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FSIGEN-489; No of Pages 4 Forensic Science International: Genetics xxx (2009) xxx–xxx
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Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig
Announcement of Population Data
Nilotes from Karamoja, Uganda: Haplotype data defined by 17 Y-chromosome STRs Vero´nica Gomes a,b,*, Cı´ntia Alves a, Anto´nio Amorim a,c, A´ngel Carracedo b, Paula Sa´nchez-Diz b, Leonor Gusma˜o a a b c
Institute of Molecular Pathology and Immunology of University of Porto (IPATIMUP), Porto, Portugal Institute of Legal Medicine, Genomics Medicine Group, University of Santiago de Compostela, Spain Faculty of Sciences, University of Porto, Portugal
A R T I C L E I N F O
A B S T R A C T
Article history: Received 17 June 2009 Accepted 2 July 2009 Available online xxx
In this work 118 Nilote male samples were genotyped from Karamoja region, in Northeast Uganda, through 17 Y-chromosomal short tandem repeats (STRs)—DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1. A total of 94 different haplotypes were found, where 19 were shared by at least two individuals, and haplotype diversity amounted to 0.9958 0.0017. When considering only the nine Y-STRs included in the minimal haplotype (YHRD) the haplotype diversity decreased to 0.9807 0.0048, a similar value to those found in other African populations such as Mozambique, Angola and Guinea-Bissau. Population comparisons were performed between our sample and nine other African populations. Significant Rst genetic distances were obtained between the Nilote population from Karamoja and all African populations used for comparison, except Xhosa sample from South Africa. In the multidimensional scaling (MDS) plot, the Karamoja sample is well separated from all other populations, standing between the Ethiopia and the Bantu samples, although closer to this last group. ß 2009 Elsevier Ireland Ltd. All rights reserved.
Keywords: Y-STRs Yfiler Nilotes Karamoja Uganda
Population: The samples used in this work were obtained with informed consent from 118 unrelated males. All these individuals are pastoralists and speak a Nilotic language. In a previous study by Gusma˜o et al. [1], 40 males included in this work were typed for YSTRs, but only for the 12 Y-STRs included in PowerPlex1 Y Systems (Promega). These samples were also studied for autosomal and Xchromosome STR markers [2,3]. Extraction: Previously described in Gomes et al. [2]. PCR: The PCR was performed using AmpFlSTR Yfiler PCR amplification kit (Applied Biosystems, Foster city, CA, USA), following manufacturer’s recommendations. Typing: Typing was achieved using an ABI 3130 Genetic Analyser (Applied Biosystems). The amplified products were compared with reference sequenced ladders provided by the manufacturer (Applied Biosystems) and the analysis was performed using GeneMapper1 ID Software v3.2. Allele’s designation for GATA H4.1 locus is in accordance to the ISFG recommendations [4].
* Corresponding author at: IPATIMUP, R. Dr. Roberto Frias, s/n. 4200-465 Porto, Portugal. Tel.: +351 225570700; fax: +351 225570799. E-mail address:
[email protected] (V. Gomes).
Results: The haplotype data are presented in Table 1. Pairwise genetic distances (Rst) and corresponding P values are presented in Table 2. Quality control: Proficiency testing of the GEP-ISFG working group (http://www.gep-isfg.org). YHRD: The Y-STR haplotype data for Karamoja population was deposited in the Y Chromosome Haplotype Reference Database (YHRD.ORG3.0—www.yhrd.org) [5], with the accession number YA003498 and population ID YP000551 (www.yhrd.org/ YP000551). Analysis of data: Haplotype diversity in our population was calculated with Arlequin v3.11 software [6]. The pairwise genetic distances (Rst) and P values were determined with the online AMOVA tool available at the YHRD.ORG3.0 [5]. For population comparison purposes only seven loci were considered (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, and DYS393), those common to all populations from Karamoja (present study), Cape Town, South Africa (Xhosa, Bantu) [7], Mozambique (general population, Bantu) [8], Guinea-Bissau (general population, Atlantic and Mande) [9], Cabinda, Angola (general population, Bantu; in YHRD), Equatorial Guinea (general population, Bantu) [10], Cameroon (unidentified, in YHRD), Ethiopia (Amharic; in YHRD),
1872-4973/$ – see front matter ß 2009 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigen.2009.07.001
Please cite this article in press as: V. Gomes, et al., Nilotes from Karamoja, Uganda: Haplotype data defined by 17 Y-chromosome STRs, Forensic Sci. Int. Genet. (2009), doi:10.1016/j.fsigen.2009.07.001
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Table 1 Y-STR Haplotypes found in Karamoja sample (N = 118). Hap
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 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
DYS
DYS
DYS
DYS
DYS
DYS
DYS
DYS
DYS
DYS
DYS
DYS
DYS
DYS
DYS
YGATA
19
389I
389II
390
391
392
393
385
438
439
437
448
456
458
635
H4.1
15 15 16 15 15 14 15 16 13 15 14 15 15 15 13 11 16 14 15 15 15 15 15 15 15 15 15 13 16 14 16 14 15 13 15 15 15 13 15 15 15 15 14 16 14 16 15 15 15 13 13 13 16 16 15 15 15 15 15 15 15 15 15 15 15 15 15 15 16 15 16 15 16 16
12 12 13 12 14 12 13 13 13 13 13 12 13 13 13 13 13 12 12 14 14 13 12 14 13 12 13 13 14 13 13 13 13 13 14 13 13 13 13 14 13 13 13 13 13 14 12 14 13 14 13 13 14 13 13 13 13 12 14 12 13 12 13 13 13 12 12 13 13 14 13 12 13 13
29 29 31 28 32 31 30 30 30 30 30 31 30 32 30 30 32 28 30 31 31 30 30 33 30 31 30 30 31 29 30 29 30 30 32 29 29 30 32 31 29 31 29 30 29 31 30 32 30 31 30 30 31 30 30 32 31 30 31 31 32 30 30 30 30 31 30 30 31 31 30 30 32 30
22 22 24 22 24 24 21 22 22 21 21 22 21 24 24 24 24 25 24 21 22 21 24 24 21 26 21 22 23 25 21 24 21 22 24 21 21 24 21 21 21 21 25 21 25 23 22 24 21 24 24 22 23 21 21 24 24 22 22 21 24 24 21 21 21 22 23 21 21 21 21 23 24 21
9 9 10 9 10 10 10 10 11 9 9 9 9 10 10 10 10 10 11 9 10 9 10 10 9 11 9 9 11 9 9 9 9 11 10 9 9 10 10 9 9 10 9 9 9 11 9 10 9 11 10 11 11 10 9 10 10 9 10 10 10 11 9 9 9 10 10 9 10 9 10 10 10 9
11 11 12 11 11 11 11 11 11 11 11 11 11 12 11 12 12 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11 12 11
13 13 13 13 13 13 13 15 13 15 16 13 15 14 13 13 13 13 12 14 13 15 13 14 15 13 14 13 14 13 13 13 15 13 13 15 16 14 13 15 16 14 13 15 13 14 13 13 15 14 14 13 14 15 15 14 13 13 13 13 13 13 15 15 16 13 13 16 14 15 15 13 13 13
12–13 12–13 10–12 12–13 11–11 14–15 16–16 17–17 10–12 12–15 12–13 12–14 12–12 11–11 16–16 16–19 10–12 15–19 15–15 12–13 15–17 12–13 11–11 11–11 12–13 15–15 12–13 14–15 11–13 11–15 11–12 11–17 12–13 10–12 11–11 12–13 12–13 16–16 17–17 12–12 12–13 17–17 11–16 12–13 11–16 11–13 12–14 11–11 12–13 16–17 14–16 10–12 11–12 17–18 12–13 11–11 11–11 12–13 15–17 16–17 10–12 15–16 12–13 12–13 12–14 15–15 15–16 13–14 17–17 12–12 17–18 15–16 10–12 12–12
10 10 10 10 10 11 11 11 10 10 10 10 10 10 10 11 10 11 11 10 11 10 10 10 10 11 10 10 10 13 11 13 10 10 10 10 10 10 12 10 10 11 13 10 13 10 10 10 10 10 10 10 10 11 10 10 10 10 11 12 10 11 10 10 10 11 11 10 11 10 11 11 10 10
12 12 10 12 11 11 11 12 11 11 11 11 10 11 12 11 10 11 11 11 13 11 12 11 11 11 11 11 11 12 12 11 11 11 13 11 11 12 12 11 12 13 12 11 12 11 11 12 11 11 12 12 11 12 10 11 11 12 12 11 10 12 12 10 11 12 12 11 13 11 11 12 11 13
15 15 16 15 15 16 14 14 14 16 16 15 16 15 14 14 16 14 16 16 14 16 15 15 16 14 16 14 15 14 15 14 16 14 15 16 16 14 14 16 16 14 14 16 14 15 15 15 16 14 14 14 15 14 16 15 15 15 14 14 16 15 16 16 16 15 14 16 14 16 14 14 16 15
20 20 19 20 21 19 21 21 20 21 21 20 21 20 20 21 19 19 19 21 21 21 21 20 21 19 21 21 22 20 21 20 21 20 23 21 21 20 21 22 19 21 20 21 20 21 20 20 20 20 20 20 22 21 21 20 21 20 21 21 19 19 22 21 20 19 19 20 21 21 21 19 19 21
15 15 14 15 13 14 15 16 14 17 17 15 18 13 15 15 14 16 15 17 15 17 13 13 16 16 17 15 16 18 15 17 17 15 14 17 17 15 15 17 17 14 16 16 18 16 15 13 17 15 15 14 16 17 17 13 13 15 15 15 15 15 18 16 18 16 16 18 15 17 16 16 14 15
16 16 16 16 18 19 17 16 19 19 17 16 19 19 17 14 17 18 17 17 18 19 17 18 18 16 17 14 14 19 18 17 17 17 19 19 16 16 16 17 17 15 18 16 18 14 16 17 19 17 16 18 14 16 19 18 17 16 17 18 17 19 19 17 18 14 17 18 15 17 16 17 17 18
19 19 17 19 17 21 21 21 20 20 20 19 20 17 22 21 17 24 22 20 21 20 18 17 20 23 20 21 17 21 20 18 20 20 17 20 20 22 20 20 21 20 21 20 21 17 19 17 20 22 23 20 17 21 20 17 17 19 21 21 17 21 20 20 20 22 22 20 21 20 21 22 17 19
21 20 19 21 21 21 21 20 20 21 21 21 22 20 20 20 19 20 21 21 21 21 20 20 21 21 21 22 21 20 22 20 21 20 21 20 20 19 21 21 21 20 20 21 20 21 21 20 21 20 19 20 21 20 21 20 20 21 20 21 19 21 21 21 21 21 22 21 21 21 20 21 19 22
Please cite this article in press as: V. Gomes, et al., Nilotes from Karamoja, Uganda: Haplotype data defined by 17 Y-chromosome STRs, Forensic Sci. Int. Genet. (2009), doi:10.1016/j.fsigen.2009.07.001
N
1 1 1 1 3 3 2 1 1 1 2 2 1 2 1 1 2 1 1 1 1 2 2 1 3 2 1 3 3 2 1 1 1 1 1 1 1 1 1 1 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 2 1 1
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Table 1 (Continued ) Hap
H75 H76 H77 H78 H79 H80 H81 H82 H83 H84 H85 H86 H87 H88 H89 H90 H91 H92 H93 H94
DYS
DYS
DYS
DYS
DYS
DYS
DYS
DYS
DYS
DYS
DYS
DYS
DYS
DYS
DYS
YGATA
19
389I
389II
390
391
392
393
385
438
439
437
448
456
458
635
H4.1
15 16 15 15 15 15 14 13 15 13 14 13 15 15 14 15 15 16 15 14
13 13 12 14 14 13 13 13 13 13 13 13 14 13 12 12 13 13 14 12
30 30 29 32 30 30 29 30 29 30 29 30 31 29 28 30 30 31 31 28
21 21 26 24 21 21 25 25 21 24 25 22 22 24 25 24 23 24 22 25
9 11 11 10 9 9 9 10 9 10 9 11 10 9 10 10 9 10 10 10
11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 13 12 11 11
14 13 13 13 15 15 13 14 15 14 13 13 13 13 13 13 9 13 13 13
12–13 11–12 15–15 11–11 12–13 12–13 11–16 16–17 12–13 16–16 11–16 10–12 15–16 11–16 15–19 11–11 14–17 10–12 15–17 15–19
10 11 11 10 10 10 13 11 10 10 13 10 11 13 11 10 9 10 11 11
12 12 12 11 12 11 12 12 11 12 11 11 13 12 11 12 11 10 13 12
16 15 14 15 16 16 14 14 16 14 14 14 14 14 14 15 14 16 14 14
21 21 20 21 21 21 20 20 21 20 19 20 21 19 19 21 19 19 21 19
17 15 16 14 16 17 18 15 17 15 17 14 15 18 15 13 15 14 15 15
18 18 16 18 19 18 19 16 16 17 18 18 18 19 18 16 20 17 17 18
20 20 23 17 20 20 21 23 20 22 21 20 21 21 24 18 21 17 21 24
21 22 21 21 21 20 20 19 21 19 20 20 21 20 20 20 20 19 21 20
N
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Table 2 Pairwise genetic distances (Rst) and P values for Karamoja and other nine African samples. The Rst values are below the diagonal and P values are above the diagonal. The significant P values after Bonferroni’s correction (
