Dr. Sarah P. Otto
ADDRESS: Department of Zoology, Room 3340 (map) University of British Columbia 6270 University Blvd. Vancouver BC V6T 1Z4, Canada FAX: (604) 822-2416 Phone: (604) 822-2778 Email: otto at zoology.ubc.ca
BookOtto, S. P. and T. Day (2007) A Biologist's Guide to Mathematical Modeling in Ecology and Evolution. Princeton University Press.
This book is intended for undergraduate and graduate students in biology who wish to learn how to develop and analyze their own mathematical models. The book is available at Princeton University Press and on Amazon. The book has been successfully used in courses at UBC, Queen's University, and University of Oregon.
Otto, S.P. (2009) The Evolution Of Sex: Recent Resolutions And Remaining Riddles. Edited Symposium Issue of the American Naturalist.
Clark, A. G. and S. P. Otto (2002) Population genetics and molecular evolution of whole genomes. Edited volume of Current Opinion in Genetics and Development.
Gerstein, A. C., Lo, D. S., and S. P. Otto (2012) Parallel genetic changes and non-parallel gene-environment interactions underlie nystatin resistance in yeast. Genetics, 192:241-252.
Hartfield, M., S. P. Otto, P. D. Keightley (2012) The maintenance of obligate sex in finite, structured populations subject to recurrent beneficial and deleterious mutation. Evolution, 65: 2421–2434.
Magnuson-Ford, K. S., and S. P. Otto (2012) Linking the investigations of character evolution and species diversification. American Naturalist, 180:225-245.
Otto, S. P. (2012) Theoretical perspectives on rapid evolutionary change. In: Singh, R. S., J. Xu, and R. J. Kulathinal, eds. Rapidly Evolving Genes and Genetic Systems. Oxford University Press, pp. 13-22.
M’Gonigle, L. K., R. Mazzucco, S. P. Otto, and Ulf Dieckmann (2012) Sexual selection enables long-term coexistence despite ecological equivalence. Nature, 484:506-509.
Hodgson, E. E., and S. P. Otto (2012) The red queen coupled with directional selection favours the evolution of sex. J. Evolutionary Biology, 25:797-802.
Jordan, C. Y., and S. P. Otto (2012) Functional pleiotropy and mating system evolution in plants: frequency-independent mating. Evolution, 66:957-972.
Roze, D., and S. P. Otto (2012) Differential selection between the sexes and selection for sex. Evolution, 66:558-574.
Gerstein, A. C., and S. P. Otto (2011) Cryptic fitness advantage: diploids invade haploid populations despite lacking any apparent advantage as measured by standard fitness assays. PLoS ONE, 6(12): e26599. doi:10.1371/journal.pone.0026599.
Immler, S., G. Arnqvist, and S. P. Otto (2011) Ploidally antagonistic selection maintains stable genetic polymorphism. Evolution, 66:55-65.
Johnson, M. T. J., R. G. FitzJohn, S. D. Smith, M. D. Rausher, and S. P. Otto (2011) Loss of sexual recombination and segregation is associated with increased diversification in evening primroses. Evolution, 65:3230-3240.
Mayrose, I., S. H. Zhan, C. J. Rothfels, K. Magnuson-Ford, M. S. Barker, L. H. Rieseberg, and S. P. Otto (2011) Recently-formed polyploid plants diversify at lower rates. Science, 333:1257.
Otto, S. P., J. R. Pannell, C. L. Peichel, T.-L. Ashman, D. Charlesworth, A. K. Chippindale, L. F. Delph, R. F. Guerrero, S. V. Scarpino, B. F. McAllister (2011) About PAR: The distinct evolutionary dynamics of the pseudoautosomal region. Trends in Genetics, 27:358-367.
Hartfield, M., and S. P. Otto (2011) Recombination and hitchhiking of deleterious alleles. Evolution, 65: 2421-2434. [Derivations in Mathematica.]
Yeaman, S., and S. P. Otto (2011) Establishment and maintenance of adaptive genetic divergence under migration, selection, and drift. Evolution, 65:2123-2129.
M'Gonigle, L., and S. P. Otto (2011) Ploidy and the evolution of parasitism. Proceedings of the Royal Society, London B., 278:2814-2822.
Gerstein, A. C., L. A. Cleathero, M. A. Mandegar, and S. P. Otto (2011) Haploids adapt faster than diploids across a range of environments. Journal of Evolutionary Biology, 24:531-540.
Mayrose, I. and S. P. Otto (2011) A likelihood method for detecting trait-dependent shifts in the rate of molecular evolution. Molecular Biology & Evolution, 28:759-770. [traitRate program]
Ally, D. C., K. Ritland, and S. P. Otto (2010) Aging in a long-lived clonal plant. PLoS Biology, 8(8): e1000454. doi:10.1371/journal.pbio.1000454
Blackburn, G. S., A. Y. K. Albert, and S. P. Otto (2010) The evolution of sex ratio adjustment in the presence of sexual antagonistic selection. American Naturalist, 176:264-275. [Derivations in Mathematica.]
Mee, J. A., and S. P. Otto (2010) Variation in the strength of male mate choice allows long-term coexistence of sperm-dependent asexuals and their sexual hosts. Evolution, 64: 2808-2819.
Smith, S. D., R. E. Miller, S. P. Otto, R. G. FitzJohn, and M. D. Rausher (2010) The effects of flower color transitions on diversification rates in morning glories (Ipomoea subg. Quamoclit, Convolvulaceae). In: Long M., ed. Darwin's heritage today: Proceedings of the Darwin 2010 Beijing International Conference. Beijing, China: Higher Education Press, pp. 202-225.
Hartfield, M., S. P. Otto, P. D. Keightley (2010) The role of advantageous mutations in enhancing the evolution of a recombination modifier. Genetics, 184: 1153-1164.
Mayrose, I., M. S. Barker, and S. P. Otto (2010) Probabilistic models of chromosome number evolution and the inference of polyploidy. Systematic Biology, 59: 132-144. [chromEvol program]
Otto, S. P. and M. C. Whitlock (2009) The impact of epistatic selection on the genomic traces of selection. Molecular Ecology, 18: 4985-4987.
FitzJohn, R., W. Maddison, and S. P. Otto (2009) Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Systematic Biology, 58: 595-611. [diversitree: R source package]
Gerstein, A. C., and S. P. Otto (2009) Ploidy and the causes of genomic evolution. Journal of Heredity, 100: 571Ð581.
Hodgins, K. A., L. Rieseberg, and S. P. Otto (2009) Genetic control of invasive plants species using selfish genetic elements. Evolutionary Applications, 2: 555-569. [R code for simulations.]
Lahti, D. C., N. A. Johnson, B. C. Ajie, S. P. Otto, A. P. Hendry, D. T. Blumstein, R. G. Coss, K. Donohue, and S. A. Foster (2009) Relaxed selection in the wild. TREE, 24: 487-496.
M'Gonigle, L. and S. P. Otto (2009) Mutating away from your enemies: The evolution of mutation rate in a host-parasite system. Theoretical Population Biology, 75: 301-311.
Hadany, L. and S. P. Otto (2009) Condition-dependent sex and the rate of adaptation. American Naturalist, 174: S71-S78.
Otto, S. P. (2009) The evolutionary enigma of sex. American Naturalist, 174: S1-S14.
Whittle, W. A., S. P. Otto, M. O. Johnston, and J. E. Krochko (2009) Adaptive epigenetic memory of ancestral temperature regime in Arabidopsis thaliana. Botany, 87: 650-657.
Greenspoon, P. and S. P. Otto (2009) Evolution by Fisherian sexual selection in diploids. Evolution, 63-4: 1076-1083.
Kouyos, R. D., M. Salathé, S. P. Otto, S. Bonhoeffer (2009) The role of epistasis on the evolution of recombination in host parasite coevolution. Theoretical Population Biology, 75: 1-13.
Otto, S. (2008) Sexual reproduction and the evolution of sex. Nature Education, 1(1).
Otto, S. P., and A. C. Gerstein (2008) The evolution of haploidy and diploidy. Current Biology, 18: R1121-R1124.
Ally, D. C., K. Ritland, and S. P. Otto (2008) Can clone size serve as a proxy for clone age? An exploration using microsatellite divergence in Populus tremuloides. Molecular Ecology, 17: 4897-4911.
The McDonnell Norms Group (2008) Antibiotic overprescribing: the influence of social norms. Journal of the American College of Physicians, 2: 265-275
Nuismer, S. L., S. P., Otto, F. Blanquart (2008) When do host-parasite interactions drive the evolution of non-random mating? Ecology Letters, 11:937-946.
Otto, S. P., M. R. Servedio, S. L. Nuismer (2008) Frequency-dependent selection and the evolution of assortative mating. Genetics, 179: 2091-2112. [Derivations in Mathematica.]
Hazzouri, K. M., A. Mohajer, S. I. Dejak, S. P. Otto, and S. I. Wright (2008) Contrasting patterns of transposable element insertion polymorphism and nucleotide diversity in autotetraploid and allotetraploid Arabidopsis species. Genetics, 179: 581-592.
Whitton, J., Sears, C. J., Baack, E. J., and S. P. Otto (2008) The dynamic nature of apomixis in the angiosperms. International Journal of Plant Sciences, 169: 169-182.
Gerstein, A. C., R. M. McBride, and S. P. Otto (2008) Ploidy reduction in Saccharomyces cerevisiae. Biol. Lett. 4: 91-94.
Otto, S. P. (2007) Unraveling the evolutionary advantage of sex. Genetical Research, 89:447-449.
Otto, S. P. (2007) The evolutionary consequences of polyploidy. Cell, 131: 452-462.
Maddison, W. P., P. E. Midford and S. P. Otto (2007) Estimating a binary character's effect on speciation and extinction. Systematic Biology, 56: 701-710.
Hadany, L. and S. P. Otto (2007) The evolution of condition-dependent sex in the face of high costs. Genetics, 176: 1713-1727.
Gandon, S., and S. P. Otto (2007) The evolution of sex and recombination in response to abiotic or coevolutionary fluctuations in epistasis.Genetics, 175: 1835-1853.
Zeyl, C. W., and S. P. Otto (2007) A short history of recombination in yeast. Trends in Ecology and Evolution, 22: 223-225.
Mandegar, M. A., and S. P. Otto (2007) Mitotic recombination counteracts the benefits of genetic segregation. Proceedings of the Royal Society, London B., 274: 1301-1307.
Hill, J. A., and S. P. Otto (2007) The role of pleiotropy in the maintenance of sex in yeast. Genetics, 175: 1419-1427.
Barrett, R. D. H., L. K. M'Gonigle, and S. P. Otto (2006) The distribution of beneficial mutant effects under strong selection. Genetics, 174:2071-2079.
Agrawal, A. F. and S. P. Otto (2006) Host-parasite coevolution and selection on sex through the effects of segregation. American Naturalist,168: 617-629.
Keightley, P. D. and S. P. Otto (2006) Selective interference among deleterious mutations favours sex and recombination in finite populations regardless of the nature of epistasis. Nature, 443: 89-92. [Preprint; Supplementary Material]
Gerstein, A. C., H.-J. E. Chun, A. Grant, and S. P. Otto (2006) Genomic convergence toward diploidy in Saccharomyces cerevisiae. PLoSGenetics, 2(9): e145.[Supplementary Material]
Currat, M., L. Excoffier, W. Maddison, S. P. Otto, N. Ray, M. C. Whitlock, S, Yeaman (2006) Comment on "Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens" and "Microcephalin, a Gene Regulating Brain Size, Continues to Evolve Adaptively in Humans." Science, 313: 172a.
Kouyos, R. D., S. P. Otto, and S. Bonhoeffer (2006) Effect of varying epistasis on the evolution of recombination. Genetics, 173: 589-597.
Otto, S. P. and A. C. Gerstein (2006) Why have sex? The population genetics of sex and recombination. Biochemical Society Transactions, 34:519-522.
Otto, S. P. (2006) Women editors: We need more female scientists. Nature (correspondence), 441: 812.
Sargent, R. D., M. A. Mandegar, and S. P. Otto (2006) A model of the evolution of dichogamy incorporating sex ratio selection, anther-stigma interference and inbreeding depression. Evolution, 60: 934-944.
Martin, G., S. P. Otto, and T. Lenormand (2006) Selection for recombination in structured populations. Genetics, 172: 593-609.
Sargent, R. D., and S. P. Otto (2006) The role of local species abundance in the evolution of pollinator attraction in flowering plants.American Naturalist, 167: 67-80.
Gilchrist, E. J., G. W. Haughn, C. C.Ying, S. P. Otto, J. Zhuang, D. Cheung, B. Hamberger, F. Aboutorabi, T. Kalynyak, L. Johnson, J. Bohlmann, B. E. Ellis, C. J. Douglas and Q. C. B. Cronk (2006) Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa. Molecular Ecology 15: 1367-1378.
Agrawal, A. F., L. Hadany, and S. P. Otto (2005) The evolution of plastic recombination. Genetics, 171: 803-812.
Albert, A. Y. K. and S. P. Otto (2005) Sexual selection can resolve sex-linked sexual antagonism. Science 310:119-121. [Available through Arianne Albert's web-site]
Nuismer, S. and S. P. Otto (2005) Host-parasite interactions and the evolution of gene expression. PLoS Biology, 3(7): e203. [Summary]
Barton, N. H. and S. P. Otto (2005) Evolution of recombination due to random drift. Genetics, 169:2353-2370.
Bull, J. J. and S. P. Otto (2005) The first steps in adaptive evolution. Nature Reviews Genetics 37:342-343.
Nuismer, S. and S. P. Otto (2004) Host-parasite interactions and the evolution of ploidy. PNAS, 101: 11036-11039 [Supplementary Material]
Sargent, R. D., and S. P. Otto (2004) A phylogenetic analysis of pollination mode and the evolution of dichogamy in angiosperms. EvolutionaryEcology Research, 6:1183-1199.
Otto, S. P. and S. L. Nuismer (2004) Species Interactions and the evolution of sex. Science, 304:1018-1020.
Otto, S. P. (2004) Two steps forward, one step back: The pleiotropic effects of favoured alleles. Proc. Roy. Soc., London B., 271: 705-714.
Vamosi, J. C., S. P. Otto, and S. C. H. Barrett (2003) Phylogenetic analysis of the ecological correlates of dioecy. Journal of EvolutionaryBiology, 16: 1006-1018.
Haywood-Farmer, E. and Otto, S. P. (2003) The evolution of genomic base composition in bacteria. Evolution, 57: 1783-1792.
Otto, S. P. (2003) In polyploids, one plus one does not equal two. TREE, 18: 431-433.
Peters, A. D. and S. P. Otto (2003) Liberating genetic variance through sex. BioEssays, 25: 533-537.
Dolgin, E. and Otto, S. P. (2003) Segregation and the evolution of sex under overdominant selection. Genetics, 164: 1119-1128.
Otto, S. P. (2003) The advantages of segregation and the evolution of sex. Genetics, 164: 1099-1118.
Otto, S. P. and M. Whitlock, M. (2003) Fixation probabilities and times. Encyclopedia of the Human Genome. Nature Publishing Group.
Otto, S. P. and P. Yong (2002) The evolution of gene duplicates. Advances in Genetics 46: 451-483 (Homology Effects, eds. J. Dunlap and C.-ting Wu, Academic Press, San Diego CA).
Otto, S. P. and T. Lenormand (2002) Resolving the paradox of sex and recombination. Nature Reviews Genetics, 3: 252-261.
Brinkman, F. S. L., J. L. Blanchard, A. Cherkasov, H. Greberg, Y. Av-Gay, R. C. Brunham, R. C. Fernandez, B. B. Finlay, S. P. Otto, B. F. F. Ouellette, P. J. Keeling, A. M. Rose, R. E. W. Hancock and S. J. M. Jones (2002). Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria and the chloroplast. Genome Research. 12:1159-1167.
Vamosi, J. C. and S. P. Otto (2002) When looks can kill: The evolution of sexually-dimorphic floral display and the extinction of dioecious plants.Proc. Roy. Soc., London B. 269: 1187-1194.
Mable, B. and S. P. Otto (2001) Masking and purging mutations following EMS treatment in haploid, diploid, and tetraploid yeast (Saccharomycescerevisiae). Genetical Research, 77: 9-26.
Otto, S. P. (2001) Genetics of Intelligence. In International Encyclopedia of the Social and Behavioral Sciences, eds. N. J. Smelser and P. B.Baltes, pp. 7651-7658. Elsevier Science Ltd. Pergamon, Oxford.
Day, T. and S. P. Otto (2001) Fitness. Encyclopaedia of Life Science. Nature Publishing Group, http://www.els.net.
Heilbuth, J. C., K. L. Ilves, and S. P. Otto (2001) The consequences of dioecy for seed dispersal: Modeling the "seed-shadow" handicap. Evolution, 55: 880-888.
Otto, S. P. and P. Jarne (2001) Haploids: Happening or hapless. Science (Perspective), 292: 2441-2443.
Otto, S. P. (2001) Eliminating the cost of sex with sexual selection. TREE (Journal Club entry), 16: 602.
Otto, S. P. and N. Barton (2001) Selection for recombination in small populations. Evolution, 55: 1921-1931.
Phillips, P. C., S. P. Otto, and M. C. Whitlock (2000) Beyond the average: The evolutionary importance of epistasis and the variability of epistatic effects. In Epistasis and the Evolutionary Process, eds. J Wolf, ED Brodie III, and M J Wade, pp. 20-38. Oxford University Press, Oxford. [Derivations in Mathematica.]
Feldman, M. W., S. P. Otto, and F. B. Christiansen (2000) Genes, culture, and inequality. In Meritocracy and Inequality, eds. K Arrow, S Bowles, and S Durlauf, pp. 61-85. Princeton University Press, New Jersey.
Lenormand, T. and S. P. Otto (2000) The evolution of recombination in a heterogeneous environment. Genetics. 156: 423-438.
Poon, A. and S. P. Otto (2000) Compensating for our load of mutations: Freezing the mutational meltdown. Evolution, 54: 1467-1479.
Otto, S. P. and C. D. Jones (2000) Detecting the undetected: Estimating the total number of loci underlying a trait in QTL analyses. Genetics,156: 2093-2107. [Derivations in Mathematica.]
Otto, S. P. (2000) Detecting the form of selection from DNA sequence data. Trends in Genetics, 16: 526-529.
Otto, S. P. and J. Whitton (2000) Polyploid incidence and evolution. Annual Review of Genetics, 34: 401-437. [Web Table; correction of typo in equation A2 (pdf, Mathematica notebook)]
Cummings, M., S. P. Otto, and J. Wakeley (1999) Genes and other samples of DNA sequence data for phylogenetic inference. Biological Bulletin, 196: 345-350.
Whitlock, M. and S. P. Otto (1999) The panda and the phage: compensatory mutations and the persistence of small populations. Trends inEcology and Evolution, 14: 295-296.
Otto, S. P. and D. Bourguet (1999) Balanced polymorphisms and the evolution of dominance. American Naturalist, 153: 561-574.
Hughes, J. S. and S. P. Otto (1999) Ecology and the evolution of biphasic life cycles. American Naturalist, 154: 306-320.
Otto, S. P. and Y. Michalakis (1998) The evolution of recombination in changing environments. Trends in Ecology and Evolution, 13: 145-151.
Christiansen, F. B., S. P. Otto, M. W. Feldman, and A. Bergman (1998) Waiting with and without recombination: The time to production of a doublemutant. Theoretical Population Biology, 53: 199-215.
Mable, B. and S. P. Otto (1998) The evolution of life cycles with haploid and diploid phases. BioEssays, 20: 453-462.
Otto, S. P. and I. Hastings (1998) Mutation and selection within the individual. Genetica, 102/103: 507-524.
Otto, S. P. and I. Hastings (1998) Mutation and selection within the individual. In Mutation and Evolution, eds. R C Woodruff and J N Thompson, pp. 507-524. Kluwer Academic Publishers, Netherlands. (Reprint of Otto and Hastings, 1998, Genetica, 102/103: 507-524.)
Feldman, M. W., S. P. Otto, and F. B. Christiansen (1997) Population genetic perspectives on the evolution of recombination. Annual Reviewof Genetics, 30: 261-295.
Otto, S. P. (1997) Unraveling gene interactions. Nature 390: 343 (News and Views).
Otto, S. P. and M. W. Feldman (1997) Deleterious mutations, variable epistatic interactions, and the evolution of recombination. TheoreticalPopulation Biology, 51: 134-147. [Derivations in Mathematica.]
Otto, S. P. and M. C. Whitlock (1997) The probability of fixation in populations of changing size. Genetics, 146: 723-733.
Feldman, M. W. and S. P. Otto (1997) Heritability from twins and other relatives. Science, 278: 1383-1384 (Correspondence).
Otto, S. P. and N. Barton (1997) The evolution of recombination: Removing the limits to natural selection. Genetics, 147: 879-906.
Otto, S. P. and J. Marks (1996) Mating systems and the evolutionary transition between haploidy and diploidy. Biological Journal of the Linnean Society, 57: 197-218.
Otto, S. P., Cummings, M., and J. Wakeley (1996) Inferring phylogenies from DNA sequence data: The effects of sampling. In New Uses for New Phylogenies, ed. P Harvey, pp. 103-115. Oxford University Press, Oxford.
Otto, S. P., F. B. Christiansen, and M. W. Feldman (1995) Genetic and cultural inheritance of continuous traits. Morrison Institute for Population and Resource Studies, Working Paper Series #0065.
Feldman, M. W., S. P. Otto, and F. B. Christiansen (1995) Statistics of discrete-valued traits under vertical transmission. Morrison Institute for Population and Resource Studies, Working Paper Series #0064.
Otto, S. P. and M. E. Orive (1995) Evolutionary consequences of mutation and selection within an individual. Genetics, 141: 1173-1187.
Bergman, A., S. P. Otto, and M. W. Feldman (1995) On the evolution of recombination in haploids and diploids. II. Stochastic models. Complexity, 1: 57-67.
Bergman, A., S. P. Otto, and M. W. Feldman (1995) On the evolution of recombination in haploids and diploids. I. Deterministic models. Complexity, 1: 49-56.
Cummings, M., S. P. Otto, and J. Wakeley (1995) The sampling properties of DNA sequence data in phylogenetic analysis. Molecular Biology and Evolution, 12: 814-822.
Orr, H. A. and S. P. Otto (1994) Does diploidy increase the rate of adaptation? Genetics, 136: 1475-1480.
Otto, S. P. (1994) The role of deleterious and beneficial mutations in the evolution of ploidy levels. Lectures on Mathematics in the Life Sciences,ed. M. Kirkpatrick, 25: 69-96.
Otto, S. P., M. W. Feldman, and F B Christiansen (1994) Some advantages and disadvantages of recombination. In Lecture Notes in Biomathematics,ed S A Levin, pp 198-211. Springer-Verlag, New York.
Otto, S. P., C. Sassaman, and M. W. Feldman (1993) Sex-ratio evolution in Eulimnadia texana. American Naturalist, 141: 329-337.
Otto, S. P. and D. B. Goldstein (1992) Recombination and the evolution of diploidy. Genetics, 131: 745-751.
Wiener, P., M. W. Feldman, and S. P. Otto (1992) On genetic segregation and the evolution of sex. Evolution, 46: 775-782.
Otto, S. P. (1991) On evolution under sexual and viability selection: A two-locus diploid model. Evolution, 45: 1443-1457.
Feldman, M. W., F. B. Christiansen, and S. P. Otto (1991) Lewontin and Kojima meet Fisher: Linkage in a symmetric model of sex determination.Genetics 129: 297-312.
Feldman, M. W. and S. P. Otto (1991) A comparative approach to the population-genetics theory of segregation distortion. American Naturalist137:00:00443-456.
Liberman, U., M. W. Feldman, I. Eshel, and S. P. Otto (1990) Two-locus autosomal sex determination: On the evolutionary genetic stability of the even sex ratio. Proceedings of the National Academy of Sciences (USA) 87: 2013-2017.
Otto, S. P. and V. Walbot (1990) DNA methylation in eukaryotes: Kinetics of demethylation and de novo methylation during the life cycle.Genetics 124: 429-437.
Feldman, M. W. and S. P. Otto (1989) More on recombination and selection in the modifier theory of sex-ratio distortion. Theoretical Population Biology 35: 207-225.