Evolution of the genomes of two nematodes in the ... - Ken Wolfe

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Declaration This thesis is submitted by the undersigned for the degree of Doctor of Philosophy at the University of Dublin. It has not been submitted as an exercise for a degree in any other university. Apart from the advice, assistance, and joint effort mentioned in the acknowledgements and in the text, this thesis is entirely my own work. I agree that the library may lend or copy this thesis freely upon request. Avril Coghlan. October, 2003. i
Acknowledgements Thankyou a billion Mum, Dad and Noel for always cheering me on during my Ph.D.. I am hugely grateful to Ken — thank you so much for your inspiration and encouragement. Thankyou Andrew for being willing to read manuscripts and discuss ideas. A special thanks to Karsten, Kevin and Simon, who kept my computer alive. Thankyou to Richard Durbin, who allowed me to join the C. briggsae Sequencing Project, and to the people with whom I worked on the project, especially Marc Sohrmann, Todd Harris, and Lincoln Stein. Thanks to Dónall MacDónaill and Nigel Buttimore, for your enthusiasm in our collaboration at the start of my Ph.D.. Thanks to all the really great members of the Wolfe lab. — it wouldn’t have been a quarter as much fun without you: Aoife, Karsten, Simon, Cathal, Antoinette, Kevin, Guillaume, Mario, Brian, Lucasz, Greg, Ailís, Devin, and Jonathen. Many thanks to my thesis examiners, Mark Blaxter and Dan Bradley, for detailed and insightful discussion of my results. ii
Page 1: Evolution of the genomes of two nem
Page 5 and 6: Table of Contents List of Abbreviat
Page 7 and 8: 4.2.3 Phases of Novel Introns . . .
Page 9 and 10: List of Figures 1.1 The model organ
Page 11 and 12: Chapter 1 Overview The biology of t
Page 13 and 14: E Chordates Hemichordates Echinoder
Page 15 and 16: 1.4 TWO Caenorhabditis GENOMES In 2
Page 17 and 18: Chapter 2 Faster Rate of Genome Rea
Page 19 and 20: Nematode fossils are extremely scar
Page 21 and 22: ends) are distributed at random alo
Page 23 and 24: Figure 2.3: (A) Location of conserv
Page 25 and 26: Frequency Frequency 60 50 40 30 20
Page 27 and 28: Breakpoint type Number of Breakpoin
Page 29 and 30: transposon (Oosumi et al., 1996). C
Page 31 and 32: effects compared with the recombina
Page 33 and 34: smaller effective population size t
Page 35 and 36: genes whose chromosomal coordinates
Page 37 and 38: did not group together and/or the D
Page 39 and 40: Chapter 3 The Caenorhabditis briggs
Page 41 and 42: predictions, we chose the predictio
Page 43 and 44: C. briggsae C. elegans WS77 ∗ C.
Page 45 and 46: WS77 WS103 New genes 1275 985 New e
Page 47 and 48: C. elegans chrom. III, 9.8-9.9 Mb *
Page 49 and 50: 4. Each exon-cluster X consisted of
Page 51 and 52: 3.5.4 Estimating the C. briggsae-C.
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Chapter 4 Origins of Novel Introns
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http://wolfe.gen.tcd.ie/avril/intro
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Of the 78 genes that have gained in
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novel introns that are either C. el
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as supporting this hypothesis are b
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4.4 METHODS 4.4.1 Sources of Sequen
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1. the outgroup for the tree was a
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Bibliography Aguinaldo, A. M., J. M
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Fedorov, A., X. Cao, S. Saxonov, S.
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Logsdon, J. M. J., M. G. Tyshenko,
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Sankoff, D. (1999). Comparative map
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Evolution of the genomes of two nematodes in the ... - Ken Wolfe

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