- Email: [email protected]
Population genetics of 17 Y-STR markers in West Libya (Tripoli region)
Forensic Science International: Genetics 7 (2013) e59–e61
Contents lists available at SciVerse ScienceDirect
Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig
Forensic Population Genetics – Short Communication
Population genetics of 17 Y-STR markers in West Libya (Tripoli region) Soumaya Triki-Fendri a, Paula Sa´nchez-Diz b, Danel Rey-Gonza´lez b, Imen Ayadi a, Suad Alfadhli c, Ahmed Rebai a,*, A´ngel Carracedo b a Research Group on Molecular and Cellular Screening Processes, Laboratory of Microorganisms and Biomolecules, Centre of Biotechnology of Sfax, BP‘1177’ route Sidi Mansour km 6, 3018 Sfax, University of Sfax, Tunisia b Institute of Forensic Sciences, Genomic Medicine Group, IDIS, University of Santiago de Compostela, Galicia, Spain c Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University, Sulaibekhat, Kuwait
A R T I C L E I N F O
A B S T R A C T
Article history: Received 24 October 2012 Received in revised form 4 January 2013 Accepted 11 February 2013
Seventeen Y-chromosomal Short Tandem Repeats (Y-STR) included in the AmpFlSTR Y-filer PCR Amplification kit (Applied Biosystems) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4) were genotyped in a population sample of 176 unrelated males from western Libya (Tripoli region). A total of 142 different haplotypes were found, 124 being unique. Haplotype diversity was 0.9950. Both RST pairwise analyses and multidimensional scaling plot show a close genetic relationship between Tripoli and North African populations. ß 2013 Elsevier Ireland Ltd. All rights reserved.
Keywords: Y-STR Libya Tripoli Haplotype Y-filer Population genetics
1. Population Libya is a North African country, bordered by the Mediterranean Sea to the north, Egypt to the east, Sudan to the southeast, Chad and Niger to the south, and Algeria and Tunisia to the west (Fig. 1). This country was first inhabited by Berbers, followed by Phenicians, Greeks, Romans, Arabs and Ottomans. After 40 years as an Italian colony, Libya achieved her independence in 1951. There are few population genetic studies undertaken in Libya [1–3]. However, this study is the first report where such a large sample of 176 unrelated healthy male individuals living in western Libya (Tripoli region) were analysed for 17 Y-STR. 2. DNA extraction Genomic DNA was extracted from blood samples using the standard phenol–chloroform method and an informed consent was obtained for each participant in the study. 3. PCR amplification The AmpFlSTR Y-filer Amplification Kit (AB, Applied Biosystems, Foster City, CA, USA) (DYS19, DYS389I, DYS389II, DYS390,
* Corresponding author. Tel.: +216 74 871 816; fax: +216 74 875 818. E-mail address: [email protected] (A. Rebai). 1872-4973/$ – see front matter ß 2013 Elsevier Ireland Ltd. All rights reserved. http://dx.doi.org/10.1016/j.fsigen.2013.02.002
DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4) was genotyped in all the samples. PCR amplification was performed according to the manufacturer’s conditions.
4. Y-STR genotyping The amplified products were separated and detected using an ABI Prism 3130 Genetic analyzer (Applied Biosystems) following the manufacturer’s recommended protocol. GeneScan 500 LIZ was used as the internal lane standard. Fragment sizes were assigned using GeneMapper1 ID v3.2.1 software (AB). Allele designations were determined by comparison of the sample fragments with those of allelic ladders provided with the kit. The nomenclature used was that of the latest recommendations for the DNA commission of the International Society of Forensic Genetics [4].
5. Quality control The data were submitted to YHRD (http://www.yhrd.org/) and received the following accession number: YA003752. The analyses were carried out at the Institute of Forensic Sciences, Genomic Medicine Group, University of Santiago de Compostela; this laboratory participates in the annual proficiency testing of the GHEP-ISFG WG (http://www.gep-isfg.org).
e60
S. Triki-Fendri et al. / Forensic Science International: Genetics 7 (2013) e59–e61
Fig. 1. Map of Libya.
6. Statistical analysis Haplotype frequencies were estimated by haplotype counting. Haplotype diversity (D) was calculated according to Nei’s formula [5]. Arlequin software (v 3.5.1.2) [6] was used to calculate population pairwise genetic distances (RST) and to perform analysis of molecular variance (AMOVA) tests. RST values were ascertained at a significance level of 0.01 using 10,000 permutations [7]. A Bonferroni adjustment (a = 0.01/231 = 0.000043) was applied to compensate for potential type I errors [8]. In genetic distance analyses, DYS385ab was not considered and the number of repeats in DYS389I was subtracted from DYS389II. To illustrate the relationship between populations, a multidimensional scaling (MDS) plot was created using SPSS software version 13 [9].
reported that although there are data suggesting that locus DYS458 may be affected by a higher mutation rate compared to other tetrameric Y-STR loci, the observed microvariants seem to reflect a single mutational event. In fact, these variant alleles show an incomplete repeat caused either by a AA insertion or GA deletion in front the third repeat from the last [27]. Moreover, a null allele was found in locus DYS448 and one duplication was observed in DYS19 locus (allele 15,16). All samples containing intermediate, duplications or null allele were reamplified for confirmation. In order to study the genetic relationship between Libya and other populations, the studied data were compared with previously published datasets (21 populations divided into 3 groups: North Africa, Middle East and Europe) (Table S2). The analysis of molecular variance (AMOVA) approach was based on the RST distance between 9 Y-STR (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS438, DYS439) haplotypes; thus, this analysis takes into account both frequency differences among haplotypes as well as relatedness of haplotypes [7]. The results showed that a high proportion of the molecular variation is due to differences within populations (88%) whereas 5.29% of the genetic variance reflects differences among groups and 6.71% of the variance is due to differences among populations within groups (P < 0.000043; 10,000 permutations). As expected, the comparative study based on pairwise genetic distance (P-value < 0.0001) revealed the close relationship of Tripoli with Tunisia (RST = 0.00133, P = 0.27195) followed by Algeria (RST = 0.01104, P = 0.03396) and Morocco (RST = 0.01117, P = 0.01376) (Table S3). The similarity between Tripoli and Tunisia was also reported by Immel et al. [2]. However, significant differences between Tripoli and Benghazi (RST = 0.04066; P < 0.00001) which is an eastern Libyan city near Egypt and Egypt (RST = 0.04861; P < 0.00001) were observed, in spite of the lower genetic distance. The significant difference between Tripoli and Benghazi has already been reported by Elmrghni et al. [1]. Moreover, Significant genetic distances between Y-chromosomes from Tripoli and neighbouring countries from Europe such as Italy (RST = 0.10282, P < 0.00001) and Malta (RST = 0.10171, P < 0.00001) calculated on the basis of 5 Y-STR markers (DYS19, DYS390, DYS391, DYS392 and DYS393) [28] were found in spite of
7. Results Y-STR haplotype distribution of western Libya is shown in Table S1. Table S2 presents the references and geographic information of the population samples used in this study to undertake interpopulation comparisons (MDS) [1,10–25]. RST values and associated P-values between pairs of populations are given in Table S3. 8. Other remarks A total 142 different haplotypes (among 176 samples) were observed, 124 of them (87.3%) were unique. Twelve haplotypes were detected twice, three haplotypes appeared three times and only three haplotypes appeared four, seven and eight times, respectively (Table S1). Haplotype diversity was calculated to be 0.9950 showing a high level of variability. Based on fragment size, four intermediate alleles, named 17.2, 18.2, 19.2 and 21.2 were observed at DYS458 locus in 50 individuals (28.4% of the dataset) (Table S1). The high frequency of intermediate alleles at this locus is noteworthy. It was also previously described in other North African populations as Algeria [11], Tunisia [26], Egypt [13], and Morocco [12]. This result is in agreement with phylogeographic analysis pointing to either a Middle East or African origin of the DYS458*.2 allelic variant [27]. In addition, Robino et al. [11]
Fig. 2. Multidimensional scaling (MDS) plot based on pairwise RST values between Libya and 21 previously published populations (stress value = 0.040 and DAF = 0.973).
S. Triki-Fendri et al. / Forensic Science International: Genetics 7 (2013) e59–e61
the genetic heterogeneity of Malta due to admixture with other populations coming from Mediterranean and northern Africa [29]. The main factor is likely the Mediterranean Sea, acting as a geographical barrier to gene flow [30]. The multidimensional scaling (MDS) analysis of genetic distances based on pairwise RST [31] illustrated the genetic relationship between the studied populations (Fig. 2). In this figure, there are three subgroups corresponding to North Africa, Iberian populations and another for Eastern Europe (Serbia and Croatia). It showed that Tripoli clustered with North African countries. This finding is also concordant with the results obtained with data from Alu insertion and apolipoprotein E gene polymorphisms [32] and with a set of 119 binary markers and 15 microsatellites from the Y chromosome [33]. In order to complete the information about male lineages of Western Libya, the analysis of Y-chromosome biallelic markers in the population of Tripoli is currently under way. The work presented here is in compliance with the update of the guidelines and recommendations on forensic analysis using Ychromosome STR [4]. This paper follows the guidelines for the publication of data requested by the journal [34]. Acknowledgements We would like to thank Mr. Mounir Kammoun and Mr. Makram Besbes for their valuable help in the sampling. This study was supported in part by the Ministry of Higher Education and Scientific Research, Tunisia, the Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University, Sulaibekhat, Kuwait and the Institute of Forensic Sciences, Genomic Medicine Group, University of Santiago de Compostela, Spain. Danel Rey Gonza´lez was supported by a F.P.U. grant (Formacio´n de Profesorado Universitario) from the Ministry of Education, Government of Spain, AP2010-2616. Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.fsigen.2013.02.002. References [1] S. Elmrghni, Y.M. Coulson-Thomas, M. Kaddura, R.A. Dixon, D.R. Williams, Population genetic data for 17 Y STR markers from Benghazi (East Libya), Forensic Sci. Int. Genet. 6 (2) (2012) 224–227. [2] U.-D. Immel, M. Erhuma, T. Mustafa, M. Kleiber, M. Klintschar, Y-chromosomal STR haplotypes in an Arab population from Libya, Int. Cong. Ser. 128 (8) (2006) 156–158. [3] YHRD: Y chromosome Haplotype Reference Database, http://www.yhrd.org (Release 39). [4] L. Gusmao, J.M. Butler, A. Carracedo, P. Gill, M. Kayser, W.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 update of the recommendations on the use of Y-STRs in forensic analysis, Forensic Sci. Int. 157 (2006) 187–197. [5] M. Nei, Molecular Evolutionary Genetics, Columbia University Press, New York, 1987, pp. 176–179. [6] L. Excoffier, H.E. Lischer, Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Mol. Ecol. Resour. 10 (3) (2010) 564–567. [7] M. Kayser, S. Brauer, H. Scha¨dlich, M. Prinz, M.A. Batzer, P.A. Zimmerman, B.A. Boatin, M. Stoneking, Y chromosome STR haplotypes and the genetic structure of U.S. populations of African, European, and Hispanic ancestry, Genome Res. 13 (4) (2003) 624–634. [8] Y. Hochberg, A charper Bonferroni procedure for multiple test of significance, Biometrika 75 (4) (1988) 800–802. [9] SPSS for Windows, Version 13.0, Chicago, SPSS Inc.
e61
[10] I. Ayadi, L. Ammar-Keskes, A. Rebai, Haplotypes for 13 Y-chromosomal STR loci in South Tunisian population (Sfax region), Forensic Sci. Int. 164 (2/3) (2006) 249–253. [11] C. Robino, F. Crobu, C. Di Gaetano, A. Bekada, S. Benhamamouch, N. Cerutti, A. Piazza, S. Inturri, C. Torre, Analysis of Y-chromosomal SNP haplogroups and STR haplotypes in an Algerian population sample, Int. J. Legal Med. 122 (3) (2008) 251–255. [12] A. Laouina, B. El Houate, H. Yahia, H. Azeddoug, R. Boulouiz, F. Chbel, Allele frequencies and population data for 17 Y-STR loci (The AmpFlSTR1 Y-filerTM) in Casablanca resident population, Forensic Sci. Int. Genet. 5 (1) (2011) e1–e3. [13] G.A. Omran, G.N. Rutty, M.A. Jobling, Diversity of 17-locus Y-STR haplotypes in upper (Southern) Egyptians, Forensic Sci. Int. Genet. Suppl. Ser. 1 (2008) 230–232. [14] S. Triki Fendri, S. Alfadhli, I. Ayadi, N. Kharrat, H. Ayadi, A. Rebai, Genetic structure of Kuwaiti population revealed by Y-STR diversity 37 (6) (2010) 827–835. [15] A.T. Fernandes, R. Gonc¸alves, S. Gomes, D. Filon, A. Nebel, M. Faerman, A. Brehm, Y-chromosomal STRs in two populations from Israel and the Palestinian Authority Area: Christian and Muslim Arabs, Forensic. Sci. Int. Genet. 5 (5) (2011) 561–562. [16] P.A. Zalloua, Y. Xue, J. Khalife, N. Makhoul, L. Debiane, D.E. Platt, A.K. Royyuru, R.J. Herrera, D.F. Hernanz, J. Blue-Smith, R.S. Wells, D. Comas, J. Bertranpetit, C. TylerSmith, Genographic Consortium, Y-chromosomal diversity in Lebanon is structured by recent historical events, Am. J. Hum. Genet. 82 (4) (2008) 873–882. [17] F. Alshamali, L. Pereira, B. Budowle, E.S. Poloni, M. Currat, Local population structure in Arabian Peninsula revealed by Y-STR diversity, Hum. Hered. 68 (1) (2009) 45–54. [18] C. Alves, V. Gomes, M.J. Prata, A. Amorim, L. Gusma˜o, Population data for Ychromosome haplotypes defined by 17 STRs (AmpFlSTR Y-filer) in Portugal, Forensic Sci. Int. 171 (2–3) (2007) 250–255. [19] L. Valverde, S. Ko¨hnemann, M. Rosique, S. Cardoso, M. Zarrabeitia, H. Pfeiffer, M.M. de Pancorbo, 17 Y-STR haplotype data for a population sample of residents in the Basque Country, Forensic. Sci. Int. Genet. 6 (4) (2012) e109–e111. [20] F. Brisighelli, A. Blanco-Verea, I. Boschi, P. Garagnani, V.L. Pascali, A. Carracedo, C. Capelli, A. Salas, Patterns of Y-STR variation in Italy, Forensic. Sci. Int. Genet. 6 (6) (2012) 834–839. [21] V. Rodrı´guez, C. Toma`s, J.J. Sa´nchez, J.A. Castro, M.M. Ramon, A. Barbaro, N. Morling, A. Picornell, Genetic sub-structure in western Mediterranean populations revealed by 12 Y-chromosome STR loci, Int. J. Legal Med. 123 (2) (2009) 137–141. [22] J. Ljubkovic´, A. Stipisic´, D. Sutlovic´, M. Definis-Gojanovic´, K. Bucan, S. Andelinovic´, Y-chromosomal short tandem repeat haplotypes in southern Croatian male population defined by 17 loci, Croat. Med. J. 49 (2) (2008) 201–206. [23] I.S. Veselinovic, D.M. Zgonjanin, M.P. Maletin, O. Stojkovic, M. Djurendic-Brenesel, R.M. Vukovic, M.M. Tasic, Allele frequencies and population data for 17 Ychromosome STR loci in a Serbian population sample from Vojvodina province, Forensic Sci. Int. 176 (2–3) (2008) e23–e28. [24] L. Kovatsi, J.L. Saunier, J.A. Irwin, Population genetics of Y-chromosome STRs in a population of Northern Greeks, Forensic Sci. Int. Genet. 4 (1) (2009) e21–e22. [25] Y.D. Alakoc, O. Gokcumen, A. Tug, T. Gultekin, E. Gulec, T.G. Schurr, Y-chromosome and autosomal STR diversity in four proximate settlements in Central Anatolia, Forensic Sci. Int. Genet. 4 (5) (2010) e135–e137. [26] S. Frigi, F. Pereira, L. Pereira, B. Yacoubi, L. Gusma˜o, C. Alves, H. Khodjet el Khil, L. Cherni, A. Amorim, A. El Gaaied, Data for Y-chromosome haplotypes defined by 17 STRs (AmpFlSTR Y-filer) in two Tunisian Berber communities, Forensic Sci. Int. 160 (1) (2006) 80–83. [27] G. Ferri, C. Robino, M. Alu`, D. Luiselli, S. Tofanelli, L. Caciagli, V. Onofri, S. Pelotti, C. Di Gaetano, F. Crobu, G. Beduschi, C. Capelli, Molecular characterisation and population genetics of the DYS458.2 allelic variant, Forensic Sci. Int. Genet. Suppl. Ser. 1 (2008) 203–205. [28] C. Capelli, N. Redhead, V. Romano, F. Calı`, G. Lefranc, V. Delague, A. Megarbane, A.E. Felice, V.L. Pascali, P.I. Neophytou, Z. Poulli, A. Novelletto, P. Malaspina, L. Terrenato, A. Berebbi, M. Fellous, M.G. Thomas, D.B. Goldstein, Population structure in the Mediterranean basin: a Y chromosome perspective, Ann. Hum. Genet. 70 (2006) 207–225. [29] M. Cassar, C. Farrugia, C. Vidal, Allele frequencies of 14 STR loci in the population of Malta, Leg. Med. 10 (3) (2008) 153–156. [30] L. Quintana-Murci, R. Veitia, M. Fellous, O. Semino, E.S. Poloni, Genetic structure of Mediterranean populations revealed by Y-chromosome haplotype analysis, Am. J. Phys. Anthropol. 121 (2) (2003) 157–171. [31] M. Slatkin, A measure of population subdivision based on microsatellite allele frequencies, Genetics 139 (1) (1995) 457–462, Erratum in: Genetics 139(3) (1995) 1463. [32] R. Bahri, E. Esteban, P. Moral, H. Chaabani, New insights into the genetic history of Tunisians: data from Alu insertion and apolipoprotein E gene polymorphisms, Ann. Hum. Biol. 35 (1) (2008) 22–33. [33] B. Arredi, E.S. Poloni, S. Paracchini, T. Zerjal, D.M. Fathallah, M. Makrelouf, V.L. Pascali, A. Novelletto, C. Tyler-Smith, A predominantly neolithic origin for Ychromosomal DNA variation in North Africa, Am. J. Hum. Genet. 75 (2) (2004) 338–345. [34] A. Carracedo, J.M. Butler, L. Gusma˜o, W. Parson, L. Roewer, P.M. Schneider, Publication of population data for forensic purposes, Forensic Sci. Int. Genet. 4 (3) (2010) 145–147.
Contents lists available at SciVerse ScienceDirect
Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig
Forensic Population Genetics – Short Communication
Population genetics of 17 Y-STR markers in West Libya (Tripoli region) Soumaya Triki-Fendri a, Paula Sa´nchez-Diz b, Danel Rey-Gonza´lez b, Imen Ayadi a, Suad Alfadhli c, Ahmed Rebai a,*, A´ngel Carracedo b a Research Group on Molecular and Cellular Screening Processes, Laboratory of Microorganisms and Biomolecules, Centre of Biotechnology of Sfax, BP‘1177’ route Sidi Mansour km 6, 3018 Sfax, University of Sfax, Tunisia b Institute of Forensic Sciences, Genomic Medicine Group, IDIS, University of Santiago de Compostela, Galicia, Spain c Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University, Sulaibekhat, Kuwait
A R T I C L E I N F O
A B S T R A C T
Article history: Received 24 October 2012 Received in revised form 4 January 2013 Accepted 11 February 2013
Seventeen Y-chromosomal Short Tandem Repeats (Y-STR) included in the AmpFlSTR Y-filer PCR Amplification kit (Applied Biosystems) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4) were genotyped in a population sample of 176 unrelated males from western Libya (Tripoli region). A total of 142 different haplotypes were found, 124 being unique. Haplotype diversity was 0.9950. Both RST pairwise analyses and multidimensional scaling plot show a close genetic relationship between Tripoli and North African populations. ß 2013 Elsevier Ireland Ltd. All rights reserved.
Keywords: Y-STR Libya Tripoli Haplotype Y-filer Population genetics
1. Population Libya is a North African country, bordered by the Mediterranean Sea to the north, Egypt to the east, Sudan to the southeast, Chad and Niger to the south, and Algeria and Tunisia to the west (Fig. 1). This country was first inhabited by Berbers, followed by Phenicians, Greeks, Romans, Arabs and Ottomans. After 40 years as an Italian colony, Libya achieved her independence in 1951. There are few population genetic studies undertaken in Libya [1–3]. However, this study is the first report where such a large sample of 176 unrelated healthy male individuals living in western Libya (Tripoli region) were analysed for 17 Y-STR. 2. DNA extraction Genomic DNA was extracted from blood samples using the standard phenol–chloroform method and an informed consent was obtained for each participant in the study. 3. PCR amplification The AmpFlSTR Y-filer Amplification Kit (AB, Applied Biosystems, Foster City, CA, USA) (DYS19, DYS389I, DYS389II, DYS390,
* Corresponding author. Tel.: +216 74 871 816; fax: +216 74 875 818. E-mail address: [email protected] (A. Rebai). 1872-4973/$ – see front matter ß 2013 Elsevier Ireland Ltd. All rights reserved. http://dx.doi.org/10.1016/j.fsigen.2013.02.002
DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4) was genotyped in all the samples. PCR amplification was performed according to the manufacturer’s conditions.
4. Y-STR genotyping The amplified products were separated and detected using an ABI Prism 3130 Genetic analyzer (Applied Biosystems) following the manufacturer’s recommended protocol. GeneScan 500 LIZ was used as the internal lane standard. Fragment sizes were assigned using GeneMapper1 ID v3.2.1 software (AB). Allele designations were determined by comparison of the sample fragments with those of allelic ladders provided with the kit. The nomenclature used was that of the latest recommendations for the DNA commission of the International Society of Forensic Genetics [4].
5. Quality control The data were submitted to YHRD (http://www.yhrd.org/) and received the following accession number: YA003752. The analyses were carried out at the Institute of Forensic Sciences, Genomic Medicine Group, University of Santiago de Compostela; this laboratory participates in the annual proficiency testing of the GHEP-ISFG WG (http://www.gep-isfg.org).
e60
S. Triki-Fendri et al. / Forensic Science International: Genetics 7 (2013) e59–e61
Fig. 1. Map of Libya.
6. Statistical analysis Haplotype frequencies were estimated by haplotype counting. Haplotype diversity (D) was calculated according to Nei’s formula [5]. Arlequin software (v 3.5.1.2) [6] was used to calculate population pairwise genetic distances (RST) and to perform analysis of molecular variance (AMOVA) tests. RST values were ascertained at a significance level of 0.01 using 10,000 permutations [7]. A Bonferroni adjustment (a = 0.01/231 = 0.000043) was applied to compensate for potential type I errors [8]. In genetic distance analyses, DYS385ab was not considered and the number of repeats in DYS389I was subtracted from DYS389II. To illustrate the relationship between populations, a multidimensional scaling (MDS) plot was created using SPSS software version 13 [9].
reported that although there are data suggesting that locus DYS458 may be affected by a higher mutation rate compared to other tetrameric Y-STR loci, the observed microvariants seem to reflect a single mutational event. In fact, these variant alleles show an incomplete repeat caused either by a AA insertion or GA deletion in front the third repeat from the last [27]. Moreover, a null allele was found in locus DYS448 and one duplication was observed in DYS19 locus (allele 15,16). All samples containing intermediate, duplications or null allele were reamplified for confirmation. In order to study the genetic relationship between Libya and other populations, the studied data were compared with previously published datasets (21 populations divided into 3 groups: North Africa, Middle East and Europe) (Table S2). The analysis of molecular variance (AMOVA) approach was based on the RST distance between 9 Y-STR (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS438, DYS439) haplotypes; thus, this analysis takes into account both frequency differences among haplotypes as well as relatedness of haplotypes [7]. The results showed that a high proportion of the molecular variation is due to differences within populations (88%) whereas 5.29% of the genetic variance reflects differences among groups and 6.71% of the variance is due to differences among populations within groups (P < 0.000043; 10,000 permutations). As expected, the comparative study based on pairwise genetic distance (P-value < 0.0001) revealed the close relationship of Tripoli with Tunisia (RST = 0.00133, P = 0.27195) followed by Algeria (RST = 0.01104, P = 0.03396) and Morocco (RST = 0.01117, P = 0.01376) (Table S3). The similarity between Tripoli and Tunisia was also reported by Immel et al. [2]. However, significant differences between Tripoli and Benghazi (RST = 0.04066; P < 0.00001) which is an eastern Libyan city near Egypt and Egypt (RST = 0.04861; P < 0.00001) were observed, in spite of the lower genetic distance. The significant difference between Tripoli and Benghazi has already been reported by Elmrghni et al. [1]. Moreover, Significant genetic distances between Y-chromosomes from Tripoli and neighbouring countries from Europe such as Italy (RST = 0.10282, P < 0.00001) and Malta (RST = 0.10171, P < 0.00001) calculated on the basis of 5 Y-STR markers (DYS19, DYS390, DYS391, DYS392 and DYS393) [28] were found in spite of
7. Results Y-STR haplotype distribution of western Libya is shown in Table S1. Table S2 presents the references and geographic information of the population samples used in this study to undertake interpopulation comparisons (MDS) [1,10–25]. RST values and associated P-values between pairs of populations are given in Table S3. 8. Other remarks A total 142 different haplotypes (among 176 samples) were observed, 124 of them (87.3%) were unique. Twelve haplotypes were detected twice, three haplotypes appeared three times and only three haplotypes appeared four, seven and eight times, respectively (Table S1). Haplotype diversity was calculated to be 0.9950 showing a high level of variability. Based on fragment size, four intermediate alleles, named 17.2, 18.2, 19.2 and 21.2 were observed at DYS458 locus in 50 individuals (28.4% of the dataset) (Table S1). The high frequency of intermediate alleles at this locus is noteworthy. It was also previously described in other North African populations as Algeria [11], Tunisia [26], Egypt [13], and Morocco [12]. This result is in agreement with phylogeographic analysis pointing to either a Middle East or African origin of the DYS458*.2 allelic variant [27]. In addition, Robino et al. [11]
Fig. 2. Multidimensional scaling (MDS) plot based on pairwise RST values between Libya and 21 previously published populations (stress value = 0.040 and DAF = 0.973).
S. Triki-Fendri et al. / Forensic Science International: Genetics 7 (2013) e59–e61
the genetic heterogeneity of Malta due to admixture with other populations coming from Mediterranean and northern Africa [29]. The main factor is likely the Mediterranean Sea, acting as a geographical barrier to gene flow [30]. The multidimensional scaling (MDS) analysis of genetic distances based on pairwise RST [31] illustrated the genetic relationship between the studied populations (Fig. 2). In this figure, there are three subgroups corresponding to North Africa, Iberian populations and another for Eastern Europe (Serbia and Croatia). It showed that Tripoli clustered with North African countries. This finding is also concordant with the results obtained with data from Alu insertion and apolipoprotein E gene polymorphisms [32] and with a set of 119 binary markers and 15 microsatellites from the Y chromosome [33]. In order to complete the information about male lineages of Western Libya, the analysis of Y-chromosome biallelic markers in the population of Tripoli is currently under way. The work presented here is in compliance with the update of the guidelines and recommendations on forensic analysis using Ychromosome STR [4]. This paper follows the guidelines for the publication of data requested by the journal [34]. Acknowledgements We would like to thank Mr. Mounir Kammoun and Mr. Makram Besbes for their valuable help in the sampling. This study was supported in part by the Ministry of Higher Education and Scientific Research, Tunisia, the Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University, Sulaibekhat, Kuwait and the Institute of Forensic Sciences, Genomic Medicine Group, University of Santiago de Compostela, Spain. Danel Rey Gonza´lez was supported by a F.P.U. grant (Formacio´n de Profesorado Universitario) from the Ministry of Education, Government of Spain, AP2010-2616. Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.fsigen.2013.02.002. References [1] S. Elmrghni, Y.M. Coulson-Thomas, M. Kaddura, R.A. Dixon, D.R. Williams, Population genetic data for 17 Y STR markers from Benghazi (East Libya), Forensic Sci. Int. Genet. 6 (2) (2012) 224–227. [2] U.-D. Immel, M. Erhuma, T. Mustafa, M. Kleiber, M. Klintschar, Y-chromosomal STR haplotypes in an Arab population from Libya, Int. Cong. Ser. 128 (8) (2006) 156–158. [3] YHRD: Y chromosome Haplotype Reference Database, http://www.yhrd.org (Release 39). [4] L. Gusmao, J.M. Butler, A. Carracedo, P. Gill, M. Kayser, W.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 update of the recommendations on the use of Y-STRs in forensic analysis, Forensic Sci. Int. 157 (2006) 187–197. [5] M. Nei, Molecular Evolutionary Genetics, Columbia University Press, New York, 1987, pp. 176–179. [6] L. Excoffier, H.E. Lischer, Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Mol. Ecol. Resour. 10 (3) (2010) 564–567. [7] M. Kayser, S. Brauer, H. Scha¨dlich, M. Prinz, M.A. Batzer, P.A. Zimmerman, B.A. Boatin, M. Stoneking, Y chromosome STR haplotypes and the genetic structure of U.S. populations of African, European, and Hispanic ancestry, Genome Res. 13 (4) (2003) 624–634. [8] Y. Hochberg, A charper Bonferroni procedure for multiple test of significance, Biometrika 75 (4) (1988) 800–802. [9] SPSS for Windows, Version 13.0, Chicago, SPSS Inc.
e61
[10] I. Ayadi, L. Ammar-Keskes, A. Rebai, Haplotypes for 13 Y-chromosomal STR loci in South Tunisian population (Sfax region), Forensic Sci. Int. 164 (2/3) (2006) 249–253. [11] C. Robino, F. Crobu, C. Di Gaetano, A. Bekada, S. Benhamamouch, N. Cerutti, A. Piazza, S. Inturri, C. Torre, Analysis of Y-chromosomal SNP haplogroups and STR haplotypes in an Algerian population sample, Int. J. Legal Med. 122 (3) (2008) 251–255. [12] A. Laouina, B. El Houate, H. Yahia, H. Azeddoug, R. Boulouiz, F. Chbel, Allele frequencies and population data for 17 Y-STR loci (The AmpFlSTR1 Y-filerTM) in Casablanca resident population, Forensic Sci. Int. Genet. 5 (1) (2011) e1–e3. [13] G.A. Omran, G.N. Rutty, M.A. Jobling, Diversity of 17-locus Y-STR haplotypes in upper (Southern) Egyptians, Forensic Sci. Int. Genet. Suppl. Ser. 1 (2008) 230–232. [14] S. Triki Fendri, S. Alfadhli, I. Ayadi, N. Kharrat, H. Ayadi, A. Rebai, Genetic structure of Kuwaiti population revealed by Y-STR diversity 37 (6) (2010) 827–835. [15] A.T. Fernandes, R. Gonc¸alves, S. Gomes, D. Filon, A. Nebel, M. Faerman, A. Brehm, Y-chromosomal STRs in two populations from Israel and the Palestinian Authority Area: Christian and Muslim Arabs, Forensic. Sci. Int. Genet. 5 (5) (2011) 561–562. [16] P.A. Zalloua, Y. Xue, J. Khalife, N. Makhoul, L. Debiane, D.E. Platt, A.K. Royyuru, R.J. Herrera, D.F. Hernanz, J. Blue-Smith, R.S. Wells, D. Comas, J. Bertranpetit, C. TylerSmith, Genographic Consortium, Y-chromosomal diversity in Lebanon is structured by recent historical events, Am. J. Hum. Genet. 82 (4) (2008) 873–882. [17] F. Alshamali, L. Pereira, B. Budowle, E.S. Poloni, M. Currat, Local population structure in Arabian Peninsula revealed by Y-STR diversity, Hum. Hered. 68 (1) (2009) 45–54. [18] C. Alves, V. Gomes, M.J. Prata, A. Amorim, L. Gusma˜o, Population data for Ychromosome haplotypes defined by 17 STRs (AmpFlSTR Y-filer) in Portugal, Forensic Sci. Int. 171 (2–3) (2007) 250–255. [19] L. Valverde, S. Ko¨hnemann, M. Rosique, S. Cardoso, M. Zarrabeitia, H. Pfeiffer, M.M. de Pancorbo, 17 Y-STR haplotype data for a population sample of residents in the Basque Country, Forensic. Sci. Int. Genet. 6 (4) (2012) e109–e111. [20] F. Brisighelli, A. Blanco-Verea, I. Boschi, P. Garagnani, V.L. Pascali, A. Carracedo, C. Capelli, A. Salas, Patterns of Y-STR variation in Italy, Forensic. Sci. Int. Genet. 6 (6) (2012) 834–839. [21] V. Rodrı´guez, C. Toma`s, J.J. Sa´nchez, J.A. Castro, M.M. Ramon, A. Barbaro, N. Morling, A. Picornell, Genetic sub-structure in western Mediterranean populations revealed by 12 Y-chromosome STR loci, Int. J. Legal Med. 123 (2) (2009) 137–141. [22] J. Ljubkovic´, A. Stipisic´, D. Sutlovic´, M. Definis-Gojanovic´, K. Bucan, S. Andelinovic´, Y-chromosomal short tandem repeat haplotypes in southern Croatian male population defined by 17 loci, Croat. Med. J. 49 (2) (2008) 201–206. [23] I.S. Veselinovic, D.M. Zgonjanin, M.P. Maletin, O. Stojkovic, M. Djurendic-Brenesel, R.M. Vukovic, M.M. Tasic, Allele frequencies and population data for 17 Ychromosome STR loci in a Serbian population sample from Vojvodina province, Forensic Sci. Int. 176 (2–3) (2008) e23–e28. [24] L. Kovatsi, J.L. Saunier, J.A. Irwin, Population genetics of Y-chromosome STRs in a population of Northern Greeks, Forensic Sci. Int. Genet. 4 (1) (2009) e21–e22. [25] Y.D. Alakoc, O. Gokcumen, A. Tug, T. Gultekin, E. Gulec, T.G. Schurr, Y-chromosome and autosomal STR diversity in four proximate settlements in Central Anatolia, Forensic Sci. Int. Genet. 4 (5) (2010) e135–e137. [26] S. Frigi, F. Pereira, L. Pereira, B. Yacoubi, L. Gusma˜o, C. Alves, H. Khodjet el Khil, L. Cherni, A. Amorim, A. El Gaaied, Data for Y-chromosome haplotypes defined by 17 STRs (AmpFlSTR Y-filer) in two Tunisian Berber communities, Forensic Sci. Int. 160 (1) (2006) 80–83. [27] G. Ferri, C. Robino, M. Alu`, D. Luiselli, S. Tofanelli, L. Caciagli, V. Onofri, S. Pelotti, C. Di Gaetano, F. Crobu, G. Beduschi, C. Capelli, Molecular characterisation and population genetics of the DYS458.2 allelic variant, Forensic Sci. Int. Genet. Suppl. Ser. 1 (2008) 203–205. [28] C. Capelli, N. Redhead, V. Romano, F. Calı`, G. Lefranc, V. Delague, A. Megarbane, A.E. Felice, V.L. Pascali, P.I. Neophytou, Z. Poulli, A. Novelletto, P. Malaspina, L. Terrenato, A. Berebbi, M. Fellous, M.G. Thomas, D.B. Goldstein, Population structure in the Mediterranean basin: a Y chromosome perspective, Ann. Hum. Genet. 70 (2006) 207–225. [29] M. Cassar, C. Farrugia, C. Vidal, Allele frequencies of 14 STR loci in the population of Malta, Leg. Med. 10 (3) (2008) 153–156. [30] L. Quintana-Murci, R. Veitia, M. Fellous, O. Semino, E.S. Poloni, Genetic structure of Mediterranean populations revealed by Y-chromosome haplotype analysis, Am. J. Phys. Anthropol. 121 (2) (2003) 157–171. [31] M. Slatkin, A measure of population subdivision based on microsatellite allele frequencies, Genetics 139 (1) (1995) 457–462, Erratum in: Genetics 139(3) (1995) 1463. [32] R. Bahri, E. Esteban, P. Moral, H. Chaabani, New insights into the genetic history of Tunisians: data from Alu insertion and apolipoprotein E gene polymorphisms, Ann. Hum. Biol. 35 (1) (2008) 22–33. [33] B. Arredi, E.S. Poloni, S. Paracchini, T. Zerjal, D.M. Fathallah, M. Makrelouf, V.L. Pascali, A. Novelletto, C. Tyler-Smith, A predominantly neolithic origin for Ychromosomal DNA variation in North Africa, Am. J. Hum. Genet. 75 (2) (2004) 338–345. [34] A. Carracedo, J.M. Butler, L. Gusma˜o, W. Parson, L. Roewer, P.M. Schneider, Publication of population data for forensic purposes, Forensic Sci. Int. Genet. 4 (3) (2010) 145–147.