Aim: The aim of this work was to study Y-STR haplotypes and Y-SNP haplogroups in a Macedonian population sample in order to analyze the present demographic structure of the male gene pool in the Republic of Macedonia (present molecular markers as a powerful tool for unraveling human history).

Material and Methods: One hundred and fifty random male DNA samples from our Human DNA Bank (www.hdnamkd.org.mk) were typed for 11 Y-STR (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439), and 30 Y-SNP markers (those described by Brion et al., IJLM, 2004, 119:10-15). DNA samples were obtained from unrelated males of Macedonian origin, with nationality and linguistic affiliation. Individuals are of Christian Orthodox religion and are residents of different geographical regions in the Republic of Macedonia. STRs were typed in a multiplex PCR reaction using the PowerPlex1 Y System (Promega GmbH, Mannheim) according to the supplier's protocols, in an AB1310 sequencer/software platform at the Institute of Legal Medicine, Faculty of Medicine (Charité). Alleles nomenclature was according to the Y-STR Haplotype Reference Database, YHRD (www.yhrd.org). The 30 Y-chromosome SNP markers were typed following a hierarchical method, in four PCR/SNaPshot multiplex reactions according to Brión et al. (IJLM, 2004, 119:10-15). SNP typing was performed at IPATIMUP. The nomenclature for Y-SNP haplogroups is according to the Y Chromosome Consortium (Genome Res., 2000, 12:339-348).

Results: The Macedonian population sample has two dominant minimal Y-STR

 haplotypes with frequencies >5% (13, 13, 30, 24, 10, 11, 13, 16–18 and 16, 

13, 31, 24, 11, 11, 13, 14–15). By haplotype extension (DYS437, DYS438, 

DYS439) both of these minimal haplotypes can be further split up into four 

different ones, 1-allele step derived profiles. The frequencies of the 20 most

 frequent minimal haplotypes in the Macedonian population were compared 

with those from four neighboring geographic regions deposited at the YHRD, 

i.e. Albania (n = 101), Bulgaria (n = 122), Croatia (n = 150) and Greece 

(n = 101). The analysis revealed that most pronounced similarities in the 

minimal haplotype frequency are with the Croatian and Albanian samples. 

The diversity for the minimal haplotype was 0.9838 and for the 11-locus

 haplotype 0.9889. The 30 Y-SNP markers allowed to discriminat 11

 haplogroups in Macedonian population. The most frequent haplogroup 

in Macedonian population was I*(xI1b2)-M170 (36.7%), followed by E3b1-M78 

(20.7%), R1b-P25 (12.0%), R1a-SRY1532 (9.3%), J2-M172 (6.7%), G-M201 

(4.0%), K2-M70 (2.7%), J*(xJ1,2)-12f2 (2.7%), L-M22 (2.0%), E3b3a-M34 

(2.0%), and R1*(xR1a,b)-M173 (1.3%).

Conclusion: The Y-STR haplotype composition found in a Macedonian sample reflects the current demography of the country. According to the Φst statistics done by AMOVA the analysed population is embedded in the Southeastern European metapopulation which is significantly different from the Eastern and the Western European clusters (Roewer et al. Hum Genet 116(2005) 279-91). Within this metacluster the Macedonians are closest to the following groups sampled in the YHRD: Albania; Romania; Hungary [Ashkenazi Jews]; Bulgaria [Turks], Bulgaria [Slavic] and Macedonian Greeks. Y chromosome SNP haplogroups in Macedonian population are typically European.