Searching for genes involved in the adaptation of Drosophila melanogaster to the European climate [Elektronische Ressource] / Nicolas Henri Svetec

Nicolas Svetec

Sujets

• Biologie

Informations

• Publié par: ludwig-maximilians-universitat_munchen
• Publié le: 01 janvier 2009
• Nombre de lectures: 35
• Langue: Deutsch
• Poids de l'ouvrage: 2 Mo

Extrait

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




Searching for genes involved in the adaptation
of Drosophila melanogaster to
the European climate





Nicolas Henri Svetec
aus
Colmar, France
2009
1
Erklärung:
Diese Dissertation wurde im Sinne von §12 der Promotionsordnung von Prof. Dr.
Wolfgang Stephan betreut. Ich erkläre hiermit, dass die Dissertation nicht einer anderen
Prüfungskommission vorgelegt worden ist und dass ich mich nicht anderweitig einer
Doktorprüfung ohne Erfolg unterzogen habe.

Ehrenwörtliche Versicherung:
Ich versichere ferner hiermit ehrenwörtlich, dass die vorgelegte Dissertation von mir
selbständig, ohne unerlaubte Hilfe angefertigt wurde.

München, ………………


Nicolas Svetec





Dekan: Prof. Dr. Jürgen Soll
1. Gutachter: Prof. Dr. Wolfgang Stephan
2. Gutachter: Prof. Dr. John Parsch
Dissertation eingereicht am: 17.03.2009
Datum der Disputation: 29.04.2009
2

3 1. Table of contents

1. Table of contents
1. Table of contents...................................................................................................... 4
2. Note.......................................................... 6
3. List of abbreviations 8
4. Zusammenfassung ................................................................................................. 10
5. Abstract.................................................................................................................. 12
6. General introduction.............................. 14
6.1 The theory of species evolution ..................................................................... 14
6.2 The population genetics approach of evolution............. 17
History of the main theories: ................................................................................. 17
Population genetics tests for selection:.................................................................. 19
In the search for footprints of selection: 21
6.3 Quantitative genetics for studying evolution ................................................. 24
The basics of quantitative genetics: ....................................... 24
QTL mapping designs:........................................................... 26
Markers for QTL analysis:..................................................... 27
Statistical analysis in QTL mapping:..................................................................... 28
6.4 Cold tolerance, an ecologically relevant adaptive trait in D. melanogaster
cosmopolitan populations .......................................................... 30
6.5 The present work........................................................... 32
7. Materials and methods 34
7.1 Selective sweep mapping............................................................................... 34
Drosophila lines and DNA sequencing: ................................................................ 34
Mapping strategy: .................................. 35
Outlier analysis:..... 35
Ascertainment bias correction: .............................................................................. 36
CLR test: ................................................ 39
SweepFinder test:................................................................... 39
Estimation of the time since fixation of the beneficial allele: ............................... 40
7.2 QTL mapping experiments ............................................................................ 42
Drosophila Lines: .................................. 42
Phenotyping:.......... 43
Genotyping: ........................................................................................................... 44
QTL Analysis:........ 45
4 1. Table of contents
8. Results.................................................................................................................... 48
8.1 Selective sweep mapping............... 48
Standard analyses of a candidate region of selection:........... 48
Application of the CLR and SweepFinder tests:.................................................... 52
Sliding window analysis: ....................................................... 54
Age of the selective sweep:................... 56
8.2 QTL mapping................................................................................................. 58
Wild Lines:............ 58
Substitution lines:.. 61
Analysis of the RILs: ............................................................................................. 63
Candidate genes:.................................... 63
9. General discussion. 66
9.1 Detection of footprints of selection on the DNA........... 66
Evidence for a selective sweep in the HDAC6 region of African D. melanogaster:
............................................................................................................................... 66
Significance of the selective sweep in relation to the function of HDAC6:.......... 68
9.2 Cold tolerance as an adaptive phenotype....................... 71
Naturally occurring variation in Chill Coma Recovery time:................................ 71
Some cold tolerance factors are located on the X chromosome:........................... 72
RILs analysis: ........................................................................ 73
QTL analysis:......................................... 74
Candidate genes:.... 74
Perspectives: .......................................................................... 76
9.3 The combination of selective sweep and QTL mapping ............................... 78
9.4 Theoretical consideration about the combined approach 83
9.5 The perspectives of studying the dynamics of complex traits in natural
populations................................................................................................................. 84
10. Bibliography.......... 86
11. Appendix A: selective sweep mapping additional figures..................................... 96
12. Appendix B: QTL mapping additional figures .................................................... 116
13. Appendix C: Protocols......................................................... 121
14. Appendix D: PCR Primer list.............. 125
15. Curriculum Vitae................................................................. 128
16. Acknowledgements.............................................................. 130

5 2. Note

2. Note
In this thesis I present my doctoral research, all of which has been done by me
except for the following: Pavlos Pavlidis performed CLR and SweepFinder tests and
ran the simulations for the sweep age estimations. Both Pavlos Pavlidis and Prof.
Wolfgang Stephan contributed to the research article cited below that served as a basis
for the present thesis manuscript. The generation of the substitution lines for the QTL
mapping experiment was a collaborative work with Dr. David de Lorenzo.

The results from my thesis have contributed to the following publication:

Svetec, N., P. Pavlidis, and W. Stephan (2009). “Recent strong positive
selection on Drosophila melanogaster HDAC6, a gene encoding a stress surveillance
factor, as revealed by population genomic analysis.” Mol. Biol. Evol. (in press)





6 2. Note



7 3. List of abbreviations

3. List of abbreviations
AFP Anti-freeze protein
bp Base pair
CCR Chill coma recovery
CI Confidence interval
CIM Composite interval mapping
CLR Composite likelihood ratio
cM Centimorgan
CV Coefficient of variation
DNA Deoxyribonucleic acid
gen. Generation
GO Gene Ontology
GOF Goodness-of-fit
HDAC Histone deacetylase
HSP Heat shock protein
IM Interval mapping
kb Kilobase pair
LD Linkage disequilibrium
LR Likelihood ratio
Mb Megabase pair
mRNA Messenger ribonucleic acid
N Effective population size e
PCR Polymerase chain reaction
QTL Quantitative trait locus
8 3. List of abbreviations

QTN Quantitative trait nucleotide
r Recombination rate
RAPDs Randomly Amplified Polymorphic DNAs
RFLPs Restriction Fragment Length Polymorphisms
RIL Recombinant inbred line
RNAi Ribonucleic acid interference
S Number of segregating sites
SFS Site frequency spectrum
SNP Single nucleotide polymorphism
THP Thermal hysteresis protein
tRNA Transfer ribonucleic acid
UTR Untranslated region
Additive variance V A
V Dominance variance D
V Environmental variance E
V Genetic variance G
V Epistatic variance I
V Phenotypic variance P
WT Wild type
θ Population mutation rate
θ Watterson estimator of θ W
π Nucleotide diversity (average number of pairwise differences)
µ Mutation rate

9 4. Zusammenfassung

4. Zusammenfassung
Ziel der vorliegenden Arbeit ist es, Gene zu identifizieren, die bei der
ökologischen Anpassung von D. melanogaster ein