alu insertion polymorphisms in anatolian turks a thesis submitted to

116 Pages·2003·1.04 MB·English

ALU INSERTION POLYMORPHISMS IN ANATOLIAN TURKS

A THESIS SUBMITTED TO
THE GRADUATE SCHOOL OF NATURAL AND APPLIED SCIENCES
OF
THE MIDDLE EAST TECHNICAL UNIVERSITY

BY

HAVVA D(cid:1)NÇ

IN PARTIAL FULLFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF
MASTER OF SCIENCE
IN
THE DEPARTMENT OF BILOGICAL SCIENCES

SEPTEMBER 2003
Approval of the Graduate School of Natural and Applied Sciences

____________________
Prof. Dr. Canan ÖZGEN
Director

I certify that this thesis satisfies all the requirements as a thesis for the degree of Master
of Science.

_____________________
Prof. Dr. Mesude (cid:1)(cid:2)CAN
Head of the Department

This is to certify that we have read this thesis and that in our opinion it is fully adequate,
in scope and quality, as a thesis for the degree of Master of Science.

__________________
Prof. Dr. (cid:1)nci TOGAN
Supervisor

Examining Committee Members

Prof. Dr. (cid:1)nci TOGAN ____________________

Prof. Dr. I(cid:3)ık BÖKESOY ____________________

Prof. Dr. Hüseyin Avni ÖKTEM ____________________

Assist. Prof. (cid:1)rfan KANDEM(cid:1)R ____________________

Dr. Ay(cid:3)e ERGÜVEN ____________________
ABSTRACT

ALU INSERTION POLYMORPHISMS IN ANATOLIAN TURKS

D(cid:1)NÇ, Havva
M. Sc., Department of Biological Sciences
Supervisor: Prof. Dr. (cid:1)nci TOGAN

September 2003, 99 pages

In the present study; ten autosomal human-specific Alu insertion
polymorphisms; ACE, APO, A25, B65, D1, FXIIIB, HS4.32, HS4.69, PV92 and
TPA25 were analyzed in approximately 100 unrelated individuals from Anatolia. Alu
insertion polymorphisms offer several advantages over other nuclear DNA
polymorphisms for human evolution studies.

The frequencies of the ten biallelic Alu insertions in Anatolians were calculated
and all systems were found to be in Hardy-Weinberg equilibrium (p>0.05).

By combining the results of this study with results of previous studies done on
worldwide populations, the genetic distance (Nei’s D ) between each pair of
A
iii
populations was calculated and neighbor joining trees were constructed. In general,
geographically closer populations were found to be also genetically similar. Principal
component analysis (PCA) was performed and Anatolia was found to be in the
European cluster. As a result of PCA; it was concluded that FXIIIB, PV92 and ACE
were the variables contributing the most to the explanation of the variation between the
populations. Additionally; canonical variates analysis (CVA) concluded that the most
discriminative markers for the groups of populations were PV92, D1, ACE and HS4.32.

Pair-wise Fst values were also calculated between Anatolians and some of the
populations for which the data was available. It was concluded that, Anatolians have
non-significant pair-wise Fst values with Swiss and French Acadian populations.

Lastly, heterozygosity vs. distance from centroid graph was constructed and it
was found that Anatolians and India-Hindu had exactly the expected heterozygosity
value predicted by the model of Harpending and Ward (1982).

Keywords: Alu insertion polymorphisms, Anatolia, neighbor joining tree, principal
component analysis, discriminant function analysis, Fst, heterozygosity vs. distance
from centroid.

iv
ÖZ

ANADOLU TÜRKLER(cid:1)’NDE ALU ARA-(cid:1)LAVE POL(cid:1)MORF(cid:1)Z(cid:1)MLER(cid:1)

D(cid:1)NÇ, Havva
Yüksek Lisans, Biyolojik Bilimler Bölümü
Tez Yöneticisi: Prof. Dr. (cid:1)nci TOGAN

Eylül 2003, 99 sayfa

Bu çalı(cid:3)mada on otozomal Alu ara-ilave polimorfizimleri (ACE, APO, A25,
B65, D1, FXIIIB, HS4.32, HS4.69, PV92 and TPA25) Anadolu’dan birbiri ile akraba
olmayan yakla(cid:3)ık 100 bireyde incelenmi(cid:3)tir. Alu ara-ilave polimorfizimlerinin insan
evrimi çalı(cid:3)malarında, di(cid:4)er nükleer DNA polimorfizimlerine kıyasla birçok avantajı
vardır.

On Alu ilavelerinin Anadolu’daki frekansları hesaplanmı(cid:3) ve hepsi de Hardy-
Weinberg (H-W) dengesinde bulunmu(cid:3)tur (p>0.05).

Bu çalı(cid:3)manın sonuçlarını daha önce dünya çapında yapılan çalı(cid:3)maların
sonuçları ile birle(cid:3)tirerek, her populasyon çifti arasındaki genetik uzaklık (Nei’nin D )
A
v
hesaplanmı(cid:3) ve kom(cid:3)u birle(cid:3)tirme a(cid:4)açları çizilmi(cid:3)tir. Genel olarak, co(cid:4)rafi olarak
yakın populasyonların genetik olarak da benzer oldu(cid:4)u görülmü(cid:3)tür. Temel ö(cid:4)eler
analizi uygulandı(cid:4)ında Anadolu’nun Avrupa grubunda oldu(cid:4)u bulunmu(cid:3)tur. Bu analiz
sonucunda, FXIIIB, PV92 ve ACE de(cid:4)i(cid:3)kenlerinin populasyonlar arası varyasyonu
açıklamada en çok katkısı olan de(cid:4)i(cid:3)kenler oldukları sonucu ortaya çıkmı(cid:3)tır. Ek olarak,
ayrı(cid:3)ım fonksiyonu analizi sonucunda ise, populasyon grupları için en ayırt edici
genetik i(cid:3)aretlerin PV92, D1, ACE ve HS4.32 oldukları görülmü(cid:3)tür.

Anadolu ve verisi mevcut olan bazı populasyonlar arasında ikili Fst de(cid:4)erleri
hesaplanmı(cid:3)tır. Sonuç olarak, (cid:1)sviçre ve Fransız Akadyan populasyonları ve Anadolu
arasında istatistiksel olarak anlamsız de(cid:4)erler elde edilmi(cid:3)tir.

Son olarak, heterozigotluk ve merkezden uzaklık grafi(cid:4)i çizildi(cid:4)inde, Anadolu
ve Hindistan-Hindu populasyonlarının heterozigotluk de(cid:4)erlerinin Harpending ve Ward
(1982) modeline göre beklenen de(cid:4)erler oldukları gözlenmi(cid:3)tir.

Anahtar kelimeler: Alu ara-ilave polimorfizmleri, Anadolu, kom(cid:3)u birle(cid:3)tirme a(cid:4)acı,
temel ö(cid:4)eler analizi, ayrı(cid:3)ım fonksiyonu analizi, Fst, heterozigotluk ve merkezden
uzaklık.
vi
To My Parents;
Nazlı and Önder Dinç

vii
ACKNOWLEDGEMENTS

First of all, I want to express my appreciation to my dear supervisor Prof. Dr.
(cid:1)nci TOGAN for guiding and understanding me so well, and for being more than a
supervisor to me. I am also grateful to Assist. Prof. (cid:1)rfan KANDEM(cid:1)R who acted as my
co-supervisor and helped a lot while doing the statistical analyses. I would also like to
thank Prof. Dr. Mark STONEKING for always replying immediately and supplying
what I have asked for.

I would like to thank my lab-mates; Evren, Emel, Ceren who were always with
me with their helpful ideas and support when I was dealing with the problems in my
experiments. And also thanks to Can, whose presence in the lab always supplied me
positive energy. I am grateful to Seral who first taught me the techniques that I have
used for this study.

Thanks to Gülen for supplying me the valuable DNA isolation protocol and also
Alper for not hesitating to drive me to the other end of Ankara. I am grateful to Damla
who thought with me and discussed every problem in my experiments.

viii
I am thankful to (cid:2)ebnem for her precious effort to help me to collect samples
and also to other friends who helped me in the sample collection. I would like to thank
everyone who gave me samples without hesitating and made this study real.

Thanks to Aydın for his support and taking care of the first bound copies of this
thesis. Of course, I can’t deny the support of Kofona!! You are always giving me
strength friends. Thank you!

I am grateful to my parents; Nazlı and Önder Dinç, my sister; Ayten, my uncle
(cid:1)lkay Gilanlıo(cid:4)lu and my whole family for their endless encouragement and support.

What are the needs of a person while writing a thesis? Patience, support,
priority, help, friendship, motivation, being loved, companionship, chocolate, coffee
and etc. It is impossible to expect all of these from people around you, however I owned
more than these during the preparation of this thesis. Banu, Aysun, Anıl and Aslı; you
were exactly like angels and became an indispensable part of me. It wouldn’t be
possible without you! THANK YOU FOR BEING WITH ME IN EVERY STEP...

ix
TABLE OF CONTENTS

ABSTRACT..........................................................................................................iii
ÖZ.........................................................................................................................v
DEDICATION......................................................................................................vii
ACKNOWLEDGEMENTS...................................................................................viii
TABLE OF CONTENTS......................................................................................x
LIST OF FIGURES...............................................................................................xiii
LIST OF TABLES................................................................................................xv
LIST OF ABBREVIATIONS................................................................................xvi

CHAPTER
1. INTRODUCTION.............................................................................................1
1.1 Brief Review of Evolutionary History of Modern Human Being.............3
1.2 Specialty of Alu Insertion Polymorphisms...............................................5
1.3 The Objective of the Study......................................................................12

2. MATERIALS AND METHODS.......................................................................14
2.1 Materials.................................................................................................14
2.2 Methods..................................................................................................15
2.2.1 DNA Isolation...........................................................................15
2.2.1.1 DNA Isolation from Blood Samples...............................15
2.2.1.2 DNA Isolation from Buccal Samples: Method I..............16
2.2.1.3 DNA Isolation from Buccal Samples: Method II............16
2.2.2 Checking the Presence of DNA..................................................18
x