Foreword; A. Meyer, Y. Van de Peer.
Early events in genome evolution.
1. Gene duplication and other evolutionary strategies: from the RNA world to the future; J. Brosius. 2. Major transitions in evolution by genome fusions: from prokaryotes to eukaryotes, metazoans, bilaterians and vertebrates; J. Spring. 3. Detection of gene duplications and block duplications in eukaryotic genomes; Wen-Hsiung Li, et al. 4. The evolutionary demography of duplicate genes; M. Lynch, J.S. Conery.
Debating the 2R and 3R genome duplication hypotheses.
5. Functional evolution in the ancestral lineage of vertebrates or when genomic complexity was wagging its morphological tail; R. Aburomia, et al. 6. Numerous groups of chromosomal regional paralogies strongly indicate two genome doublings at the root of the vertebrates; L.-G. Lundin, et al. 7. Are (all) fishes ancient polyploids? Y. Van der Peer, et al. 8. More genes in vertebrates? P.W.H. Holland. 9. 2r or not 2R: testing the hypotheses of genome duplication in early vertebrates; A.L. Hughes, R. Friedman. 10. The 2R hypothesis and the human genome sequence; K. Hokamp, et al.
Plant genome evolution.
11. Introns in, introns out in plant gene families: a genomic approach of the dynamics of gene structure; A. Lecharny, et al. 12. Investigating ancient duplication events in the Arabidopsis Genome; J. Raes, et al. Case studies. 13. Crystallin genes: speciallization by changes in gene regulation mat precede gene duplication; J. Piatigorsky. 14. Expansion of the epidermal growth factor receptor family by genome and gene duplication in fish; J.-N. Volff, M. Schartl. 15. The role of gene duplication in the evolution and function of the vertebrate Dlx/distal-less bigene clusters; K. Sumiyama, et al. 16. Dopamine receptors for every species: gene duplications and functional diversification in craniates; S. Le Crom, et al. 17. Nuclear receptors are markers of animal genome evolution; H.E. García, et al. 18. The fates of zebrafish Hox gene duplicates; C. Josefowicz, et al. 19. Phylogenetic analysis of the mammalian Hoc8 non-coding region; Chang-Bae Kim, et al.
Gene networks and evolution.
20. Maximum likelihood methods for detecting adaptive evolution after gene duplication; J.P. Bielawski, Ziheng Yang. 21. Approach of the functional evolution of duplicated genes in Saccharomyces cerevisiae using a new classification method based on protein-protein interaction data; C. Brun, et al. 22. Developmental gene networks and evolution; J.P. Rast.
In the years since the publication of Susumu Ohno's 1970 landmark book Evolution by gene duplication tremendous advances have been made in molecular biology and especially in genomics. Studies of genome structure and function prerequisite to testing hypotheses of genome evolution were all but impossible until recent methodological advances.
This book evaluates newly generated empirical evidence as it pertains to theories of genomic evolutionary patterns and processes. Tests of hypotheses using analyses of complete genomes, interpreted in a phylogenetic context, provide evidence regarding the relative importance of gene duplication. The alternative explanation is that the evolution of regulatory elements that control the expression of and interactions among genes has been a more important force in shaping evolutionary innovation.
This collection of papers will be of interest to all academic and industry researchers working in the fields of molecular biology, biotechnology, genomics and genome centers.
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