Gene Duplication

Gene Duplication events provide abundant genetic variation upon which evolution can act. The existence of large gene families attests to the importance of this process in the prodution of phenotypic variation. In this seminar course we will explore the mechanisms that produce duplicated genes, the models that explain persistence of duplicated genes, the evolutionary fate of duplicated genes, the role of gene duplicates in adaptive phenotypes and the lab techniques to identify and charaterie duplicated genes. The format will emphasize student lead discussion and includes a 3 week genomics lab experiment to identy gene duplicates among African Cichlid Species.

How do new genes evolve?
What happens to genes when they are duplicated?
Which genes are duplicated?
Is gene duplication "adaptive"?

After we gave read a few review papers and a collection of specific examples, students will read a current NSF-funded grant proposal of which the goal is to identify a role for gene duplication in the adaptive radiation of African Cichild Fishes.

Students will then go into the lab and preform Comparative Genomic Hybridization to identify gene duplicates in 4 fish species. After analysis of the data, students will write up their results to be integrated with the ongoing research projec.

The following reviews and example papers are meant to provide ideas and inspiration.
Students are not restricted to this reference list

Students will work in pairs.
Students will lead a discussion based on one primary research paper.
Students may also choose to suggest one related review for necessary background.

Review Articles
Hurles M. (2004) Gene duplication: the genomic trade in spare parts. PLOSBiology 2:0900-0904

Taylor, J.S. and Raes, J. (2004) Duplication and divergence: The evolution of new genes and old ideas. Annual Review of Genetics 38:615-643.

Conant G.C. and Wolf, K.H. (2008) Turning a hobby into a job: How duplicated genes find new functions. Nature Reviews Genetics 9:938-950.

Lynch, M. and Conery, J.S. (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.

Moore RC, Purugganan MD (2005) The evolutionary dynamics of plant duplicate genes. Current Opinion in Plant Biology 8:122-128.

Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y.L. and Postlethwait J. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545.

Korbel, J., Kim, P.M., Chen, X., Urban, E.A., Weissman, S., Snyder, M and Gerstein, M.B. (2008) The current excitement about copy-number variation: how it relates to gene duplications and protein families.

Fanciulli M., Tetretto, E., Aitman, T.J., (2010) Gene copy number variation and common human disease. Clin Genet 77:201-213.

Examples of Gene duplication studies.
Some of these are focused on one or a few genes while others take a genome wide approach to address patterns and others take a comparative approach between species.

Poliseno, L., Salmena, L., Zhang, J., Carver, B., Haveman, W.J., Pandolfi, P.P. (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465:1033-1038.

Chen, Z.Z., Cheng ,C.H.C., Zhang, J.F., Cao, L.X., Chen, L., Zhou, L.H., Jin, Y.D., Ye, H., Deng, C., Dai, Z.H., Xu, Q.H., Hu, P., Sun, S.H., Shen, Y. and Chen, L.B.(2008) Transcrintomic and genomic evolution under constant cold in Antarctic notothenioid fish. Proceedings of the National Academy of Sciences of the United States of America 105:12944-12949.

Emerson, J.J., Cardoso-Moreira, M., Borevitz, J.O. and Long, M (2008) Natural Selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster Science 320, 1629-1631.

Hurley, I., Hale, M.E., Prince, V.E. (2007) Duplication events and the evolution of segmental identity. Evolution and Development 7-6:556-567.

Blomme, T., Vandepoele, K., De Bodt, S., Simillion, C. Maere, S., Van de Peer, Y., (2006) The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biology, 7:R43(doi:10.1186/gb-2006-7-5-r43)

Dumas L, Kim YH, Karimpour-Fard A, Cox M, Hopkins J, Pollack JR, Sikela JM (2007) Gene copy number variation spanning 60 million years of human and primate evolution. Genome Research 17:1266-1277.

Monson, R.K. (2003) Gene Duplication, neofunctioalization, and the evolution of C4 photosynthesis. International Journal of Plant Science. 164:S43-S54.

Sandve SR, Rudi H, Asp T, Rognli OA (2008) Tracking the evolution of a cold stress associated gene family in cold tolerant grasses. Bmc Evolutionary Biology 8.

Perry, G.H, Ben-Dor, A., Tsalenko, A., Sampas, N., Rodriguies-Revenga, L., Tran, C.W., Scheffer, A., Steinfeld, I., Tsang, P., Yamada, N.A., Park, H.S., Kim, J., Seo, J.S., Yakhini, Z., Laderman, S., Bruhn, L., and Lee, C (2008) The fie-scale and complex architecture of human copy-number variation. The American Journal of Human Genetics. 82:1-11.

Li, J., Musso, G. and Zhang, Z (2008) Preferential regulation of duplicated genes by microRNAs in mammals Genome Biology 9:R132.

Makova, K.D. and Li, W.H. (2008) Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Research 13:1638–1645

Shoja, V., Murali, T. M. and Zhang, L. (2007) Expression divergence of tandemly arrayed genes in human and mouse. Comparative Functional Genomics 2007:60964(8pages).

Ames RM, Rash BM, Hentges KE, Robertson DL, Delneri D, Lovell SC. 2010. Gene duplication and environmental adaptation within yeast populations. Genome Biol Evol 2:591-601.

Hasselmann M, Lechner S, Schulte C, Beye M. 2010. Origin of a function by tandem gene duplication limits the evolutionary capability of its sister copy. Proceedings of the National Academy of Sciences of the United States of America 107:13378-83.

Meisel RP, Hilldorfer BB, Koch JL, Lockton S, Schaeffer SW. 2010. Adaptive Evolution of Genes Duplicated from the Drosophila pseudoobscura neo-X Chromosome. Molecular Biology and Evolution 27:1963-78.

Watson CT, Lubieniecki KP, Loew E, Davidson WS, Breden F. 2010. Genomic organization of duplicated short wave-sensitive and long wave-sensitive opsin genes in the green swordtail, Xiphophorus helleri. Bmc Evolutionary Biology 10.

Yuan JA, He ZZ, Yuan XN, Jiang XY, Sun XW, Zou SM. 2010. Speciation of Polyploid Cyprinidae Fish of Common Carp, Crucian Carp, and Silver Crucian Carp Derived from Duplicated Hox Genes. Journal of Experimental Zoology Part B-Molecular and Developmental Evolution 314B:445-56.

Zhou X, Lin Z, Ma H. 2010. Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants. Genome Biology 11

Hughes, A,L, (2010) Origin and diversification of the L-amino oxidase family in innate immune defenses of animals. Immunogenetics 62:753–759