The selective and demographic history of Drosophila melanogaster [Elektronische Ressource] / Lino Ometto

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

The selective and demographic
history of Drosophila melanogaster
Lino Ometto
aus
Vicenza, Italien
2006Erklärung
Diese Dissertation wurde im Sinne von §13 Abs. 3 bzw. 4 der Promotionsordnung von Prof.
Dr. Wolfgang Stephan betreut.
Ehrenwörtliche Versicherung
Diese Dissertation wurde selbstständig, ohne unerlaubte Hilfe erarbeitet.
1. Gutachter: Prof. Dr. Wolfgang Stephan
2. Gutachter: Prof. Dr. John Parsch
Dissertation eingereicht am: 16.12.2005
Tag der mündliche Prüfung: 17.02.2006a elisa,
mare
Table of Contents
Summary 1
Note 3
Introduction 5
List of abbreviations 11
1. A survey of DNA variation in the X chromosome of Drosophila
melanogaster 13
1.1. The impact of demography and natural selection on the genetic
variation of Drosophila melanogaster 15
1.1.1. Materials and Methods 15
1.1.1.1. Population samples 15
1.1.1.2. PCR amplification and DNA sequencing 16
1.1.1.3. Statistical analysis 16
1.1.1.4. Recombination rate 17
1.1.1.5. Demographic modeling of the European population 17
1.1.2. results 18
1.1.2.1. Polymorphism patterns in the African population 19
1.1.2.2. Polymorphism patterns in the European population 23
1.1.2.3. Comparison of the African and European populations 27
1.1.3. discussion 27
1.1.3.1. Demography 27
1.1.3.2. Selection 28
1.2. Inferring the effects of demography and selection on Drosophila
melanogaster populations 31
1.2.1. Materials and Methods 31
1.2.1.1. Data collection 31
1.2.1.2. Statistical analysis 32
1.2.1.3. Demographic modeling of the African population 33
1.2.1.4. Demographic modeling of the European population 34
1.2.2. results 38
1.2.2.1. Polymorphism patterns of the African population 38
1.2.2.2. Polymorphism patterns of the European population 42
1.2.2.3. Estimating the parameters of a simple bottleneck model for the European
population 45
1.2.2.4. Identifying candidate sweep regions in the European population 47
1.2.3. discussion 52
1.2.3.1. Demographic history of the African population 53
1.2.3.2. Demographic and selection history of the European population 54
1.2.3.3. Estimating the frequency of adaptive substitutions 57
1.2.3.4. Is recombination mutagenic in D. melanogaster? 58
2.1. Characterization of a selective sweep in a European population
of Drosophila melanogaster 59
2.1.1. Materials and Methods 60
2.1.1.1. Data collection and analysis 60
2.1.1.2. Testing the European population against demography 61
2.1.1.3. Gene expression analysis 62
2.1.2. results 65
2.1.2.1. Nucleotide diversity pattern across the candidate region 65
2.1.2.2. Testing the polymorphism pattern against demography 66
2.1.2.3. Expression of the gene CG9509 70
2.1.3. discussion 71
2.1.3.1. Indications that the valley of reduced variation corresponds to a selective
sweep 72
2.1.3.2. Candidate genes associated to the selective sweep 73
3. The effects of neutral and selective forces on the genome
evolution of Drosophila melanogaster 75
3.1. Insertion/deletion and nucleotide polymorphism data reveal
constraints in introns and intergenic
regions 77
3.1.1. Materials and Methods 78
3.1.1.1. Drosophila data set 78
3.1.1.2. Analysis of insertion and deletion variation 78
3.1.1.3. Modeling of selective constraints 79
3.1.2. results and discussion 81
3.1.2.1. Introns and intergenic regions show a similar polymorphic deletion bias
81
3.1.2.2. Insertions have smaller sizes and higher frequencies than deletions 81
3.1.2.3. Estimates of indel and nucleotide sequence variation 84
3.1.2.4. Introns, but not intergenic sequences, are larger in D. melanogaster than
in D. simulans 85
3.1.2.5. Analysis of selective constraints 87
3.2. Mutational pattern and substitution dynamics in the non-coding
DNA of Drosophila melanogaster 91
3.2.1. Materials and Methods 92
3.2.1.1. Data collection and analysis 92
3.2.1.2. Statistical analysis 92
3.2.2. results 93
3.2.2.1 Divergence correlates with recombination rate in intergenic regions 93
3.2.2.2. Differences in size among homologous loci in Drosophila 94
3.2.2.3. In intronic regions, GC content is lower than in intergenic regions and
does not correlate with recombination 95
3.2.2.4. Substitution patterns in Drosophila 95
3.2.2.5. Comparing the fixation pattern of D. melanogaster and D. simulans 99
3.2.2.6. Base composition of indels 99
3.2.2.7. Inferring constraints in conserved intergenic and intronic regions 100
3.2.3. discussion 102
3.2.3.1. Intergenic and intronic regions have different base composition but similar
mutation patterns 102
3.2.3.2. GC content affects nucleotide diversity and the insertion/deletion
dynamics 102
3.2.3.3. Replication time and transcription-associated mutation bias have
negligible effects on the mutation pattern 104
3.2.3.4. Longer introns are under more constraints 105
3.2.3.5. Evidence for selective constraints in non-coding DNA 105
3.2.3.6. Positive correlation between divergence and recombination rate in
intergenic regions 106
Conclusions 107
Literature cited 111
Appendix 125
Curriculum vitae 167
Publications 168
Acknowledgments 171v