16 0.01

26 0.020 13/17 0.03

13/18 0.04

14/14 0.02

14/15 0.01

14/17 0.01

15/15 0.01

15/16 0.01

16/16 0.02

16/17 0.03

17/18 0.02

h 0.588 0.573 0.584 0.719 0.406 0.599 0.597 0.654 0.625 0.836

Table 2

List of 92 Y-chromosome STR haplotypes detected in 100 unrelated males from the Acores Islands on the basis of the 10 selected markers

Haplotypes DYS19 DYS389I DYS389II DYS390 DYS391 DYS392 DYS393 DYS385 DYS438 DYS439 N

H1 13 12 29 24 11 10 13 11-14 11 11 1

H2 13 12 30 25 11 11 13 11-14 11 10 1

H3 13 12 30 25 11 11 13 17-18 10 11 2

H4 13 13 28 25 11 11 11 13-18 9 11 1

H5 13 13 29 23 10 11 13 13-17 9 11 1

H6a 13 13 29 24 9 11 13 13-14 10 10 1

H7 13 13 30 22 11 13 13 12-14 12 11 1

H8 13 13 30 23 11 11 14 16-17 10 12 1

H9 13 13 31 24 10 10 13 16-16 10 11 1

H10 13 13 31 24 10 11 14 16-16 10 12 1

H11 13 14 30 21 11 12 13 13-14 12 11 1

H12 13 14 30 22 11 13 13 13-16 9 11 1

H13 13 14 30 24 9 11 12 13-14 10 10 1

H14 14 12 28 21 11 11 13 13-15 10 11 1

H15a 14 12 28 24 11 13 13 11-14 13 11 1

H16a 14 12 28 24 11 13 13 11-14 12 12 1

H17b 14 12 28 24 11 13 13 10-14 12 11 1

H18a 14 12 28 24 11 13 13 12-14 12 12 1

H19 14 12 28 25 11 11 13 13-14 10 11 1

H20b 14 13 28 23 11 13 13 11-14 12 12 1

H21a 14 13 29 22 11 13 13 11-14 12 11 1

H22a 14 13 29 22 11 13 13 11-14 12 12 1

240 A. Fernandes, A. Brehm / Forensic Science International 135 (2003) 239–242

Table 2 (Continued )

Haplotypes DYS19 DYS389I DYS389II DYS390 DYS391 DYS392 DYS393 DYS385 DYS438 DYS439 N

H23b 14 13 29 23 11 11 12 13-18 9 11 1

H24b 14 13 29 23 11 11 12 13-18 9 12 1

H25b 14 13 29 23 11 13 12 11-14 12 11 2

H26 14 13 29 23 11 13 12 12-13 12 11 1

H27a 14 13 29 23 11 13 13 11-14 12 12 4

H28a,c 14 13 29 23 11 13 13 12-14 12 11 1

H29 14 13 29 24 10 10 13 11-14 12 11 1

H30a,c 14 13 29 24 10 13 13 11-14 12 12 1

H31c 14 13 29 24 10 13 13 11-16 12 12 1

H32c 14 13 29 24 11 13 12 11-13 12 11 1

H33a 14 13 29 24 11 13 12 11-14 11 12 1

H34a 14 13 29 24 11 13 12 11-14 12 13 1

H35a,c 14 13 29 24 11 13 13 11-14 10 13 1

H36a,c 14 13 29 24 11 13 13 11-14 12 12 1

H37 14 13 29 24 11 13 13 8-11 12 12 1

H38a 14 13 29 24 11 13 14 11-14 12 12 1

H39 14 13 29 25 10 11 11 13-13 9 11 1

H40a 14 13 29 25 11 13 13 11-14 12 11 1

H41b 14 13 30 23 11 11 12 13-18 10 11 1

H42b 14 13 30 23 11 13 12 11-14 11 12 1

H43b 14 13 30 23 11 13 13 12-14 12 12 2

H44b 14 13 30 23 11 14 13 11-14 12 12 1

H45b 14 13 30 24 10 13 14 11-14 12 12 1

H46a 14 13 30 24 11 13 13 11-14 12 12 1

H47a 14 13 30 24 11 13 13 12-14 12 13 1

H48 14 13 30 25 11 13 13 13-13 12 11 1

H49b 14 13 30 25 11 13 13 11-14 12 11 1

H50b 14 13 30 25 11 13 13 11-14 12 12 1

H51 14 13 30 26 11 12 12 13-13 9 12 1

H52 14 13 32 23 10 11 12 13-17 9 9 1

H53 14 14 29 23 10 10 12 11-14 12 11 1

H54 14 14 29 23 11 13 12 14-17 9 11 1

H55 14 14 30 24 10 13 14 11-13 12 11 1

H56b 14 14 30 24 11 13 12 11-14 12 12 2

H57c 14 14 30 24 11 13 12 12-15 11 11 1

H58a,c 14 14 30 24 11 13 13 11-14 12 13 1

H59a,c 14 14 30 24 11 13 13 11-14 12 12 1

H60 14 14 30 24 11 13 13 14-15 9 13 1

H61 14 14 30 24 11 14 13 12-13 12 12 1

H62 14 14 30 24 11 14 13 13-13 12 12 1

H63 14 14 30 25 9 13 13 11-11 12 12 1

H64 14 14 31 24 11 11 12 13-15 9 11 2

H65 14 14 31 24 11 13 12 11-14 12 12 1

H66 15 12 28 21 10 11 12 13-15 11 11 1

H67 15 12 28 21 11 12 14 11-13 10 11 1

H68 15 12 28 24 10 11 11 13-15 9 12 1

H69 15 12 28 24 11 11 12 12-17 9 12 1

H70 15 12 28 26 11 12 13 13-15 10 12 1

H71a 15 12 29 21 10 11 15 13-17 9 11 1

H72 15 12 29 21 11 11 14 13-15 10 11 1

H73b 15 12 29 22 10 11 14 12-14 10 13 1

H74 15 12 30 23 11 13 13 11-14 12 13 1

H75 15 13 28 24 11 13 13 14-14 12 11 1

H76 15 13 29 22 10 11 12 12-19 10 11 1

H77 15 13 29 22 10 11 13 12-19 10 11 1

H78b 15 13 29 23 10 11 12 13-13 11 11 1

H79a 15 13 29 23 11 13 13 11-14 12 13 1

H80 15 13 29 24 10 13 13 14-14 12 11 1

A. Fernandes, A. Brehm / Forensic Science International 135 (2003) 239–242 241

statistically significant differences (P < 0:0001). A compar-

ison of our data with a Y-STR Europe database [5], and thus

excluding DYS438 and DYS439, allows additional infer-

ences: 18 haplotypes are found in mainland Portugal (only

four are common to Madeira), and 18 do not exist in Portugal

but appear in Europe mainly in Germany and Italy (see

Table 2). Finally, the kits used are wrongly labelled for

DYS391, DYS389I, DYS439 and DYS392 in which concerns

particular fragment size lengths. In the 4 loci mentioned, all

fragments in the range of 250 pb length have 4 base pairs

more then stated in the manual.

References

[1] M. Aler, A. Salas, P. Sanchez-Diz, A. Carracedo, M. Gisbert,

E Murcia, Y-chromosome STR haplotypes from a Western

Mediterranean population sample, Forensic Sci. Int. 119 (2001)

254–257.

[2] A. Fernandes, A. Brehm, L. Gusmao, A. Amorim, Y

chromosome STR haplotypes in the Madeira Archipelago

population, Forensic Sci. Int. 122 (2001) 178–180.

[3] J.J. Gamero, J.L. Romero, J.L. Gonzalez, M. Carvalho, M.J.

Anjos, F.C. Real, M.C. Vide, Y-chromosome STR haplotypes

in a southwest Spain population sample, Forensic Sci. Int. 125

(2002) 86–89.

[4] A. Gonzalez-Neira, L. Gusmao, M. Brion, M.V. Lareu, A.

Amorim, A. Carracedo, Distribution of Y-chromosome STR

defined haplotypes in Iberia, Forensic Sci. Int. 110 (2000)

117–126.

[5] L. Gusmao, C. Alves, S. Beleza, A. Amorim, Forensic

evaluation and population data on the new Y-STRs DYS434,

DYS437, DYS438, DYS439 and GATA A100, Int. J. Legal

Med. 116 (2002) 139–147.

[6] B. Quintans, S. Beleza, M. Brion, P. Sanchez-Diz, M. Lareu,

A. Carracedo, Population data of Galicia (NW Spain) on the

new Y-STRs DYS437, DYS438, DYS439, GATA A10, GATA

A7.1, GATA A7.2, GATA C4 and GATA H4, Forensic Sci. Int.

131 (2003) 220–224.

[7] M. Raymond, F. Rousset, GENEPOP, J. Heredity 86 (1995)

248–249.

[8] S. Schneider, J.-M. Kueffer, D. Roessli, L. Excoffier, Arlequin:

A Software for Population Genetic Data Analysis, Genetics

and Biometry Laboratory, University of Geneva, Switzerland,

2000.

[9] http://ystr.charite.de/index_gr.html.

Table 2 (Continued )

Haplotypes DYS19 DYS389I DYS389II DYS390 DYS391 DYS392 DYS393 DYS385 DYS438 DYS439 N

H81a 15 13 29 24 10 13 13 11-14 12 12 1

H82 15 13 29 24 11 11 12 16-17 9 13 1

H83 15 13 29 25 9 11 12 12-12 10 11 1

H84a 15 13 30 24 10 12 15 15-15 10 11 1

H85b 15 13 30 24 11 13 13 11-14 12 12 1

H86 15 13 30 24 11 13 14 11-15 12 12 1

H87 15 14 29 24 11 13 12 11-14 12 11 1

H88 16 12 27 22 10 11 12 12-14 10 11 1

H89 16 13 29 23 11 11 13 15-16 10 11 1

H90b 16 13 31 25 11 11 14 11-14 11 10 1

H91 16 14 31 21 11 11 13 16-17 11 12 1

H92 17 14 32 25 11 12 13 12-15 10 12 1

GD 0.998

H is the haplotype, N is the number of individuals observed with that haplotype, GD is the genotype diversity.a Haplotypes appearing in mainland Portugal.b Haplotypes appearing in Europe.c Haplotypes appearing in Madeira Island.

242 A. Fernandes, A. Brehm / Forensic Science International 135 (2003) 239–242