United Arab Emirates University
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Theses
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8-2014
Y-Chromosome Polymorphism in United Arab
Emirates
Safa Yaqoub Yousif Alkhayyat AL Hammadi
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Alkhayyat AL Hammadi, Safa Yaqoub Yousif, "Y-Chromosome Polymorphism in United Arab Emirates" (2014). Theses. Paper 134.
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United Arab Emirates University
College of Scienct:
Biology Department
Y-CHROMOSOlV
OL YMORPI-IISM IN UNITED
ARAB EMIRATES
Safa Yaqoub Yousif Alkha:yat Alhammadi
This thesis is submitted in partial fulfillment of the requirements for the
Degree
of Master of Science in Environmental Sciences
'-
Under the direction of Dr. Khaled Amiri, Dr. Ahmed AI Marzouqi and
Dr. Abdulmaj eed Al Khajch.
August 2014
DECLARATION OF ORIGINAL WORK
L
afa Yaqou b
at the
n iled
ou i f
I k ha))at
rab E m i rate
I ham madi. the unders igned, a graduate stu dent
niversit) ( A E
a " Y -ch romosome pol) m orphi m in
thi
n i ted
), and the author o f the thesis t i t led
rab E mirates" , hereby I declare that
thes i s i a n orig i nal \\ ork done a n d prepared b y me under t h e guidance o f D r .
Khaled
Dr.
m i ri, D r . Abdulmajeed
hilled
I Marzoll qi in
I K haj eh, in t h e Col lege of c ience a t
E U and
bu Dhabi general head q uarter. T h i s work has not
pre jOll I) formed as the ba is for the award of any degree, d i ploma or sim i lar tit le
at th i or an) other u n i \ ersit) in the
oure
A E . The materi a l s borrowed from the other
and i n luded in 111) the i ha\ e been properl ac know ledged .
:;ifrr
Student's Signature
'-:,-2......
. .
Date
II
.....:...!.!� �(?!.?!.':f. .
. ..
Copyright ©20 1 4 by Safa Alhammadi
All Rights Reserved
III
Approved by
Thesis Examining Committee:
1)
Advisor (Committee Chair):
Dr. Khaled Amiri
Department of :
Biology
College of :
Science
Signature :
2)
_
_
-=--"==:...=-==--___
Member:
Date:
1- 1
\«
JuIY
Dr. Sofyan Alyan
Biology
Science
Date:
3)
Member (External Examiner):
'
Division of :
��
: ---z.c,,�
-" �"""=:;...-
Institution:
Signature
...
...
/...."-....,
"'----
Dr. Mohsin Sulaiman Alaamri
DNA fingerprinting & forensic
Advanced Biotechnology Centre
Accepted b.
J1h�
1a ter's Program Coord inator:
ignature
lo
Oate . .
I �.! ;);,.1':1 .............
.
Dean of the Col lege:
.
-1�
. ��
�
J gnatur
··· · ······· · · ·
.
· . .
· . . . . · .. ..
·
· . . ·
·
O
Date
Cop . . . . . of . . . . . .
v
v'
. . . . . . . . .
(et/
,... ('t
. . . . . . . . . . . . . . . . . . . . . . . . . . ..
A B STRACT
Human Y c hromosome is a pec ific male marker and it con ists of the largest
non-reco m b i n i n g egment in human genome that is the ha l lmark of Y chromosome
populat i on-ba ed stud ies.
Th is
tud ) estab l i he
an extensive Y pol)-morp h i sm pro fi l e o f the
population and t o our knowledge, t h i
AE
is the largest study carried out in the U A E .
o A samples were genotyped for 1 7 polymorph ic STR from 3 4 5 unrelated E m irati
male.
I n UAE popu l ation, the analysi o f the al lele freque ncy c learly shows that each
10 u
ha
a p red o m i nant al le le .
It i s also apparent t hat a l l e les for most loci are
clustered over a narrow range \ here approxi mate l y 60% - 80% of the population is
sharing a spec i fi c a l le le for the locus.
M o reover, the h ighest di ers ity were observed at locus D Y S 4 5 8
A
=
0.9 a n d D Y 3 8 5 -B
=
0.9.
=
0.9, DYS3 8 5 -
Therefore they should be consi dered a s t h e most
variable and most i n formative m arkers for foren s i c test i ng.
W h i le, loc i w i th the
lo\\er d ivers it are the least i n formative loci ( i .e . DYS392 which equal 0 . 4 3 7 ) .
T h e U A E population i s largely heterogeneous a n d a tota l o f 3 0 1 d i fferent
haplotypes were ident i fied . There are 271 un ique haplotypes and 22 haplotypes were
shared between 1:\\ 0 i n d ividua ls .
There are t h ree cases \ here four. five and six
ind ividua l s are sharing identical hap lotype.
hapl otypes shared by five i nd ividuals.
M o reover, th ere are th ree d i fferent
Th is is l i ke l y due to the sharing o f mo t
common recent ancestors. This brings the d i sc r i m i nation capac ity to approxi mate ly
90% and hap lotype d ivers ity 99. 8 85%.
This is fundamental to understand i ng the
VI
degree o f heterogeneity in
E popu lation and can refl ect the pattern of the
m i grat ion, geograph ic i nfl uen e, and cu ltural i nfluen e .
an array of haplot) pe that can
rab E mirate
cOlll1trie .
p p u l ation i
na l ) i
d l fferen e \\ ith in
econd l ) . the tud) pro\ ide
ne a databa e for forensic u e . To thi end.
n ited
d iver e and are genet ical l ) clo e to neigh boring
o f molecular variance ( M V A )
how no
igni ficant genetic
A E population or popu lat ion res i d i ng the A rabian Gulf region.
VII
Ded icat ion
I lov i ng ded icate 111) the i to m} beloved parent, i ter and brothers \\ ho ha\e
never faded to g i \e me a moral upport and for g l \ ing me a l l I need and encouraging
me to cont i nue m) h i gher education.
loreo\ er, J dedicate thi thesis to the person \\ ho i s m y manager, fr iend and brother
I brah i m
1-110 a n i \\ ho ha real l ) been there through the hard t i mes.
IX
1.10
Y - T R Markers:
1.11
Bac kground of
1.12
Objecti ves:
. . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
n i ted Arab E m i rates: .
.
13
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. .
. .
15
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
17
..
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
A D MATE R I A L.
H PTER I I : M ET H O D
am ple Co l lection:
2. 1
.
. . . .
.
.
. . . . . . .
. .
. . . . . . . . . . . . . .
.
18
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ..
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . .
19
2. 2
Consent Fonn: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . 19
2.3
Bucc al
2 .4
Preparat ions and
2.5
Storage Condit ion:
2.6
General
2.7
2.10
. . . . . . . . . . .
.
. . . . . . . . . . .
ample Batc h i ng:
.
.
. .
.
. . . . . . . . . . . . . .
20
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
20
. . .. . . . . . . . . . . . . . . . . . . . . . . . . . .. .
.
. . . . . . . . . . . . . .
.
.
. . . . . . . . . . . . . . . .
.
20
D A Extract ion Process:
2.6. 2
Quanti fication Process:
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.6. 3
A m p l i ficat ion Process:
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Detection o f A m p F LS T R
tatist ical A nalysis:
. . . .
.
. . .
Y fi ler
. .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
k i t PC R Product: .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
.
. .
Profi l ing
3.2
Y STR a l le les Freq uenc ies:
3.3
Y
.
. . . . . . . . . . . . . . . .
.. .
.
. .
.
. . . . . . . . . . . . . .
. .. .
. .
. . .
24
28
33
. . . .
. . . . . . . . . . . . . . . . . . . .
. 34
.
. . . . . . . . . . . . . . . . . . . . . . . . . .
36
.38
39
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
40
T R hap lotype o f U A E popu lation:
3.3 . 1
Hap lotype Freq uency:
3.3 .2
Hap lotype D i versity:
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
.
23
. . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
D i scri m i nation Capac i ty:
. 21
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . .
.
.
. . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . .
1easure o f d i vers ity between and w it hin populat ion:
67
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
67
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
68
. . . . . . . .
.
70
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Shared haplotype in UAE popu lation :
3 . 5 .0
. . . . . . . . . . . . . . . . . . .
.
Ana ly s is o f Popu lation genet ic parameters: .
amp les:
.
. . . . . . . . . . . . . . . . .
. . . . .
3. 1
3.5
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C H A PT E R I I I: R E S U LTS A N D D I S C U S S ION
3.4
19
. . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
a m p l e Procedures:
. . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . .
2.6. I
2.8
2.9
\\ abs Packagi ng:
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
.
. . . . . . . . .
Shared haplotype compared w ith other popu l ations:
3 .6
Gene d i versity i n U A E popu lat ion and i n sub-popu lation:
3.7
AMOVA resu l ts in U A E popu lation:
.
. . . . . . . . . . . . . . . . . . . . . .
. . 76
. .
. .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Xl
71
. . . . . . . . . . . . . . . . . . .
.
. . . . . . . . . . . . ...
77
78
C HA PTER I V : CO C L U 10
Con clusio n:
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Bibl iograp h ) :
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
XII
79
81
84
L I ST OF TAB L E
Tab le 1 : D i fferent types of T R loc i
. . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . .
Table 2: T total vol u m e for m u lti-mix 0[96 react ions
. . . . . . . . . .
.
. . . . . . . . . . . .
.
. . . . . . . . . . . . . . . . . . . . . . . .
Tab le 3 : Demon trate the Polymerase Chain React ion cyc l ing parameters
Tab le 4 : AmpFL TR
Y fi ler
k it loc i and al leles
13
25
. . . . . . . . . . . . . . . .
26
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ..
27
Tab le 5: Total o l u mes of D A am p l i fied plate in a C E step
.
Tab le 6: Total n u m ber of a l leles for each loc i in UAE pop u l at ion
.
. . . . . . . . . . . . . . . . . . . . . . .
32
. . . . . . . . . . . . . . . . . . . . . . . . . . . . .
42
. . . . . . . . . . .
Tab le 7: Predom i nant a l le l e i n UAE popu lat ion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Tab l e 8: A l l Ie frequenc of d i fferent l oc i" itb pie charts for U A E popu lat ion :
Tab le 9:
. . . . . .
44
l le l e F req uencies for tbe su b-popu lations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Tab l e 1 0: oc i
.
. . . . .
61
Tab l e 1 1 : A l le l e frequency of U A E popu lat ion compared w it h other populat ions
. . . . .
66
. . . . . . . . . .
68
\
it h a l leles that are not shared between all regions
.
. . . . . . . . . . . . . . . . . . . . . . .
Tab l e 1 2 : H ap lotype freq uency for shared hap lotype in the U A E popu lation
. .
Table 1 3: Pairw i se Popu lat ion Matrix of Nei Genetic D istance for sub -popu lat ion
Tab le 1 4 : D iscr i m i nation Capac ity and H aplotype D ivers i ty in U A E popu lat ion
Tab le 1 5(A-E): Hap lotypes that are shared i n the population
71
73
78
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
79
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
79
.
. . . . . . . . .
.
70
. . . . . . . . . . .
Tab l e 1 7: A M OVA design a nd resu lts (average over 1 7 loc i ):
XI I I
. . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Tab le 1 6 : Genetic diversity i n U A E population and i n su b-popU lat ion
Tab le 1 8: AMOVA res u l ts i n other popu lation:
. . .
LIST OF FIGURES
Figure I : Com ponent of the 0
Figure 2 :
c hemat i c o f
structure
...............................................................................
a nd Y sex chromosomes
. ................................................................
Figure 3: Relat ive po it ions of 1 7 markers TRs loc i
Figure 4 : t\1ap o f the U n ited
.
............................................ ............
6
8
14
rab E m i rates . ....... .......................... . . . . . . . . . ............................... 1 5
Figure 5 : Analy i s wo rkflow for a l l sample . ..... ...... ........... ................. ................ ...... ............ 2 0
Figure 6 : 1 7 loc i of Am p F L S T R
Y file
PC R w i th ladder and internal control
. ....
Figure 7 : Gen Mapper l O-X soth are plot the A m p FIST R Y fi ler A l le l ic Ladder.
Figure 8 : Y
T R p ro fi l generated us ing A m p FI S T R
Y filer™
31
....
32
. ....................... .........
39
.
Figure 9 : A llele frequency for the predom inant a l leles i n t he U A E population
...........
43
F igure 1 0( A-Q) : A l lele frequency of d i fferent loc i i n sub-populations .
. 58
Figure 1 1 : Variance d i stribut ion of the UAE population
.. 63
.
F i gure 1 2: Variance d i stribut ion o f the three reg ions
...................... .
. .................................................
.
. .
. ............ ........ . . . . .. ............................
Figure 1 3 : Total num ber o f U n ique and Shared H aplotype
.............................. .. .... ........
72
Figure 1 4 : Matc h ing versus U n ique Haplotypes by Locus .
...............................................
76
XI V
. . .
64
C H A PTER I : INTRODUCTION
1
1.1
L i t e r a t u res review :
A
the 1 920s began. the existence of the Y chromosome was debated and
Theop h i l us Painter pub l i hed a very short art i c l e c la i m ing the presence of Y
chromosome in hu mans and other pri mate .
Y c h romosome unl ike m i tochondrial
genome. i inherited patern a l l y and approximatel
95% percent of Y chromosome is
inherited as one hap lotype (Rosa et aI., 2007). Therefore Y c h romosome represents
an invaluable record of a l l mutations that have taken p lace along male l ineages
throughout the e olut ion. The i m portance of Y c h romosome is not l i m ited to
determ ining the ex of a spec ies, but invol ves the d i fferent i a l gene dosage, and shows
a characteristic pattern of inheritance in males and fem a les.
Y chromosome
consti tutes approx imately 2% of the human genome and cons ists of h ighly
polymorp h i c loc i . Therefore, Y chromosome analys is i s used in many app l i cat ions
panning d i fferent fields and inc l udes patern ity determ ination, human m igrat ion,
archeogenet ics, and pa leontology (Rosa et a I . , 2007). Another i m portant app l ication
of Y c hromosome analysis i s in forens ic science it i s used to solve murder case, rape,
and e en exonerat ion of convicted felons (Carva l ho-S i lva et a I . , 2001).
There are a flu rr
of stud ies involv ing Y c h romosome and human popu lat ion
such as stud ies in human m i gration, influence of geographical location, and shap ing
of h u man c u lture (Gaetano et a l . 2009). The beauty of Y c h romosome studies lends
itse l f to several s lowly m utating a l leles on non-recombin ing Y chromosome (N RY )
that c a n be used to group human Y chromosomes into veliical paternal l ineages cal led
Y c h romosome haplotype.
Many more stud ies are ava i l ab l e t hat address the
2
i m pol1ance of Y c h romosome stud ies (Jobl ing et a I ., 200 3 ) .
The Y chromosome
tudy is a lso u ed to determ ine d i sea e assoc iat ion in a population ( ezgin et a l . ,
20 1 0). The e stud ie provide i m portant ind icators of human uscept i b i l i ty to d i seases
and response to d rugs ( K rausz et aI., 2004 ).
Despite the i m portance of Y
chromosome stud ies. there is a dearth of informat ion on the popu lat ion of Arabian
Gu l f regions. The a i m of this study is to characterize Y chromosome spec i fic loc i
that can dec ipher d i vers it
o r uniqueness o f the U A E populat ion structure.
For a
comprehensi ve su rvey of Y c hromosome polymorph ism, it is i m portant to study a
larger populat ion ac ross the U A E . Th i s
the UAE popu lation
\ \ h ic h
\
i l l dec i pher patri l ineage geneti c d i ersity in
is one of the i mportant elements to e l uc idate cu ltura l
infl uence, t h e origin of surnames. d ialect, d i sease assoc iat ion, popu lat ion structure,
and esta b l i shment of forens ic databases.
1.2
Hu m an G e n om e :
H u man genome i s d i ploid and contains two copies o f chromosomes, each
inherited from a parent.
Du ring gametogenes is, the genome is red uced, to haploid
9
state that com prises of 3 x 10 bp ( K rawczak et a I . , 1994) .
Genet ic informat ion
(except for m i tochond rial genome) res ides in the nuc leus of the cel l and is organized
into physical structures cal led c hromosomes
cel l d i v is ion.
v,
hose structural state c hanges du ring
In general , Chromosomes contain the genetic informat ion of cel ls
cal led Deoxyri bonuc leic Ac id ( DN A ), and it controls many cel lu lar funct ions ( Daniel,
2008).
C h romosomes are norm a l l y transm itted as an intact unit from parent to
c h i ld ren. A ccord ing to the random assortment princ i p l e, these markers res id ing on
one ch romosome are inheri ted together and they exh i b it geneti c l inkage. In contrast,
3
markers on d i fferent chromosomes are general ly inherited independent ly of one
another and they do not demonstrate l inkage ( Stryer, 1999). Con ersel y, markers that
ho\',
genet ic
chromoso me.
l inkage,
L inked
imply ing that these are c lose together on the same
loc i are transm itted
in c l usters or haplotypes unless
recomb inat ion proces es changes their pha ing ( Bac ker et a I . , 199 5 ) . That is, the) are
associated together more often than chance wou ld pred ict.
H u m an genome i s d i stributed over 46 chromosome and 23 homologous pai rs
(Daniel, 2008). Tv. enty-two pa i rs of these chromosomes are cal led autosomes and
labeled accord ing to length, longest to shortest, and one pa i r is c a l l ed sex
chromosomes, X and Y . A norm a l person receives two copies of chromosomes, one
set i s derived paternal l y and one set maternal ly. The d iploid cel l s results from the
fusion of 2 haploid cel ls sperm (23 c h romosomes) and egg (23 c h romo omes) to have
an em bryo or gametes of 46 c h romosomes. Y chromosome determ ines the sex of the
em bryo. Ma les have one X and one Y chromosome ( X Y ), w h i le females have two X
chromosomes ( X X ).
Therefore, the gender of the embryo is determ ined by the
paterna l contribution and 0 A test ing in the l aboratory can determ ine th i s . H u man
genome are very s i m i lar to one another and on average two ind i v idual share 99.7% of
the sequence of their DN A . The remaining 0.3% (�10 m i l l ion nuc leotides) bears the
variation that exi sts among ind i v iduals (Tishkoff et a I . , 2004 ) .
Some extranuc lear
DNA is a lso present in the m i tochondria that are located in the c ytoplasm of the cel ls,
and can be used for human ident i ficat ion. A lthough the majority of these nuc leotide
d i fferences are neutra l .
4
1 .3
Th e t r u ct u re an d com p o it ion of h u m an ge n om e :
I n 1869, Frederich 1ie c her a German b ioc hem ist \\ a the fir t to obsene D
and unfortun ate l ) , re earchers d i d not rea l ize the i m portance of t h i
long t l lne
In 195 3 James Wat on, an
mer ican b iologi t. and Fran c i
Briti h ph) SI ist. propo ed a model ror the tructure of t he D
model \\ a
molecule for a
Crick, a
molecu le.
This
ba ed on re earch by Rosa l i nd Fran k l in, Maurice W i l k ins, and other
c ienti t ( Daniel, 2008). Thei r \"or"-s opened the doors to a ne\\ field of re earch
and one of the e fields i
kno" n as molecu lar genet ics, w h i c h i s the tud; of the
fu nct i on-structure relat ionsh ip and the tudy of in heritance and variat i on at molecu lar
le\ e l .
t t h e mo t b a ic le\ el, D
"ru e . D
i
found i n nearly a l l - l i v i ng cel l except R A
i s a molec u l e that is sh aped l ike a 1:\\ i ted ladder and i t cons ists of t\\ O
eparate trands that i ntert\\ ine to form a dou b le hel ix, a stru ture that resemb les a
p i ra l taircase a shown in figure I . Each strand of D A is com posed of a eries of
smal ler molecu les c a l led nucleotides.
[n turn, each nuc leot ide i s itse l f made up of
three smal ler molec u les or cal led
prl mar)
components:
monosaccharide deox) ri bose, and a pho phate group.
a n itrogenou
ba e,
The nuc leotide are jOllled
together b) co a l ent bonds to form polynuc leotide c h a i ns. There are four different
D A nuc leotide , each defined by a spec ific n itrogenous ba e:
den i ne ab bre lated
as ( A ), Thy m i ne abbre iated as (T), Guan ine abbrev i ated as (G), and C ) 10 i ne
abbreviated as ( C) . D A contains t\\ O types of n itrogen-contai n i ng bases. Aden ine
and Guan i ne, \\ hose ring-sh aped molec u les h ave
i:\. mem ber , are c a l l ed purine;
\,h i le C ) 10sine and Th) m i ne with fused fi ve- and six-mem ber ri ngs are cal led
p) r i m i d i nes. A ccord i n g to complementary base pairing concept, A denine and
5
Th�l1linc ah\a�
C) to
111C
bd e pair \\ ith each oth r h) t\\O h)drogen boneL \\hil'. guaninc an I
art! attache I togcth·r b:- three h)drogen hond: :ee figurc I (Dani -I. 200R).
r
I'igure I: Component of th
J
a ckbOfl
Dl IA ::,tructurc
'.ltLlrall�. compkmentar:- base-p<liring is responsibk for the abilit) to accuratel)
replicate D, '1\ n1()ICCllk�. \\ith its genctic inlormation and pas: it on to the next
gcneration (I),lI1iel,
IA
200X).
Human V-Chromosome:
The human Y chroll10::'OlllC is onc or the 1:1. test c\oh ing part::. of til
!.!enome.
.....
human
In the In t decade. Y chrolllosome ha. been increasil1!.!h
...... .. used to ill\ c. ti!.!atc
'-
the migration . e\ lliution. and range c, 'pansions of modern human' <tIld it al. 0 ha
dttrdctcd a great ckal of attention 0\\ ing to it. supremac:- in mak
,md unique haplot) pc statu� in the genome.
mcahHlrm.1 mchrio molitor at Br� n �1a\\r College.
6
1905
[n
,
.
c
.
dckn11lnation
during cI ::,tuJ)
'etlie StC\ cn. ha
or the
id -ntili -d
Y
hromosome as a sex-determ ining chromo orne. and named it Y becau e it ah\ays
c. I
ted
111
paIrs \\ ith X
hromo orne.
Whi h \\a d i sco\ered in 1890 by H ermann
Hcnk ing ( Ha ley et a l . . 20 I 0). There are eyeral interesting attributes and b iological
feature of the human Y chromosome: one of the e features i s carrying a l im i ted
number of fun t ional gene
\\ ith a high proport ion of repeat element
( I i et aI.,
2003 ) . Add it iona l l y , it ha i m portant b iological male- pec i fi c funct ion \.\ ith d i rect
con equence
on male fitne s inc lud ing male fert i l ity and test is determ ination .
Feat ure . l ike pattern of i nheri tance among other . make the study o f Y chromo ome
poly morphi m
\ery
usefu l
for
inference
of population
hi tor ies.
foren ic
app l icat ions and patern ity analysi ( I i et a l . . 2003 ).
1 .5
t r u c t u re of t h e Y -Ch ro m osom e :
Y Chromo ome i
( H rrie et a l . . 1986).
one o f the sma l le t chromo omes In the human genome
It repre ents on l) 2�'0 of the human genome in male and it
contains about 60 m i l l ion base pairs ( her et al.. 2002 ) .
d i\.ided into two sma l l tips kno\ n a
Y Chromo ome can be
pseudoautosomal region ( PAR) and non­
p eudoauto omal region (male-spec ifi c ) that are man) t imes larger than PAR. There
are 1\\0 region in the pseudoautosom a l region cal led PAR I \\ hich is located at the tIP
of the short arm (Yp) w i th approximatel} 2.5 m i l l ion ba e pairs in length and PA R2
\\ h ich i s less than I m i l l ion base pairs in length and it i s located at the long arm (Yq)
of the Y chromo ome ( A l i et aI., 2003; see figure 2).
On the other hand, the rest of the Y chromosome (about 95°/0) \.\ hich is termed
the non-recombining portion ( RY ) or ma le-spec i fic region ( M Y ) does not undergo
sexual recom b inat ion during meiosis. [t is ah a} in a haploid state, and therefore. is
7
transm itted intact through paternal l ineages.
The
RY remains the same from the
father to on unless a m utat ion occurs (Butler, 201 1 ).
(a)
x
Non-recombining
Pseudoaulosomal
1 (PAR1) portion of Y-chromosome region 2 (PAR2)
(NRY)
Pseudoaulosomal
region
Male-specific region of the Y
(MSY)
(b)
Yp
r-L-
Centromere
Yq
:cx=
___
__
HeterochromallC region
Euchromatic region
(not sequenced)
(23 Mb)
-30 Mb
F i gure 2: Sc hemat ic of X and Y sex chromosomes.
The Y c h romosome is com posed of both euc hromat ic and heterochromatic
regions of \\ hich onl y the 23 Mb of euchromat in has been sequenced (But ler. 2011).
The Y chromosome sequence composit ion. l i ke any other c h romosome, consists of
unique sequence (norm a l l y represent cod ing sequence), and repet it ive. The repetition
are either repeated randem ly or interspersed and general ly they are referred to as
sate l l i te and its subset depend ing on the length of unit repeat. The fol low ing sections
a im at introd uc ing satel l i tes 0 A characteristics and its su bset (for revie\
Job l ing et a!., 2003 ).
8
see
a t eJl i t e
1.6
DNA:
There are four major c lasses o f tandem D
\\
repeats that have been cia sified
ith in the human genome: satel l i te 1, sate l l ite 2, satel l ite 3 and sate l l ite 4 ( 1 i l kos et
aI., 1997). Around 2 0% of the human genome is composed of \ arious sate l l ite D A
fam i l ies ( Ba l lantyne et a I . , 1 989).
ate l l ite D As were origina l l y ident i fied by the
eparate band ing of part of the genom ic D A in eq u i l ibrium dens ity grad ient
centrifugatio n.
Sate l l ite DNA is c lass i fied accord ing to their genom ic local izat ion,
such a centromeric, telomeric or d i sper ed along the chromosome. Satel l ite D A is
pri m ly located near the centromeric regions of the c h romosomes and the repeat unit
length can extend for se eral t housand base pa i rs ( W i lJared et aI., 198 7 ) . A lphoid
c lass is another major tandem repeat DNA spec ies, 'Wh ich
approx i matel
is composed of
2% of the whole genome (M anue l i d i s. 19 8 7 ) . The A l phoid satel l ite
cons ists of tandem arrays of approximately 17 1 bp monomers ( Yang et a I . , 1982), and
it i
local ized to the pericentromeric region of each human chromo ome (Job l ing et
a I. , 1998).
1.7
M i n i s a t e llite DNA :
M inisatel l ite term refers to the Variable
a c las
of h ighly repet i t ive satel l ite DNA.
umber Tandem Repeat ( VNTR) that is
By definition. m inisatel l ite means the
section of DNA that cons ists of a short series (10-60 base pa i rs) of nuc leotide. These
occur at more t han 1,000 locat ions in the human genome.
There are two types of
m inisatel l ite; the fi rst is cal led "H ypervariable M in isate l l i te' that have a core unit 924bp long and are found mainly at the centromeric regions, and the second is cal led
'Telol l1eric M inisatel l ite" that have core units 6 bp long, and have t housands of
9
repeated sequences at the telomeres. During the last two decades. a number of h igh ly
variable regions in the human genome ha e been detected and character ized. The use
TR polymorph isms, subsequent l), ha
of
become one of the most succes ful
changes in the fie l d of forensic medicine for persona l identification and paternity
testing. In Y chromosome two m i nisate l l ites have been described.
The first \\ as
M Y l ( D Y FI 5 5 I ) and which has a 1% mutation rate per generat ion. Accord ing to
Jobling, this marker was reported as the most variable 10cLls in Y chromosome
( Jobl i ng et aI., 1 996).
W h i le the other m i n isatel lite described is M Y 2 ( DY S440)
conta in on ly two units of three or four cop ies of 99- 1 1 0bp repeating unit (Gi l l et aI.,
1 995).
One of the m a ll1 advantages of these markers is that they are h igh ly
pol morph ic in som e lineages.
1.8
Microsa t e l l ites DNA :
Microsate l l ite is defined as S i m p l e Sequence Repeats ( SRs) or also
Tandem Repeats ( S TRs).
hort
It is another source of polymorph isms of the human
genome, which be long to the family of repetitive non-coding DNA sequence. They
can be found in coding and non-coding regions. Microsate l lite is characterized by the
length variation in tandem arrays of simple repeat sequences of 2-6 base pair. STRs
provide a rich source of polymorphic markers resulting from variations in the number
of cop ies of the repeated pattern.
They are simi lar to V NTR loci and m i nisate l lite
loci but the latter contain longer repeat units.
STR loci display several ad vantages
that m ake them attractive as genetic markers. They are very plentiful , averaging one
trinuc leotide tandem repeat locus for every 1 5 kb in the human genome, and they are
amenable to peR amp lificat ion by using flanking sequence primers. The resulting
10
ampli fication by fragment of the indi idual
TR loci ranges from 1 00 to -.fOObp. The
characterization of a l arge number of highl
I
polymorphic
TR loc i along w ith the
construction of \ \-e l l -defined a l lelic ladders for several of the m ost eas i l y interpreted
loci, al lo\\ s for an increased use of these system
determina tion. The Y c hromosome is
seque nce.
in forensic anal}sis and paternity
ery rich in several c lasses of repeated D A
Using these microsate l l i te loci is a very useful tool in the forensic
ident ification of male D A in rape cases \ ith male and female fractions (see sect ions
be lo\\ : Butler, 20 1 1 ).
1 .9
S h ort Ta n de m R e p e a ts ( STRs):
The human genome is ful l of repeated DNA sequences. STR is one example of
these short repeated sequences. The nature of STR give rise to high ly polymorph ism
region . These tandem repeats c lusters are characterized by b locks of DNA of some
common sequence \ hic h is repeated over and over in tandem.
These repeated
sequences come in various sizes and are c lassified according to the length of t he core
repeat units.
Short tandem repeats are found around the chromosoma l centromere
and consist of a short repeat un it ranging approximately 2 to 6 base pairs in length
(Butler. 20 I I ) . The number of repeats in
individuals,
\
TR markers can be highly variable among
h ic h make these STRs effective tools for studying polymorph i sm and
genet i c variation between individuals and populations. A t the beg i n n i n g of 1 996, the
FBI Laboratory launched a nationwide forensic science effort to establish core STR
loci for inclusion within the national database known as CO DTS (Comb i ned DNA
fndex System).
The 1 3 CO DIS loci are: C S F I PO, FGA, T H O I, TPOX, V WA,
D3 S 1 3 5 8, D 5 S 8 1 8 D7S820, D8 S 1 1 79, D 1 3 S3 1 7, D 1 6 S 5 3 9, DI 8 S 5 1 and D2 1 1 1 .
11
These loc i are nat ionally and internationa l l y recognized as the standard for human
ident i fication (Co l l i n et a!. . 2004). Ho\\ e \ er. the number of loc i that are u ed for
genet ic \ariation a the kno\\ ledge of the poly morph ic loc i is increasing.
1 .9.1
Types of STR loc i :
M icrosate l l ites c a n b e c lass i fied based o n s ize, t h e nature of the repeated un it or
their pos it ion w ithin the genome. The m i crosate l l i te, based on its repeat un iform ity.
can be c lustered i nto four categories as shown in tab le I ( U rquhart et a!., 1 994).
Often the repeats are inte rrupted with fe\ base pairs.
1.9.2
S i m p l e STR loc i :
Genera l ly it contains one repeat ing unit with equa l length and sequence and they
are not i nterrupted by ot her sequences. Exam p les of t his type are D 5 S 8 1 8, D l 3 S3 1 7,
D7S820, 0 1 6 539. TPOX and C SFIPO loc i . The s i m p le STR can be further
subd iv ided into s i m p le one repeat i ng sequences such as H U M F E IFPS and simple
with non-consensus a l le les l i ke H U M T H O 1 .
1.9.3
Compou n d STR loc i :
T h i s type of STR loc i consi sts of two o r more adjacent s i m p l e repeat sequences
( H U MG ABRB 1 5 ) or consists of a compound with
on-consensus a l le les. such as
( H U M v W FA3 1 /.A) .
1 . 9.4
Complex STR loci:
This type of STR loc i al lele com mon ly consi sts of regular tetra nuc leot ide repeat
units
\
ith i nterspersion of d i mer, trimer and hexamer i nvariants.
12
H y p erva riable
1 . 9.5
TR lo c i :
T h i s locus is h ighly polymorphic and contains com plex compound regions that
can sho\\ many a l leles that d iffer by one base pair.
HU 1ACTBP2 or
Examples of this ty pe are
E 3 3 and 0 1 1 554 loc i .
Tab le 1 : D ifferent type o f T R loci
Loci
Type
No
Repeat E x a m p les
1
S i m p le
D5S8 1 8
( AGATh-16
2
Com pound
H U M v WA
(ATCT)2 (G TCTh-.J(ATCTk 1 3
3
Complex
02 1
(TCTA )-I-6(TCTG )S_6[(TCTA)3 TA(TCTA )3
1 1
TCA(TCTA)2TCCA] (TCTA )s_16(TATCTA)o_l TC
A common repeat structure (AAAG) with
ACTBP2
Hypervariable
4
d if ferent mono, d i , tri, tetra and hexamer
invariants that are scattered throughout the locus.
1 .10
Y-STR Ma rkers :
There are two categories of DNA markers, which are used to exam1l1e Y
chromosome d i ve rs ity. The fir t marker is cal led b i -a l l e l ic loci, \ h ich exhibits two
poss ib le
B i-al lelic
a l l e les.
markers
are also
referred
(0 as un ique event
polymorp h i ms ( U E Ps ) and that is due to their low m utat ion rates, which is est imated
from 1 0-
to 1 0
-9
per generation.
The exam ple of t h i s marker i nc ludes single
nucleot ide polymorph isms ( Y-S P) and A lu e lement insert ion ( Y A P ). The second
marker cal l ed multi-a l l e l ic loci, wh ich includes two m i n i sate l l ites, and several
hund red STR markers.
The ir results are characterized as haplotypes and it can be
used to d ifferentiate Y chromosome hap lotypes w i t h h igh resolut ion d ue to the ir
h igher mutat ion rates (But ler, 20 1 1 ).
13
Y chromo ome 0 A analysis can be performed
defines hap lot) pe or Y -
\\
ith either Y -STRs \�hich
Ps \ \-hich def ine hap logroup. Y -STRs re ults exhibit more
3
\ ariabI l it) due to the rapid change in mutation of Y - TRs (mutation rate ::::: 1 in 1 0
compared to Y-
Ps (mutation rate::::: 1 in 1 09 ) (But ler, 20 1 1 ) . Thus, Y - TRs ha\ e a
greater use in forens ic identification of male 0 A such as in rape cases and patern it)
determ ination in deficiency cases where the al leged father is m i ssing. The majority
of Y- TRs result in a single polymorphic fragment upon peR amplification, but
there are some Y - TRs \\ h ich originate from regions that are dup l icated on the Y
chromosome,
result ing in the
presence of
h 0
ampl icons of variable s ize
(i.e.DY 3 8 5 , DY 459 and recently DYS464 (Butler 20 1 1 ) . The fol lowing figure 3
i l lustrates the relative pos itions of 1 7 markers
TRs loci commonly used in human
identification setting.
PAR1
-
5
DYS393
DYS456
�AMELY
- DYS458
cenlror;le'8
10
DYS19
DYS391
15
20
'2
5
DYS635
DYS437
DYS439
DYS3891111
--
DYS390
GATA-H4
DYS438
-
DYS385a
DYS385b
DYS392
DYS448
PAR2
Figure 3: Relative positions of 1 7 markers STRs loci
14
1.1 1
Bacl-(Jrollnd of United Arab Emirate (UAE):
0
,
0
N
tt
W
E
5
R
BIA
GULF
• ABU OHA I"
•
Uw....s
UNI
ARAB
INA
A
'lAY 0
IRA
I
A
Figure -.f: l\lap of the United Arab Emirates.
The United Arab Emirates (UAE) is one part of the Gulf Cooperation Council
(GCC ) \\hich consists of si-..;: gulf countries including Bahrain, KLl\\ait. Qatar. Saudi
Arabia. and Ol11an.
In addition. the United Arab Emirate is located in the eastem
part of the Arabian Peninsula. extends along part of the Gulf of Oman and the
southern coast of th' Arabian Gulf.
The United Arab Emirates i. a constitutional
federation of Se\ en emirates: Abu Dhabi. Dubai. Sharjah. Ajman. l mill al-Qai\\ain.
.
,
Ras al-Khail11ah and Fujairah. The federation \\(1-' formally established on the 2 of
December 1971. The ll:\E occupies an area of 71023.6 Sq. km along the southeastern tip of the Arabian Peninsula.
As 5ho\\n in figure -.f. Qatar lies to the v,est.
, audi Arabia to the south and west. and Oman to the north and east. The CAE lies
bet\\e
" en
ea.·t (lfAE
statistical center. 20 10). Furthermore. the capital and the largest cily of the federation
l�
in the U E is
J Iov. ever,
bu Dhabi. \\ hich accounts for 8 7 percent of the
Els total area.
jman is the smal lest em irate, encompassing onl; 2 5 9 square kilometers.
Accord ing to se era l studies, researchers discovered that the
nited Arab
Emirates has a long history, recent fi nd ings on the eastern side of the Hajar
10untains and in the , \-'estern region of Abu Dhab i having pushed the earliest
evidence of Man in the Emirates back by hundreds of thousands of years. The arrival
of envoys from the Prophet Muha mmad ( PBU H ) in 630 AD hera lded the conversion
of the region to Islam. By 6 3 7 AD Islamic armies were using Julfar (Ras al-Khaimah
Em irate) as a staging post for the conquest of Iran.
Over man
centuries, Julfar
became a ,,,, e althy port and pearling center from which great wooden dhows ranged
far and \ ide across the Ind ian Ocean.
The U A E population can be d i vided into three sectors Urban (had har),
nomadic ( bedu) and rura l . Bedouin people are traditiona l l y inhabitants of the Arabian
Gulf who claim descent from t\ 0 male lineage: A dnani and Qahtani (N ature, 20 1 0) .
In addition, these nomadic peop le are cal led people of the desert, w ho are animal
owners and move about with their came ls, sheep and goats in search of graz ing and
concentrate around t heir we l ls. Some of them used to gather firewood from the scrub
and bring it into the coasta l tow ns. H owever, H adhar peop le made their l i ving from
the sea. M oreover, they lived by fish ing and pearl industry. In contrast, rural people
used agriculture as a main way of life in the eastern mountain area and oases.
However, what was overwhe l m ingly rural and bedu a generat ion ago is now
preponderantly urban ( AI-Sayegh,
1 998).
Therefore, in this study the UAE
population was divided into three regions Northern, Eastern and Western based on the
prox i mit ies.
Ib
l n thi stud
\
e are address ing the heterogeneity of the
regard to paternal linage inher itance. The
E popu lation
\\ ith
A E population as per our know ledge has
not been genetica l l) characterized on a large scale. This stud) is one step in a series
of studies of the U E population. The specific aim of this study is to define the U A E
population structure a n d hie rarchy th rough anal ysis o f 1 7 STR of Y chromosome.
1.12
O bj ec t ives :
Se eral objectives of this study can be defined as the fol low ing:
J - To establish a thorough profi le of Y polymorphism in the U A E .
2- T o stud y t h e pattern o f migrat ion a n d geograph ic in fluence .
3 - To eva luate the anal ysis of paternal lineages for forensic purpose.
4- To investigate the variance of 1 7 short tandem repeat (STR) loci in the
U A E population.
5- To study hap lotype and hap lotype frequency in the UAE population
th rough the anal ysis of 1 7 polymorphic short tandem repeat (STR) loci.
17
CH A PTER II: M ETHODS AND M ATERIAL
18
a m ple Colle c t io n :
2.1
Buccal s\\ ap samples were col lected from 723 nati e males from the U nited
Arab Emirates population of \\ hich 345 were analyzed for this study. This is the
largest
tud) in the region . The samples \\ ere obtained randomI) from unrelated
individua ls encompassing the U A E population (A bu- Dhabi, DubaL
Ra
harjah, FUJurah,
AI kaimah, Aj man, Um A lqawaen, Khalba and K horfakkan).
The random
sample col lection complies with the regulations of many scie ntific communities such
as the I nternational
ociety for Foren sic Genetics ( ISF G ) and the
ational Research
Council (NRC). According to these bodies a l l sam p les deposited in the international
databases should be col l ected randomly in order to eliminate biases.
2.2
C o n s e n t Form :
The buccal samp les were col lected \ ith written consent from the subjects. The
consent Form was approved by AI-Ain Medica l District Human Research Ethical
Committee which is an accredited organization of Federal Wide Assurance ( F WA)
and comp liant with IC H/GC P Standards. The consent form \ as written in Eng lish
and transl ated into Arabic. The subjects were informed of the nature of study before
the relevant information, such as name, family name, place of origin, was obtained .
2.3
B u ccal Swa bs Packa g i n g :
Samp les col lected from outside of AI-Ain city were trans ferred i n a n icebox to
the National DNA Database (NDNAD) Laboratory. On arrival, consent forms w ere
separated from the samp l e and the sam p les were stored at -20°C for further use.
19
2.4
P r e p a r a t i o n a n d Sa m p le B a t c h i n g :
Once the amples were received i n the lab, a unique barcode \v a ass igned to
ubsequent ly. the samp les were batched together b) robot ic pro ess
each sam pl e.
cal led Tube tar.:R' ( manufactured by Peak Analysis & Automation, U K ) and placed in
an extraction rack for processing. Briefl y, TubeStar
that al lo\\
is a pos i tional logging station
batch D A extraction simultaneously. The samples are distri buted in an
extraction rack that consist of 96 \ve l l s of wh ich 86 \\ e l l s are for D A samples and
1 0 w e l l are for controls (positive and negative extraction controls, blank tubes for
Ile l ic Ladders and PCR controls).
2 .5
S t o rage C o n d i t i o n :
DNA sam ples were analyzed b y AmpFISTR Y filer kit (Life Tech nology) . The
°
kit is stored at -20 C and inc ludes AmpFl STR Y fi ler Primer set, Amp liTaq Gold
D A pol) merase. A m p FISTR Y filer PCR Reaction Mix, A m p FISTR Control DNA
007 and AmpFISTR Y fi ler A l le lic Ladder. On d e l i very to the lab, AmpFISTR Y
fi ler
lIelic Ladder was isolated and stored at 4°C for post amplification as to prevent
cross contamin ation . A l l other reagents \ ere stored at 2-8 °C . Chemicals that contain
fluorescent (i.e. A m p FISTR Y fi ler A l le lic Ladder and Pico Green etc. ) are sensitive
to l ight and were stored in a dark area.
2.6
G e n e ra l S a m p l e P roced u re s :
B
Batch i g
n
E x t rac t i O n
Q u a n t i fil c a h·
A m p l i fil c a t i o
C a p i l la ry
n".... ..
o,n."-....
_
_____
__________
________ ,. '--__________
Figure 5 : A nal ysis workflow for a l l samples.
20
E l e c t ro p h o resi
The workflow in figure 5 sho\ s the general sample processing. The D A for each
ith si lica mem brane method in
batch \ a
extracted
Biorobet
nive rsa l r nstrument; then the batch is mO\led for quantification \\ ith Pico
\
D A D Laboratory \ \ ith
Green fluores cence on I nfi nite pre 200 Inst rument platform . A fter quant ification of
D A, the D A (96-we l l Quant D A ) is amp lified on Tetrad peR machine.
Final ly, the amplifie d D
p late was loaded on 3 5 00 X L Genetic Analyzer \\ h ich
(24 capi l lary capac ity) for fragment resolution.
2.6. 1
D N A E x t ra c t i o n P roce
s:
A l l the D A extracted processes were performed according to the manufacture' s
protocol . The first step o f analyzing t h e genomic D A is to isolate D A from t i ssues
or ce l l
using a comb i nat ion of physical and chemica l methods.
platforms and technologies are availab le.
One of the p latforms is cal led
Membrane Matrix. Biorobet Universa l System from Qiagen
u es sil ica mem brane m atrix method.
Many different
ilica
is an instrument that
It is designed to perform ful ly automated
medium for high throughput app licat ions in 96-we l l format.
from swabs, b l ood, and forensic sam p les etc.
DNA can be purified
Moreover, it provides a rapid and
efficient method for D A extraction from nuc leated cells. The basic princIple of
si lica m atrix can be described in four stages. The first stage is to lyse the tissue by
breaking up the ce l l s \ ith reagents l i ke A TL
presence of proteinase K.
ATL
buffer, physica l agitation in the
buffer contains sodium dodecyl sulfate (SDS)
detergent that disrupts ce l l mem brane and dissociates protein D A comp lex.
Proteinase K solution, meanwh i le, degrades prote ins includ i ng DNA scaffolding
proteins and other p rote in debris. The second stage is to isolate D A from the ce l l by
21
adding A L'& l ysis buffer and Ethanol .
inactivates nuc l eases.
A L:& buffer is u ed to l yse the ce l l and
It contains guanidinium hydroch loride chaotropic salt \\ h ich
removes \\ ater from hydrates molecules in a solution and renders D A susceptible to
bindin g to ilica matrix in the spin plate. As D A is insoluble in alcohol, ethanol is
used to prec ip itate DNA out of fluid suspension. Therefore, it increa es D A affinity
to bind to i l ica spin column for further e lution of D A through the spin plate. The
third stage is D A Puri fication . The purification step uses wash buffer (A W l and
A W2).
Each of the buffers has a different ethanol concentration.
A W l being the
more concentrated buffer fol lowed by A W2. This ensures the DNA rema ins bound to
the silica matrix on the column.
The buffers act to disso l ve and remove ce l lular
debris and contam inants that are not bound to the s i l ica matr ix. The vacuum d raws
these th rough the spin column. The result of this stage is to leave c lean and purified
D A bound to a si lica matrix.
AW
aminomethane,(HOC H 2)3CN H2]
and
buffer conta ins Tris[tris(hydroxymethyl)
Ethylenediaminetetraacetic
acid
(EDTA ) .
EDTA removes debris b y chelation metal ions (attaching molecules t o itse lf using the
ionic charge) . The final stage of DNA extract ion is e lut ion . In t his step
uclease free
water (N F W ) is used . Water was added to change the bind ing cond itions th rough re­
hydrating the D A and removing hydrogen bonds, and subsequently eluting the D A
from the column. The last step ' as performed at 60° C and p H 8 . 3 for a maximum
efficiency.
22
2.6. 2
Q u a n t ific a t i o n P roce
:
D A quanti fication is critica l for mol ecular analy is" h ich il1\oh es
TR
ampli ficatIOn. There are se eral methods used to establish the concentration of the
D A
in
solut ion .
The most common
spectrophoto metric quantification.
method
of
D A
quantification
IS
Howe er, there are several other methods to
spectro photome tric quant ificat ion including F l uorometry, A luQuant, Quantitative
PCR (qPCR) and U V fluorescence in presence of a D A dye.
In this stud , DNA
\\ as quantified by usi ng DNA-bind ing dye, name ly, PicoGreen
( Life Technolog ) .
One of the advantages of this method is its abi l ity t o quantify a small amount of
doubl stranded DNA as l ittle as 2 5 pg/m l of dsDNA i n the presence of ssDNA. The
a say is linear
0
er three ord ers of magnitude and has litt le sequence-dependence,
which al lo\\ s it to accurately measure 0 A from many sources, inc lud ing genomic
DNA, v iral DNA, m i n i prep DNA, or peR amplification products.
DNA -dye
complex is then subjected to l ight at 480nm D A/PicoG reen \\ hich emits light at
520nm. The light emitted correlates w i th the concentration of the D A .
tandard
D A concentration curve is generated with Sonicated Human p l acenta DNA (SH P).
Fluorescence p late reader software.
PicoGreen® registers em ission of the light .
Fluorescence material are l ight sensitive and work ing solutions were prepared fresh ly
each t i m e b y add i ng 5 0).l1 of P ico G reen
immed iately w rapped in aluminum foi l .
23
and 1 0 m l of
uc lease-free water and
A m p l ifi c a t i o n P roce
2.6. 3
2.6.3 . 1
:
DNA A m p l i fi c a t io n us i n g A m p F LSTR
This
AmpF L TR
amplif) 1 7
tep involve
Yfile
Y fi l e
P C R ki t :
specific amp lification of fluorescentl), tagged D A .
PCR Amplification Kit ( Life Technologies) ,\. as used to co­
hOl1 tandem repeat ( TR) loci plus a sex determining (Ame logenin)
locus. These loci are: DYS456, DYS389 1 DY 390, DYS389 1 f , DYS4 5 8, DY 1 9.
DYS3 8 5 aJb, DYS393 DY 39 1 , DY 439, DYS63 5, D Y S392, GATA-H4. DYS437,
DYS43 8 and D Y 448.
The AmpFL TR® Yfiler® includes AmpFI TR Y filer
Primer sets ( 1 5 -30bp) that are locus-specific, and A m p l iTaq Gold
(an
DNA Polymerase
nz) me responsib le for D A rep lication which is obtained from exp ression of
Thermos Aquatics DNA polymerase gene cloned in E . coli). The other components of
the D A amplification assay is A mpFISTR Y filer PCR Reaction Mix which contains
magnesium ch loride as a cofactor for polymerase, deoxyribonucleotide triphosphates
(dNTPs). bovine serum a lbumin to stabilize the polymerase, sodium azide as
preservati\ e, TE buffer to maintain optimum buffe ring capacity, A m p FISTR Control
DNA 007, and A m p FISTR Y filer a l le lic ladder.
2 .6.3.2
M u l t i plex PCR Protocol:
A l l of the DNA amplification reactions were performed in multiplex fashion.
The Multip lex PCR technology was introduced in 1 98 8 (C ham berlain, 1 988).
Multip lexing PCR reaction a l lows simultaneous amplification of more than one locus
in a single tube unde r the same conditions. In this study amplification of the 1 7 loci
and amelogenin locus were performed accord ing to manufacturer ' s protocol with
24
minor modi fication to adapt for automation. Multi-m ix solution \\ as prepared for a
\\ hole batch that contained the fol low ing volume a sho\\ n in tab le 2 .
Tab le 2 : Represent tota l volume for multi -mix of 96 reactions.
Plate Size
React ion Mix ( )..d )
Primer ( �L l )
TaqGold (�d )
96
984 ( ng/ j..l l )
5 1 5 ( ng/ j..l l )
46 ( ngl �t1 )
Mult i-Mix reaction tubes were vortexed for a mini mum of 1 0 seconds and briefly
spun to 5 000rpm to ensure homogeneity of the components. The num ber of reactions
per batch was 96 including positive and negative controls.
Fifteen m icrol iters of
I\ l ulti-mix \\ as added to each "v e i l, fol lowed by the addition of 1 0 �d of 0 A ( 1 . 5
ng/ l Oj.. l I ) to a total olume of (25 j..l 1). The p late then was sealed by alum inum foi l and
centrifuged for 1 0 seconds and placed in the Bio-Rad Tetrad for h igh -throughput PC R
app lications.
2 .6.3.3 T h e r m a l Cy c l i n g P a r a m e t e rs fo r A m p F L STR® Y fi l e r® PC R k i t :
All PC R react ions consisted of hot-start cycle at 95° C for I I m i nutes fol lowed
b) 29 c cles of denaturation at 94°C, anneal ing at 59° C for 1 minute, and extension
at n° C for I minute per cycle.
The PCR reactions were comp leted by post-
extension for 45 minutes at 60° C as shown in table 3 .
25
Tab le 3 : Demonstrate the Polymerase Chain Reaction cyc l i n g parameters.
Cy c le
S t age
Tempera t u re
D u ra t i on
Des c r i pt i o n
Once
Hot Start
95°C
I I min.
Reconftguration of enz} me
Denaturation
94°C
1 min.
ds6NA strands split to ssDNA
P . An nealing
59°C
I min.
P. Extension
nOc
Primers anneal t o binding site
1 min.
Prim ers extended b y enzyme
Once
Post- e tension
60°C
45 min.
Once
Hold
4°C
00
28
2 .6.3.4
A l l strands extended to inc lude
extra Adenine base
Temperature decrease to denote
end of process
Lo c i a m p l i fied by A m p F L STR® Y fi l e r® k i t :
The fol lowing tab l e shows the loc i ampl ified o n Y chromosome, and the
corresponding f luorescent marker dyes. The A m p F I STR® Y fi l er
A l le lic Ladder is
used to genotype and score the sam ples. The al lele sizes represented in the al lelic
ladder and the genotype of the AmpFISTR® Control DNA 007 are also l i sted in table
4.
26
Tab le 4: A m p F L R 'E. Yfi le
manufacture protoco I).
kit loci and al leles (The tab le is adopted from
Locus
Alleles included in AmpFLSTR® Yfiler®
Dye
designation
Allelic Ladder
la bel
DYS456
DYS389 I
DYS390
6- FA
1 3, 1 4, 1 5, 1 6, 1 7, 1 8
1 0, 1 1 , 1 2, 1 3, 1 4, 1 5
1 8, 1 9, 20, 2 1 , 22, 23, 24, 25, 26, 27
DYS389 II
24, 25, 26, 27, 28, 29, 30, 3 1 , 32, 33, 34
DYS 1 9
1 0, 1 1 , 1 2, 1 3, 1 4, 1 5, 1 6, 1 7, 1 8, 1 9
DYS458
DYS385 alb
DYS393
DYS391
1 4, 1 5, 1 6, 1 7, 1 8, 1 9, 20
21 , 22, 23, 24, 2 5
8, 9, l a, 1 1 , 1 2, 1 3, 1 4, 1 5, 1 6
7, 8, 9, 1 0, 1 1 , 1 2, 1 3
DYS392
7, 8, 9, 1 0, 1 1 , 1 2, 1 3, 1 4, 1 5, 1 6, 1 7, 1 8
DYS437
DYS438
DYS448
15
13
VIC®
29
17
15
1 1,14
NEO™
13
11
12
8, 9, 1 0, 1 1 , 1 2, 1 3, 1 4, 1 5
Y GA A H4
007
24
7, 8, 9, 1 0, 1 1 , 1 2, 1 3, 1 4, 1 5, 1 6, 1 7, 1 8, 1 9, 20,
DYS439
DYS635
M TM
Con trol D NA
24
20, 2 1 , 22, 23, 24, 25, 26
8, 9, 1 0, 1 1 , 1 2, 1 3
1 3, 1 4, 1 5, 1 6, 1 7
8, 9, l a, 1 1 , 1 2, 1 3
1 7, 1 8, 1 9, 20, 2 1 , 22, 23, 24
27
PET®
13
13
15
12
19
D e t ec t i o n o f A m p FLSTR
2.7
Y fi le r
k i t p e R P rod u c t :
The m U l t i p lex ampl i fied D A fragments are resolved o n a pol) mer-based
electro phore i
as oc iated
\\
techn ique in
\\
h ich the la er beam act i vates d ifferent fluorophase
ith each D A fragments.
P r i n c i p l e of electro p h o re i
2 . 7.1
E lectrop horetic separat ion is based on the princ i p l e t hat a charged pal1icle in a
solution
\\
i l l m i grate towards one of the electrodes when placed in an electrical field.
In our experi ments, the DNA fragments
(CE).
\
ere resolved by cap i l lary e lectrophoreses
The fundamental pri nciple of CE is identical to the concept of gel
electrophoreses.
Br iefly, the speed and d irect ion a charged part icle mo es is
determ i ned by its net charge. size, shape and molecular weight as we l l as external
factors such as the composit ion of the buffer, the voltage used among other variables.
The fragments m igrates across CE, where at a specific poi nt a long the cap i l lary length
the argon ion laser passes t hrough clear sect ions in the array and excites the
fluorescent dyes attached to the DNA fragments wh ich result in em ission of l ight at
d ifferent detectable \ ave lengths.
d ifferent for each dye.
The specific wavelength of the e m i tted l ight is
The l ight is col lected and separated accord ing to its
\� avelength b) a spectrograph onto a charge coupled dev i ce (C C D ) camera, and a l l
types of fluorescent e m i ssions can b e detected w ith one burst of the laser. The data
col lect ion software col lects the l ight i ntensities from specific areas on the CCD
camera, correspon d i ng to the d iffere nt wavelengths of l ight. T h i s i s i m i lar to Llsing a
phys ical f i l ter to separate the l ight wave lengths, referred to as v i liual filter.
28
2.7.2
G e n e t i c A n a lyze r:
The separation and detection of
u ing the 3 - 00 L Genetic
mpFL TR
Y fi ler
nalyzer ( Life Tech nologies).
PCR kit \\ as performed
It is highly automated
system and ea y-to-use format a l lows for its , ide usage in the laboratory. It Includes
a 24 capi l lar) 3 6cm in length, it ana l ) es 24 samples e ery 2 5 -3 0 minutes.
addition. it proces es one
ample per run a
to reduce cross contamination.
In
The
fragment re olution are rather quick due to the high voltages. Previous ly this \\ as not
po ible main l ) due to heat generated at higher vol tages w hich ultimate l
the D A fragment migration . Capi l l ar
a l lo\\
hampered
has a large surface area (volume ratio) that
efficient heat di sipation that reduces the time required for DNA fragment
re olution.
Moreo er, t here is 3 5 00 X L Data Col l ection Software,
hich is a Del l ­
b a e d workstation and monitors a s the parameter of the C E o
2.7.3
Capi l l a ry E lectropho res i s Reage n t s :
1 . Pe rfo r m a n c e O p t i m i zed polymer ( PO P- 4 ) :
Capil lar electrophoresis ( C E ) uses the same principles m entioned above. The
samples are separated as they pass th rough a f i n e bore silica tube or (capi l l ary)
containing a liquid separation medium ca l led Perform ance Optimized Polymer ( PO P 4).
POP-4 reagent i s a separation medium a n d i t used b y capi l lary e lectrophoresis
POP-4 is th e most suitab l e medium for D A fragment resolution as it is non -cross
lin ked liquid polymer. POP-4 contains denaturant, such as urea and Pyrrolidone that
keeps D N A single stranded during resolution . The pol mer is made of a non -cross
linked / Acry l amide ( N , N -dimethy lacrylamide ). Other reagents that are essential for
capil l ary e lectrophoresis circuit are Anode ( positive charge) and Cathode ( negative
29
charge) b uffer. Both
E DT
node Buffer and part of the Cathode Buffer contain Tris-based
and Boric acid buffer. It i req u i red mai nl) for
pH 8. , \\ hich allo\
h\ 0
reasons: first, it has a high
D A to ex hibit a net negati e ch arg .
econd, it creates a
com plete e l ectrical circuit a llow ing e lectrophoresis to take place.
2 . 7 . .t
a m p l e p re p a ra t i o n befo re Ca p i l l a ry E lec t ro p h o re
a m ple preprarat ion in olves a couple of steps: the first is denaturation of
double tranded a m p lified D A to single trands and the second is the preparation of
appropriate references for fragment scoring. They are:
1-
H iD i- F o nn a m id e :
H i - D i Formamide i s a highly de-ion ized form o f t h e denaturing agent formamide.
Formamide is a n ucle ic denaturant and changes, in t h i s case. the DNA or R A
conformation to single stranded molec u l es D N A denaturat ion i s an i m portant
com ponent of analysi because s i ngle stranded D N A red uces the b i ases mobi lity sh i ft
d u e t o D A conformation and enhance analytical resol ution .
2- G e n eSca n T M 600 L I Z ® Size Sta n d a rd :
D A fragment scor i ng is based on reference standard fragment. It is a sol ution
of d ye
\\ ith
labeled D A fragm ents of known and varying lengt h s that is produced
from bacter i al p l asmid restriction enzyme d igestion. T h i s results in a generation of
fragments for size references that in conju nction with the a l lelic ladder allows
verification of unknown STR lengths. In other words it acts as an internal ru ler for
each samp l e allo\ ing the size of the unknown fragments in the samp le to be
calcu l ated.
Figure 6 i l l ustrates the fl uorescent dye label color and rel ative PCR
prod uct size ranges for the various STR loci present in this partic u l ar kit.
30
Am p FtSTR® Yfi l e r ™
I
I
I
200 bp
1 00 bp
I
300 bp
400 bp
6- Fam
r"
DYS 393
DYS 3 9 1
DYS439
, -
:
DYS635
'
VIC
' ./ 1
,
DYS 392
PET
I
G S500-internal lane sta ndard
I
rigure 6: 1 7 loc i of AmpFLS TR R Yfi l er R p e R \\ ith ladder and i nternal contro l .
2.7.5
A m p FlSTR Y fi l e r A l l e l i c L a d d e r :
Fragment cal l i ng accuracy L rei n forced by AmpFLSTR:R' Y fi ler a l l e l i c ladder
and i nternal contro l . [he ladder con�ist of D N A rra�ment
of
\\ ith kno\\ n designation
�
�
the 1l10,'t commonly fonnd al lele,' per loc Lls as sho\\ /1 i n Figure 7, These .'tandard
allele :sizing are obtai ned from large population base stud) ,
31
_
,.-..?Wtr'
il
"
___
III
j
lIS
IG
j
____--=---_
-.�_=r
I��
l l ,, "
F i gure 7 : GeneMapper I O- X software p lot the AmpFISTR Y fi ler A l l e l i c Ladder.
fable
5:
Total \ ol umes requ i red for 0 A amp l i fied plate i n a CE step.
Cockta i l
Plate S i7e
H i O i ( �L l )
S ize Standard ( �d )
A l le l i c Ladcler( p l )
96
1 40-+
36
1 .S
B i O i and i ze standard reagcnts (cocktai l ) were m i xed. \'ortexed. and spun i n steri le
m i cro fugc tube for 1 0 second .. Each sam p l e consist o f 1 3 . S u l from the cocktail and
I . S u l from A l l e l i c Lad(kr as shown in table 5 . Thc plate was then pulse-spunned and
32
firm l} seated w ith a co er s l i p
Then the p late \\ as subj ected to heat ( for
) for 2 m i n ute at 9 - oC in thermo-cyc ler \\ ithout c losing the l i d
denaturat ion of D
and then
epta .
naps cooled b y p lac ing t h e p late on a i c e b l ock.
p laced in a
F i nal ly, t h e plate was
pec i a l p late holder and p l ate reta iner p l aced on top, and the assembly
p laced onto the equencer and started the run. The 3 5 00 Data Col lect io n software
\\ orh.s alongside other o ftware to control the mechanical operat ion of the instrument,
u h as mo\ ing the auto ampler and s\ itc h i ng on the oven for D A denaturat ion. I t
c ol lect the n uorescence em i ssion data from the CCD camera and processes it before
storage a both tables ( i n the m ac h i nes own database) and as sample fi les on the hard
driv e . W i t h i n the c o l lection software, there are numerous modules conta i n i ng pre -set
i nstructions to the seq uencer, go e rn ing parameters such as vol tage, te mperature of
the oven, and the l aser power. From the run w i n dow, the appropr iate module can be
se lected for the p late check, pre-run and the run step. The co l lection software also
mon itors and d i sp l ays the status of the instrument and saves it to the i nstrument
database as E PT data.
2.8
S t a t i s t i c a l A n a lysis :
For statistical analys i s, U A E popu lation ,: as fi rst d i v i ded into three regions,
orthern that inc l ude · ( Dubai, Sharjah, Aj man, Ras A l k h a i m a and Um A l qaw i n),
Eastern \\ h ic h i n c l ude ( F uj u rah, K a l baa and Khorfakkan) and Western region inc l ude
(Abu Dhab i and A l A i n c i ty) and interchangeab l y they are cal led population 1 , 2, and
3 respec t i e l y .
The popu lation was grouped based on the h i story, geograph ic
prox i m i t i es, and probab le m i gration ro utes.
hapl otype
were
performed
w ith
statistical
33
The analysis o f a l l e l e frequency and
and
popu lation
genetic
software.
Gene
apper
!\,
1 0-X
er ion 1 .2 analysi
o ftware carried out data analysis. It
ana lJZc data generated on human ident i fication cap i l lary e l ectrophoresis platform
such a 3 500 L Genetic Anal zer. I n this project, the u age o f th i s o fu\ are \\ as to
anal yze the r su Its and to generate ra\ data for a l l samples and the parameter was set
to I SO Relat i \ e F l uore cent U n i t (rfu).
The raw data fi le that generated from the
was analyzed using macro progra m m ing i n M i c rosoft Excel and
Gene r-.. l appe ·
1 0-
an i n tegrated
o ft\\ are package for popu lat ion genet ics data anal sis
ver i o n 3 . 5 . 1 . 3 . ( Excoffi er. 2005).
Pad .age for
oc i a l
c iences)
A LEQ U f N
Moreover, statistical program S P S ( Statistical
w a s used t o generate t h e descriptive parameter o f
popu lation su h a Me a n, Standard de ialion, a l lele frequency charts and tables for
eac h 10 i .
2.9
A n a lysis o f P o p u l a t i o n g e n e t i c pa ra m ete rs :
The fie l d o f popu lat ion genet ics has come a long way s i nce the early part o f the
2 0th century. The c o m b i nation o f Mende l ian genet ics and b i ometric studies led to the
b i rth of population genet ics "vhose father i s R. F isher ( H a l d , 1 99 8 ) .
popu lation genet ic
I n itial ly,
stud ie s concentrated on study i n g the a l lele freq uenc ies in
populations, subpopu lation, a nd gro ups ( Prov i ne, 1 9 7 8 ) . There fore, it is i m portant to
de e lop the not io n of al l e l e freq uenc ies computat ion even though our current study
i n v o l ves a haploid system man i fested in Y c hromoso m a l STR analysis.
It is
i m portant to desc r i be H ardy and W e i n berg E q u i l i b r i u m ( H W E) as many of the
m athematical treatments in population genet ics stems from H WE .
The H W E m ethod i s used to calcu late the ex pected proport ion o f d i fferent
genotypes in a g i ve n popu lat io n.
A populat ion to w h i c h the H W E i s app l icable
34
con i t
o f d i p lo id
assumption
ystems. sexua l l } reprod uc ing i n d i iduals. and a score of other
such as independence of a l le l e freq uenc ies transm i slon from one
generat ion to the next from the common geneti c poo l who has not been under any
se lection force.
In the I I W E , the probabi l ities o f the genot pes can be g iven by the
equat i o n :
p
2
2pq
+
Y here: p
q
:!
=
2pq
:!
q
=
�
=
1,
percentage of hom ozygous dom i nant i nd i v i d ua l s
percentage o f homozygo us recess i ve ind i v iduals
=
And p
percentage of heterozygous i n d i v iduals;
+
q
=
I
W here:
p
=
frequenc)
0 f the
dom i nant a l l e l e in the popu lation and
q
=
tl'equen )- of the recess i ve al le le in the population.
The total frequency o f a l le les in a populat i on is equal to one.
I n add i t i on, H W E
depends m a i n l y o n the ex istence o f a very large s i ze and random ly mating
populations ( H am mond et aI., 1 994).
There are tv 0 i m portant facets to Hardy- W e i n berg mode l .
F i rst and the most
i m p oltant fac et, i s that i t sho\\ s that the M end e l ian mechan ism preserves genet ic
variabi l ity.
Second, i t pro v i des a usefu l fu nctional re lat i o n s h i p between genotype
frequencies and gene (al le le ) frequenc ies where p
2
+
2pq
+
q
2
=
(p+q)
2
=
I.
It shows
that, everyt h i ng e lse being equal, the population w i l l q u i c k l y reach equ i l i brium and
stay there. Ho wever, H W E works i n an ideal s i tuation, t hat does no t usua l ly occur
natura l l y and thus H W E i s used as a n u l l model to test various population structure
ass u mpt ions such genet ic forces and populat io n constra i nts.
35
The
econd point \\ hich is mo tl) im portant to population genet ic ists is the
a b i l ity to d e
ri be the state o f a popu lation entire l y i n terms of a l l e l e freq uencies
rather than genotype freq uenc ies.
A l le l e (". h ich are much fe\\ er than genotypes)
freq uencies o f the popu lation can derive the expected heterogeneity o f popu lation.
2. 1 0
M e a u re o f d iv e rs i ty betw e e n a n d w i t h i n p o p u l a t io n :
0 \ e r the past few decades. m ic ro ate l l. ites h a e been the cho ice fo r popu lation
tud ies. due to the i r h igh level o f variab i l ity and the re lat i ve ease o f devel opment and
coring i n non-mod e l system .
everal methods have been used to score the
\ ariation and d i \ er ity of m i c ro sate l l ite in popu lations. Fsl or fi xation index is one
of the mo t u ed b iometric method . Fsl simply measu res the level o f hetrozygosity or
d i fferent iation ben een population and its subpopu lat io n. It was origina l ly devel oped
to mea ure genetic d i stance using b i a l l e l ic markers ( Wright, 1 969), but the equation
\Va su bseq uent l y genera l ized for m u l t i p le al le les (Nei, 1 97 3 ) . FSI ranges from 0.0 to
1 .0, a expected . w i th 0 ind icating no d i fferences i n a l l e l e freq uenc ies between two
populations and 1 .0 ind icati ng that the two populations are fi xed for alternate al le les.
2
FSI is often 0. 1 -0 . 2 . For m i c rosatel l ites w i th high m utation rate ( i n the range o f 1 0. _
6
1 0. ) other measures of hetrozygosity or d i versity has been int roduced to study
popu lation structure .
S u bsequent mathemat ical derivation, namely, RST, is used to
account for m utat ion u n der the assumption o f step-wise mutations, that is, single
m utation at a time and that each su bseq uent mutat ion is dependent on the prev ious
one -that is the s ize o f m ic rosate l l ite d ictates the future m utat ion ( S latkin, 1 997). The
previous popu lation mode l i ng eventua l l y d i ve rted from mere a l l e l i c frequency stud ies
to genet i c d i stance among and between populations wh ich is m a i n l y derived from
36
a l l e l ic varIance bet\'v een subpopu lations.
I n the c u rrent
tudy, we ha e est imated
haplot) pe freq uenc ies, varian es, and used ana l ) sis of molecular variance (AMOV A )
t o tud) the
E popu lation and its subgroups. Furthermore, ' e have compared the
AE popu lation \\ ith other popu lation i n d i fferent parts o f the , orld . Our analysis
\\a
conducted on A L E Q j
(vers ion 3 . 5 . 1 . 3 . ) \Vh ic h is an integrated soft\\ are
pad.age for population genet ics data analysis ( Excoffi er, 2005) and SPS
package.
37
stat istical
C H A PT E R III: R E SULTS AND DISCUS SION
38
I his t:hapt�r descri h�: the \\.!su l ts o f the 00:A pro fi l i ng o f 345 samplec obtai ned from
unre lated mal es i n the l IA E . ,\ 1 1
Y
ii i
rT\I
the sampl e: \\ ere genotyped \\ i th Amp!' ! S T R f{
of
k i t ( L i fe Technol og� ) ror 1 7 h igh l � polymorph i c l oc i . This i s
ont: o f
the
l argest : i ngle populatil'1l studied tim. 1�tr.
3. I
P r o fi l i n g Sa 111 p i e s :
A l l the 3 -\. 5 samples \\ e re
STP
R
Y
k i t . Fi gure 8
fi l e rl\(
success fu l l y
p resents
The same reaction \\ as perfo rmed for
flOCtl
• •
.,
•
�I .I
�I
.
CU:O'Z
,tD;'Z
,.
•
•
...
.
"
•
II
•
•
"
.1
.
"
j .!
•
•
U
'"
�.
.I
1!21
•
'30
'"
,�
u
•
@
�
n.
!
subj ect.
'"
J
0
I!!.
a
samples .
N
..I
.!
Ctn!Z
345
.�
'"
an example of Y STR p ro fi le for
•
E
..
pro fi led for al l 1 7 loc i w i th the AmpFI
�
[£
[iiJ
."
.!
"
>I,
!
C>
....'..
�
fjj
!
F igure R : Y STR p ro fi l e generated using . mprl STR R Y fi l e rT:\( at optimal n�action
conditions. The figure sho\\ s l abd lcd i nd i ,i dual S I"R and the peak height.
39
3.2
Y S TR a l l e l e
Freq uencie :
I n genera l . al le le freq uenc ies are u ed to study the popu lat ion structure and its
\ ariance is a key i n d icator o f gcnet ic d i ver it)' at the i n d i v idual, population, and
peC le I vel and dcmonstrate the ric hness o f the popu lation gene poo l ( H euertz et
a l . . 2004). The popu lation genet ic parameters are com puted \ ith stat istical package
for the
c ia l sc ience ( PS ) and po pu lation genet ics o ft\\ are Arleq u i n ( Excoffier,
2005) for a l l 1 7 a m p l i fiable loc i .
The computations are carried out for the whole
popu lation a we l l as eac h ubpopulation (sect ions 3 . 2 . 1 and 3 . 2 . 2 respec t i ve ly). I t is
i m portant to note that i n t h i s study, the state o f hetroz) gos ity o f a l lele freq uenc ies o f
345 E m i rati
amples were estimated by count i n g the n u m ber o f i n d i v idual al lele
observed and d i v i d ing it by the total number o f samples fo r the respect ive popu lation.
W e have observed a tota l number of 1 24 al leles d i stri buted across the 1 7 loc i i n the
UAE popu lation ( see table 6).
3. 2 . 1
A l l e l e Freq u e n cy o f Y H a p lotype i n t h e U A E p o p u l a t i o n :
The analysis o f the a l le le frequency in the U A E popu lation c l early shows that
eac h loc u s has a p red o m i nant al lele ( see table 7 and fi g ure 9 ) .
I t is also apparent that
the a l l e les o f m ost loc i are c l ustered over a narrow range where appro x i mate ly 60%
8 0°'0 of the population i s sharing a spec i fi c a l lele for the locus.
-
For example, a l l ele
1 4 of D YS43 7 is shared a m o ng 7 9 % o f the po pulation; s i m i larly al lele 1 1 o f D Y S392
i s shared among 79% o f the UAE population, al l e l e 1 3 o f D Y S 3 8 9 1 locus i s shared
in 72% of the population, and a l le le 1 0 of D Y S3 9 1 is shared bet\ een 72% of the
popu lat ion.
A lthough to a lesser degree, other loc i a l so have predom i nant al leles.
40
These loci are DY 4 3 8 (allele l O is shared among 59% of popu lation), DY 448
(al lele 20 i
hared among 56% of popu lat ion), DY 1 9 (al lele 1 4 is sh ared among
- - % of popu lation), GA TA_H4 (al lele I I is shared among 54% of popu lation),
DY 393 ( a l lele I I i
hared in 48% of popu lation), and D Y 4 5 6 ( a l lele 1 5 is shared
in 4 7°/0 of population).
I n other ca es, there i a b i moda l or even rn u l t i modal d i str i bution of a l leles (see table
8 : i .e. D Y 4 5 8 locu ) ; that is al le les that are not c l ustered and their d i stribution
appears d i sconti nuou
and c hunky.
For i nstance, D Y S 4 5 8 locus shows two pre­
dom i nant a l le les ( 1 6 and 1 7) w ith freq uencies of 68 and 72 respectively (where
34 - ) .
W h i l e the most common al le les at D Y S439 locus are I J and 1 2
freq uenc ie
of 1 5 1 and 1 1 8 respec tive l y.
\
ith
Moreover, fo r DY 4 5 8 locus the two
common a l leles are 1 7 w ith the freq uency of 72 and a l lele 1 6 w ith the frequency of
68 and for the D Y S 3 8 5 - B locus the pred o m i nant a l leles are 1 8 and 1 7 w i th
freq uencie of 8 8 and 68 respec tive l y. The bimodal a l lele predom i nance d i stribution
is characteristic o f gene flow from other popu lations. That is there are groups of the
popu lation. arguably. t hat m igrated i nto the UAE fro m d i fferent region and fLlli h er
stu d ies are req u i red to ident i fy the most l i ke l y a l le les that are associated w ith each
a l l e l ic mod a l . Tab l e 8 (A-Q) p resents a detai led description of a l l e l ic d i stribution for
each loci and the co rrespon d i ng pie c harts.
41
rable 6: Total num ber of a l le les for each loc i i n U A E popu lation
Lo c us #
#
of a l l e l e
D YS456
5
DYS3891
4
D Y S390
6
D Y S389 I I
8
D Y S 45 8
13
D YS 1 9
6
D Y S385-A
1 1
D Y S385- B
II
D Y S393
8
DYS39 1
7
D YS439
7
D Y S635
9
D Y S392
7
GATA H 4
5
D Y S4 3 7
-l
D Y S438
5
D Y S448
8
Mean
7.294
S.D.
2.568
42
'I able 7 : Prt.!dom i nanl allele i n U
Locus
OYS456
D YS389 1
E populalion.
V rc <l o rn i n a n t
F req u e n cy
15
0.475
13
0 . 7 '22
'") "
- -'
0.-+4 1
30
0 . -+ 3 2
1 7 . 1 6*
0 . 2 09. 0 . 1 97 *
DYS1 9
14
0.554
D \'S.38':--.\
13
0.3 7 7
D YS385-R
18
0.255
D YS393
12
0.4 75
O YS39 1
10
0 . 6- U
D YS-B9
II
0 .-+3 8
O YS635
21
004 1 7
DYS392
I I
0.783
1 1
0.539
DYS-B7
14
0 . 7 86
DYS43 8
10
0 . 5 86
O YS448
20
0 . 5 65
D YS390
OYS389 1 1
DYS458
GATA H4
F re q u e n cy of P re d o m i n a te A l l e l e i n U A E P o p u l a t i o n
0.8
>u
c
(l)
:::J
u
�
u..
0.6
0.4
0.2
0
Locus
Figurt.! C): A l lele frequency for the predom inant al l el es in the UAE pupu latiun
43
I abl , X : \ l i c k Ih�q u 'ne) o f o i fkrcn t l oe i w i t h p i c c harb fur l), E po p u l a t i o n :
\11 k
I rcqu':l L)
l '':I\.Cl1t
I�
I I
X�
::! � . J
f---.
I " (l
1 6�
I� 5
1 6 ()
(J:\
1 <) 7
15
.t 3
.H 5
1 00.(1
-
Ij 0
�.
I 1 0
-
f---
1 � ()
l ot ti l
B.
L o c u s DYS389 J
\ I k l .:
I n:qucI1L)
I'CIC.:1ll
I ::! ()
� ::!
I ::! . ::!
I ., 0
::!�l)
1 -1 0
:1
IH
I :) ()
2
6
3 15
1 00.0
I ut,1i
-, ,
- -
C. L o c u s D Y S 3 9 0
I
\Ikle
! I cquenL)
1'':lccnt
::! I
6 I
26
- 5
1 52
-I I I
::!-I
101
29 3
2�
41
1 1 9
:!6
I
J
3-15
1 00 (I
::! !
"
') '
_.1
i
I
i
T ol,tI
I
44
D. Loc u s D YS3R9 J J
\ ! I.:lc
I l eqll-:n<.:�
l 'el L 'nt
), 0
2
(,
2
h
2�
- 0
_
-0
..
2S ( l
1
-1
I
-
---
2() ()
S
< ''
2I I
� (l ()
I -It)
-l � )
;1 0
55
I � <)
� 2 [)
20
:5 R
l ' ,n
-I
I 2
I ,'t.ll
3 -1 5
l oo n
E . L o c u s DYS.tS8
I
I
\ I k l <:
rrcqll-:ne�
I\:recnt
I l,O
I
,
-'
1 -1 0
"
,
,9
1 5 1l
51
1 -1 X
I (, ( )
('S
I <J,7
1 6, �
I
,,
1 - I)
72
20 'J
1 -,2
36
104
�5
7 2
IS 2
-18
1 3 <J
1 'J,n
(,
1 7
1 9, 2
") ''
-.
6 7
20,0
-I
1 .2
20 2
h
I -
l ot II
34 5
I ()(),fl
IS 0
I
45
F.
L O C LJ
\IU�
DYS 1 9
I r 'qllt:IlL \
I \:r..:.:nl
-
'
II
2
()
l , tl
iI
') !l
I t (I
19l
�5 l
1 - ()
,'.,2
21 X
l 6 ()
lU
X -
1 - ()
-
2 0
,45
l OO.O
l
1 Illal
." 0
a.
D• •
• • -a
_
.
.-
a.
G. Locu.' DYS385 1
I
I
\ 1 1..: 1 .:
rr.:qu':I1':�
f\:r.:.:nt
X ()
I
,
-'
100
.2
.6
l i n
52
15 I
1 2 .0
25
.2
11 U
U ti
....' .... ...,.
I .J ()
39
I I -'
I: 0
20
I f> 0
,,
1 () 7
1 - [)
35
1 (1. 1
I S [)
,
-
(,
IYO
I
3
3l �
I IH ) (I
I lll i l
I
__ x
46
•
•
I I . L o c lI. D) S3S:- 2
r-
f--I I ()
Per, ' nt
I rnlUenn
\11 -1 '
-...
.,
(,
--
1 2 ()
�
I ) ()
-
�'r -
1
!
(,
.1 \ , .\
IX
I , l)
+- -�
20
:; X
_, t)
I I .'
6X
1 <)
_.
()
XX
�5 :>
I li n
�X
13 9
21l 0
IX
5 ..,
21 0
.,
-
,(,
H)
1 00 0
1 .", , 0
I ()O
_
1 7 (l
IX
I lltdl
I.
,.'-
--- --,-=.
I
I
t
-�- -
-
L o c u s D Y 393
\ I kk:
rrC'lllCl1t:�
I 'crc:cl1t
l) ()
2
(,
10U
2
(,
1 1 0
12
3 :>
1 2 ()
1 6..j
..j 7 .:i
1 3 ()
1 26
36 :>
l HI
30
I - (I
I II ()
I (11 ..11
-
I
• •
• ••
OlIO
., .
� .
• 11 0
, .
OI�O
X -
2 0
I
1
'15
1 (I( I ( )
47
.J.
,..---
L O C H . D YS39 1
r-- -
�
\Ikl
I n:qll ':I'�)
1 '':: 1 <:1':111
(, ( )
I
\
7 0
I
,
� o
I
i
\) (J
I ,
3 X
I I I ()
222
(, � 3
1 1 0
96
2- N
12 0
10
2 l)
1 01,11
315
1 (10 0
--
-
�
t--
f--.
K L o cu� D YS ..B 9
\ l I d .:
F t CL]lI 'IlL)
Pt:ILCllt
l) 0
I
.J
1 0 (I
39
I I 3
1 1 .0
151
.+3 �
1 2 (l
I IX
34 2
13 0
2�
I' (I
I � ()
7
2 0
150
2
(,
3�5
1 00 I I
l otal
L.
LOCH
D Y 392
\Ikk
I l cqll 'nt:�
<) 0
2
I
I '..:r.:.:nt
I
2 <)
I I CJ
2 70
7X :;
12 0
.+
I ::
1 3 ()
3U
X,I
"
-
1 1 0
1 5 0
I Ol.1I
I
•
•
o
• •
o •
•
...
b
10
100
• •
"'.
OIl)
.' .
ou
."
,.
,
(, 7
,
-
(,
3�5
1 0( 1 [)
48
1 . L o c lI
D YS635
I
'1
.rI.:411.:nL�
l'aLcilI
1 <) 0
I
,
20 II
"1
I - 1
21 0
1�4
II �
22 ( )
��
11 9
21 ()
66
1 <)
,
-" ' ,
I
,,
2 1 0
19
- 'i
2 ') ()
6
I �
2 () 0
I
3
3 -1 5
I OO ll
\11
I--
'-
\ "1"1\
I
Locu. DYS-t-t8
\ 1 1 .: 1 .:
l'n:ljllcIlC)
Paceill
160
2
(,
\- 0
-'
l)
I S ()
-1
1 2
1 9 ()
89
2: X
20 0
1 95
56 5
2 1 (J
32
q 3
22 0
5
I I
2, 0
(,
I -
3�5
1 (10 0
I (11,11
�
I
49
O. L O C H
Y G \T
1 14
--------,
I I (ljlleIlL)
liel -
I '�rc�nl
20
100
- X
1 11(,
1 1 0
�
P.
�
-
r-
.5 , lJ
� �
120
l Oll
2 () ()
H O
16
10 �
I I ()
.1
l)
I Ol . 1
H-
1 00 (l
L o c u .· D YS43 7
\ I kk.
I n:Lju':Il<':�
J \:r<.:.:nl
1 )( 1
I
,
-'
I � (l
2�1
- 1' . 6
1 5 I)
50
I �. S
1 6. 0
21
6 1
315
I OU (l
r,'l.11
Q. L o c u · DYS438
\ I kle
I r 'qLI 'nc�
I'cn:cnl
X U
.2
(,
39
I I :>
20�
5 1' . 6
90
I
100
I
1 1 0
R .2
1 2 ()
1 1'
1 0[ ,11
3 -1 S
I
I
• •
• •
C' ••
• o.
o •
.2JR
- �
J _
1 (1) 0
50
It is evident from the predo m i nant al lele freq uencies and bi modal it) d i stribution
of e \ eral al le les at s pec i fic locus that (here are at least m i n i ma l common hap lot) pes
compn I Ilg
A E pop u l ati o n. I n fact, our analysi
ho\\
the popu lation hare at l ea t 5 -7 a l l e les acro s the 1 7
further d i cu
structur
that approx imate ly half of
TR loci ( see section 3 . 2 . 2 for
ion). Based on this ev idence, t\\ O scenarios are v iable to explain the
of the U A E popu lation.
F i r t, a
teady popu lation i nc rease in the past
sev eral thousand years w i t h i n the boundaries of what const itutes the U A E . The i n itial
popu lation shared common hap lot) pe that eventual ly m utated to estab l ish the genetic
d i \ r it) of today ' s population. The second scenario i n v o l ves recent ad m i xture and
gene flo\\ for m u l t i ple neighboring reg ions \\ ith in the past century.
second
cenario i s the most p lausible, it is i m po rtant
(0
A l though the
stress the im portance of
co ering a larger popu lation at h igher popu lation h ierarc hy w i t h i n the reg ion at higher
molecular reso l ut ion
(0
dec ipher the population structure and estab l ish deep ancestry
( U nderh i l l , 2007). A l ternat i vely, both scenarios at \ ork a l though the fi rst scenario
prov ided the d i versity o f a l l e les, contributed to a l esser degree to the hap lotypes
d i vers i ty. T h i s latter assettion stems from an observat ion of a narrow range of a l le les
c l ustering \\ ith i n each locus (see table 8).
The a l lele c l ustering and narrow range
d i stribution assumes a step" i se m utation as opposed to i nfi n ite a l ie Ie model ( V aldes
et . a l . 1 993 ; J arne, et. a l . 1 996).
1or·eover, the UAE popU lation, as is the case i n any other population,
demonstrates a l l e le frequencies and genetic variance that is d i stinct from other
popU l at i o ns in d i fferent cont inents. The resu lt reflec ts the genet ic d i stance between
these popU l at ions, which i m p l ies the separat ion of popu lation i n habiting the U A E
51
regions and the urround ing area at least in the past several thou and years ( Eckert
and l I i le 2009;
re lativel)
adenas, 2008; Bosc h, 2000).
hort period (se eral thou and
Di ver ity of this magn itude in a
ears) is in agreement w it h h i gher mutat ion
4
2
rate or m i c ro ate l l ite ( 1 0. _ 1 0. per gen rat io n) as opposed to single nuc leotide
mutat ion ( B ri n kmann et al., 1 998; Dupu) et a I . , 2004).
A l lele Freq u e n cy fo r u b pop u l a t i o D s i n t h e U A E :
3.2.2
The a l le l ic p ro fi le, freq uency, and d i stribution for each locu
ubpopulation of the U
I n the three
E fo l lo\\ s s i m i lar patterns ( see tab l e 9 and fi gure 1 0. A -Q).
The a l le le frequency among the three subpo pulat ions, however, shows smal l
fl uctuat ions espec i a l l y for spec i fi c loc i . A l though, our study demonstrates that there
are u n i q ue a l leles to a subpopu lation or a l le les not shared by a l l regions, the profi le of
the a l le le frequency and d i stribution are s i m i lar.
I t is im portant to note that the
ample ize of Eastern subpopu lat ion ( n=2 5 ) is smal ler com pared to Western ( n= 1 89)
and
orthern (n= 1 3 9 ) reg ions; therefore, we attempt to d i scuss the results of Eastern
region w i th caution e ven though it is not uncommon to see a popu lation of s i m i lar
size d i sc ussed for i n ferences i n the l i terature. Table 1 0 demonst rates the al leles that
are u n ique or not shared betvveen a l l the reg ions in the U A E population.
For
examp le, a l lele 1 5 of D Y S 3 8 9 I , i s p resent o n l y in Western reg ion, wh i le a l leles 26 of
DYS390 is p resent i n
orthern reg ion on ly.
I nteresti n g ly, a l l e les 1 3 and 1 6 .2 o f
DYS45 8 locus a n d a l le les 9 and 1 6 of D Y S393 locus are present o n l y i n Western
region.
M oreover, a l l e l es ( 1 0 and 1 9) of DYS3 8 5 -A locus are un ique to
region o n l y \\ h i l e a l le les 8 and 1 8 are o n l y present in W estern region.
orthern
We have
exc l uded the Eastern region i n t h i s comparison as the popu lation size is smaller
52
(n=2 5 ) than
o lihern and We tern regions. H o\ ever, the absence o f an al lele frOI11 a
region \\ ith h i gh populatio n does \ arrant its ab ence i n the Eastern region popu lation
(Tab le 1 0) that th re are al l e l e only spec i fic to Eastern region. A l arger pop u lation
ize \\ i l l u l t i mate ly identi Cy the uniquenes
subpopu lation .
53
of these al l el es in t he respective
Tab le 9 : A l lele Freq uenc ies for the ub-popu lations.
N o rt h e rn ( n= 1 3 1 )
E a s t e r n ( n= 2 S )
W e s t e rn ( n = 1 89 )
A l l eles for t h e locus 1 : D YS�5 6 :
Fl'e q .
s.d.
A l lele:
N o.
F l'eq.
s.d.
A l le l e :
No.
F re q .
s.d.
A llele:
I
0.06 1
0 . 02 1
1 3 .0
I
0.000
0.000
1 3 .0
I
0.032
0.007
1 3 .0
2
0 214
0.036
1 4 .0
'2
0.320
0.067
1 4 .0
2
0.254
0.0 1 8
1 4 .0
3
0 . 466
0. 044
1 5 .0
3
0.480
0.07 1
1 5 .0
3
0.4 8 1
0.02 1
1 5 .0
N o.
4
0.206
0.03 5
1 6.0
4
0. 1 60
0.052
1 6. 0
4
0 . 1 96
0.0 1 7
1 6 .0
5
0.053
0 . 020
1 7.0
5
0.040
0.028
1 7 .0
5
0.037
0.008
1 7.0
A l leles fo r t h e locus 2: D YS389 1 :
No.
F req.
s.d.
A l le l e :
N o.
F req.
s.d.
A l lele:
N o.
F re q .
s.d.
A l lele:
I
0. 1 2 2
0.029
1 2 .0
1
0.040
0.028
1 2 .0
I
0. 1 3 2
0.0 1 4
1 2 .0
2
0. 763
0.037
1 3 .0
2
0.680
0.067
1 3 .0
2
0 . 698
0.0 1 9
1 3 .0
3
0. 1 07
0.027
1 4 .0
3
0.280
0.064
1 4 .0
3
0. 1 5 9
0. 0 1 5
1 4 .0
4
0. 000
0.000
1 5 .0
4
0.000
0.000
1 5 .0
4
0. 0 1 1
0.004
1 5 .0
A l leles fo r t h e l o c u s 3: D Y S3890 :
No.
F re q .
s.d.
A llele:
N o.
F req.
s.d.
A l le l e :
No.
F re q .
s.d.
A l lele:
1
0.06 1
0.02 1
2 1 .0
1
0.080
0.039
2 1 .0
I
0.058
0.0 1 0
2 1 .0
2
0.053
0.020
22.0
'2
0.040
0.028
22.0
2
0.095
0.0 1 2
22.0
3
00420
0.043
23.0
3
0.520
0 . 07 1
23.0
3
0.444
0.02 1
2 3 .0
4
0.282
0.039
24.0
4
0.280
0.064
24.0
4
0 . 3 02
0.0 1 9
24 .0
5
0. 1 68
0.033
25.0
5
0.040
0.028
25.0
5
0. 095
0. 0 1 2
2 5 .0
6
0.008
0 . 008
26.0
6
0.000
0.000
26.0
6
0 . 000
0.000
26.0
No.
F r·eq .
s.d.
A l lele:
A l leles for t h e l o c u s 4: D YS389 I 1
No.
F req.
1
0. 0 1 5
0. 0 1 1
0.000
0.000
3
0.084
0.024
4
0.252
5
0.405
6
s.d.
No.
F req.
s.d.
A llele:
2 5 .0
1
0.000
0.000
25.0
I
0 . 000
0 . 000
25.0
27.0
2
0.000
0.000
27.0
2
0. 0 1 1
0 . 004
27.0
28.0
3
0.000
0.000
28.0
J
0.069
0. 0 1 1
2 8 .0
0 . 03 8
29.0
4
0.280
0.064
29.0
4
0.228
0.0 1 8
29.0
0 . 043
30.0
5
00 400
0.070
30.0
5
0.455
0.02 1
30.0
0. 1 5 3
0.032
3 1 .0
6
0.240
0 . 06 1
3 1 .0
6
0. 1 53
0 .0 1 5
3 1 .0
7
0.069
0.022
32.0
7
0.000
0.000
32.0
7
0.058
0.0 1 0
32.0
8
0.008
0 . 00 8
33.0
8
0.040
0.028
3 3 .0
8
0. 0 1 1
0.004
33.0
:2
A l lele:
"
A l le les fo r the locus 5 : D YS458
No.
F re q .
s.d.
Allele:
No.
F req.
s.d.
A l le l e :
No.
F re q .
s.d.
A l lele:
I
0 . 000
0.000
1 3 .0
I
0.000
0.000
1 3 .0
1
0 . 005
0.003
1 3 .0
'2
0.008
0.008
1 4 .0
2
0.000
0.000
1 4 .0
2
0 .0 1 1
0.004
1 4 .0
3
0 . 1 76
0.033
1 5 .0
3
0. 1 20
0.046
1 5 .0
3
0. 1 3 2
0.0 1 4
1 5 .0
54
�
0.�29
0.037
1 6 .0
�
0. 1 60
0.05�
1 6.0
4
0 . 1 80
0.0 1 6
1 6 .0
5
0 . 000
0 . 000
1 6. 2
5
0.000
0.000
1 6.2
5
0.005
0.003
1 6 .2
6
0.229
0.037
1 7. 0
6
0. 1 60
0.052
1 7.0
6
0.20 1
0. 0 1 7
1 7 .0
7
0.092
0.025
1 7.2
7
0.080
0.039
1 7 .2
7
0. 1 1 6
0. 0 1 3
1 7. 2
8
0.069
0 . 022
1 8.0
8
0.040
0.028
1 8.0
8
0 . 079
0. 0 1 1
1 8.0
9
0. 099
0.0�6
1 8.2
9
0.032
0.067
1 8 .2
9
0. 1 43
0. 0 1 5
1 8 .2
1 9 .0
10
0 . 008
0.008
1 9. 0
10
O.O�O
0.028
1 9.0
10
0.02 1
0.006
I I
0 . 069
0 022
1 9.2
I I
0.040
0 02 8
1 9 .2
I I
0 . 069
0 .0 1 1
1 9 .2
12
0.008
0.008
20.0
12
0.040
0.028
20.0
12
0.0 1 1
O.OO�
20.0
13
0.0 1 5
0.0 1 1
20.2
13
0.000
0.000
20.2
13
0.02 1
0.006
20.2
A l le les fo r t h e loc u s 6 : D Y S 1 9
N o.
F req.
s.d.
A llele:
No.
F req.
s.d.
A l lele:
N o.
F re q .
s.d.
A llele:
I
0.000
0.000
1 2 .0
I
0.000
0.000
1 2 .0
I
0.0 1 1
0.004
1 2 .0
2
0. 1 07
0.027
1 3 .0
2
0. 1 2 0
0.046
1 3 .0
2
0.074
0. 0 1 1
1 3 .0
3
0.5-+2
0.04�
1 4.0
3
0. 560
0.07 1
1 4 .0
3
0.56 1
0.02 1
1 4 .0
-+
0.200
0 . 060
1 5 .0
�
0.280
0.064
1 5 .0
4
0.228
0. 0 1 8
1 5 .0
5
O. 084
0.024
1 6. 0
5
0.040
0.028
1 6 .0
5
0.095
0 .0 1 2
1 6 .0
6
0 .0 1 5
0. 0 1 1
1 7. 0
6
0.000
0.000
1 7. 0
6
0.026
0.007
1 7 .0
F re q .
s.d.
A l lele:
A l leles fo r t h e l o c u s : 7 D YS385-A
F req.
A l lele:
No.
0 . 000
8.0
I
0.000
0. 0 1 1
1 0 .0
2
0.000
I 1 .0
3
0. 1 2 0
N o.
F req.
s.d.
I
0.000
2
0. 0 1 5
3
0. 1 98
0.035
A llele:
No.
0.000
8 .0
I
0.005
0 . 003
8 .0
0.000
1 0. 0
2
0.000
0.000
1 0 .0
0.046
1 1 .0
3
0 . 1 22
0. 0 1 4
1 1 .0
s.d.
4
0.076
0.023
1 2 .0
4
0.200
0.057
1 2 .0
4
0.053
0.009
1 2 .0
5
0.3 5 1
0 . 042
1 3 .0
5
0.360
0.069
1 3 .0
5
0.397
0.02 1
1 3 .0
6
0.084
0 . 024
1 4 .0
6
0.080
0 . 039
1 4 .0
6
0. 1 3 8
0. 0 1 4
1 4 .0
7
0.03 8
0.0 1 7
1 5 .0
7
0. 1 20
0 . 046
1 5 .0
7
0 . 063
0.0 1 0
1 5 .0
8
0.099
0.026
1 6 .0
8
0 . 1 20
0.046
1 6 .0
8
0. 1 1 1
0.0 1 3
1 6 .0
9
0. 1 2 2
0 . 029
1 7. 0
9
0.000
0.000
1 7 .0
9
0. 1 0 1
0.0 1 3
1 7.0
10
0 . 000
0 . 000
1 8 .0
10
0.000
0 . 000
1 8 .0
10
0.0 1 1
0.004
1 8 .0
I I
0 . 00 8
0.008
1 9 .0
II
0.000
0.000
1 9.0
1 1
0.000
0.000
1 9.0
N o.
F req.
N o.
F re q .
s.d.
A llele:
A l l e l es for t h e l o c u s 8: D YS385- B
No.
F req.
s.d.
A l lele:
s.d.
A l lele:
1
0.008
0.008
1 1 .0
1
0.000
0.000
1 1 .0
I
0 . 005
0.003
1 1 .0
2
0 . 023
0.0 1 3
1 2 .0
2
0.000
0.000
1 2.0
2
0.0 1 6
0.005
1 2 .0
3
0.008
0.008
] 3.0
3
0.000
0 . 000
1 3 .0
3
0.02 1
0.006
1 3 .0
4
0. 1 60
0.032
1 4 .0
4
0.200
0.057
1 4.0
4
0. 1 1 6
0.0 1 3
1 4 .0
5
0.084
0.024
1 5 .0
5
0.000
0.000
1 5 .0
5
0.048
0.009
1 5 .0
6
0.099
0.026
1 6 .0
6
0.080
0.039
1 6 .0
6
0. 1 2 7
0.0 1 4
1 6.0
7
0. 1 83
0.034
1 7 .0
7
0 . 1 60
0.052
1 7 .0
7
0.2 1 2
0.0 1 7
1 7.0
8
0.267
0.280
0 . 064
8
0.243
0.0 1 8
1 8 .0
0.039
1 8 .0
8
55
1 8 .0
9
0. 1 3 0
0.029
1 9.0
9
0. 200
0.057
1 9.0
9
0. 1 3 8
0.0 1 4
1 9.0
10
0.03 1
0 .0 1 5
20.0
10
0.080
0.039
20.0
10
0.063
0.0 1 0
20.0
1 1
0.000
0.000
2 1 .0
j 1
0.000
0.000
2 1 .0
11
0.0 1 1
0.004
2 1 .0
Al le les for t h e locus 9 : D YS393
N o.
F req.
s.d.
A l lele:
N o.
F req.
s.d.
A l lele:
No.
F req.
s.d.
A l lele:
1
0.000
0.000
9.0
1
0.000
0.000
9.0
1
0 .0 1 1
0 . 004
9.0
0.005
0.003
1 0.0
2
0 . 008
0.008
1 0.0
2
0.000
0.000
1 0 .0
2
3
0.03 8
0 .0 1 7
1 1 .0
3
0.Q40
0.028
1 1 .0
3
0.032
0.007
I 1 .0
4
0.435
0.043
1 2 .0
4
0.520
0.07 1
1 2 .0
4
0. 497
0.02 1
1 2.0
1 3 .0
5
0.405
0.043
1 3 .0
5
0.280
0.064
1 3 .0
5
0.349
0.020
6
0 . 084
0.024
1 4 .0
6
0. 1 20
0.046
1 4 .0
6
0.085
0.0 1 2
1 4 .0
7
0.023
0 .0 1 3
1 5 .0
7
0.040
0.028
1 5 .0
7
0.0 1 6
0.005
1 5 .0
8
0.000
0 . 000
1 6. 0
8
0.000
0.000
1 6. 0
8
0.005
0.003
1 6 .0
No.
F re q .
s.d.
A l lele:
A l leles fo r t h e locus 1 0 : D Y S39 1
N o.
F req.
s.d.
A l lele:
No.
F req.
s.d.
A l lele:
1
0.000
0 . 000
6.0
1
0.000
0.000
6.0
I
0.005
0.003
6.0
2
0 . 000
0.000
7.0
2
0.000
0.000
7.0
2
0.005
0 . 003
7.0
8.0
3
0.000
0 . 000
8.0
3
0.000
0.000
8.0
3
0.005
0.003
4
0 . 03 1
0.0 1 5
9.0
4
0.040
0.028
9.0
4
0.042
0.008
9.0
5
0.679
0.04 1
1 0.0
5
0.640
0.069
1 0 .0
5
0 .6 1 9
0.020
1 0 .0
6
0 . 260
0 . 03 8
1 1 .0
6
0 . 2 80
0.064
1 1 .0
6
0.29 1
0. 0 1 9
1 1 .0
7
0.023
0 .0 1 3
1 2.0
7
0.040
0.028
1 2 .0
7
0.032
0 . 007
1 2 .0
A l lele:
A l l e l es fo r t h e l o c u s 1 1 : D Y S439
No.
F re q .
s.d.
Allele:
No.
F req.
s.d.
A l lele:
N o.
F re q .
s.d.
I
0.000
0.000
9.0
I
0.000
0.000
9.0
I
0.005
0 . 003
9.0
2
0. 1 22
0.029
1 0 .0
2
0.080
0.039
1 0.0
2
0. 1 1 1
0.0 1 3
1 0 .0
3
0.420
O.O ..B
1 1 .0
.J�
0.520
0.07 1
1 1 .0
3
0.439
0.02 1
1 1 .0
4
0.336
0.04 1
1 2 .0
4
0.240
0.06 1
1 2.0
4
0 . 3 60
0.020
1 2 .0
5
0.092
0.025
1 3 .0
5
0.080
0.039
1 3 .0
5
0.053
0.009
1 3 .0
6
0.023
0.0 1 3
1 4 .0
6
0.040
0.028
1 4 .0
6
0. 0 1 6
0 . 005
1 4 .0
7
0 . 000
0.000
1 5 .0
7
0.000
0.000
1 5 .0
7
0.0 1 1
0.004
1 5.0
No.
F re q .
s.d.
A l lele:
A l leles fo r t h e locus 1 2 : D Y S635
No.
F re q .
s.d.
A l le l e :
N o.
F req.
s.d.
A llele:
1
0.008
0.008
1 9 .0
1
0.000
0. 000
1 9 .0
I
0 . 000
0.000
1 9 .0
2
0. 1 76
0.033
20.0
2
0.080
0.039
20.0
2
0. 1 4 8
0. 0 1 5
20.0
3
0.374
0.042
2 1 .0
3
0. 440
0.07 1
2 1 .0
3
0.444
0.02 1
2 1 .0
4
0. 1 3 7
0.030
22.0
4
0. 1 20
0.046
22.0
4
0. 1 4 3
0.0 1 5
22.0
5
0.2 1 4
0.036
23.0
5
0.240
0.06 1
23.0
5
0. 1 69
0. 0 1 6
2 3 .0
6
0.000
0. 000
24.0
6
0.040
0.028
24.0
6
0.05 8
0. 0 1 0
24.0
7
0.023
0.0 1 3
25.0
7
0.000
0.000
25.0
7
0.0 1 6
0.005
2 5 .0
56
8
0 000
0 . 000
26.0
8
0.040
0.028
26.0
8
0 . 000
0.000
26.0
Allele:
A l l e l es fo r t h e locus 1 3 : D Y S392
N o.
F req.
s.d.
A l lele:
N o.
F req.
s.d.
A l lele:
No.
Freq.
s.d.
I
0 . 000
0.000
9.0
I
0.000
0.000
9.0
I
0. 0 1 1
0.004
9.0
2
0.023
0.0 1 3
1 0.0
2
0.080
0.039
1 0 .0
2
0.026
0.007
1 0.0
1 1 .0
3
0.779
0.036
1 1 .0
3
0.720
0.064
1 1 .0
3
0. 794
0. 0 1 7
4
0.008
0 . 00 8
1 2 .0
4
0.040
0.028
1 2.0
4
0. 0 1 1
0.004
1 2 .0
5
0 . 099
0.026
1 3 .0
5
0.080
0.039
1 3 .0
5
0 . 079
0. 0 1 1
1 3 .0
6
0.084
0.024
1 4 .0
6
0.000
0.000
1 4 .0
6
0 . 063
0.0 1 0
1 4 .0
7
0.000
0 . 000
1 5 .0
7
0.040
0.028
1 5 .0
7
0 . 00 5
0 . 003
1 5 .0
No.
F re q .
s.d.
A l le l e :
No.
F req.
s.d.
A l lele:
No.
F re q .
s.d.
A l lele:
1
0.092
0.025
1 0.0
1
0.040
0.028
1 0 .0
I
0.037
0.008
1 0 .0
A l l e les fo r t h e locus 1 4 : G H TA - H 4
2
0.48 1
0.044
1 1 .0
2
0.680
0.067
1 1 .0
2
0.56 1
0.02 1
1 1 .0
J�
0 . 290
0 . 040
1 2 .0
3
0 .080
0.039
1 2 .0
3
0.3 1 7
0.020
1 2 .0
4
0. 1 3 7
0.030
1 3 .0
4
0. 1 _0
0.046
1 3 .0
4
0.079
0. 0 1 1
1 3 .0
O. 00
0.000
1 4 .0
5
0.080
0.039
1 4 .0
5
0.005
0.003
1 4 .0
No.
F re q .
s.d.
A l le l e :
-
A l l e les fo r t h e locus 1 5 : D Y S437
No.
F re q .
s.d.
A l lele:
N o.
F req.
s.d.
Allele:
I
0.000
0.000
1 3 .0
I
0 . 000
0.000
1 3 .0
I
0.005
0 . 003
1 3 .0
2
0. 763
0.037
1 4 .0
2
0 . 800
0.057
1 4 .0
2
0.799
0.0 1 7
1 4 .0
3
0. 1 68
0.033
1 5 .0
3
0.080
0.039
1 5.0
3
0. 1 3 8
0.0 1 4
1 5 .0
4
0.06 1
0 . 02 1
1 6 .0
4
0.080
0.039
1 6. 0
4
0.058
0 .0 1 0
1 6.0
F re q .
s.d.
A llele:
A l leles fo r t h e locus 1 6 : D Y S438
No.
1
F req.
s.d.
A llele:
N o.
F req.
s.d.
A l lele:
N o.
0 . 000
0.000
8.0
1
0.040
0.028
8.0
I
0 . 00 5
0.003
8 .0
0 . 1 07
0.027
9.0
2
0.040
0.028
9.0
2
0. 1 27
0.0 1 4
9.0
0.550
0 . 044
1 0.0
3
0,480
0.07 1
1 0 .0
3
0.624
0.020
1 0 .0
-l
0.260
0 . D3 8
1 1 .0
4
0 . 3 60
0 . 069
I 1 .0
4
0.206
0 .0 1 7
1 1 .0
5
0.076
0.023
1 2 .0
5
0.080
0.039
1 2 .0
5
0.032
0.007
1 2 .0
2
3
A l l e les fo r t h e locus 1 7 : D Y S448
No.
Freq.
s.d.
A llele:
No.
F req.
s.d.
A l le l e :
No.
F req.
s.d.
A l le l e :
I
0 . 008
0 . 008
1 6 .0
I
0.000
0.000
1 6 .0
I
0.005
0 . 003
1 6 .0
2
0.0 1 5
0 .0 1 1
1 7 .0
2
0.000
0 . 000
1 7 .0
2
0.005
0 . 003
1 7 .0
1 8 .0
3
0 . 00 8
0.008
1 8 .0
3
0 . 040
0.028
1 8 .0
3
0. 0 1 1
0.004
4
0.275
0.039
1 9.0
4
0. 1 60
0.052
1 9.0
4
0.259
0. 0 1 8
1 9.0
5
0 . 5 80
0.043
20.0
5
0.640
0.069
20.0
5
0.545
0.02 1
20.0
6
0.053
0.020
2 1 .0
6
0.080
0.039
2 1 .0
6
0. 1 2 2
0.0 1 4
2 1 .0
7
0.000
0.000
22.0
7
0.040
0.028
2 2 .0
7
0 . 005
0 . 003
22.0
8
0. 0 1 5
0. 0 1 1
2 3 .0
8
0.000
0.000
2 3 .0
8
0 . 02 1
0.006
2 3 .0
57
Allele Frequency for 3 regions at locus DYS456
.9
Allele Frequency for 3 regions at lOCUS DYS3890
Allele Frequency for 3 regions at locus DYS3891
�,c;
J
�
.,. n
c
5
�
. �!I III �II ...
< �.
n
,.)
14
"
�
04
.:: 03
�
O�
1.1
11
�:iele Nu:nber
••
'!h/r�
N
8
�
" �le l.',rn�'
(8)
Allele Frequency for 3 regions at locus DYS38911
(C)
Allele Frequency for 3 regions at locus DYS458
025
0.60
Allele Frequency for 3 regions a t locus DYS19
050
0.2
). 035
v
� 03
� O.i�
�
.: 02
� 0.15
>-
0.1
0.05
o
n
• ':1It.�e- • E.iSln U 'ellem
• Eas!efn • NIIt
0.1
«
.:1
n
IS
:3
:: ili I I tl
.11
A1lele 'l,mbtr
I [allO:' I W£;1e
(A)
05
O .!5
.1.
1.1
.7
16
c.!
•
25
26
27
I I III1 [ I I I
2B
19
lC
Allele Number
I Norther� I Ealtern
( 0)
I Western
31
32
>- o �o
g
0.15
"
c
�
�
0.1
u.
�
/j
�
� O.30
�
� 0.05
!
IJ .I IL
�
c
B
•
• I
II
13 14 15 16 16.2 17 17 2 18 IB.2 19 19.2 20 20.2
Allele Number
!
!
<
020
0.10
_
000
12
III I�I I�I 1.1
13
14
15
Allele Number
I Norther� I Ea>tern
58
I Western
(b)
I Northern
I Ealtern
I We�wn
(F)
16
.
•
II
0.4
c,o
03
� lS
� OJ
§ '�25
f VI
..
).
u
OS
0,],
� 004
� 0.2
c
�
�
� 0.15
, 5
:§� v.l
1 1\1 \;I II I�I I] II ..
< 0.1
� O�
-
I
10
11
12
13
14
IS
16
17
'"
UI
�
l id
01
;(
0,05
. .
I I
11
II
18
.
I
n
14
�
�
:;
�
�
Allele Frequency for 3 regions at locus DYS391
0.6
19
20
11
10
1l
• Northern
Allele Frequency for 3 regions at locus DYS439
Z
0.4
0.2
lui
10
I Northern l [a�lrn II/estern
m
11
I fallern
16
15
I Weswn
0.5
Allele Frequency for 3 regions at locus DYS635
04
).
�
�
�
c
�
�
OJ
14
13
Allele Number
I ••
( I)
). 0 4
Allele N um btl
II I
o
21
05
05
c
18
0,45
0.6
0,1
17
0.1
(II)
0.7
�
�
I:
16
Iii
I Notr?rn I EaSVln I We�e"
((i)
).
15
O..l
Allele Nu mber
Allele N um4er
I N')ll�e'n IHastern I Mstern
08
� 03
tI
�
UI
�
.:. 0.1
�
� OJ5
0.2
OJ
12
OJ
�
:r 0.25
OJ
<
.L I
035
I�I I�I lUI
10
11
13
Allele Number
I �)rl.ner� • Eastern I We�ern
(.I )
( K)
59
<:
OJ
0.05
•••
\4
15
19
M III III
20
21
22
I
13
Allele Number.
I �ortl:ern I rmr� I'\\eltern
(L)
24
II.
25
..�
..)
u.s
.4
-; �3
03
<
01
..,. I�I I I
•L.
"
14
13
Ilil
. 1 1.
II
15
•
10
ALele �'Jmbt
I \;::iel I taS!m I\\' �ll ern
I:
I K,rtho>r
I.I b
11
�
cd)
I
�1
13
14
!4
13
0.7
Allele Frequency for 3 regions at locus DYS448
0.6
>
u
c:
04
.:c OJ
.
8
_
1.1
9
• Northern
111 111
10
11
0.4
�
0.3
«
0.2
ill
�
0.1
•• .
o
•
16
12
Allele Number
I Weslern
_ __
17
18
• Northern
I Eastern
( P)
05
�
c�
60
I I m .01
19
20
Allele Number
Eastern I Western
•
(0)
21
•
22
.
•••
.Ii
15
ele llum�
I NG,�r� I [alt�rn • N""..n
( 0)
Allele Frequency for 3 regions at locus DYS438
05
� ::
,2
A!lele Numbe
• [aster� 'I \\'elte�
0.6
>
u
c:
03
(N)
( f\ I )
07
ILl
C.4
•
23
Table
1 0:
Pre
nts a U l11 l11ar) of loc i \\ ith a l le les that are not hared bet\\ een a l l
regIOns.
Loc u s
Allele
N orthern N= 1 3 1
Eastern N = 25
W e s t e rn N = 1 3 9
O Y S456
13
0 .06 1
0
0.032
O Y S3 89 1
15
0
0
0 .0 1 1
O Y S390
26
0.008
0
0
25
0.0 1 1
0
0
27
0
0
0 .0 1 1
28
0 .084
0
0.069
32
0.069
0
0.058
13
0
0
0.005
OY 3 89 1 1
D
OY
458
19
D Y 3 85-A
D Y 385- B
D Y S393
OY 3 9 1
DY
439
O Y S635
14
0 .008
0
0 .0 1 1
1 6. 2
0
0
0.005
20.2
0.0 1 5
0
0.02 1
12
0
0
0.0 1 1
17
0 .0 1 5
0
0.026
0 .0053
8
0
0
10
0 .0 1 5
0
0
17
0 . 1 22
0
0. 1 0 1
0 .0 1 1
18
0
0
19
0 .008
0
0
1 1
0 .008
0
0 .005
12
0.023
0
0 .0 1 6
13
0.008
0
0.02 1
15
0.084
0
0 .048
21
0
0
0 .0 1 1
9
0
0
0 .0 1 06
10
0
0.008
0 .005
16
0
0
0 .005
6
0
0
0 .005
7
0
0
0 .005
8
0
0
0 .005
9
0
0
0.005
15
0
0
0.0 1 1
24
0
0 .040
0.058
19
0.008
0
0
25
0 .023
0
0 .0 1 6
9
0
0
0.0 1 06
14
0.024
0
0.63
15
0
0 .040
0 .005
G ATA H 4
14
0
0.080
0.005
D Y S437
13
0
0
0.005
D Y S·t38
8
0
0.040
0.005
16
0.008
0
0 .005
17
0. 0 1 1
0
0 .005
22
0
0.040
0 .005
O Y 392
DY 448
61
The
ariation in a l l e le di tri bution, or a lternat ively uniq ueness, can stem from
e\ eral factor .
There are more common rare al le les that are
orthern and Eastern region rather than Western region (see table 1 0).
hared between
Iternati ely,
there are man) rare a l l e les that are o nl . pre ent i n We tern region and absence from
other t\\ O region
de pite the fact that
orthern popu lation s i ze is re latively large.
1 10\\ e e r, one m i ght sti I I argue that these a l ie les are rare and the popu lation size i not
repr sentative of the ubpopulation. Tn fact, most of the ' u n i que a l lele freq uenc ies
are
<I
0 0.
H owever, a l l e les frequenc ies that are
mai ler Ea tern subpop u l ation ( n=2 5 ) .
a l lele
<I
% also do show u p only in the
A l ternatively, it c a n be argued that those
that are not shared between the regions are the resu lt of new m u tations
( K u ri hara, 2 004; G usmao et a I . , 2005; for re v i ew see E l legren, 2000).
Other
explanations for the p resence or absence of a l l e les in any of the subpopu lations can
I t can re nect a recent gene fl ow from
tem m a i n l y from popu lation structure.
neighboring regions that contri butes m i n i m a l ly to tota l hap lotype freq uenc ies.
F u rthemlOre, the gene flow to spec i fic regions are fro m spec i fic neighboring areas .
For exam p le. the Eastern and
olthern are coasta l areas and it is ex pected that
ad m i xture rate i s h i gher i n those regions. Further analysis and experiments at h igher
molecular levels i s requ i red to e l uc idate the structure of the popu lation w ith respect to
rare a l le les.
3.2.3
V a r i a n ce of a l le l e freq u e n cy i n U A E p o p u l a t i o n and i n s u b ­
po p U l a t i o n :
A l le le variance i s a parameter that desc ribes the d istribution o f a n observed
population and its mathemat ical treatment can deci pher genetic distance bet\-\ een
pop U lat ion and groups w i t h i n a population.
62
I n the recent years, genet ic d i stance
m an i fested i n a l l ek \ari ance rather than a l l e l e frequenc) i s i nc reas i n g l y u t i l i7cd i n
p() p U l al i o n genetic stud i es ( S latk i n , 1 9 9 5 : 1\ k i rmans,
.2006:
Exco 11i er,
2005 ).
We
han: c u m p u kd \ ariance of a l l d cs ('or each l oc us for the 3 4 5 sam p l es . S PS S so ftware
was u ed to c a l c u l at e the \ ariance for each l oc u s : variance is s i m p l y the square root
o f t h e standard variat i o n , 'I he \ ariance i s o b ta i n e u fu r t h e U A E pop u l at i o n as a whole
as we l l as tor t h e th ree reg i o ns (I orthe rn , E astern and Weste rn ) ( F i gure 1 1 and 1 2) .
[ t i s c l ear t h a t the variances fo r e a c h l o c u s i s d i fTe rent a n d re flects t h e n u m be r o f
a l l c ks and d i s t r i b u t i o n () f a l l e l es for t h e respe c t i ve loc us.
H owc\'Cr. t h e c o m parison
or t h e \ a r i a n ce bet\\ ecn subpo p u l a t i o n s d e m onstrates c l ustering fo r a l1lunber of loc i
\\ h i l e the) a re s p read fo r other loc i ( F i g ure 1 2 ) .
Va r i a n ce of U A E P o p u l a t i o n
8
•
Q)
u
C
ttl
. ;::
ro
1
>
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
0.125
Locus N a m e
F i g u re
1 1:
Variance d i s t r i b u t i o n o r t h e U A E popu l a t i o n .
63
•
Va r i a n ce of t h e t h ree Reg i o n s
• Northern Va riance
8
• Eastern Va riance
Western Variance
•
<lJ
u
C
III
·c
�
•
•
•
•
>
•
•
•
•
•
•
•
0.125
1.0
lJ"I
<;t
VI
>a
0;
CXl
(Y')
V'!
>a
0
<:1'
(Y')
V'!
>a
0;
CXl
f')
VI
>a
CXl
lJ"I
<;t
VI
>a
.....
Ci'
VI
>a
.....
If'I
CXl
(Y')
lI'l
>a
I
N
If'I
CXl
(Y')
VI
>a
I
(Y')
Ci'
(Y')
V)
>a
.....
0'1
(Y')
VI
>a
Ci'
(Y')
<;t
VI
>a
Locus N a m e
lJ"I
(Y')
1.0
V)
>a
N
0'1
(Y')
lI'l
>a
<;t
:r:
<r
f<r
\.9
"
I
..,.
(Y')
VI
>a
CXl
(Y')
<;t
VI
>a
CXl
<;t
<;t
lI'l
>a
Figu re 1 2 : Variance d istribution o f the llm:: e regions.
S i nce the non-recombi n i ng part o f Y chromosome is i n herited as a unit haplotype and
provided that se\eral o f the loc i ' s variance are clustered (sim i l ar) bet\\"een
sUbpopu iali ons w ith no sign i fi cant di fference. then it fo l l o\\'s that the varIance
observed for other loc i i s probably due to h i gher suscept i b i l i ty of those loci to
mutation ( Gusmao et a l . . '200.5 ) . Normal l y . STR has a h igher rate of mutation than
2
I
single nucl eot i dcs: it is esti mated from I x l O- - l X I O-- . These variations depend on
the allele i tsel [ position. moti f size. sequence composition, and stab i l ity oC STR
( Eckert and H i l e 2009: G usmao et aL 200.5 ) . Founder e ffect and geneti c drift are not
p lausible explanations in the UAE popui ation as the genetic d i \"ersity of the 1 7 STR is
high and relati vely smal l members o f populations are sharing identical haplotypes
(see below).
Loci \\ ith greater a l l e l e \·ariance bet\\ cen the subpopulatioll arc
DY , 4 3 8 . DYS...J. 3 7 . GATA 1 1 1 4. DYS I 9.
However. it should be noted that the
\\'estern ' s population a l l e l e \ ariance for DYS43 8 . DYS...J. 3 7 . GATA_I I I 4. DYS 1 9
luci show departure from Eastern and Northern regions. A l though. these results are
sti l l I nconcl usive it warrants further i nvesti gat ion at a higher m o l ecular resol ution
( S N P ) . The S'\JP studies w i l l e l uc idate \\·hether the vari ance departure ror
64
<l
spec i li c
regIOn
due to ne\\ m utation ba ed on one- tep mutat ion model or to recent gene
flo\\ .
3 . 2 0 4 A l le l e F req u e n c
population :
of U A E p o p u l a t i o n co m p a red w i t h o t h e r
P redom inant a l le les ob er ed in the U A E populat ion sam p l e were com pared to
other predom i nant a l leles in the
rab ian Pen insula popu lat ions and to surround ing
areas u ing data from other tudie performed o n the ame loci in V -Chromosome.
o m pari on of a l l e le freq uenc ies \ ith other popu lations in the region of the A rabian
Pen i n Li la and its neighboring countries ( oares et a L 2008; H ed man et a I . , 2004;
Fad h laou i
t a l . , 2 0 1 2 ; A m brosio e t a l . . 2 0 1 2 ; I m ad e t a I . , 20 1 3 ; Y u n i s et a I . , 20 1 3 ;
H a l lenberg et a I . , 2005; Rosa et a I . , 2006; Rahman el a I . , 2 0 1 2 ; Donbak et a I . , 2006;
Turrina et a l . . 2006; Chang et al. 2007; Abd in et a I . , 2003 ) show s i m i lar preva lence
of predom i nate al le les across the loc i . I t can b e seen that the U A E po pu lation share
most of its predom i nant a l le les w ith Tu rkey ( shares 1 3 loc i), Tunisia (s hares 1 0 loc i),
yria (shares 9 loc i), I raq and I nd i a (they hare 9 loc i ) . I n general, they share more
than 5 0% o f their p red o m i nant a l le les " ith the U A E popu lation ( see tab le 1 1 ).
Howe\ er. it shou l d be noted that each po pu lation reta in their part i c u larit ies of al lele
v ariance and freq uencies that can p lace them at part icu lar genetic d i stance.
65
Ta b k
1 1 : l TAE
ro p u i a l i o l l a l k k rn.: q w':I1l: Y C l l l l 1 p a n.:d \" i t h o t h e r po p u l a t i on s . A l l e l es shared between t TA E and o t h e r p o P U ia t i llllS �II\.'
h ighl ighkd.
Popu lation
G ni nc;!
lJA I,:
Bissa u
N=3 .t 5
. --
1 .5
D Y S�56
D YS390
D Y S3 S 9 1 I
f----
D Y S�58
i---
D YS 1 9
D YS385 - A
D Y S385-B
-
-
D YS3 8 9 1
N .-- 2 1 5
-
. � --
,
T n l'l((�y
Syria
Somalia
Spain
T u n is i a
Brafil
Finland
P a ki s t a n
Colom b i a
I ta ly
I l i d ia
N= S6
N= 1 1 3
N= 2(J 1
N�3.t7
N=2 1 8
N - ..t 1 2
'i .=o..t O O
"" 7 1
1'\ = 1 73
N � 1 55
'i � 1 0 6
15
-
-
13
13
-
I raq
N=.ttlO
-
)
- -
�o
30
-� -
1 7. 1 6*
14
I ")
.
1S
14
---- -- --
21
"
23
29
-
15
14
14
-
13
-
14
f-- -
15
-
- -
13
13
13
")
-"
j
,"
29
30
25
31
16
-
14
10
- .)
15
13
24
25
24
24
17
14
11
14
13
16
27
15
18
30
-
-
15
14
15
15
-
11
II
18
-
13
14
14
10
10
10
10
10
10
11
9
D YS�39
I I
13
10
11
12
11
12
10
D Y S635
21
-
24
21
-
D Y S392
II
I1
II
11
1I
13
14
1 1
-
12
II
-
-
12
1 1
-
II
D Y S39 1
G ATA H �
1 1
12
12
13
-
13
22
13
21
13
10
-
-
13
14
14
14
13
14
14
15
14
D Y S�38
10
II
10
10
9
11
12
10
-
D Y S -U8
20
-
19
20
-
-
19
20
-
N u m b er of
S h a red
loci
6
17
--- �- --
S
13
9
>" Two predo m i na n t a l l e l e i n the U A E pop u l a t i o n .
--
- -
�
-
-
30
13
24
20
- -
-- --
15
IJ
----
13
-
-
-
14
-
24
22
:-;0
-
16
14
15
12
11
29
-
-
-
14
-------
-
D YS437
24
29
13
14
13
--
12
D Y S393
15
--
14
16
28
-
13
-
-
--
-
13
31
18
--
-
16
-
I1
14
-
-4
10
14
13
13
II
II
11
10
10
14
-
21
24
11
13
10
13
10
-- --
12
11
--
-
-
II
II
20
-
14
12
13
14
15
15
12
14
10
11
13
-
II
-
20
-
-
19
14
-
-
-
3
5
7
2
-t
I 'V
. . .. 8;-. �' - ,
' . I- � I�
" 1 - ··_ ,_ >
--
66
I
3.3
Y
TR h a p l o t y p e o f U A E p o p u l a t i o n :
B rie fl) , the word "hap loty pe" desc ribes a genetic u n i t or com b i nation of al le les
at adja ent locat ion
single parent.
or loci on the chromo ome that are in herited together from a
uto omal haploty pe are prone to recom b i nation and therefore the
ero ion of its gamet ic pha ing ( H art l , 1 997). On the other hand, an organ ism
\V
ith
heterogamete , one of the hromo omes that is most ly non -reco mbin ing is inherited
a one hap lotype ( K ayser et a I . , 1 997). Haplotype can appear in many d i fferent ways
uch a , one locus, se era l loc i or an entire c hromosome depend i ng on recombi nation
numb r i n a set of loc i . There are three primary reasons for considering the hap lotype
organ izat ion of a variat i o n . F i rst is that, the u n it of b io logical fu nction, the prote ln ­
cod i ng gene, p roduce p rote i ns whose seq uences correspond to matern al and paternal
hap lotypes. Second, the variation i n a pop u l at ion is i n fact, structured into hap lotypes
that are l i ke l y transmitted as a uni t.
Last ly, regard less of the po pulat i on genetic
reason , haplotypes serve to red uce the d i mensional ity of the prob lem of test ing
assoc iation, and so they may i nc rea e the power of those tests (C lark, 2004) .
I n t h i s study, 3 4 5 haplotypes each wit h 1 7 a l leles were analyzed u s i n g A rleq u i n
soth\ are ( Ex.coffi er, 2005).
The analysis measures t h e freq uency of a l l eles and
genetic variations between popu lations, w i t h i n a pop u lation, and among groups.
3.3. 1
H a p loty p e Fre q uency:
H a p l otypes o n non- psuedoautosomal region of Y c h romosome passes from one
-
generation to another i ntact except where m utat ion events have taken p lace.
This
study measures s i m i l arities or d i ssim i larities between haplotypes to describe the
67
geneti
tructure of U A E popu lat ion.
A lthough in our study, the popu lation shO\\ s
re lativel) d i ver e hap lotype, there are a number o f hap lot pe shared at lea t bet\ een
t\\ O i n d i v idu a l \\ ho are not related (see table 1 2 ) .
Table 1 2 . H ap lot p e freq uen y fo r
hared hap lotype I n the U A E po pu lat ion. (fi
repre ent nu m ber o f count am p Ies ti mes quared freq uency).
H a p lo t y pe
S h a red
1
H ap lo t \ pc
F req.
2
(Freq.)
4
5
6
Tota l
0.005 797
0.008696
0 .0 1 1 5 94
0.0 1 4493
0.0 1 73 9 1
-
-06
.05
05
7 . 5 6 1 0.
0 .000 1 3 4
0.0002 1
0.000302
-
8.4* 1 0
fi
3
0 .002899
3 . 36* 1 0
27 1
22
5
1
1
I
301
0 . 002277
0.00073 9
0.000378
0.000 1 3 4
0.0002 1
0.000302
0 .00404 1
27 1
44
15
4
5
6
345
co u n t
N
3.3. 2
2
F req u e n cies
H a p loty p e D iv e rs i ty :
The presence o f identica l hap lotypes warrant the i n est igat ion of hap lotype
d i ve rs ity. H ap lot 'pe d iversit i s a measure of the u n i q ueness o f a part i c u lar hap lotype
in a g iven population. This measure of gene d i vers i ty is ana logous to hetrozygosity at
a single locus. The hap lotype d i versity ( H ) in o ur population was c a l c u lated us i ng the
fo l lo\\ ing fo rm u la :
H
=
Y
-
-Y
_ 1
(1
-
�
L..,
I
T;'J )
W here .2\ is the re lative hap lotype freq uency of each haplotype i n the sam ple
{
and ." is the n um ber of sam p le (Nei et aI., 1 98 7 ) .
Hap lotype d i vers ity i n t h e U A E
population is e q ua l to 9 9 . 8 8 5 % (see tab le 1 4 i n section 3 . 4),
is a large geneti c d i vers ity in U A E popu lat io n.
68
"
h i ch means that there
However, we have also compared
genet ic d i tance bet\\ een the subpopu lation in the three regIOns.
( I icro o ft �)
o ft\\ are G E A L
matrix ( Peakal l and
di tance anal) i
Excel - based
6 was used t o compute N i e ' s pairw i se genetic
mou e, 2006). The re u l ts of pairw ise population
e i ' s genetic
sho\\ a re latively sm a l l d i ffe rence between popu lation .
The
pa in\ i e genetic d i stan e computat ion is based on stepwise mutation models ( ei,
1 978). It hould be noted that region 2 ( Eastern) demon strates h i ghest d i stance " hen
ompared to We tern region and not as large of a genet ic d i stance when com pared to
o rthern ( ee tab l e 1 3 ) .
locat ion of the latter
1\\0
This can be attributed to sam p l e size but geographical
region ( Eastern and
ort h e rn ) may account for the genetic
si l1l i laritie , a the e t\\ 0 regions are coastal regions and may have shared t he same
m igratory paths. N ie's genetic d i stance (Takezak and N e i , 1 996; Nei, 1 97 8 ; Peaka l l
mouse, 2006), howe e r measures the summation o f a l l genet ic loci exam ined for
the popu lation under stud
and i t i s prone to b iases for two fu ndamenta l reasons: 1 )
the sam p l e s ize and 2 ) the num ber of genet ic loci exam i ned. A l t hough, t his study h as
experimented
\\
ith genetic d i stance w it h i n the U A E
po pulat ion, the cu rrent
i n format ion m u st be caut iously i nterpreted but warrant fUl iher i n vest igat ion at h i gher
molec u lar reso lution ( i .e.
P, copy Dumber variat i o n ) .
appreciate that the geographical location of d i fferent region
I t is a l so i m poliant to
in the U A E provi ded
d i fferent resou rces and attracted d i fferent interests fo r imm igrants. Th is is espec i a l l y
true for t h e periods before 1 97 0 ' s d i stance (Nei, 1 9 7 8 ) .
69
Tab le 1 3 : Repre ent the res ults Pain\ i e Population Matrix of
for
e i Genetic D i stance
orthern ( I ), Eastern (2), and We tern ( 3 )
P a i r" ise Popu l a t i o n M a t ri x o f N e i G e n e t i c D i s t a n c e a n d I d e n t ity
Pop2
N e i ge n e t i c i d e n t i t y
# Pop l
I
2
N e i ge n e t i c D i s t a n ce
0.069
0.934-
131
25
I
3
0.043
0.958
131
1 89
..,
j
0. 1 3 9
0 . 8 70
25
1 89
Pop l
')
-
3.4
# Po p 2
D i c r i m i n a t i o n C a p a c i ty :
B)
de fi n i tion,
D i scri m i nation Capacity ( DC) means that the number of
hap lot) pes obse rved o nly once i n the popu lation, w here designated as " U n ique
hap lotype".
The DC calculated for the
1 7 loci stud i ed a a percentage of unique
hap lot) pe by d i v i d i ng the nu mber o f un ique hapl otype over the total number of the
hap lotypes.
F ro m tab le 1 3 the percentage of DC is equal to 90.03 w h i c h i nd icates
that the U A E population is com prised of a re lative ly large num ber of unique
hap lot) pes.
I n t h i s study none of the shared hap lotypes comes from fi rst degree
re latives ( fathers/son brother. paternal cousins). T h i s i n formation has a sign i ficance
im pact i n fo rensic analysis and other loc i on Y c hromosome shou l d be used i n
conj u nction w ith t h e 1 7 l o c i ut i l ized.
FLII1 h ermore, t h e DC ind icates that there are
common hap lotypes i n the U AE popu lation that is probabl y contri buted by sharing
recent ancestors.
The UAE population demography, soc ial structure, and c ulture
strengthen \\ hy DC is not approaching 1 00%.
70
Table 1 4 · sho\\ s t he percentage of Discr i m i nation Capa it)' and Haplotype D i versit)
In
3.5
E popu lation
S h a re d h a p l o t y p e i n U A E p o p u l a t i o n :
Common hap lotype among c l ose ly located popu l at ions may i m p ly common
paternal ancestry ( Fured i et a I . , 1 999). The fi n d i ng o f hared identical hap lotype i n a
popu lation ha
probab i l i t)
a s i g n i ficant connotation on forensic i n vest igat ions
o f identity bet\ een d i fferent popu lation .
invest igated in this study i s comprised of 3 0 1 hap lotypes.
(n=3 0 1 ). 2 7 1 haplot) pes are u nique wh i le
t\\"o i n d i, idual
(see figure 1 3 ) .
�
v
ith regard to
The U A E popu lation
Of the total haplotype
haplotypes are shared at least ben een
W h i l e the majority of shared haplotypes occ urs
bet\\ een n\'o i nd i v iduals there are three cases w here four or more ind i v i duals are
sharing identical hap lot pe. Moreover, there are three d i fferent hap lotypes shared by
fi e i n d i idu a ls (see Table 1 5 ( A-E). In most case t hese i n d i v i duals are not from the
same c l a n . H o\\ e er, in one i nstance t here are three i n d i v i d u a l s with the same tribe
name \\ ho are shari ng the same hap lotype; upon fu rther i n vest igat ion, t he three
i n d i v i d u a l do not share father or grandfather names.
71
N U M B E R O F S H A R E D H A P LOTY P E
..........
N
LJ.J
0..
>to
--'
0<:t
I
u..
0
0
Z
N
N
1
2
.....
CJ)
4
3
5
6
N O . OF I N D I V I D U LAS
F i gure 1 3 : Tot<1l n um b e r o f U n i q ue and S hared I f a p l olypc
72
Tab le 1 5( A - E ) : Presents the haplotypes that are shared in the population. J\ ) l I ap lot) pes shared between two i n d i \ lduals:
11) I l ap iotypes shared between three of I nd i v i duals; C ) l l aplotypes shared between fOLl r of I n d i vi d uals ; D) l I ap lot) pes
shared between five or I nd i v i duals. E) I Iaplotypes shared between six I n d i v iduals. The order of al leles i n the tables are
DYS 1 9, D Y S 3 8 9 1 , D Y S 3 89 1 1 , DY S390, DYS39 J , D Y S 392, D Y S393, D Y S 3 8 5 A , DY S 3 8 5 B, DYS43 8, DYS439,
DYS437, DYS44 8 , D Y S4 56, DYS4 5 8, DYS635 and G A T A - I 14.
A
No.
F r�.
S.D
0.005 79 7
0.004093
0.004093
16
15
0 .004093
0.004093
0.004093
0.004093
15
14
26
42
0. 005 797
44
46
0.005797
0.005 79 7
57
59
63
1 00
0.005 797
0.005 797
0.005 797
0. 005 79 7
0 . 00 5 797
0. 005 797
0 . 00 5 79 7
1 27
0.005 797
0.004093
0. 004093
0 . 004093
0 . 004093
0.004093
0 .004093
1 39
0.00579 7
0 . 004093
1 45
0.005 797
1 60
161
0 . 00 5 797
14
16
16
14
13
23
31
13
13
12
23
30
23
24
31
28
30
29
14
14
13
13
13
13
13
13
14
15
13
13
14
0. 004093
16
14
0 .004093
15
0.005 797
0. 004093
1 78
0.00579 7
0.004093
1 84
1 90
0 . 0 0 5 797
0 . 00 5 797
0.005 797
0 .005797
0 .004093
0 . 004093
0. 004093
0.004093
0 .004093
86
89
91
217
280
7
0.005 797
23
23
25
23
23
23
23
30
29
30
30
30
24
24
30
29
14
23
25
16
13
24
30
16
14
13
14
13
14
14
24
23
30
31
25
24
23
29
32
31
24
30
15
13
15
17
13
13
1 72
1 72
14
13
14
15
18
16
15
14
14
13
II
16
13
12
16
13
1 82
17
15
1 82
1 82
1 82
1 82
15
13
14
14
14
14
13
13
13
17
14
14
30
1 82
14
13
32
16
15
16
14
I I
17
17
14
1 82
16
17
17
15
14
15
15
14
13
73
15
11
17
13
I I
I I
14
15
H a �I oJype
17 12 10
16
15
20
19
14
17
18
20
18
18
17
14
12
13
12
12
12
13
12
12
12
12
13
12
12
10
10
9
1I
I I
10
10
1 1
10
I I
11
10
1 1
I I
10
12
11
13
I I
I 1
I I
I I
1 1
12
15
20
20
23
21
21
23
21
21
I I
14
14
10
10
20
20
14
14
14
14
14
14
14
14
14
14
I I
9
20
19
20
19
20
20
20
20
19
15
14
10
12
10
10
10
10
10
10
12
10
20
19
19
22
21
21
22
1
I
I
I
14
11
1 1
13
12
11
13
10
10
1 1
I I
1 1
12
12
11
I I
I I
12
14
14
I I
10
20
20
I I
I I
I I
1 1
13
I I
12
1 1
13
12
I I
I I
14
14
14
14
14
14
10
10
I I
10
10
10
20
20
19
23
19
II
I I
23
22
13
10
10
23
17
13
10
12
20
18
18
15
12
16
17
13
12
14
13
13
13
10
I I
1I
10
10
10
12
I I
10
12
11
11
20
21
24
18
14
I I
11
?
21
22
I I
1 1
1 1
13
1 1
1 I
1
I
I
I
12
20
B
N o.
Freq.
S.D
1 83
0.0087
0.0050
25
0.0087
0.0050
1 18
0.0087
0 .0050
n
0 .0087
0.0050
9
0.0087
0 .0050
H aplotype:
14
13
23
14
13
23
30
14
13
23
30
IS
13
23
30
14
13
23
30
30
14
13
19
1 82
14
13
1 92
14
13
1 72
14
1 82
14
1 92
12
I I
19
12
18
12
13
17
13
18
c
D
E
74
I I
21
I I
I I
I I
I I
22
I I
I I
12
12
21
I I
I I
12
10
I I
20
I I
I I
12
I I
I I
21
I I
I I
10
20
14
10
20
14
10
20
14
10
20
14
10
20
14
I hi l� l i ke l ) cil! ' t o t he sharing o f most C0111m011 rec�llt ancestors. I Illwc\'er. i n the
maj orit: or cas 's. the trihes name does not pred ict a spec i li c hapl otype. This is not
surpri� i ng
,L
tri bal names. al though it stems from a cOlll mon founder: i t i 'i given to
i l1li i \ iuuals that do not ha\'e d i rect blood re lati onsh ip. These results have signi ficant
i m p l ications l)n Curensic science practices
These resul ts cal l for more thorough
analysis that sht) ll l d i n c l ude Sl P stud i es alongside the 1 7 Y chromosome STR
analysis. We also have found that approx i matdy 5 0% o t' thl.:! lTAE popu lation share
bctm:en 6 tl) 7 loc i the result. which should restrict the usage of m i n i mal pand o f
S T R t see F i gurc 1 4 ) . Tbe data \\ as anal)- zed b y GENALEX 6 which i s b u i l t as Excel
( i\ l icro�ot \{ ) add-in program ( Peab l l and Smouse. 2006).
Figure 1 4 presents the
number of matc h i ng hapl o types yerSllS un i q ue haplotype by l oc lls.
N o . M a t ch i n g vers u s U n i q u e H a p l otypes by locus
'
'
'
'
,
'), '),x"v -:vx'? '})xt>< x,?x . ,?x '· x,?x '· ,?x .· ,?x '· ,?x '· ,?x '" '?x '" x'?x '" '?x '" x,?x .,· x,?x .·· x":: '"
x
x
x
x
x
x
x
� x� "-;� "-;� "-;� "-;� "-;� "-;� "-;� "-;� "-;� "-;� "-;� "-;� "-;�
'),
Locus Combination
-+- ItWi th m a t c h i n g h a p l otype
_ It W i t h u n i q u e h a p l otype
Fig ure 1 4 : ;-"Iatching \'�rsus U nique H ap l ot) pes by Loclls.
7S
3.5.0
h a red h a p l o ty p e of
A E popu l a t i o n c o m p a red w i t h o t h e r
population :
I n our popu lation, 3 0 1 d i fferent haplot) pes were ident ified, 2 7 1 of wh ich were
unique. The 1110st freq uent hap lotype \\ as found in 22 in tances. The second most
frequent hap lot) pe "" ere 4 ,
, 6, \\ h ich they shared o n ly o n e hap lotype. I n addit ion
b) comparison \\ ith other popu lat ions, \\ e found that in L i bya (n= 1 76 i n d i v iduals),
they have a total of 1 42 d i fferent haplotype and 1 24 \ as un ique (Tri k i et a I . , 20 1 3 ) .
Howe\ er, i n C h i na ( n= 1 1 2 indi iduals) a tota l o f 9 9 hap lot pes were found and 8 8 of
them \\ re u n iq ue hapl otypes (Tie et aI., 2003 ) .
In add itio n, Syria with 1 1 3
i n d i i d ua ls . the) ob erved that there are 1 0 8 d i fferent haplot pes and 1 04 haplot) pes
\\ ere found to be un iq ue ( bd i n et a l . 2 003 ) . M o reover, i n the Kuwa it i popu lat ion a
total of 1 0 1 d i fferent hap lotypes, among wh ich 7 8 where un ique, e i ght haplotypes
were shared between two i nd i v iduals, three i n d i v i d ual
.
i n d i v idual
shared fou r haplotypes, four
hared o n l y one hap lotype and the most freq uent haplot ype was shared by
7 i n d i v i d ua ls ( oumaya et aI., 2 0 1 0 ) . I n Tunisa, they found that the total number of
hap lot) pe \\ ere 1 5 4, o f wh ich 1 2 7 were un ique, the most common haplotype was
represented b
1 4 i n d i i d u a l s ( Fadh laou i -Z id et a I . , 20 1 2 ) .
76
3.5
G e n e d iv e r ity fo r 1 7 poly m or p h i c l o c i i n UAE p o p u l a t i o n and in
1I b-po p li l a t i o n :
Gene d i \ e rsity for a11 3 4 - sample were calculated lIsing the fo l lo w i ng form u l a :
H
.Y
Y - 1
=
Where
•
. 1' ,
i
( 1 - "'"'
L .1'2 )
1
I
the freq uency of each al lele in the locus and iV i
pre ented i n the !OCLI (
ei et a I . , 1 987). Accord i n g to measures o f genetic d i versi ty,
the h i ghest d i er ity were o bserved at locus DY 4 5 8
OY 3 8 5 - 8
=
0.9 .
the number of al lele
=
0 . 9 , D Y S 3 8 5 -A
Therefore, t hey shou ld be considered a
. mo t i n format ive marker for forensic test i ng.
=
0.9 and
the most variab le and
W h i le, loc i with the 10\ er di ersity
are the least informat i ve loci (OY 392 \ hich eq u a l 0.437; see table 1 6 ) .
nother parameter t hat can b e calcu lated is t h e tota l gen t ic d i versity and we
calculated it by d i i d ing the number of observed hapl otype over the total sam ples
\\ h ich i
equal i n t hi s study 87%.
In the sub-pop u l ation, there are varieties of the
h ighest and lowest of al l e les frequencies. For exam p le, in Northern region, there are
n ine loc i w it h h ighest and 1\\ 0 loc i w i th 10\ est d i er i ty. W h i le i n Eastern region, the
h ighe t gene d i versity i s in O Y S 3 89 I I
\
ith a value of 1 .00 and the lowest i nvol es t he
DY S43 7 locus; moreover i n Western region, the highest gene d i versity is assoc iated
\\ ith five d i fferent l oc us ( ee table 1 6) .
The t rend of gene d i ver ity in the sub-
population i not d i ffe rent from the \\ hole U A E popu lation. H owever, the d i fferential
d i ve rs ity per locus rei nforces a stepwise mutation mod e l i n which the memory of the
pre ious event o f m utation is mainta i ned ( V a ldes, 1 993 ) as op posed to infin ite
mutation model ( H udson, 2002 ) .
77
Table 1 6 : Genet ic d i versity for J 7 pol} morphic loci i n
popu lation.
UAE p_op_u l a t i o n
Nort h e rn
Eastern
D Y S456
0.8
0.9
D Y S38 9 I
0.6
0.5
0.9
0.7
D Y S390
0.8
0.9
0.8
0.9
D YS389 1 I
0.8
0.9
1 .0
0.8
Lo c us
3.6
A E pop u lation and in sub­
Wes t e rn
0.8
0.6
D YS458
0.9
0.9
1 .0
0.9
DYS 1 9
0.7
0.8
0.7
D YS 3 8 5 A
0.9
0.9
0.8
1 .0
D Y S385 B
0.9
0.9
1 .0
D Y S393
0.7
0.7
0.8
D Y S39 1
0. 6
0 .6
0.7
0.9
0.9
0.7
D Y S-J39
0.8
0.9
0.8
0.6
0.8
D Y S635
0.8
0.9
0.9
0.9
D Y S392
0. 4
0.5
0.6
GATA H4
0.8
0.9
0.6
0.3
0.7
D Y S437
0.5
0.6
0.5
0.5
DYS438
0.7
0.8
0.8
0.7
DYS448
0.7
0.7
0.7
0.7
A M OV A res u l ts i n U A E p o p u l a t io n :
nal) i of M o lecular V ariance ( A M O V A ) was calcu lated i n A rleq u i n software
o\ er h\ o sources of ariation among the population and w i t h i n population as shown
in tab le 1 7 . A M OY A measures hap lotype d i vers ity rather than j u st a l lele freq uenc ies
that prov ides an oppoJ1Ll I1 i ty to measure the d i fference in haplotype
in a paitw i se
manner. Furtherm ore, the analysis accommodates and re l ies l ess o n d i ffere nt types of
assumption about the evo l ut i o n of genet ic models. It is c lear fro m the A MOY A that
the m ajority >99 . 5% of the variations w i th i n a po pulation rather than between
populations. T h i s re i n forces our earl ier d i scussion that N i e ' s ( 1 9 8 7 ) geneti c d i stance
calculations suffered fro m : 1 ) number of loc i , 2), population size (espec i a l l y for
Eastern regions), and 3 ) the assumptions that are an i ntrinsic part o f m athemat ical
78
treatment. I n ad d it ion the average F- tat istics ov er a l l loc i F ixat ion Ind ices ( F t
0 . 002 80).
A l lhough Fst calcu lation depend
con ordance \\ ith l a c k of h ierarchy in the
Table 1 7:
=
on the al lele freq uencies, it is i n
E ub-population.
M O A design and resu lts (average
0
er 1 7 loc i ) :
Sou ,"ce o f V a r i a t i o n
S u m of squa res
V a r i a n ce c o mpo n e n ts
Pe rce n t age V a ri a t io n
0 .0 1 5
0.280
A m o n g po p u l a t io n s
1 5 .065
Within populations
3978.80 I
5.34 1
99.720
To t a l
3 99 3 . 866
5.356
1 00
Howe er, there are apprec iable genet ic d i ersity i n the U A E population as a whole
that reflect h i gh rate o f ad m i xture d i fferent geographical regions.
(tab le 1 8 ) that
fl o\\ account
A M OYA shows
E popu lation i s c losest to Yemen, Kuwait, I raq and I ran.
for these s i m i larit ies and reflects the h i story of the U A E which is in
accordance with the hi tory of A rabian Pen i n s u l a ' s h i story.
Table 1 8 :
MOYA results in other popu lation:
Pop u la t io n
A fg h a n is t a n
Gene
A fg h a n i s t a n
I ra n
I raq
Kuwa i t
Yemen
UAE
0
ha n
0. 0026
0
I ra q
0.0027
0.0002
0
K uwait
0.0039
0 . 00 1 4
0.00 1 4
0
Yemen
0.003 1
0 . 0006
0.0006
0.00 1 8
0
UAE
0. 003 1
0 . 0008
0.0008
0.00 1 9
0.00 1
79
0
C H A PTER I V : CONCLUSION
80
Co n c l u i o n :
In thi
tud } . buccal s\\ ap sample
i n d i \ iduals from the
were obta ined from 3 4 5 unre lated
n i ted Arab E m i rates population.
II of the ON
performed in m u l t i p lex fashio n using A m p F L TR
Y fi l e
peR
( L i fe
tandem
repeats
Te hno logies)
to
co-am p l i fy
17
hort
sa mples , ere
m p l i fication K it
( TRs)
loc i .
Experimental variation \\ as red uced w i th the use o f h i gh l y automated system cal led
3 5 00
L Genetic Analyzer ( L i fe Techno logies).
The U A E pop u l at ion was d i v ided
into three region accord ing to geographical region and prox i m ity, namely, Northern,
Ea tern and Western reg ion .
frequency . haplot} pe frequenc ies,
(AMO
I n the current study, , e have esti mated
a l lele
ariances. and used analysis o f m o lecu lar variance
) t o trati fy t h e popu lati o n.
T h e 1 7 Y c h romosome S T R s analyzed in t h i s study proved t o be h ighly
i n forlnati e markers, , ith h i gh val ues fo r gene d i vers ity w i th re lat i vely h igh
d iscrim i natory capac it
Thus. based on th is study, the appl ication 1 7 Y c hromosome
TRs analysis for foren sic and patern ity ana l ys i s proves to be usefu l in the U A E .
H o " e er. further. genetic analYSIS such a s S P or copy n u m ber variation such as A l u
seq uence is req u i red for defi n itive confi rmation i n forens i c
i n vestigation o r deep
ancestry stud ies.
The a l l e l i c p ro fi le. freq uency, and d istri bution for each locus in the three
sUbpopu lations of the U A E fo l low s i m i lar patterns. The a l lele frequency among the
three subpo p u l atio ns, however, shows sm a l l fl uctuat ions espec i a l l y for spec ifi c loci
and that cou ld be because of the number o f sam p les.
A lthough, our study
demonstrates that there are un ique a l leles to a subpo pulat i on or not shared by a l l
regions. the pro fi l e of the a l lele frequency and d i stri bution are very s i m i lar.
81
We
strongl) be l ieve that a larger popu lat ion
ize from d i fferent e m i rates w i l l u lt i mate ly
iden t if) the u n iq ueness o f the e a l leles in the respecti e subpopu l ations.
A l though in our tud) , the popu lation shO\\ s relatively di erse haplotype, there
are 2 7 1 unique hap lotype. T\\ enty-two of the haplotypes are shared between two
i n d i iduals.
There are other hap lot)'pes that are shared between at least two
ind i , iduals. H a p l ot) pe d i ver ity in the U A E po pulation is equal to 99 . 8 8 5 %, which
mean that there is a large genetic di ers ity in U A E popu lat i o n . On the other hand
the percentage of d i sc r i m i nat ion capac ity i
eq ual to 90.03%, w h ich ind icates that
U E population con i sts of i n d i v iduals who share ident i c a l hap lotype \ h ich are not
related a j u dged by the names.
Th i s stud) i s very i m pOltant and it contri butes to other st ud ies around the G u l f
A rea to stud_ t h e geneti c d i vers ity of pop u lat i o n . H owever, t his study c a l l s fo r more
extens i ve genet ic study of the region i n order to elaborate on genet ic d i stance
between population, d isease-assoc iated haplotypes, archeological, and h i storical
stud ies.
82
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