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Y chromosome haplotypes in Albanian population from Kosovo

DOI:10.1016/j.forsciint.2004.04.006
Authors:
Marijana Pericic Salihovic at Institute for Anthropological Research
Marijana Pericic Salihovic
Lovorka Barac-Lauc at Croatian Science Foundation
Lovorka Barac-Lauc
  • Croatian Science Foundation
Irena Martinović Klarić at The Institute for Social Research, Croatia
Irena Martinović Klarić
Branka Janićijević
Branka Janićijević
Branka Janićijević
  • This person is not on ResearchGate, or hasn't claimed this research yet.
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Abstract and Figures

Eight Y chromosome short tandem repeat (STR) polymorphisms (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, and DYS393) were analyzed in the sample of 117 unrelated Albanian males living in Kosovo. A general STR allelic frequency pattern in the Albanian population from Kosovo corresponds to other European populations. Fourty six haplotypes were observed in single copy. The most frequent haplotypes were (DYS19-DYS385-DYS389I-DYS389II-DYS390-DYS391-DYS392-DYS393) 14-11/11-13-29-24-11-13-13 (10.26%), 14-14/17-12-28-24-10-11-12 (9.40%), 13-16/18-13-30-24-10-11-13 (9.40%), and 14-17/17-13-31-24-10-11-13 (9.40%).
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Announcement of population data
Y chromosome haplotypes in Albanian population from Kosovo
Marijana Peric
ˇic
´
a,*
, Lovorka Barac
´Lauc
a
, Irena Martinovic
´Klaric
´
a
,
Branka Janic
´ijevic
´
a
, Ibrahim Behluli
b
, Pavao Rudan
a
a
Institute for Anthropological Research, Amrus
ˇeva 8, 10000 Zagreb, Croatia
b
School of Medicine, Institute of Anatomy, University of Prishtina, Prishtina, Kosovo, Croatia
Received 16 February 2004; received in revised form 26 March 2004; accepted 5 April 2004
Available online 4 June 2004
Abstract
Eight Y chromosome short tandem repeat (STR) polymorphisms (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391,
DYS392, and DYS393) were analyzed in the sample of 117 unrelated Albanian males living in Kosovo. A general STR allelic
frequency pattern in the Albanian population from Kosovo corresponds to other European populations. Fourty six haplotypes
were observed in single copy. The most frequent haplotypes were (DYS19-DYS385-DYS389I-DYS389II-DYS390-DYS391-
DYS392-DYS393) 14-11/11-13-29-24-11-13-13 (10.26%), 14-14/17-12-28-24-10-11-12 (9.40%), 13-16/18-13-30-24-10-11-
13 (9.40%), and 14-17/17-13-31-24-10-11-13 (9.40%).
#2004 Elsevier Ireland Ltd. All rights reserved.
Keywords: Y chromosome; Short tandem repeats (STRs); Haplotypes; Kosovo
Population: 117 unrelated, autochthonous healthy adult
Albanians from Kosovo (Prishtina, Vitia and Gjakova areas)
participated in this study and gave their informed consent.
Extraction: The whole blood was obtained by venipunc-
ture and collected into EDTA tubes, followed by DNA
extraction using the salting-out procedure [1].
PCR: Seven tetranucleotide loci (DYS19, DYS385,
DYS389I, DYS389II, DYS390, DYS391, and DYS393)
and one trinucleotide (DYS392) were typed in two multiplex
reactions according to the Y STR Haplotype Reference
Database (http://www.ystr.org [2]). PCR reactions were
carried out in a GeneAmp PCR System (Applied Biosys-
tems, Foster City, CA) according to conditions described in
the YHRD.
Typing: PCR products were detected on an ABI PRISM
310 sequencer (Applied Biosystems). The GeneScan version
3.7 software (Applied Biosystems) was used to analyze
fragment sizes. The alleles were named according to the
number of repeat units based on the sequenced allelic ladders
as suggested by deKnijff et al. [3].
Results: The results are shown in Tables 1 and 2.
Data analysis: Allelic frequencies were estimated by
gene counting method. Haplotype and locus diversity within
population and exact test of population differentiation were
calculated using Arlequin 2.0 package [4].
Other remarks: Eight studied loci showed the allelic
frequency distribution (Table 1) similar to those previously
reported in other European populations [5,6] with the excep-
tion of loci DYS389II and DYS385. At DYS389II the most
frequent was the allele 30 as opposed to the most frequent
allele 29 [5,6], but similar to the finding of Croatians (as an
example of a Southeastern European population) where the
most frequent were alleles 30 and 31 [7]. At DYS385 the
most frequent was 11/11 as opposed to the most frequent 11/
14 [5].
The highest diversity (Table 2) that corresponds to the
highest discrimination value was found for the locus
DYS385 (0.916). The rest of the diversity values are in
concordance with the previously reported results [8–10].
Twenty two out of the sixty Albanian haplotypes were not
previously observed in the Y STR Haplotype Reference
Database (http://www.ystr.org [2]) among 13,986 minimal
haplotypes in a set of 94 European populations. Four most
Forensic Science International 146 (2004) 61–64
*
Corresponding author. Tel.: þ385-1-4816-904;
fax: þ385-1-4813-777.
E-mail address: mpericic@luka.inantro.hr (M. Peric
ˇic
´).
0379-0738/$ – see front matter #2004 Elsevier Ireland Ltd. All rights reserved.
doi:10.1016/j.forsciint.2004.04.006
Tab le 1
Allele frequencies at eight Y chromosome STRs in Albanians from Kosovo
Locus DYS19 Frequencies DYS385 Frequencies DYS389I Frequencies DYS389II Frequencies DYS390 Frequencies DYS391 Frequencies DYS392 Frequencies DYS393 Frequencies
Alleles 13 0.333 10/11 0.009 12 0.214 26 0.009 22 0.009 8 0.009 11 0.752 12 0.248
14 0.556 10/15 0.060 13 0.692 28 0.197 23 0.103 9 0.017 13 0.239 13 0.744
15 0.060 10/18 0.009 14 0.094 29 0.239 24 0.718 10 0.726 14 0.009 14 0.009
16 0.043 11/11 0.162 30 0.333 25 0.137 11 0.248
17 0.009 11/14 0.034 31 0.188 26 0.034
11/15 0.009 32 0.026
11/16 0.009 33 0.009
13/14 0.009
14/14 0.026
14/15 0.034
14/16 0.009
14/17 0.128
14/18 0.026
14/20 0.009
15/15 0.009
15/16 0.009
15/17 0.026
15/18 0.034
16/16 0.009
16/17 0.034
16/18 0.137
16/19 0.009
17/17 0.120
17/18 0.068
17/19 0.009
17/20 0.009
62 M. Peric
ˇic
´et al. / Forensic Science International 146 (2004) 61–64
Table 2
Y STR haplotypes in Albanians from Kosovo
Haplotype nFrequencies
of halotype
DYS19 DYS385 DYS389I DYS389II DYS390 DYS391 DYS392 DYS393
1 1 0.0085 13 14/20 13 30 24 10 11 12
2 1 0.0085 17 11/14 13 31 24 11 11 13
3 11 0.0940 14 14/17 12 28 24 10 11 12
4 1 0.0085 15 11/15 13 30 24 11 11 13
5 1 0.0085 13 16/17 13 30 24 10 11 13
6 1 0.0085 14 11/11 13 29 25 11 13 13
7 1 0.0085 15 15/17 14 30 22 10 11 12
8 1 0.0085 13 15/18 13 30 24 10 11 13
9 2 0.0171 14 11/11 13 29 24 10 13 13
10 1 0.0085 13 16/17 13 32 24 10 11 13
11 1 0.0085 13 17/19 13 30 26 10 11 13
12 2 0.0171 15 14/17 12 28 24 10 11 12
13 4 0.0342 13 16/18 13 30 25 10 11 13
14 11 0.0940 13 16/18 13 30 24 10 11 13
15 12 0.1026 14 11/11 13 29 24 11 13 13
16 1 0.0085 13 13/14 14 30 24 9 11 13
17 1 0.0085 13 17/18 13 31 24 10 11 13
18 3 0.0256 14 14/15 12 28 23 10 11 13
19 1 0.0085 15 10/15 13 29 25 11 13 12
20 5 0.0427 14 10/15 13 29 25 11 13 12
21 11 0.0940 14 17/17 13 31 24 10 11 13
22 1 0.0085 14 16/17 13 31 24 10 11 13
23 1 0.0085 14 10/11 13 29 24 11 13 13
24 1 0.0085 16 14/16 13 31 25 11 11 13
25 1 0.0085 13 17/18 14 32 24 10 11 13
26 2 0.0171 13 17/18 14 31 24 10 11 13
27 2 0.0171 13 17/18 14 31 23 10 11 13
28 1 0.0085 14 17/18 13 30 24 10 11 13
29 2 0.0171 13 15/18 13 30 25 10 11 13
30 1 0.0085 14 10/15 13 29 25 10 13 12
31 1 0.0085 13 17/17 13 30 25 10 11 13
32 1 0.0085 14 17/17 13 29 24 10 11 13
33 1 0.0085 16 14/15 13 32 24 10 11 13
34 1 0.0085 16 15/15 14 33 24 10 11 13
35 1 0.0085 14 14/17 12 28 24 10 11 13
36 2 0.0171 14 14/14 12 28 23 10 11 13
37 1 0.0085 14 17/17 13 31 23 10 11 13
38 1 0.0085 14 11/16 13 30 24 11 13 12
39 2 0.0171 14 14/18 12 28 24 10 11 12
40 1 0.0085 14 11/14 14 30 23 11 13 13
41 1 0.0085 15 14/18 12 28 24 10 11 12
42 1 0.0085 15 10/18 12 29 24 10 11 12
43 1 0.0085 13 16/19 13 30 24 10 11 13
44 1 0.0085 14 14/17 12 26 24 10 11 12
45 1 0.0085 13 15/17 13 30 26 10 11 13
46 1 0.0085 13 15/18 13 29 24 10 11 13
47 1 0.0085 14 17/18 13 31 24 10 11 13
48 1 0.0085 14 11/11 14 30 24 11 13 12
49 1 0.0085 13 15/16 13 30 23 10 11 13
50 1 0.0085 14 11/11 13 29 24 11 14 13
51 1 0.0085 13 15/17 13 30 24 10 11 13
52 1 0.0085 13 16/18 13 29 24 10 11 13
53 1 0.0085 14 14/14 12 28 23 8 11 13
54 1 0.0085 14 11/11 14 30 24 11 13 13
55 1 0.0085 13 16/17 13 30 23 10 11 13
56 1 0.0085 13 16/16 13 30 24 9 11 14
M. Peric
ˇic
´et al. / Forensic Science International 146 (2004) 61–64 63
frequent haplotypes (DYS19-DYS385-DYS389I-DYS389II-
DYS390-DYS391-DYS392-DYS393) 14-11/11-13-29-24-
11-13-13 (10.26%), 14-14/17-12-28-24-10-11-12 (9.4%),
13-16/18-13-30-24-10-11-13 (9.4%), and 14-17/17-13-31-
24-10-11-13 (9.4%) had 30, 3, 74, and 1 matches, respec-
tively. Forty six haplotypes were observed in a single copy.
Total haplotype diversity was estimated at 0:9621 0:0079.
Exact test of population differentiation based on haplo-
type frequencies did not reveal significant difference
between Albanian male population living in Kosovo and
first-generation Albanian immigrants living in Italy [11].
Exact test by locus showed significant differences at loci
DYS19 (P¼0:002) and DYS385 (P¼0:000).
This study is reported by following the guidelines for
publication of population data requested by the journal [12].
Acknowledgements
This work was supported by the Ministry of Science and
Technology of the Republic of Croatia grant to P.R. (project
title: Population Structure of Croatia—Anthropogenetic
Approach, no. 0196005).
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Table 2 (Continued )
57 1 0.0085 13 17/20 13 30 24 10 11 13
58 1 0.0085 14 11/11 13 30 24 11 13 13
59 1 0.0085 16 11/14 13 30 26 10 11 13
60 1 0.0085 16 11/14 13 31 26 10 11 13
LDV 0.580 0.916 0.470 0.764 0.458 0.414 0.380 0.389
n: number of individuals and LDV: locus diversity values.
64 M. Peric
ˇic
´et al. / Forensic Science International 146 (2004) 61–64
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Full-text available
  • Jun 2010
In our previous population study, we have used twelve Y-chromosomal short tandem repeats loci incorporated in the PowerPlex Y System to determine Y-STR diversity in B&H human population. With intent to obtain additional verification of the previously obtained results as well as to establish specific reference for a local B&H population, we have decided to test DNA samples collected from 100 unrelated healthy male Canton Sarajevo residents (from Sarajevo region) for the same twelve Y-linked short tandem repeats loci. Qiagen DNeasy Tissue Kit (Qiagen, GmbH, Hilden, Germany) was used for DNA extraction from buccal swabs and PowerPlex Y System (Promega Corp., Madison, WI) has been used to simultaneously amplify Y-STR loci by PCR. PowerPlex Y System includes 12 STR loci: DYS19, DYS385a, DYS385b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439. The total PCR reaction volume was 5 microL. PCR amplifications were carried out in PE GeneAmp PCR System Thermal Cycler (ABI). Electrophoresis of the amplification products was preformed on an ABI PRISM 310 genetic analyzer (ABI, Foster City, CA) according to the manufacturer's recommendations. The raw data were compiled and analyzed using the accessory software: ABI PRISM Data Collection Software and Genemapper version 3.2. In addition, we have compared the obtained "Sarajevo" dataset with the data previously generated for the entire Bosnian and Herzegovinian population, as well as with the available data on geographically close (neighboring) European populations. The results of this study will be used as guidelines in additional improving of research into genetic relationship among recent local B&H populations, both isolated and open, which is a long-term project in our country.
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Y-STR diversity in the Himalayas
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Linguistic and ethnic diversity throughout the Himalayas suggests that this mountain range played an important role in shaping the genetic landscapes of the region. Previous Y-chromosome work revealed that the Himalayas acted as a biased bidirectional barrier to gene flow across the cordillera. In the present study, 17 Y-chromosomal short tandem repeat (Y-STR) loci included in the AmpFlSTR® Yfiler kit were analyzed in 344 unrelated males from three Nepalese populations (Tamang, Newar, and Kathmandu) and a general collection from Tibet. The latter displays the highest haplotype diversity (0.9990) followed by Kathmandu (0.9977), Newar (0.9570), and Tamang (0.9545). The overall haplotype diversity for the Himalayan populations at 17 Y-STR loci was 0.9973, and the corresponding values for the extended (11 loci) and minimal (nine loci) haplotypes were 0.9955 and 0.9942, respectively. No Y-STR profiles are shared across the four Himalayan collections at the 17-, 11-, and nine-locus resolutions considered, indicating a lack of recent gene flow among them. Phylogenetic analyses support our previous findings that Kathmandu, and to some extent Newar, received significant genetic influence from India while Tamang and Tibet exhibit limited or no gene flow from the subcontinent. A median-joining network of haplogroup O3a3c-M134 based on 15 Y-STR loci from our four Himalayan populations suggests either a male founder effect in Tamang, possibly from Tibet, or a recent bottleneck following their arrival south of the Himalayas from Tibet leading to their highly reduced Y single-nucleotide polymorphism and Y-STR diversity. The genetic uniqueness of the four Himalayan populations examined in this study merits the creation of separate databases for individual identification, parentage analysis, and population genetic studies.
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Human Y-Chromosome Short Tandem Repeats: A Tale of Acculturation and Migrations as Mechanisms for the Diffusion of Agriculture in the Balkan Peninsula
Article
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Southeastern Europe and, particularly, the Balkan Peninsula are especially useful when studying the mechanisms responsible for generating the current distribution of Paleolithic and Neolithic genetic signals observed throughout Europe. In this study, 404 individuals from Montenegro and 179 individuals from Serbia were typed for 17 Y-STR loci and compared across 9 Y-STR loci to geographically targeted previously published collections to ascertain the phylogenetic relationships of populations within the Balkan Peninsula and beyond. We aim to provide information on whether groups in the region represent an amalgamation of Paleolithic and Neolithic genetic substrata, or whether acculturation has played a critical role in the spread of agriculture. We have found genetic markers of Middle Eastern, south Asian and European descent in the area, however, admixture analyses indicate that over 80% of the Balkan gene pool is of European descent. Altogether, our data support the view that the diffusion of agriculture into the Balkan region was mostly a cultural phenomenon although some genetic infiltration from Africa, the Levant, the Caucasus, and the Near East has occurred.
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Evaluation of Y-chromosomal STRs: A multicenter study
Article
Full-text available
  • Jun 1997
A multicenter study has been carried out to characterize 13 polymorphic short tandem repeat (STR) systems located on the male specific part of the human Y chromosome (DYS19, DYS288, DYS385, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393, YCAI, YCAII, YCAIII, DXYS156Y). Amplification parameters and electrophoresis protocols including multiplex approaches were compiled. The typing of non-recombining Y loci with uniparental inheritance requires special attention to population substructuring due to prevalent male lineages. To assess the extent of these subheterogeneities up to 3825 unrelated males were typed in up to 48 population samples for the respective loci. A consistent repeat based nomenclature for most of the loci has been introduced. Moreover we have estimated the average mutation rate for DYS19 in 626 confirmed father-son pairs as 3.2 × 10–3 (95% confidence interval limits of 0.00041–0.00677), a value which can also be expected for other Y-STR loci with similar repeat structure. Recommendations are given for the forensic application of a basic set of 7 STRs (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393) for standard Y-haplotyping in forensic and paternity casework. We recommend further the inclusion of the highly polymorphic bilocal Y-STRs DYS385, YCAII, YCAIII for a nearly complete individualisation of almost any given unrelated male individual. Together, these results suggest that Y-STR loci are useful markers to identify males and male lineages in forensic practice.
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Chromosome Y microsatellites: Population genetic and evolutionary aspects
Article
Full-text available
  • Jan 1997
By means of a multicenter study, a large number of males have been characterized for Y-chromosome specific short tandem repeats (STRs) or microsatellites. A complete summary of the allele frequency distributions for these Y-STRs is presented in the Appendix. This manuscript describes in more detail some of the population genetic and evolutionary aspects for a restricted set of seven chromosome Y STRs in a selected number of population samples. For all the chromosome Y STRs markedly different region-specific allele frequency distributions were observed, also when closely related populations were compared. Haplotype analyses using AMOVA showed that when four different European male groups (Germans, Dutch, Swiss, Italians) were compared, less than 10% of the total genetic variability was due to differences between these populations. Nevertheless, these pairwise comparisons revealed significant differences between most population pairs. Assuming a step-wise mutation model and a mutation frequency of 0.21%, it was estimated that chromosome Y STR-based evolutionary lines of descent can be reliably inferred over a time-span of only 1950 generations (or about 49000 years). This reduces the reliability of the inference of population affinities to a historical, rather than evolutionary time scale. This is best illustrated by the construction of a human evolutionary tree based on chromosome Y STRs in which most of the branches connect in a markedly different way compared with trees based on classical protein polymorphisms and/or mtDNA sequence variation. Thus, the chromosome Y STRs seem to be very useful in comparing closely related populations which cannot probably be separated by e.g. autosomal STRs. However, in order to be used in an evolutionary context they need to be combined with more stable Y-polymorphisms e.g. base-substitutions.
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A Simple salting out procedure for extracting DNA from Human Nucleated Cells
Article
We investigate the contribution of the Iberian bat fauna to the cryptic diversity in Europe using mitochondrial (cytb and ND1) and nuclear (RAG2) DNA sequences. For each of the 28 bat species known for Iberia, samples covering a wide geographic range within Spain were compared to samples from the rest of Europe. In this general screening, almost 20% of the Iberian species showed important mitochondrial discontinuities (K2P distance values > 5%) either within the Iberian or between Iberian and other European samples. Within Eptesicus serotinus and Myotis nattereri, levels of genetic divergence between lineages exceeded 16%, indicating that these taxa represent a complex of several biological species. Other well-differentiated lineages (K2P distances between 5–10%) appeared within Hypsugo savii, Pipistrellus kuhlii and Plecotus auritus, suggesting the existence of further cryptic diversity. Most unsuspected lineages seem restricted to Iberia, although two have crossed the Pyrenees to reach, at leas...
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Miller SA, Dykes DD, Polesky HF. A simple salting-out procedure for extracting DNA from nucleated cells. Nucleic Acids Res 16: 1215
Article
  • Mar 1988
Full textFull text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (113K), or click on a page image below to browse page by page. 1215
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Y-Chromosome STR haplotypes in an Italian population sample
Article
  • Feb 1999
Seven Y-chromosome STRs were investigated in a male population sample from the Modena area by means of one quadruplex reaction (systems DYS19, DYS390, DYS391, DYS393), one duplex reaction (systems DYS389-II, DYS392) and two single PCR reactions (DXYS156 and DYS389-I/II). In 100 males, 71 different haplotypes could be observed, 57 of which were seen only once. The haplotype diversity/discrimination index is 0.97. The resulting database could be used for routine forensic application like paternity testing and stain investigation.
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Y chromosome STR haplotypes: Genetic and sequencing data of the Galician population (NW Spain)
Article
  • Feb 1999
Recently described Y-STR polymorphisms can be analysed as informative haplotypes which are useful in the forensic field. In order to include these systems in our forensic routine, we have carried out a population study in Galicia (NW Spain) analysing seven Y-STR polymorphisms (DYS19, DYS389-I, DYS389-II, DYS390, DYS393 and DYS385: two loci). The results were compared with other population studies. In addition various alleles for each system (except DYS385) were sequenced and the corresponding allelic ladders constructed.
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Haplotype frequencies and population data of nine Y-chromosomal STR polymorphisms in a German and a Chinese population
Article
Y-chromosomal STR loci are of increasing interest in paternity testing, forensic casework, anthropological and evolutionary studies. We participate in a cooperation to establish an international reference database of at least nine Y-chromosomal STR loci to be used for biostatistic calculations. We present frequency distributions of nine Y-chromosome specific STR polymorphisms and frequencies of compound haplotypes in two populations. We chose the loci DYS393, DYS19, DYS392, DYS385I, DYS385II, DYS390, DYS391 and DYS389I and II. Blood samples were taken from 136 unrelated male individuals from Cologne (Germany) and of 63 unrelated males from Chengdu (Sichuan Province, PR China). DNA was extracted by a salting out procedure or chelex extraction. PCR was carried out in two multiplex reactions. Fragment analysis was conducted on an ALF- or ALF-express sequencer. Frequency profiles of the German men showed no significant differences compared to most European populations. Mean exclusion chances were between 0.44 for DYS393 and 0.94 for DYS385. Haplotype diversity for the complete haplotype was 86.66% in Germans and 98% in Chinese. The Chinese men showed for all analysed loci except for DYS389I and DYS390 remarkably different allele distributions.
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