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1 Chapter 11 Evolution by Gene Duplication Chau-Ti Ting Unless noted, the course materials are licensed under Creative Commons Attribution-NonCommercial-ShareAlike.

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Presentation on theme: "1 Chapter 11 Evolution by Gene Duplication Chau-Ti Ting Unless noted, the course materials are licensed under Creative Commons Attribution-NonCommercial-ShareAlike."— Presentation transcript:

1 1 Chapter 11 Evolution by Gene Duplication Chau-Ti Ting ctting@ntu.edu.tw Unless noted, the course materials are licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Taiwan (CC BY-NC-SA 3.0)Attribution-NonCommercial-ShareAlike 3.0 Taiwan

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

3 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.

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

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

6 Unequal Crossing-over Wikipedia Lee M. Silver

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

8 = = 2N Parent4N Parent Meiosis N Gamete 2N Gamete 3N Zygote Mating Uneven Chromosome Number National Taiwan University Chau-Ti Ting

9 Autopolyploidy Mitosis (Failure of cell division) 2N4N Meiosis 2N4N Fertilization National Taiwan University Chau-Ti Ting

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

11 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 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. 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.

12 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 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. 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.

13 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.

14 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. 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.

15 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. 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.

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

17 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.

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

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

20 (Pseudogenization) Fates of Gene Duplication 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.

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

22 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.

23 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.

24 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.

25 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

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

27 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? 2.How does an entirely new function originate after gene duplication? 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. Source: J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292. Source: J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292.

28 Outstanding questions about the evolution of duplicate genes (II) 4.How does genetic buffering function? 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. Source: J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292.

29 Copyright Declaration WorkLicensingAuthor/SourcePage National Taiwan University Chau-Ti Ting P2 W. H. Freeman and P. Benjamin 2005. Genetics: A Conceptual Approach, 2nd ed., p. 239. W. H. Freeman and Company. New York, USA. http://www.nature.com/scitable/topicpage/dna-deletion-and-duplication-and- the-associated-331 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 Scitable by Nature Education Terms of UseTerms of Use Nature Terms and Conditions The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf P4 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 StatementCopyright Statement The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf P5 Wikipedia Lee M. Silver http://en.wikipedia.org/wiki/File:Unequalcrossingover.gif 2012/06/28 visited P6

30 30 WorkLicensingAuthor/Source National Taiwan University Chau-Ti Ting P7 National Taiwan University Chau-Ti Ting P8 National Taiwan University Chau-Ti Ting P9 National Taiwan University Chau-Ti Ting P10 “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=43f1093b-ba99- 4437-b8ea-b728b4aa468f It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 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 OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf P14 Wikipedia M. A. Clark http://en.wikipedia.org/wiki/File:Susumu_Ohno.png 2012/06/28 visited P16

31 31 WorkLicensingAuthor/Source J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292. http://www.sciencedirect.com/science/article/pii/S0169534703000338 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 Cell Press Terms and ConditionsTerms and Conditions Elsevier Website Terms and ConditionsTerms and Conditions The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf P18 J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 293. http://www.sciencedirect.com/science/article/pii/S0169534703000338 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 Cell Press Terms and ConditionsTerms and Conditions Elsevier Website Terms and ConditionsTerms and Conditions The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf P19 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 OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf P20

32 32 WorkLicensingAuthor/Source J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 294. http://www.sciencedirect.com/science/article/pii/S0169534703000338 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 Cell Press Terms and ConditionsTerms and Conditions Elsevier Website Terms and ConditionsTerms and Conditions The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf P21 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/v4/n11/pdf/nrg1204.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 OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf P22 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/v4/n11/pdf/nrg1204.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 OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf P23

33 33 WorkLicensingAuthor/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/v4/n11/pdf/nrg1204.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 OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf P24 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/v4/n11/pdf/nrg1204.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 OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf P25 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/v11/n2/pdf/nrg2689.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 OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf P26

34 34 WorkLicensingAuthor/Source What is the relative importance of positive darwinian selection and relaxation of purifying selection in functional divergence of duplicated genes? J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292-298. http://www.sciencedirect.com/science/article/pii/S0169534703000338 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 Cell Press Terms and ConditionsTerms and Conditions Elsevier Website Terms and ConditionsTerms and Conditions The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf P27 How does an entirely new function originate after gene duplication? J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292-298. http://www.sciencedirect.com/science/article/pii/S0169534703000338 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 Cell Press Terms and ConditionsTerms and Conditions Elsevier Website Terms and ConditionsTerms and Conditions The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf P27 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 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292-298. http://www.sciencedirect.com/science/article/pii/S0169534703000338 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 Cell Press Terms and ConditionsTerms and Conditions Elsevier Website Terms and ConditionsTerms and Conditions The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf P27

35 35 WorkLicensingAuthor/Source How does genetic buffering function? J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292-298. http://www.sciencedirect.com/science/article/pii/S0169534703000338 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 Cell Press Terms and ConditionsTerms and Conditions Elsevier Website Terms and ConditionsTerms and Conditions The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf P28 How important is gene duplication to the origin of species-specific features and speciation? J. Zhang 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292-298. http://www.sciencedirect.com/science/article/pii/S0169534703000338 It is used subject to the fair use doctrine of: Taiwan Copyright Act Articles 52 & 65 Cell Press Terms and ConditionsTerms and Conditions Elsevier Website Terms and ConditionsTerms and Conditions The "Code of Best Practices in Fair Use for OpenCourseWare 2009 (http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf)" by A Committee of Practitioners of OpenCourseWare in the U.S. The contents are based on Section 107 of the 1976 U.S. Copyright Acthttp://www.centerforsocialmedia.org/sites/default/files/10-305-OCW- Oct29.pdf P28


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