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Y-Chromosomal STR Haplotype Profiling in Yousafzai’s living in Swat Valley Pakistan

Authors:
Presentations from the 22nd Congress of the IALM (July 5-8, 2012, Istanbul, Turkey)
Y-Chromosomal STR Haplotype Profiling in Yousafzai’s living in
Swat Valley Pakistan
Ilyas M.1*, Shahzad M.S.1, Israr M.1, Jafri S.S.1, Shafeeq M.1, Zar M.S.1, Ali A1,
Rahman Z.1 and Husnain T.1
1. Forensics Research Group, National Centre of Excellence in Molecular Biology, 87-West Canal Bank
Road, Thokar Niaz Baig, Lahore-53700, Pakistan
*Muhammad Ilyas, National Centre of Excellence in Molecular Biology, 87-West Canal Bank Road, Thokar
Niaz Baig, Lahore-53700; Pakistan Email: ilyas@cemb.edu.pk; URL: www.cemb.edu.pk
Abstract:
Haplotype, allele frequencies and population data of 17 Y-chromosome STR loci DYS456, DYS3891,
DYS390, DYS389II, DYS458, DYS19, DYS385a, DYS385b, DYS393, DYS391, DYS439, DYS635, DYS392,
YGATAH4, DYS437, DYS438 and DYS448 were determined from 71 unrelated male individuals belong to
Yousafzai tribe living in Swat Valley. Statistical analysis was performed and as many as 45 haplotypes were
identified and 41 of them were observed only once, accounting for 91% unique haplotypes. The most common
haplotypes were observed seventeen times (23.9%). Y chromosomal haplotypes diversity for 17 Y STRs locus
set ranged from 0.232 to 0.577 in Yousufzai population indicating haplotypes among unrelated males. The
Yousafzai allele frequency database was then compared with other populations of the world.
Keyword: Y-Chromosome, STR, Yousafzai, Pathan, Swat, Khyber Pakhtoonkhwa
Introduction:
Yousafzai (literally meaning “Sons of Joseph”) is a sub-tribe of Pashtuns (Pathans) present in the
Northern parts of Khyber Pakhtoonkhwa, Pakistan [1]. There are a variety of cultural and ethnic similarities
between Jews and Pashtuns [2]. Many currently active Pashtun traditions may have parallels with Jewish
traditions [3]. The code of Pashtunwali is strikingly similar in content and subject matter to the Mosaic Law.
Various studies have proved that human DNA is a way to explore historical movements of populations by
studying their genetic make-up. Many Pakistani haplotypes have been added to YHRD database that are very
likely to be G2c [4]. Some genetic lineage research also showed minor contribution to the Pathan genome from
Iranian, Arab, Turkish and Greek peoples [5]. Theory of Pathan lineage with Israel is currently being studied by
researchers in India [6].
A huge number of Y-STR loci (>400) have been shown by many groups and added into public
databases such as the Genome Database (www.gdb.org) and Y-Haplotype Reference Database (www.yhrd.org).
A complete annotated STR physical map of the human Y chromosome shows the detailed position of each locus
along the chromosome [7].
Methodology:
Buccal swab samples from 71 healthy unrelated individual belong to the Yousafzai tribe currently living
in different areas of Swat and Malakand districts i.e. Mingora City, Manglor, Kabal, Batkhela, Dargai, Odigram
and Khwaza Khela (Fig.1). Proper consent forms were signed from them. Dinc method was used to extract DNA
from buccal swabs samples [8]. Nanodrop ND 1000 spectrophotometer was used to check DNA quantity.
Seventeen Y-STR loci kit i.e. AmpFlSTR® Yfiler™ was used to do this study. Locus information found was
then added to Y-STR Haplotype Reference Database (YHRD) web site (www.yhrd.org) under the accession
number: YA003748. DNA was amplified and genotyped using the AmpFlSTR® Yfiler™ kit, according to the
recommended protocol of the manufacturer. ABI Prism Genetic Analyzer 3130 was used to analyze PCR
product. Gene Mapper v3.2 software (Applied Biosystems, Foster City, CA) was used to analyze the data raw
data. Further statistical tests were applied on genetic data using Arlequin, SPSS and Microsoft Excel.
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Fig. 1: Map of Khyber Pathoonkhwa, Pakistan and its neighbor countries. The “Red Color” shows study area.
Results and Discussion:
Total 45 different haplotypes were observed in which 41 were unique, accounting for 91% unique
haplotypes (Table 1). The most common haplotypes was observed seventeen times (23.9%). The highest locus
diversity value was 0.577 at locus DYS391 while the lowest locus diversity value was 0.232 for DYS389I locus.
Allele frequencies calculated from each population and all haplotypes for the 17 Y-STR loci in 71 males are
listed in Table 2. It was observed that our findings were not consistent with results from Iran and Afghanistan
[9][10] concerning the most frequent allele appearance and the highest locus diversity value being 0.591 for
DYS391 locus in our results. H1 is also found reported in Afridi pathans in India and 2 haplotypes in Northern
African pathans. H2 is reported 1 in Tibetean China and 1 in Dhaka Bangladesh.
The observed low Y-STR diversity of the Yousafzai’s compared in table 3 with other populations like
Afghanistan, Iran, Israel, Greeks and India could be explained by genetic drift resulting from small effective
population sizes [11][12]. A Y-STR 20-plex have been developed that increased the power of discrimination
compared with reported Y-STR multiplex [13].
Y-chromosomal relationships between the populations were then investigated. A multidimensional
scaling plot (MDS) of the transformed distances is shown in Fig. 2. Most of the populations form a loose cluster
towards the center, with the Yousafzai’s. Analysis of molecular variance (AMOVA) reveals a considerable
regional stratification within the country as well as between different Pashtun (Pathan) groups living in Pakistan
(Table 3).
Presentations from the 22nd Congress of the IALM (July 5-8, 2012, Istanbul, Turkey)
Table 1. Haplotypes distribution of the Y -Chromosome analyzed in Yousafzai’s (Pathan) population of Swat Valley, Pakistan (n=71)
ID No DYS19 DYS389I DYS
389II DYS
390 DYS
391 DYS
392 DYS
393 DYS
385ab DYS
438 DYS
439 DYS
437 DYS
448 DYS
456 DYS
458 DYS
635 YGATAH4
H1 17 15 13 30 24 11 11 13 11,14 11 10 14 20 15 15 23 12
H2 7 15 13 30 24 10 11 13 11,14 11 10 14 20 15 15 23 12
H3 4 15 13 30 24 12 11 13 11,14 11 10 14 20 15 15 23 12
H4 2 15 13 31 24 11 11 13 11,14 11 10 14 20 15 15 23 12
H5 1 16 13 29 20 10 11 12 15, 14 8 11 14 18 15 16 21 11
H6 1 14 13 29 22 10 11 12 14, 16 9 11 15 19 15 16 20 11
H7 1 15 13 30 22 10 11 12 14, 18 10 10 14 19 16 16 21 11
H8 1 15 13 30 22 10 11 12 14, 18 10 11 14 19 16 17 20 11
H9 1 15 13 29 22 10 11 12 14, 17 9 12 14 20 15 17 20 12
H10 1 15 14 30 22 10 11 12 14, 16 9 12 14 20 15 17 20 12
H11 1 15 14 30 22 10 11 12 14, 17 9 12 14 20 15 17 20 12
H12 1 15 13 30 25 10 11 14 08, 15 11 11 14 18 16 15 20 11
H13 1 14 12 29 24 10 12 12 14, 16 10 12 14 22 15 16 21 11
H14 1 15 13 29 22 10 11 13 11, 14 10 12 16 20 15 15 21 12
H15 1 15 13 29 22 10 11 15 13, 20 10 10 14 19 15 17 24 10
H16 1 15 13 29 21 10 14 12 09, 16 10 13 16 19 15 15 21 12
H17 1 15 13 30 22 10 16 12 14, 18 10 11 14 19 15 17 20 11
H18 1 15 12 30 24 11 11 13 11, 14 11 10 14 20 15 15 23 12
H19 1 14 13 30 24 11 11 13 11, 14 11 10 14 20 15 15 23 12
H20 1 15 13 29 24 11 11 13 11, 14 11 10 14 20 15 15 23 12
H21 1 15 13 30 24 11 11 13 09, 14 11 9 14 20 15 15 23 12
H22 1 15 14 30 25 10 11 12 14, 17 9 12 14 20 15 17 20 12
H23 1 14 13 29 23 10 10 14 13, 18 11 10 16 19 15 17 24 11
H24 1 15 13 29 24 11 11 13 11, 14 11 10 14 20 15 16 23 12
H25 1 14 13 29 23 10 10 14 12, 17 11 11 16 19 15 16 24 12
H26 1 15 13 30 24 11 11 13 11, 16 11 10 14 20 15 15 23 12
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H27 1 13 13 29 22 10 15 13 12, 16 11 12 14 19 15 18 23 10
H28 1 14 12 29 24 10 12 12 14, 16 10 12 16 22 15 16 21 12
H29 1 15 13 30 24 11 11 13 11, 14 11 11 14 20 15 15 23 12
H30 1 14 12 28 22 11 14 11 13, 18 10 13 15 19 17 15 25 12
H31 1 15 13 31 24 11 11 13 11, 14 11 10 14 20 15 15 23 12
H32 1 15 13 31 24 11 11 12 11, 14 11 10 14 20 16 15 23 12
H33 1 15 13 31 25 11 11 13 11, 14 11 10 14 20 15 15 23 12
H34 1 15 13 31 24 11 11 13 11, 14 11 11 14 20 15 15 23 12
H35 1 15 13 30 24 12 11 13 11, 14 11 10 14 20 16 15 23 12
H36 1 15 13 30 25 11 11 13 11, 14 11 10 14 20 15 15 23 13
H37 1 15 13 30 24 11 11 13 11, 14 14 10 13 20 15 15 23 12
H38 1 16 13 31 25 11 11 13 11, 15 11 10 14 20 15 15 23 13
H39 1 16 13 30 25 10 11 13 11, 14 11 10 14 20 16 16 24 12
H40 1 15 14 30 25 10 11 13 12, 15 9 11 14 20 16 20 21 13
H41 1 13 13 29 24 10 17 13 12, 16 11 13 15 19 15 17 23 10
H42 1 16 13 31 25 12 11 13 11, 15 11 10 14 20 15 16 23 12
H43 1 15 13 31 25 11 11 13 11, 13 11 10 14 20 16 17 23 13
H44 1 15 13 30 23 11 11 13 14, 18 10 11 16 21 15 20 24 11
H45 1 16 14 31 23 10 11 13 14, 16 10 11 14 21 16 20 25 12
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Table 2: Allele frequency distribution, Genetic Diversity and contribution to Discrimination Capacity for 17 Y-STR loci in Pashtoon (Pathan) Yousufzai Population (n = 71)
Alleles DYS456 DYS389I DYS390 DYS389II DYS458 DYS19 DYS385a DYS385b DYS393 DYS391 DYS439 DYS635 DYS392 YGATAH4 DYS437 DYS438 DYS448
8 0.0141 0.0141
9 0.0282 0.0141 0.0845
10 0.4085 0.6761 0.0282 0.0423 0.1549
11 0.6761 0.0141 0.507 0.1549 0.8732 0.1268 0.7324
12 0.0563 0.0563 0.1831 0.0845 0.1127 0.0282 0.7746
13 0.8732 0.0282 0.0423 0.0141 0.7465 0.0423 0.0563 0.0141
14 0.0704 0.0986 0.169 0.6479 0.0423 0.0282 0.8592 0.0141
15 0.8592 0.662 0.8028 0.0141 0.0563 0.0141 0.0141 0.0423
16 0.1268 0.1408 0.0704 0.1268 0.0845
17 0.0141 0.1408 0.0282 0.0563 0.0141
18 0.0141 0.0845 0.0282
19 0.1549
20 0.0141 0.0423 0.0141 0.1127 0.7606
21 0.0141 0.986 0.0282
22 0.1549 0.0282
23 0.0563 0.6901
24 0.6338 0.0704
25 0.1268 0.0282
28 0.0141
29 0.1972
30 0.662
31 0.1268
GD 0.24909 0.23259 0.56257 0.51388 0.52756 0.34486 0.51549 0.55814 0.41287 0.57706 0.51146 0.50261 0.23782 0.3843 0.25633 0.43822 0.4008
DC: discrimination capacity = 60.56%; HD: Haplotype Diversity = 0.860465
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Fig. 2: Multidimensional Structure (MDS)
Table 3: Comparative AMOVA of Yousufzai Population with other populations
Population Afghan [Pathan] India
[Afridi Pathan] Afghanistan Greece Iran Israel Mongolia Yousafzai
Afghan
[Pathan] --- 0.0000 0.0000 0.0055 0.0682 0.0000 0.0000 0.0000
India
[Afridi Pathan] 0.0080 --- 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000
Afghanistan 0.0079 0.0007 --- 0.0000 0.0000 1.0000 0.0000 0.0000
Greece 0.0232 0.0181 0.0180 --- 0.0126 0.0000 0.0001 0.0000
Iran 0.0013 0.0051 0.0050 0.0151 --- 0.0000 0.0000 0.0000
Israel 0.0079 0.0007 -0.0060 0.0180 0.0050 --- 0.0000 0.0000
Mongolia 0.0080 0.0008 0.0007 0.0180 0.0051 0.0007 --- 0.0000
Yousafzai 0.0080 -0.0062 0.0007 0.0181 0.0051 0.0007 0.0008 ---
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Conclusion:
The results obtained in this study can be utilize in crime investigation, personal identification and
paternity testing where it will help in providing information which cannot be taken from autosomal DNA
systems. In addition, genetic genealogical studies can also be done using Yousafzai population data generated in
this research.
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1. Tokayer, R.M. (2007). Mystery of the Ten Lost Tribes. Nihon-Yudaya, Huuin no Kodaishi.
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3. Prusher, I. (2007). Is One of the Lost Tribes the Taliban?. Moment Magazine. www.momentmag.com
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genetic influence of central asian pastoralists". Am. J. Hum. Genet. 78 (2): 202–21.
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