Chapter 11 Evolution by Gene Duplication ChauTi Ting

Chapter 11 Evolution by Gene Duplication Chau-Ti Ting ctting@ntu. edu. tw Unless noted, the course materials are licensed under Creative Commons Attribution-Non. Commercial-Share. Alike 3. 0 Taiwan (CC BY-NC-SA 3. 0) 1

The Bar Locus in Drosophila National Taiwan University Chau-Ti Ting +/+, wild-type B/+, heterozygous Bar B/B, homozygous Bar

Unexpected Observations Occasionally the homozygous stock gives rise to wild-type appearance. More rarely the stock gives rise to a more extreme reduction in eye-size, Ultra-Bar. Sturtevant and Morgan • both wild-type and Ultra-Bar flies recovered from the Bar stock were associated with crossing over.

Hypothesis: Unequal Crossing-over Source: W. H. Freeman and P. Benjamin 2005. Genetics: A Conceptual Approach, 2 nd ed. , p. 239. W. H. Freeman and Company. New York, USA.

Cytological Evidence (Bridges 1936) Source: C. B. Bridges 1936. The Bar “gene” a duplication. Science 83: p. 210.

Unequal Crossing-over Wikipedia Lee M. Silver

Genome duplication • Kuwada (1911) – Maize (Zea mays) was an ancient tetraploid • two sets of paralogous chromosomes in its karyotype. Diploid Parent (2 N) Tetraploid Parent (4 N) National Taiwan University Chau-Ti Ting

2 N Parent 4 N Parent Meiosis N Gamete 2 N Gamete Mating = 3 N Zygote Uneven Chromosome Number National Taiwan University Chau-Ti Ting

Autopolyploidy Mitosis (Failure of cell division) 2 N Meiosis 4 N National Taiwan University Chau-Ti Ting Fertilization 2 N 4 N

Allopolypoidy Species B 2 N = 4 Species A 2 N = 6 Failure of cell division Hybrid Chromosome = 7 4 chromosome gamete Normal gamete Chromosome = 3 7 chromosome gamete National Taiwan University Chau-Ti Ting Fertile hybrid Chromosome = 10

Evolution by Gene duplication (Historical View I) In 1918, Bridges wrote that the main interest in duplications lay in their offering a method for evolutionary increase in lengths of chromosomes with identical genes, which could subsequently mutate separately and diversify their effects Source: J. S. Taylor and J. Raes 2004. Duplication and divergence: The evolution of new genes and old Ideas. Annual Review of Genetics 38: p. 615. Muller further proposed that the redundant loci produced by the duplication of chromosomes parts could experience divergent mutations and eventually be regarded as nonhomologous genes Source: J. S. Taylor and J. Raes 2004. Duplication and divergence: The evolution of new genes and old Ideas. Annual Review of Genetics 38: p. 615.

Evolution by Gene duplication (Historical View II) In 1932, Haldane suggested that duplication events might be favorable because they produce genes that could be altered without disadvantage to the organism Source: J. S. Taylor and J. Raes 2004. Duplication and divergence: The evolution of new genes and old Ideas. Annual Review of Genetics 38: p. 615. In 1938, Serebrovsky proposed that selection could be relaxed in genes that occur in duplicate (achaete-scute complex) Source: J. S. Taylor and J. Raes 2004. Duplication and divergence: The evolution of new genes and old Ideas. Annual Review of Genetics 38: p. 615.

Evolution by Gene duplication (Historical View III) Stephens (1951) proposed the only way of achieving “evolutionary progress” would be by increasing the number of genetic loci, either by the synthesis of new loci from nongenic material or by the duplication and subsequent differentiation of existing loci via genome duplication or unequal recombination Source: J. S. Taylor and J. Raes 2004. Duplication and divergence: The evolution of new genes and old Ideas. Annual Review of Genetics 38: p. 615.

Gene Duplication and DNA Content Britten and Davidson (1969) summarized DNA content from widely diverse species, with a plot showing that a great increase in DNA is “a necessary concomitant to increased complexity of organization. ” Ohno noted a twofold to threefold increase in genome size between Ciona intestinalis and placental mammals and concluded that this difference was due to extensive gene duplication, possibly polyploidization Source: J. S. Taylor and J. Raes 2004. Duplication and divergence: The evolution of new genes and old Ideas. Annual Review of Genetics 38: p. 615.

GENE DUPLICATION AND ISOZYME ELECTROPHORESIS Duplicated isozyme loci produced more bands than single-copy genes, and many isozyme electrophoresis studies uncovered gene duplicates in polyploids Data from isozyme studies not only uncovered new examples of gene duplication, it also shed light on the consequences of gene duplication (PGI in fish) Source: J. S. Taylor and J. Raes 2004. Duplication and divergence: The evolution of new genes and old Ideas. Annual Review of Genetics 38: p. 615.

Susumu Ohno (大野 乾) 1928 -2000 http: //www. nap. edu/html/biomems/sohno. html

• J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292 -298. • M. Long, E. Betran, K. Thornton, and W. Wang 2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: p. 865 -875.

Source: J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292.

Mechanisms of Gene Duplication Source: J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292.

Fates of Gene Duplication (Pseudogenization) Source: A. Force, M. Lynch, F. B. Pickett, A. Amores, Y. Yan, and J. Postlethwait 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: p. 1531.

Division of expression after gene duplication Source: J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292.

Source: M. Long, E. Betran, K. Thornton, and W. Wang 2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: p. 865.

The origin of jingwei Source: M. Long, E. Betran, K. Thornton, and W. Wang 2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: p. 865.

Accelerated evolution of new genes Source: M. Long, E. Betran, K. Thornton, and W. Wang 2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: p. 865.

The biased distribution of retroposition events Source: M. Long, E. Betran, K. Thornton, and W. Wang 2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: p. 865.

Source: H. Innan and F. Kondrashov 2010. The evolution of gene duplications: classifying and distinguishing between models. Nature Review Genetics 11: p. 97.

Outstanding questions about the evolution of duplicate genes (I) 1. What is the relative importance of positive darwinian selection and relaxation of purifying selection in functional divergence of duplicated genes? Source: J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292. 2. How does an entirely new function originate after gene duplication? Source: J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292. 3. What roles does gene duplication play in the establishment of complex gene expression networks and protein–protein inter- action networks, which are key characteristics of biological systems? Source: J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292.

Outstanding questions about the evolution of duplicate genes (II) 4. How does genetic buffering function? Source: J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292. 5. How important is gene duplication to the origin of species-specific features and speciation? Source: J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292.

Copyright Declaration Work Licensing Author/Source Page P 2 National Taiwan University Chau-Ti Ting W. H. Freeman and P. Benjamin 2005. Genetics: A Conceptual Approach, 2 nd ed. , p. 239. W. H. Freeman and Company. New York, USA. http: //www. nature. com/scitable/topicpage/dna-deletion-and-duplication-andthe-associated-331 It is used subject to the fair use doctrine of: • Taiwan Copyright Act Articles 52 & 65 • Scitable by Nature Education Terms of Use • Nature Terms and Conditions • The "Code of Best Practices in Fair Use for Open. Course. Ware 2009 (http: //www. centerforsocialmedia. org/sites/default/files/10 -305 -OCWOct 29. pdf)" by A Committee of Practitioners of Open. Course. Ware in the U. S. The contents are based on Section 107 of the 1976 U. S. Copyright Act P 4 C. B. Bridges 1936. The Bar “gene” a duplication. Science 83: p. 210. http: //www. sciencemag. org/content/83/2148/210. extract It is used subject to the fair use doctrine of: • Taiwan Copyright Act Articles 52 & 65 • Science/AAAS Copyright Statement • The "Code of Best Practices in Fair Use for Open. Course. Ware 2009 (http: //www. centerforsocialmedia. org/sites/default/files/10 -305 -OCWOct 29. pdf)" by A Committee of Practitioners of Open. Course. Ware in the U. S. The contents are based on Section 107 of the 1976 U. S. Copyright Act P 5 Wikipedia Lee M. Silver http: //en. wikipedia. org/wiki/File: Unequalcrossingover. gif 2012/06/28 visited P 6

Work Licensing Author/Source P 7 National Taiwan University Chau-Ti Ting P 8 National Taiwan University Chau-Ti Ting P 9 National Taiwan University Chau-Ti Ting P 10 National Taiwan University Chau-Ti Ting “a necessary concomitant to increased complexity of organization. ” Roy J. Britten and Eric H. Davidson 1969. Gene Regulation for Higher Cells: A Theory. Science 25: p. 349. http: //www. sciencemag. org/content/165/3891/349. extract? sid=43 f 1093 b-ba 994437 -b 8 ea-b 728 b 4 aa 468 f It is used subject to the fair use doctrine of: • Taiwan Copyright Act Articles 52 & 65 • The "Code of Best Practices in Fair Use for Open. Course. Ware 2009 (http: //www. centerforsocialmedia. org/sites/default/files/10 -305 -OCWOct 29. pdf)" by A Committee of Practitioners of Open. Course. Ware in the U. S. The contents are based on Section 107 of the 1976 U. S. Copyright Act P 14 P 16 Wikipedia M. A. Clark http: //en. wikipedia. org/wiki/File: Susumu_Ohno. png 2012/06/28 visited 30

Work Licensing Author/Source J. Zhang P 18 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292. http: //www. sciencedirect. com/science/article/pii/S 0169534703000338 It is used subject to the fair use doctrine of: • Taiwan Copyright Act Articles 52 & 65 • Cell Press Terms and Conditions • Elsevier Website Terms and Conditions • The "Code of Best Practices in Fair Use for Open. Course. Ware 2009 (http: //www. centerforsocialmedia. org/sites/default/files/10 -305 -OCWOct 29. pdf)" by A Committee of Practitioners of Open. Course. Ware in the U. S. The contents are based on Section 107 of the 1976 U. S. Copyright Act J. Zhang P 19 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 293. http: //www. sciencedirect. com/science/article/pii/S 0169534703000338 It is used subject to the fair use doctrine of: • Taiwan Copyright Act Articles 52 & 65 • Cell Press Terms and Conditions • Elsevier Website Terms and Conditions • The "Code of Best Practices in Fair Use for Open. Course. Ware 2009 (http: //www. centerforsocialmedia. org/sites/default/files/10 -305 -OCWOct 29. pdf)" by A Committee of Practitioners of Open. Course. Ware in the U. S. The contents are based on Section 107 of the 1976 U. S. Copyright Act A. Force, M. Lynch, F. B. Pickett, A. Amores, Y. Yan, and J. Postlethwait 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: p. 1534. http: //www. genetics. org/content/151/4/1531. full. pdf It is used subject to the fair use doctrine of: • Taiwan Copyright Act Articles 52 & 65 • The "Code of Best Practices in Fair Use for Open. Course. Ware 2009 (http: //www. centerforsocialmedia. org/sites/default/files/10 -305 -OCWOct 29. pdf)" by A Committee of Practitioners of Open. Course. Ware in the U. S. The contents are based on Section 107 of the 1976 U. S. Copyright Act P 20 31

Work Licensing Author/Source J. Zhang P 21 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 294. http: //www. sciencedirect. com/science/article/pii/S 0169534703000338 It is used subject to the fair use doctrine of: • Taiwan Copyright Act Articles 52 & 65 • Cell Press Terms and Conditions • Elsevier Website Terms and Conditions • The "Code of Best Practices in Fair Use for Open. Course. Ware 2009 (http: //www. centerforsocialmedia. org/sites/default/files/10 -305 -OCWOct 29. pdf)" by A Committee of Practitioners of Open. Course. Ware in the U. S. The contents are based on Section 107 of the 1976 U. S. Copyright Act M. Long, E. Betran, K. Thornton, and W. Wang 2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: p. 866. http: //www. nature. com/nrg/journal/v 4/n 11/pdf/nrg 1204. pdf It is used subject to the fair use doctrine of: • Taiwan Copyright Act Articles 52 & 65 • Nature Terms and Conditions • The "Code of Best Practices in Fair Use for Open. Course. Ware 2009 (http: //www. centerforsocialmedia. org/sites/default/files/10 -305 -OCWOct 29. pdf)" by A Committee of Practitioners of Open. Course. Ware in the U. S. The contents are based on Section 107 of the 1976 U. S. Copyright Act P 22 M. Long, E. Betran, K. Thornton, and W. Wang 2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: p. 867. http: //www. nature. com/nrg/journal/v 4/n 11/pdf/nrg 1204. pdf It is used subject to the fair use doctrine of: • Taiwan Copyright Act Articles 52 & 65 • Nature Terms and Conditions • The "Code of Best Practices in Fair Use for Open. Course. Ware 2009 (http: //www. centerforsocialmedia. org/sites/default/files/10 -305 -OCWOct 29. pdf)" by A Committee of Practitioners of Open. Course. Ware in the U. S. The contents are based on Section 107 of the 1976 U. S. Copyright Act P 23 32

Work Licensing Author/Source M. Long, E. Betran, K. Thornton, and W. Wang 2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: p. 869. http: //www. nature. com/nrg/journal/v 4/n 11/pdf/nrg 1204. pdf It is used subject to the fair use doctrine of: • Taiwan Copyright Act Articles 52 & 65 • Nature Terms and Conditions • The "Code of Best Practices in Fair Use for Open. Course. Ware 2009 (http: //www. centerforsocialmedia. org/sites/default/files/10 -305 -OCWOct 29. pdf)" by A Committee of Practitioners of Open. Course. Ware in the U. S. The contents are based on Section 107 of the 1976 U. S. Copyright Act P 24 M. Long, E. Betran, K. Thornton, and W. Wang 2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: p. 872. http: //www. nature. com/nrg/journal/v 4/n 11/pdf/nrg 1204. pdf It is used subject to the fair use doctrine of: • Taiwan Copyright Act Articles 52 & 65 • Nature Terms and Conditions • The "Code of Best Practices in Fair Use for Open. Course. Ware 2009 (http: //www. centerforsocialmedia. org/sites/default/files/10 -305 -OCWOct 29. pdf)" by A Committee of Practitioners of Open. Course. Ware in the U. S. The contents are based on Section 107 of the 1976 U. S. Copyright Act P 25 H. Innan and F. Kondrashov 2010. The evolution of gene duplications: classifying and distinguishing between models. Nature Review Genetics 11: p. 100. http: //www. nature. com/nrg/journal/v 11/n 2/pdf/nrg 2689. pdf It is used subject to the fair use doctrine of: • Taiwan Copyright Act Articles 52 & 65 • Nature Terms and Conditions • The "Code of Best Practices in Fair Use for Open. Course. Ware 2009 (http: //www. centerforsocialmedia. org/sites/default/files/10 -305 -OCWOct 29. pdf)" by A Committee of Practitioners of Open. Course. Ware in the U. S. The contents are based on Section 107 of the 1976 U. S. Copyright Act P 26 33

Work Licensing Author/Source What is the relative importance of positive darwinian selection and relaxation of purifying selection in functional divergence of duplicated genes? J. Zhang P 27 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292 -298. http: //www. sciencedirect. com/science/article/pii/S 0169534703000338 It is used subject to the fair use doctrine of: • Taiwan Copyright Act Articles 52 & 65 • Cell Press Terms and Conditions • Elsevier Website Terms and Conditions • The "Code of Best Practices in Fair Use for Open. Course. Ware 2009 (http: //www. centerforsocialmedia. org/sites/default/files/10 -305 -OCWOct 29. pdf)" by A Committee of Practitioners of Open. Course. Ware in the U. S. The contents are based on Section 107 of the 1976 U. S. Copyright Act How does an entirely new function originate after gene duplication? J. Zhang P 27 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292 -298. http: //www. sciencedirect. com/science/article/pii/S 0169534703000338 It is used subject to the fair use doctrine of: • Taiwan Copyright Act Articles 52 & 65 • Cell Press Terms and Conditions • Elsevier Website Terms and Conditions • The "Code of Best Practices in Fair Use for Open. Course. Ware 2009 (http: //www. centerforsocialmedia. org/sites/default/files/10 -305 -OCWOct 29. pdf)" by A Committee of Practitioners of Open. Course. Ware in the U. S. The contents are based on Section 107 of the 1976 U. S. Copyright Act What roles does gene duplication play in the establishment of complex gene expression networks and protein–protein inter- action networks, which are key characteristics of biological systems? J. Zhang P 27 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292 -298. http: //www. sciencedirect. com/science/article/pii/S 0169534703000338 It is used subject to the fair use doctrine of: • Taiwan Copyright Act Articles 52 & 65 • Cell Press Terms and Conditions • Elsevier Website Terms and Conditions • The "Code of Best Practices in Fair Use for Open. Course. Ware 2009 (http: //www. centerforsocialmedia. org/sites/default/files/10 -305 -OCWOct 29. pdf)" by A Committee of Practitioners of Open. Course. Ware in the U. S. The contents are based on Section 107 of the 1976 U. S. Copyright Act 34

Work Licensing Author/Source How does genetic buffering function? J. Zhang P 28 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292 -298. http: //www. sciencedirect. com/science/article/pii/S 0169534703000338 It is used subject to the fair use doctrine of: • Taiwan Copyright Act Articles 52 & 65 • Cell Press Terms and Conditions • Elsevier Website Terms and Conditions • The "Code of Best Practices in Fair Use for Open. Course. Ware 2009 (http: //www. centerforsocialmedia. org/sites/default/files/10 -305 -OCWOct 29. pdf)" by A Committee of Practitioners of Open. Course. Ware in the U. S. The contents are based on Section 107 of the 1976 U. S. Copyright Act How important is gene duplication to the origin of species-specific features and speciation? J. Zhang P 28 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292 -298. http: //www. sciencedirect. com/science/article/pii/S 0169534703000338 It is used subject to the fair use doctrine of: • Taiwan Copyright Act Articles 52 & 65 • Cell Press Terms and Conditions • Elsevier Website Terms and Conditions • The "Code of Best Practices in Fair Use for Open. Course. Ware 2009 (http: //www. centerforsocialmedia. org/sites/default/files/10 -305 -OCWOct 29. pdf)" by A Committee of Practitioners of Open. Course. Ware in the U. S. The contents are based on Section 107 of the 1976 U. S. Copyright Act 35