Selection and population structure in Drosophila melanogaster [Elektronische Ressource] / Steffen Beißwanger

Beisswanger, Hans Steffen

Informations

• Publié par: ludwig-maximilians-universitat_munchen
• Publié le: 01 janvier 2006
• Nombre de lectures: 26
• Langue: Deutsch
• Poids de l'ouvrage: 15 Mo

Extrait

Dissertation zur Erlangung des Doktorgrades
der Naturwissenschaften an der Fakultät für Biologie der
Ludwig-Maximilians-Universität München






Selection and population structure in
Drosophila melanogaster






















Steffen Beißwanger
aus München
2006

Erklärung

Diese Dissertation wurde im Sinne von § 12 der Promotionsordnung von Herrn
Prof. Dr. Wolfgang Stephan betreut. Ich erkläre hiermit, dass die Dissertation nicht
einer anderen Prüfungskommission vorgelegt worden ist und dass ich mich
anderweitig einer Doktorprüfung ohne Erfolg nicht unterzogen habe.


Ehrenwörtliche Versicherung

Ich versichere hiermit ehrenwörtlich, dass die vorgelegte Dissertation von mir
selbständig und ohne unerlaubte Hilfe angefertigt wurde.

München, 12.10.2006


Steffen Beißwanger





Dissertation eingereicht am: 12.10.2006

1. Gutachter: Prof. Dr. Wolfgang Stephan
2. Gutachter: Prof. Dr. John Parsch


Mündliche Prüfung am: 05.12.2006 vii
Table of Contents
Summary 1
Preface 3
Introduction 5
List of Abbreviations 15
1 Evidence for a selective sweep in the wapl region of Drosophila
melanogaster 17
1.1 MATERIAL AND METHODS 18
1.1.1 Fly strains ..................................................................................................................... 18
1.1.2 Molecular methods ...................................................................................................... 19
1.1.3 Data analysis ................................................................................................................ 19
1.1.4 Estimation of the parameters of a selective sweep model......................................... 20
1.1.5 Position of selected site ............................................................................................... 21
1.1.6 Demographic modeling of the European population................................................. 21
1.2 RESULTS 22
1.2.1 Nucleotide variation around the wapl fragment......................................................... 22
1.2.2 Standard neutrality tests for the European sample..................................................... 26
1.2.3 Standard neutrality tests for the African sample........................................................ 29
1.2.4 Can the severe reduction in variation observed in the European sample be
explained by a population size bottleneck? ............................................................... 29
1.2.5 Estimation of selection parameters............................................................................. 32
1.2.6 Position of selected site ............................................................................................... 33
1.3 DISCUSSION 33
1.3.1 Evidence for a selective sweep in the wapl region .................................................... 34
1.3.2 Estimating the strength and target site of selection ................................................... 36
1.3.3 Genes near the target site of selection ........................................................................ 37
1.4 SUMMARY 37
2 The wapl region revisited 39
2.1 MATERIAL AND METHODS 41
2.1.1 Fly strains ..................................................................................................................... 41
2.1.2 Molecular techniques................................................................................................... 42
2.1.3 Statistical analysis........................................................................................................ 42
2.1.4 Likelihood analysis of selective sweep ...................................................................... 43
2.1.5 Pinpointing the target of selection .............................................................................. 43
2.1.6 Age of selective sweep ................................................................................................ 43
2.1.7 Analysis of gene expression........................................................................................ 44
2.2 RESULTS 45
2.2.1 Polymorphism in the ph-d – Pgd region .................................................................... 45
2.2.2 Haplotype structure...................................................................................................... 47
2.2.3 Standard neutrality tests .............................................................................................. 50
2.2.4 Likelihood and strength of selective sweep ............................................................... 50
2.2.5 Target of selection ....................................................................................................... 52
2.2.6 Age of selective sweep ................................................................................................ 54
2.2.7 Analysis of gene expression........................................................................................ 55 viii
2.3 DISCUSSION 57
2.3.1 Positive selection in the ph-d – Pgd region................................................................ 57
2.3.2 Strength of selection .................................................................................................... 58
2.3.3 Localizing the target of selection................................................................................ 60
2.3.4 Time since the fixation of the selected site ................................................................ 62
2.4 SUMMARY 63
3 Population structure of Southeast Asian D. melanogaster 65
3.1 MATERIAL AND METHODS 67
3.1.1 Fly samples................................................................................................................... 67
3.1.2 Molecular techniques................................................................................................... 67
3.1.3 Analysis of genetic variation....................................................................................... 68
3.1.4 Population structure..................................................................................................... 69
3.1.5 Demographic analysis.................................................................................................. 70
3.2 RESULTS 70
3.2.1 Nucleotide varitation ................................................................................................... 72
3.2.2 Neutrality tests ............................................................................................................. 75
3.2.3 Population structure..................................................................................................... 75
3.2.4 Frequency spectra ........................................................................................................ 82
3.2.5 Demographic analysis.................................................................................................. 83
3.2.6 Heterozygosity across the wapl region....................................................................... 84
3.3 DISCUSSION 85
3.3.1 Nucleotidy diversity..................................................................................................... 85
3.3.2 Population differentiation............................................................................................ 87
3.3.3 When was SE Asia colonized?.................................................................................... 88
3.3.4 Historical context of the wapl region ......................................................................... 90
3.4 SUMMARY 91
Conclusions 93
Literature cited 97
Appendix 113
Curriculum vitae 135
Publications 136
Acknowledgements 137 1

Summary




In this thesis I scrutinized a specific region of the X chromosome of
Drosophila melanogaster for evidence of positive directional selection. In addition, I
analyzed the structure of six Southeast (SE) Asian populations of this species.
In the first chapter, I analyzed a region that showed no polymorphism in a
previous scan of the X chromosome in a European D. melanogaster population. This
region, which I named the wapl region, is located on the distal part of the X
chromosome, in cytological division 2C10 – 2E1. I observed a 60.5 – kb stretch of
DNA encompassing the genes ph-d, ph-p, CG3835, bcn92, Pgd, wapl and Cyp4d1 that
almost completely lacks variation in the European sample. Loci flanking this region
show a skewed frequency spectrum at segregating sites, strong haplotype structure,
and high levels of linkage disequilibrium. Neutrality tests revealed that these patterns
of variation are unlikely under the neutral equilibrium model or simple bottleneck
scenarios. In contrast, newly developed likelihood ratio tests suggest that strong
positive selection has acted recently on the region under investigation, resulting in a
selective sweep. Evidence is presented that this sweep may have originated in an
ancestral population in