1 chapter 11 evolution by gene duplication chau-ti ting [email protected] unless noted, the course...
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Chapter 11Evolution by Gene Duplication
Chau-Ti Ting
Unless noted, the course materials are licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Taiwan (CC BY-NC-SA 3.0)
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National Taiwan University Chau-Ti Ting
The Bar Locus in Drosophila
+/+, wild-type B/+, heterozygous Bar B/B, homozygous Bar
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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.
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Hypothesis: Unequal Crossing-over
Source: W. H. Freeman and P. Benjamin2005. Genetics: A Conceptual Approach, 2nd ed., p. 239. W. H. Freeman and Company. New York, USA.
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Cytological Evidence(Bridges 1936)
Source: C. B. Bridges1936. The Bar “gene” a duplication. Science 83: p. 210.
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Unequal Crossing-over
Wikipedia Lee M. Silver
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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
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=
2N Parent 4N Parent
Meiosis
N Gamete 2N Gamete
3N Zygote
Mating
Uneven Chromosome Number National Taiwan University Chau-Ti Ting
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Autopolyploidy
Mitosis(Failure of cell division)
2N 4N
Meiosis
2N 4N
Fertilization
National Taiwan University Chau-Ti Ting
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Allopolypoidy
Species A2N = 6
Species B2N = 4
Failure of cell division
4 chromosome gameteHybrid
Chromosome = 7
Normal gameteChromosome = 3
7 chromosome gamete
Fertile hybrid Chromosome = 10
National Taiwan University Chau-Ti Ting
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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. Raes2004. Duplication and divergence: The evolutionof new genes and old Ideas. Annual Review of Genetics 38: p. 615.
Source: J. S. Taylor and J. Raes2004. Duplication and divergence: The evolutionof new genes and old Ideas. Annual Review of Genetics 38: p. 615.
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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. Raes2004. Duplication and divergence: The evolutionof new genes and old Ideas. Annual Review of Genetics 38: p. 615.
Source: J. S. Taylor and J. Raes2004. Duplication and divergence: The evolutionof new genes and old Ideas. Annual Review of Genetics 38: p. 615.
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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. Raes2004. Duplication and divergence: The evolutionof new genes and old Ideas. Annual Review of Genetics 38: p. 615.
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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 evolutionof new genes and old Ideas. Annual Review of Genetics 38: p. 615.
Source: J. S. Taylor and J. Raes2004. Duplication and divergence: The evolutionof new genes and old Ideas. Annual Review of Genetics 38: p. 615.
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GENE DUPLICATION AND ISOZYME ELECTROPHORESIS
Duplicated isozyme loci produced more bands than single-copy genes, and many isozyme electrophoresis studies uncovered gene duplicates in polyploidsData 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. Raes2004. Duplication and divergence: The evolutionof new genes and old Ideas. Annual Review of Genetics 38: p. 615.
Source: J. S. Taylor and J. Raes2004. Duplication and divergence: The evolutionof new genes and old Ideas. Annual Review of Genetics 38: p. 615.
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Susumu Ohno ( 大野 乾 )1928-2000
http://www.nap.edu/html/biomems/sohno.html
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• J. Zhang2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292-298.• M. Long, E. Betran, K. Thornton, and W. Wang2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: p. 865-875.
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Source: J. Zhang2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292.
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Mechanisms of Gene Duplication
Source: J. Zhang2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292.
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(Pseudogenization)
Fates of Gene Duplication
Source: A. Force, M. Lynch, F. B. Pickett, A. Amores, Y. Yan, and J. Postlethwait1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: p. 1531.
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Division of expression after gene duplication
Source: J. Zhang2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292.
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Source: M. Long, E. Betran, K. Thornton, and W. Wang2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: p. 865.
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The origin of jingwei
Source: M. Long, E. Betran, K. Thornton, and W. Wang2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: p. 865.
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Accelerated evolution of new genes
Source: M. Long, E. Betran, K. Thornton, and W. Wang2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: p. 865.
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Source: M. Long, E. Betran, K. Thornton, and W. Wang2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: p. 865.
The biased distribution of retroposition events
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Source: H. Innan and F. Kondrashov2010. The evolution of gene duplications: classifying and distinguishing between models. Nature Review Genetics 11: p. 97.
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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. Zhang2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292.
Source: J. Zhang2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292.
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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. Zhang2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292.
Source: J. Zhang2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292.
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Copyright DeclarationWork Licensing Author/Source Page
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W. H. Freeman and P. Benjamin2005. 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-331It 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 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 Act
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C. B. Bridges1936. The Bar “gene” a duplication. Science 83: p. 210.http://www.sciencemag.org/content/83/2148/210.extractIt 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 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 Act
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Wikipedia Lee M. Silverhttp://en.wikipedia.org/wiki/File:Unequalcrossingover.gif2012/06/28 visited
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“a necessary concomitant to increased complexity of organization.”
Roy J. Britten and Eric H. Davidson1969. 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-b728b4aa468fIt is used subject to the fair use doctrine of:•Taiwan Copyright Act Articles 52 & 65It 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 Act
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Wikipedia M. A. Clarkhttp://en.wikipedia.org/wiki/File:Susumu_Ohno.png2012/06/28 visited
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J. Zhang2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292.http://www.sciencedirect.com/science/article/pii/S0169534703000338It 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 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 Act
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J. Zhang2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 293.http://www.sciencedirect.com/science/article/pii/S0169534703000338It 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 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 Act
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A. Force, M. Lynch, F. B. Pickett, A. Amores, Y. Yan, and J. Postlethwait1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: p. 1534.http://www.genetics.org/content/151/4/1531.full.pdfIt 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 Act
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J. Zhang2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 294.http://www.sciencedirect.com/science/article/pii/S0169534703000338It 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 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 Act
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M. Long, E. Betran, K. Thornton, and W. Wang2003. 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.pdfIt 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 Act
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M. Long, E. Betran, K. Thornton, and W. Wang2003. 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.pdfIt 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 Act
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M. Long, E. Betran, K. Thornton, and W. Wang2003. 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.pdfIt 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 Act
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M. Long, E. Betran, K. Thornton, and W. Wang2003. 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.pdfIt 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 Act
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H. Innan and F. Kondrashov2010. 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.pdfIt 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 Act
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What is the relative importance of positive darwinian selection and relaxation of purifying selection in functional divergence of duplicated genes?
J. Zhang2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292-298.http://www.sciencedirect.com/science/article/pii/S0169534703000338It 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 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 Act
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How does an entirely new function originate after gene duplication?
J. Zhang2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292-298.http://www.sciencedirect.com/science/article/pii/S0169534703000338It 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 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 Act
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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. Zhang2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292-298.http://www.sciencedirect.com/science/article/pii/S0169534703000338It 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 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 Act
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Work Licensing Author/Source
How does genetic buffering function?
J. Zhang2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292-298.http://www.sciencedirect.com/science/article/pii/S0169534703000338It 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 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 Act
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How important is gene duplication to the origin of species-specific features and speciation?
J. Zhang2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292-298.http://www.sciencedirect.com/science/article/pii/S0169534703000338It 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 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 Act
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