Evolution and Population Genetics Seminar

Genetics 590

Autumn, 1999

The Evolution and Population Genetics seminar will meet on Tuesdays in Autumn quarter in Hitchcock 316 from 12:30pm - 1:20pm. This quarter the topic will be mathematical/computational/population models of genomic evolution and comparative genomics. Participants will read papers in this area and will be expected to lead discussion once during the quarter. Some of the material we hope to cover is models of genome rearrangement (papers by Sankoff and by Pevzner), models of tandemly duplicated genes, both their numbers and their genetic differences, models of microsatellite arrays, and so on. I will try to make a list of references available at the first meeting and on the course web page.

Note that the emphasis will not be on empirical papers but on the papers dealing with populational models or computational questions, because (1) that's just the way I am, and (2) models and computations are important.

The weekly references will be available to be copied in the copy room of the Genetics Department, J205 Health Sciences Building, and they are to be listed below.

The course will presuppose knowledge of elementary statistics and genetics. It is a graduate course with prerequisite Genetics 562 or permission of the instructor.

Joe Felsenstein (joe@genetics.washington.edu)

Readings for the sessions (session leader given for each):

September 28

will be an organizational session with some background by me on the kinds of chromosome rearrangements.

October 5

(Joe Felsenstein)

Nadeau, J. H. and D. Sankoff. 1997. Landmarks in the Rosetta Stone of mammalian comparative maps. Nature Genetics 15: 6-7.
Nadeau, J. H., and D. Sankoff. 1998. The lengths of undiscovered conserved segments in comparative maps. Mammalian Genome 9: 491-495.
Nadeau, J. H. and D. Sankoff. 1998. Counting on comparative maps. Trends in Genetics 14: 495-501.

October 12

(Lindsey Dubb)

Sankoff, D. M. N. Parent, I. Marchand, and V. Ferretti. 1997. On the Nadeau-Taylor theory of conserved chromosome segments. Pp. 262-274 in Combinatorial Pattern Matching. Proceedings of the 8th Annual Symposium, CPM 97. Springer-Verlag, Berlin.
Sankoff, D. and J. H. Nadeau. 1996. Conserved synteny as a measure of genomic distance. Discrete Applied Mathematics 71: 247-257.
Sankoff, D., V. Ferretti, and J. H. Nadeau. 1997. Conserved segment identification. Journal of Computational Biology 4: 559-565.

October 19

(Eric Anderson)

Sankoff, D. and M. Goldstein. 1989. Probabilistic models of genome shuffling. Bulletin of Mathematical Biology 51: 117-124.
Sankoff, D. R. Cedergren, and Y. Abel. 1990. Genomic divergence through gene rearrangement. pp. 428-438 in R.F. Doolittle (ed.), Methods in Enzymology, vol. 183. Academic Press, New York.

October 26

(Arran McPherson)

Sankoff D., G. Leduc, N. Antoine, B. Paquin, B. F. Lang, and R. Cedergren. 1992. Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. Proceedings National Academy Sciences, USA 89: 6575-6579.
Kececioglu, J. and D. Sankoff. 1995. Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement. Algorithmica 13: 180-210.

November 2

(Benno Schwikowski)

Hannenhalli, S., C. Chappey, E. V. Koonin, and P. A. Pevzner. 1995. Genome sequence comparison and scenarios for gene rearrangements: a test case. Genomics 30: 299-311.
Hannenhalli, S. and P. A. Pevzner. 1999. Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. Journal of the ACM 46: 1-27.
Hannenhalli, S, and P. A. Pevzner. 1995. Transforming men into mice (polynomial algorithm for genomic distance problem). Proceedings of the 36th Annual Symposium on Foundations of Computer Science. IEEE Computer Society Press, Los Alamitos, California.
Bafna, V., and P. A. Pevzner. 1996. Genome rearrangements and sorting by reversals. SIAM Journal on Computing 25: 272-289.
Bafna, V. and P. A. Pevzner. 1998. Sorting by transpositions. SIAM Journal on Discrete Mathematics 11: 224-240.

November 9

November 16

(Mathieu Blanchette)

Sankoff, D. and M. Blanchette. 1998. Multiple genome rearrangement and breakpoint phylogeny. Journal of Computational Biology 5: 555-570.
Blanchette, M., T. Kunisawa, and D. Sankoff. 1999. Gene order breakpoint evidence in animal mitochondrial phylogeny. Journal of Molecular Evolution 49: 193-203.
Sankoff, D., G. Sundaram, and J. Kececioglu. 1996. Steiner points in the space of genome rearrangements. International Journal of Foundations of Computer Science 7: 1-9.

November 23

(Joe Felsenstein)

Imai, H. T. and T. Maruyama. 1978. Karyotype evolution by pericentric inversion as a stochastic process. Journal of Theoretical Biology 70: 253-261.
Imai, H. T. and R. H. Crozier. 1980. Quantitative analysis of directionality in mammalian karyotype evolution. American Naturalist 116: 537-569.
Imai H. T., T. Maruyama, T. Gojobori, Y. Inoue, and R. H. Crozier. 1986. Theoretical bases for karyotype evolution. 1. The minimum-interaction hypothesis. American Naturalist 128: 900-920.
Imai, H. T., N. Takahata, T. Maruyama, A. Daniel, T. Honda, Y. Matsuda, and K. Moriwaki. 1988. Theoretical bases for karyotype evolution. 2. The fusion burst in man and mouse. Japanese Journal of Genetics 63: 313-342.
Sankoff, D. and V. Ferretti. 1996. Karyotype distributions in a stochastic model of reciprocal translocation. Genome Research 6: 1-9.

November 30

(Hollie Walsh)

Christiansen, F. B., and O. Frydenberg. 1977. Selection-mutation balance for two nonallelic recessives producing an inferior double homozygote. American Journal of Human Genetics 29: 195-207.
Clark, A. G. 1994. Invasion and maintenance of a gene duplication. Proceedings of the National Academy of Sciences, USA 91: 2950-2954.

December 7

(Linda Park and lab)

Walsh, J. B. 1995. How often do duplicated genes evolve new functions? Genetics 139: 421-428
Nadeau, J. H. and D. Sankoff. 1997. Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution. Genetics 7: 1259-1266.
El-Mabrouk, N., J. H. Nadeau, and D. Sankoff. 1998. Genome halving. pp. 235-250 in Combinatorial Pattern Matching. Proceedings of the 9th Annual Symposium, CPM 98. Springer-Verlag, Berlin.

References

The future readings of the seminar will largely be from among these papers:

Conserved chromosome segments

Nadeau, J. H. and B. A. Taylor. 1984. Lengths of chromosome segments conserved since divergence of man and mouse. Proceedings of the National Academy of Sciences, USA. 81: 814-818.
Zakharov, I. A. and A. K. Valeev. 1988. Quantitative analysis of the evolution of mammalian genome by comparing genetic maps (in Russian). Doklady Akademiya Nauk SSSR 301: 1213-1218.
Sankoff, D. M. N. Parent, I. Marchand, and V. Ferretti. 1997. On the Nadeau-Taylor theory of conserved chromosome segments. Pp. 262-274 in Combinatorial Pattern Matching. Proceedings of the 8th Annual Symposium, CPM 97. Springer-Verlag, Berlin.
Sankoff, D. and J. H. Nadeau. 1996. Conserved synteny as a measure of genomic distance. Discrete Applied Mathematics 71: 247-257.
Sankoff, D., V. Ferretti, and J. H. Nadeau. 1997. Conserved segment identification. Journal of Computational Biology 4: 559-565.
Ehrlich, J., D. Sankoff, and J. H. Nadeau. 1997. Synteny conservation and chromosome rearrangements during mammalian evolution. Genetics 147: 289-296.
Nadeau, J. H. and D. Sankoff. 1997. Landmarks in the Rosetta Stone of mammalian comparative maps. Nature Genetics 15: 6-7.
Nadeau, J. H. and D. Sankoff. 1998. Counting on comparative maps. Trends in Genetics 14: 495-501.
Nadeau, J. H., and D. Sankoff. 1998. The lengths of undiscovered conserved segments in comparative maps. Mammalian Genome 9: 491-495.

Rearrangement of genomes

Sankoff, D. and M. Goldstein. 1989. Probabilistic models of genome shuffling. Bulletin of Mathematical Biology 51: 117-124.
Sankoff, D. R. Cedergren, and Y. Abel. 1990. Genomic divergence through gene rearrangement. pp. 428-438 in R.F. Doolittle (ed.), Methods in Enzymology, vol. 183. Academic Press, New York.
Hannenhalli, S., C. Chappey, E. V. Koonin, and P. A. Pevzner. 1995. Genome sequence comparison and scenarios for gene rearrangements: a test case. Genomics 30: 299-311.
Hannenhalli, S. and P. A. Pevzner. 1999. Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. Journal of the ACM 46: 1-27.
Hannenhalli, S, and P. A. Pevzner. 1995. Transforming men into mice (polynomial algorithm for genomic distance problem). Proceedings of the 36th Annual Symposium on Foundations of Computer Science. IEEE Computer Society Press, Los Alamitos, California.
Bafna, V., and P. A. Pevzner. 1996. Genome rearrangements and sorting by reversals. SIAM Journal on Computing 25: 272-289.
Bafna, V. and P. A. Pevzner. 1998. Sorting by transpositions. SIAM Journal on Discrete Mathematics 11: 224-240.
Ferretti, V., J. H. Nadeau, and D. Sankoff. 1996. Original synteny. Pp. 159-167 in Combinatorial Pattern Matching. Proceedings of the 7th Annual Symposium, CPM 96. Springer-Verlag, Berlin.
Sankoff, D., G. Sundaram, and J. Kececioglu. 1996. Steiner points in the space of genome rearrangements. International Journal of Foundations of Computer Science 7: 1-9.
Sankoff, D., and M. Blanchette. 1998. Multiple genome rearrangement. RECOMB 98. Pp. 243-247 in Proceedings of the Second Annual International Conference on Computational Molecular Biology. ACM, New York, NY.
Sankoff, D. and M. Blanchette. 1998. Multiple genome rearrangement and breakpoint phylogeny. Journal of Computational Biology 5: 555-570.
Kececioglu, J. and D. Sankoff. 1995. Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement. Algorithmica 13: 180-210.
Blanchette, M., T. Kunisawa, and D. Sankoff. 1999. Gene order breakpoint evidence in animal mitochondrial phylogeny. Journal of Molecular Evolution 49: 193-203.
Gray, M. W., B. F. Lang, R. Cedergren, G. B. Golding, C. Lemieux, D. Sankoff M. Turmel, N. Brossard, E. Delage, T. G. Littlejohn, I. Plante, P. Rioux, D. Saint-Louis, Y. Zhu, and G. Burger. 1998. Genome structure and gene content in protist mitochondrial DNAs. Nucleic Acids Research 15: 865-878
Blanchette, M., T. Kunisawa, and D. Sankoff. 1996. Parametric genome rearrangement. Gene 12: GC11-GC7.
Sankoff, D. 1993. Analytical approaches to genomic evolution. Biochimie 75: 409-413.
Sankoff D., G. Leduc, N. Antoine, B. Paquin, B. F. Lang, and R. Cedergren. 1992. Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. Proceedings National Academy Sciences, USA 89: 6575-6579.

Karyotype evolution

Imai, H. T. and T. Maruyama. 1978. Karyotype evolution by pericentric inversion as a stochastic process. Journal of Theoretical Biology 70: 253-261.
Imai, H. T. and R. H. Crozier. 1980. Quantitative analysis of directionality in mammalian karyotype evolution. American Naturalist 116: 537-569.
Imai H. T., T. Maruyama, T. Gojobori, Y. Inoue, and R. H. Crozier. 1986. Theoretical bases for karyotype evolution. 1. The minimum-interaction hypothesis. American Naturalist 128: 900-920.
Imai, H. T., N. Takahata, T. Maruyama, A. Daniel, T. Honda, Y. Matsuda, and K. Moriwaki. 1988. Theoretical bases for karyotype evolution. 2. The fusion burst in man and mouse. Japanese Journal of Genetics 63: 313-342.
Sankoff, D. and V. Ferretti. 1996. Karyotype distributions in a stochastic model of reciprocal translocation. Genome Research 6: 1-9.

Loss or divergence of duplicate genes

Christiansen, F. B., and O. Frydenberg. 1977. Selection-mutation balance for two nonallelic recessives producing an inferior double homozygote. American Journal of Human Genetics 29: 195-207.
Clark, A. G. 1994. Invasion and maintenance of a gene duplication. Proceedings of the National Academy of Sciences, USA 91: 2950-2954.
Walsh, J. B. 1995. How often do duplicated genes evolve new functions? Genetics 139: 421-428
Nadeau, J. H. and D. Sankoff. 1997. Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution. Genetics 7: 1259-1266.
El-Mabrouk, N., J. H. Nadeau, and D. Sankoff. 1998. Genome halving. pp. 235-250 in Combinatorial Pattern Matching. Proceedings of the 9th Annual Symposium, CPM 98. Springer-Verlag, Berlin.

Possible other topics to cover (may be little time for these):

Expansion and homogenization of tandem repeat families (papers by Ohta and others)
Microsatellite arrays
Theories for degeneration of Y chromosomes