The use of low-copy nuclear genes in the radiation of the Macaronesian Crassulaceae Sempervivoideae [Elektronische Ressource] : phylogeny and evolutionary processes / presented by Korinna Esfeld

Tadele

Sujets

• Biologie

Informations

• Publié par: ruprecht-karls-universitat_heidelberg
• Publié le: 01 janvier 2009
• Nombre de lectures: 12
• Langue: English
• Poids de l'ouvrage: 10 Mo

Extrait

The use of low-copy nuclear genes in the
radiation of the
Macaronesian Crassulaceae
Sempervivoideae –
Phylogeny and evolutionary processes













Dissertation

Korinna Esfeld
Born in Lutherstadt Wittenberg

2009








Dissertation
submitted to the
Combined Faculties for the Natural Sciences and for Mathematics
of the Ruperto-Carola University of Heidelberg, Germany
for the degree of
Doctor of Natural Sciences




















presented by
Diplom-Biologin Korinna Esfeld
born in: Lutherstadt Wittenberg
Oral-examination: .......................................
i


The use of low-copy nuclear genes in the radiation of the
Macaronesian Crassulaceae Sempervivoideae –
Phylogeny and evolutionary processes






















Referees:

Prof. Dr. Marcus Koch
Prof. Dr. Claudia Erbar
ii









... für meine Familie und meine Freunde,
die geduldig daran geglaubt haben!












Am Ende ist alles gut und wenn es
nicht gut ist, dann ist das nicht das Ende....

iiiContents
Contents

Contents................................................................................................................................iv
Figures ...................................................................................................................................v
Tables .................................................................................................................................. vii
0.1. Summary...................................................................................................................... viii
0.2. Zusammenfassung.........................................................................................................ix
1. Introduction ....................................................................................................................... 1
2. Materials and Methods .....................................................................................................21
2.1. Study species ............................................................................................................21
2.2. Molecular methods ....................................................................................................26
2.2.1. RNA material ......................................................................................................26
2.2.2. DNA material ......................................................................................................26
2.2.3. Amplification of the low-copy nuclear genes........................................................27
2.2.4. Cloning of the low-copy nuclear genes................................................................30
2.2.5. Colony PCR........................................................................................................31
2.2.6. Amplification of nrITS and cpDNA regions ..........................................................32
2.2.7. Sequencing.........................................................................................................32
2.2.8. Sequence analysis..............................................................................................32
2.2.9. Definition of the gene regions .............................................................................33
2.2.10. Improvements of the datasets...........................................................................33
2.2.11. Partition Homogeneity Tests .............................................................................34
2.2.12. Phylogenetic reconstructions ............................................................................34
2.2.13. Blast analyses...................................................................................................35
2.2.14. Neighbor-joining reconstructions for homologs of PEPC, AP1, and AP3...........35
2.2.15. Species phylogeny............................................................................................36
2.2.16. Nucleotide differences, replacements, and amino acid substitutions.................36
2.2.17. Relative Rate Tests...........................................................................................37
2.2.18. Selection pressure ............................................................................................37
3. Results .............................................................................................................................39
3.1. Datasets ....................................................................................................................39
3.2. Phylogenetic reconstructions .....................................................................................45
3.3. Blast and Neighbor-joining analyses..........................................................................64
3.4. Species phylogeny based on nrITS ...........................................................................66
3.5. Gene duplications......................................................................................................67
3.6. Nucleotide differences, replacements, and amino acid substitutions..........................69
3.7. Relative Rate Tests ...................................................................................................73
3.8. Ka/Ks-values .............................................................................................................74
3.9. Selection pressure.....................................................................................................76
4. Discussion........................................................................................................................78
4.1. Phylogenetic reconstructions .....................................................................................78
4.2. Gene duplications......................................................................................................86
4.3. Selection pressure.....................................................................................................97
4.4. Regulatory versus structural genes..........................................................................103
5. Summary........................................................................................................................108
Literature............................................................................................................................110
Abbreviations .....................................................................................................................125
Overview of scientific contributions.....................................................................................127
Appendices ........................................................................................................................128
Acknowledgment................................................................................................................150
iv Figures
Figures

Fig. 1: Map of Macaronesia and the Canary Islands after Mort et al. (2002). Taken from
the website http://www.eiu.edu/~bio_data/posters/2002/poster_016.htm............................... 2
Fig. 2: Maximum parsimony phylogram of the MCS species based on cpDNA/nrITS data
(from Mort et al. 2002)........................................................................................................... 9
Fig. 3: MIKC-like structure of the plant MADS-box proteins (adapted after Purugganan
et al. 1995). ..........................................................................................................................15
Fig. 4: The extended ABCDE model adapted after Erbar (2007)..........................................17
Fig. 5: Schematic exon and intron structure of the MCS_PEPC gene sequences. Exons
are shown as boxes and introns as lines. The relative length of the respective parts is
given in table 4. ....................................................................................................................40
Fig. 6: Schematic exon and intron structure of the MCS_AP1 gene sequences. Exons
are shown as boxes and introns as lines. The relative length of the respective parts is
given in table 6. ....................................................................................................................42
Fig. 7: Schematic exon and intron structure of the MCS_AP3 gene sequences. Exons
are shown as boxes and introns as lines. After the last exon box the 3´-UTR is indicated
as line. The relative length of the respective parts is given in table 8....................................44
Fig. 8: BI phylogram based on the full-length MCS_PEPC data. Posterior probabilities
are given at the nodes........