1 Chapter 11 Evolution by Gene Duplication Chau-Ti Ting [email protected] Unless noted, the course...

1

Chapter 11Evolution by Gene Duplication

Chau-Ti Ting

[email protected]

Unless noted, the course materials are licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Taiwan (CC BY-NC-SA 3.0)

http://creativecommons.org/licenses/by-nc-sa/3.0/tw/deed.en







National Taiwan University Chau-Ti Ting

The Bar Locus in Drosophila

+/+, wild-type B/+, heterozygous Bar B/B, homozygous Bar

http://creativecommons.org/licenses/by-nc-sa/3.0/tw/


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. Benjamin2005. Genetics: A Conceptual Approach, 2nd ed., p. 239. W. H. Freeman and Company. New York, USA.

http://get.nccu.edu.tw:8080/getcdb/handle/getcdb/127023

Cytological Evidence(Bridges 1936)

Source: C. B. Bridges1936. The Bar “gene” a duplication. Science 83: p. 210.




Unequal Crossing-over

Wikipedia Lee M. Silver

http://creativecommons.org/licenses/by-sa/3.0/deed.en



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



=

2N Parent 4N Parent

Meiosis

N Gamete 2N Gamete

3N Zygote

Mating

Uneven Chromosome Number National Taiwan University Chau-Ti Ting



Autopolyploidy

Mitosis(Failure of cell division)

2N 4N

Meiosis

2N 4N

Fertilization




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




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.




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)





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



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.




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)





Susumu Ohno ( 大野乾 )1928-2000

http://www.nap.edu/html/biomems/sohno.html



• 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.

Source: J. Zhang2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18: p. 292.



Mechanisms of Gene Duplication




(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.


Division of expression after gene duplication



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 origin of jingwei



Accelerated evolution of new genes





The biased distribution of retroposition events



Source: H. Innan and F. Kondrashov2010. 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?

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.






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?





Copyright DeclarationWork Licensing Author/Source Page


P2

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

P4

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

P5

Wikipedia Lee M. Silverhttp://en.wikipedia.org/wiki/File:Unequalcrossingover.gif2012/06/28 visited

P6

http://www.nature.com/scitable/topicpage/dna-deletion-and-duplication-and-the-associated-331

http://www.nature.com/scitable/topicpage/dna-deletion-and-duplication-and-the-associated-331

http://www.nature.com/scitable/viewTermsOfUse

http://www.nature.com/info/tandc.html

http://www.centerforsocialmedia.org/sites/default/files/10-305-OCW-Oct29.pdf


http://www.sciencemag.org/content/83/2148/210.extract

http://www.sciencemag.org/site/help/about/copyright.xhtml



http://en.wikipedia.org/wiki/File:Unequalcrossingover.gif





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Work Licensing Author/Source

National Taiwan University Chau-Ti TingP7




“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

P14

Wikipedia M. A. Clarkhttp://en.wikipedia.org/wiki/File:Susumu_Ohno.png2012/06/28 visited

P16

http://www.sciencemag.org/content/165/3891/349.extract?sid=43f1093b-ba99-4437-b8ea-b728b4aa468f

http://www.sciencemag.org/content/165/3891/349.extract?sid=43f1093b-ba99-4437-b8ea-b728b4aa468f



http://en.wikipedia.org/wiki/File:Susumu_Ohno.png







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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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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

P20

http://www.sciencedirect.com/science/article/pii/S0169534703000338

http://www.cell.com/cellpress/TermsandConditions

http://www.elsevier.com/wps/find/termsconditions.cws_home/termsconditions








http://www.genetics.org/content/151/4/1531.full.pdf






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P21

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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http://www.nature.com/nrg/journal/v4/n11/pdf/nrg1204.pdf











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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?


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?


P27



















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How does genetic buffering function?


P28

How important is gene duplication to the origin of species-specific features and speciation?


P28













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1 Chapter 11 Evolution by Gene Duplication Chau-Ti Ting [email protected] Unless noted, the course...

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