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Dr. Sarah P. Otto
(Nickname: Sally)

	Department of Zoology)
	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


Otto, 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.

Panel reports and edited volumes (Link to blogs and op-eds)

BC COVID-19 Modelling Group (2020-2021) Reports on COVID-19 in British Columbia.

Potvin, C. et al. (2017) Re-Energizing Canada: Pathways to a Low-Carbon Future. Sustainable Canada Dialogues, pp. 67.

Potvin, C. et al. (2015) Acting on Climate Change: Solutions from Canadian Scholars. Sustainable Canada Dialogues, pp. 58.

The Expert Panel on Biodiversity Science (2010) Canadian Taxonomy: Exploring Biodiversity, Creating Opportunity. Council of Canadian Academies.

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.

Research Publications

de Haas, F., L. Kläy, F. Débarre, and Otto, S. P. (2024) Modelling daisy quorum drive: a short-term bridge across engineered fitness valleys. PLoS Genetics, in press.
Otto, S. P., A. MacPherson, and C. Colijn (2024) Endemic does not mean constant as SARS-CoV-2 continues to evolve. Evolution, in press.
Ehrlichman, A., L. Sandell, S. P. Otto, and O. Ronce (2024) Planting long-lived trees in a warming climate: the importance of stage-dependent climatic tolerance. Evolutionary Applications, in press.
Zhong, K., A. Chan, B. Collicutt, M. Daspe, J. Finke, M. Foss, T. Green, C. Harley, A. Hesketh, K. Miller, S. P. Otto, K. Rolheiser, R. Saunders, B. Sutherland, and C. Suttle (2024) The prokaryotic and eukaryotic microbiome of Pacific oyster spat is shaped by ocean warming but not acidification. Applied and Environmental Microbiology, 90:e00052-24.
Urquhart-Cronish, M., A. L. Angert, S. P. Otto, A. MacPherson (2024) Density-dependent selection during range expansion affects expansion load in life-history traits. The American Naturalist, 203:382-392.
Urban, M. et al. (2024) When and how can we predict adaptive responses to climate change? Evolution Letters, 8:172-187.
Sandell, L., S. G. König, and S. P. Otto (2023). Schrödinger's yeast: the challenge of using transformation to compare fitness among Saccharomyces cerevisiae that differ in ploidy or zygosity. PeerJ, 11:e16547.
Kulmuni, J., B. Wiley, and S. P. Otto (2023) On the fast track: hybrids adapt more rapidly than parental populations in a novel environment. Evolution Letters, 8:128-136.
Zhan, S. H., A. Ignatieva, Y. Wong, K. Eaton, B. Jeffery, D. S. Palmer, C. L. Murall, S. P. Otto, and J. Kelleher (2023) Towards pandemic-scale ancestral recombination graphs of SARS-CoV-2. bioRxiv. https://doi.org/10.1101/2023.06.08.544212
Rolland, J. et al. (2023) Conceptual and empirical bridges between micro- and macroevolution. Nature Ecology and Evolution, 7:1181-1193.
Lamb, C. et al. (2023) Braiding Indigenous rights and endangered species law: Recovery targets fall short of culturally meaningful abundance. Science, 380:694-696.
Anderson, B. et al. (2023) Opposing effects of plant traits on diversification. iScience, 26:106362.
Helmstetter, A., et al. (2023) Trait-dependent diversification in angiosperms: Patterns, models and data. Ecology Letters, 26:640-657.
van Heusden, K., G. E. Stewart, S. P. Otto, and G. A. Dumont (2023) Effective pandemic policy design through feedback does not need accurate predictions. PLoS Global Public Health, 3(2): e0000955.
Yamaguchi, R., B. Wiley, and S. P. Otto (2022) The phoenix hypothesis of speciation. Proc. R. Soc. B, 289: 20221186.
Kreiner, J., S. M. Latorre, H. A. Burbano, J. R. Stinchcombe, S. P. Otto, D. Weigel, & S. Wright (2022) Rapid weed adaptation and range expansion in response to agriculture over the last two centuries. Science, 378: 1079-1085.
Tafreshi, A. G., S. P. Otto, M. Chapuisat (2022) Unbalanced selection: the challenge of maintaining social polymorphism in silver ants. Philosophical Transactions B., 377: 20210197.
Dekens, L., S. P. Otto, V. Calvez (2022) The best of both worlds: combining population genetic and quantitative genetic models. Theoretical Population Biology, 148: 49-75.
MacPherson, A., S. Wang, R. Yamaguchi, L. H. Rieseberg and S. P. Otto (2022) Parental population range expansion before secondary contact promotes heterosis. The American Naturalist, 200:E1-E15.
Colijn C., D. J. D. Earn, J. Dushoff, N. H. Ogden, M. Li, N. Knox, G. Van Domselaar, K. Franklin, G. Jolly, S. P. Otto (2022) The need for linked genomic surveillance of SARS-CoV-2. Can Commun Dis Rep, 48(4):131-9. https://doi.org/10.14745/ccdr.v48i04a03
Bessho, K., and S. P. Otto (2021) Fixation probability in a haploid-diploid population with asexual reproduction. Theoretical Population Biology, 143, 30-45.
Tuper, P., S. P. Otto, and C. Colijn (2021) Fundamental Limitations of Contact Tracing for COVID-19. FACETS, 6:1993-2001.
Otto, S. P., T. Day, J. Arino, C. Colijn, J. Dushoff, M. Li, S. Mechai, G. Van Domselaar, J. Wu, D. J. D. Earn, and N. H. Ogden (2021). The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic. Current Biology, 31: R918-R929.
Grainger, T. N., A. Senthilnathan, P.-J. Ke, M. A. Barbour, N. T. Jones, J. P. DeLong, S. P. Otto, M. I. O'Connor, K. E. Coblentz, N. Goel, J. Sakarchi, M. C. Szojka, J. M. Levine, and R. M. Germain (2021) An empiricist's guide to using ecological theory. The American Naturalist, 199:1-20.
Silva, W. T. A. F., S. P. Otto, and S. Immler (2021) Evolution of plasticity in production and transgenerational inheritance of small RNAs under dynamic environmental conditions. PLoS Genetics, 17(5): e1009581.
Germain, R. M., S. P. Hart, M. M. Turcotte, S. P. Otto, J. Sakarchi, J, Rolland, R. Usui, A. L Angert, D. Schluter, R. Bassar, M. T. Waters, F. Henao-Diaz, A. M. Siepielski (2021) On the origin of coexisting species. Trends in Ecology and Evolution, 36:284-293.
MacPherson, A., M. J. Keeling, and S. P. Otto (2021) Feedback between coevolution and epidemiology can help or hinder the maintenance of genetic variation in host-parasite models. Evolution, 75:582-599.
MacPherson, A., M. J. Keeling, and S. P. Otto (2021) Coevolution fails to maintain genetic variation in a host-parasite model with constant finite population size. Theoretical Population Biology, 137:10-21.
Otto, S. P. (2021) Selective interference and the evolution of sex. J. of Heredity, 112:9-18.
Yamaguchi, R., and S. P. Otto (2020) Insights from Fisher's geometric model on the likelihood of speciation under different histories of environmental change. Evolution, 74-8: 1603-1619.
Day T, Gandon S, Lion S, Otto SP (2020) On the evolutionary epidemiology of SARS-CoV-2. Current Biology, 30:R841-R870
Sutherland, B. G. J., C. Rycroft, A.-L. Ferchaud, R. Saunders, L. Li, S. Liu, A. M. Chan, S. P. Otto, C. A. Suttle, and K. M. Miller (2020) Relative genomic impacts of translocation history, hatchery practices, and farm selection in Pacific oyster Crassostrea gigas throughout the Northern Hemisphere. Evolutionary Applications, 13:1380-1399.
Osmond, M. M., S. P. Otto and G. Martin (2020) Genetic paths to evolutionary rescue and the distribution of fitness effects along them. Genetics, 214: 493-510. [Highlighted in Genetics]
Kattge, J. et al. (S. P. Otto one of 720 authors) (2020) TRY plant trait database - enhanced coverage and open access. Global Change Biology, 26: 119-188.
Otto, S. P., and A. Rosales (2020) Theory in service of narratives in evolution and ecology. American Naturalist, 195: 290-299.
Zareyan, S., S. P. Otto, and C. Hauert (2019) A sheep in wolf's clothing: levels of deceit and detection in the evolution of cue-mimicry. Proc. R. Soc. B, 20191425.
Otto, S. P. (2019) Evolutionary potential for genomic islands of sexual divergence on recombining sex chromosomes. New Phytologist, 224: 1241-1251.
Otto, S. P., and B. Payseur (2019) Crossover interference: shedding light on the evolution of recombination. Annual Review of Genetics, 53:19-44.
Hanlon, V. C., S. P. Otto, and S. N. Aitken (2019) Somatic mutations substantially increase the per-generation mutation rate in the conifer Picea sitchensis. Evolution Letters, 3-4: 348-358.
Urquhart-Cronish, M. and S. P. Otto (2019) Gender and language use in scientific grant writing. FACETS, 4:442-458. [Covered in University Affairs]
Bradshaw, C. J. A., S. P. Otto, Z. Mehrabi, A. A. Annamalay, S. Heft-Neal, Z. Wagner, P. N. Le Souef (2019) Testing the socio-economic and environmental determinants of better child-health outcomes in Africa: a cross-sectional study among nations. BMJ Open, 9(9), e029968.
Bazzicalupo, A. L., F. Carpentier, S. P. Otto, and T. Giraud (2019) Little evidence of antagonistic selection in the evolutionary strata of fungal mating-type chromosomes (Microbotryum lychnidis-dioicae). G3, 9:1987-1998.
Coristine, L. E., S. Colla, N. Bennett, A. Carrlsson, C. Davy, K. T. Davies, B. Favaro, D. T. Flockhart, K. Fraser, D. Orihel, S. P. Otto, W. J. Palen, J. L. Polfus, O. Venter, and A. T. Ford (2019) National contributions to global ecosystem values. Conservation Biology, 33:1219-1223.
Westwood, A. R., S. P. Otto, A. Mooers, C. Darimont, K. E. Hodges, C. Johnson, B. M. Starzomski, C. Burton, K. M. A. Chan, M. Festa-Bianchet, S. Fluker, S. Gulati, A. L. Jacob, D. Kraus, T. G. Martin, W. J. Palen, J. D. Reynolds, and J. Whitton (2019) Protecting biodiversity in British Columbia: recommendations for developing species at risk legislation. FACETS, 4: 136-160. [See also Report submitted to the Government of British Columbia for consideration as it develops species at risk legislation for the province]
Altenberg, L., et al. (2019) Some topics in theoretical population genetics: editorial commentaries on a selection of Marc Feldman's TPB papers. Theoretical Population Biology, 129:4-8.
Otto, S. P. (2018) Adaptation, speciation and extinction in the Anthropocene. Proc. R. Soc. B 285: 20182047.
Immler, S., and S. P. Otto (2018) The evolutionary consequences of selection at the haploid gametic stage. American Naturalist, 192: 241-249.
Scott, M. F., M. M. Osmond, and S. P. Otto (2018) Haploid selection, sex ratio bias, and transitions between sex-determining systems. PLoS Biol 16(6): e2005609.
Sharp, N. P., L. Sandell, C. G. James, and S. P. Otto (2018) The genome-wide rate and spectrum of spontaneous mutations differs between haploid and diploid yeast. PNAS 115(22) E5046-E5055.
MacPherson, A., and S. P. Otto (2018) Joint coevolutionary-epidemiological models dampen Red Queen cycles and alter conditions for epidemics. Theoretical Population Biology, 122:137-148.
Coristine, L., et al. (2018) Informing Canada's commitment to biodiversity conservation: A science-based framework to help guide protected areas designation through Target 1 and beyond. FACETS, 3: 531-562.
Vamosi, J.C., S. Magallón, I. Mayrose, S. P. Otto, and H. Sauquet (2018) Macroevolutionary patterns of flowering plant speciation and extinction. Annual Review of Plant Biology, 69:685-706.
MacPherson, A., S. P. Otto, and S. Nuismer (2018) Keeping pace with the Red Queen: identifying the genetic basis of susceptibility to infectious disease. Genetics, 208:779-789.
Sharp, N. P., and S. P. Otto (2018) Zeroing in on the rate of genome doubling. Current Biology [non-peer reviewed Dispatch], 28: R306-R327.
Scott, M., and S. P. Otto (2017) Haploid selection favors suppressed recombination between sex chromosomes despite causing biased sex ratios. Genetics, 207: 1631-1649.
Van Den Elzen, C. L., E. J. Kleynhans, and S. P. Otto (2017) Asymmetric competition impacts evolutionary rescue in a changing environment. Proceedings of the Royal Society, London B., 284: 20170374. http://dx.doi.org/10.1098/rspb.2017.0374
Osmond, M. M., S. P. Otto, and C. A. Klausmeier (2017) When predators help prey adapt and persist in a changing environment. American Naturalist, 190:83-98.
Mee, J. A., S. P. Otto, and D. Pauly (2017) Evolution of movement rate increases the effectiveness of marine reserves for the conservation of pelagic fishes. Evolutionary Applications, 10:444-461.
Goldberg, E. E., S. P. Otto, J. C. Vamosi, I. Mayrose, N. Sabath, R. Ming, and T.-L. Ashman (2017) Macroevolutionary synthesis of flowering plant sexual systems. Evolution, 71: 898-912.
Bessho, K., and S. P. Otto (2017) Fixation probability in a haploid-diploid population. Genetics, 205:421-440.
Ono, J., A. C. Gerstein, and S. P. Otto (2017) Widespread genetic incompatibilities between first-step mutations during parallel adaptation of Saccharomyces cerevisiae to a common environment. PLoS Biology, 15(1): e1002591. doi:10.1371/journal.pbio.1002591.
Potvin, C., et al. (2017) Stimulating a Canadian narrative for climate. FACETS, 2:131-149.
Sandell, L., and S. P. Otto (2016) Probing the depths of biological diversity during the second Century of GENETICS. Genetics, 204:395-400.
Kleynhans, E. J., Otto, S. P., Reich, P. B., and M. Vellend (2016) Adaptation to elevated CO2 in different biodiversity contexts. Nature Communications, 7:12358.
Ostevik, K. L., Andrew, R. L., Otto, S. P., and L. H. Rieseberg (2016) Multiple reproductive barriers separate recently diverged sunflower ecotypes. Evolution, 70: 2322-2335.
Zhan, S. H., Drori, M., Goldberg, E., Otto, S. P., and I. Mayrose. (2016) Phylogenetic evidence for cladogenetic polyploidization in land plants. American Journal of Botany, 103:1252-1258.
Sharp, N. P., and S. P. Otto (2016) Evolution of sex: Using experimental genomics to select among competing theories. Bioessays, 38: 751-757.
Kindsvater, H., Braun, D., Otto, S., and J. Reynolds (2016) Costs of reproduction explain the correlated evolution of semelparity and egg size: theory and a test with salmon. Ecology Letters, 19: 687-696.
Débarre, F., and S. P. Otto (2016) Evolutionary dynamics of a quantitative trait in a finite asexual population. Theoretical Population Biology, 108:75-88.
Rothfels, C. J., and S. P. Otto (2016) Polyploid speciation. In: Encyclopedia of Evolutionary Biology, 73. R. Kliman, head editor, D. Ortiz-Barrientos, section editor, Elsevier.
Sabath, N., E. Goldberg, L. Glick, M. Einhorn, T.-L. Ashman, R. Ming, S. Otto, J. Vamosi, I. Mayrose (2016) Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms. New Phytologist, 209: 1290-1300.
Bailey, M., B. Favaro, S. P. Otto, A. Charles, R. Devillers, A. Metaxas, P. Tyedmers, N. C. Ban, T. Mason, C. Hoover, T. J. Duck, L. Fanning, C. Milley, A. M. Cisneros-Montemayor, D. Pauly, W.W. L. Cheung, S. Cullis-Suzuki, L. Teh, and U. R. Sumaila (2016) Canada at a crossroad: The imperative of realigning ocean policy with ocean science. Marine Policy, 63: 53-60. [Highlighted in the Huffington Post.]
Wellenreuther, M. and S. P. Otto (2016) Women in evolution - Highlighting the changing face of evolutionary biology. Evolutionary Applications, 9:3-16.
Otto, S. P., M. F. Scott, and S. Immler (2015) Evolution of haploid selection in predominantly diploid organisms. PNAS 112: 15952-15957
Osmond, M. M. and S. P. Otto (2015) Fitness-valley crossing with generalized parent-offspring transmission. Theoretical Population Biology, 105:1-16.
Veen, T. and S. P. Otto (2015) Liking the good guys: Amplifying local adaptation via the evolution of condition-dependent mate choice. Journal of Evolutionary Biology, 28:1804-15.
Pennell, M. W., M. Kirkpatrick, S. P. Otto, J. C. Vamosi, C. L. Peichel, N. Valenzuela, and J. Kitano (2015) Y fuse? Sex chromosome fusions in fishes and reptiles. PLoS Genetics, 11(5): e1005237.
Gerstein, A. C., J. Ono, D. S. Lo, M. L. Campbell, A. Kuzmin, and S. P. Otto (2015) Too much of a good thing: The unique and repeated paths toward copper adaptation. Genetics, 199: 555-571.
Immler, S., and S. P. Otto (2015) The evolution of sex chromosomes in haploid dioecious organisms. Evolution, 69:694-708. [Highlighted in The Molecular Ecologist blog.]
Otto, S. P. (2015) Biodiversity protects. Species loss endangers all of us. Alternatives Journal, 41: 21-25.
Mayrose, I., S. H. Zhan, C. J. Rothfels, N. Arrigo, M. S. Barker, L. H. Rieseberg, and S. P. Otto (2015) Methods for studying polyploid diversification and the dead end hypothesis: a reply to Soltis et al. (2014). New Phytologist, 206: 27-35.
Scott, M. F., and S. P. Otto (2014) Why wait? Three mechanisms selecting for environment-dependent developmental delays. J. Evolutionary Biology, 27:2219-2232.
Kindsvater, H., and S. P. Otto (2014) The evolution of offspring size across life-history stages. American Naturalist, 184: 543-555.
Hardy, N., and S. P. Otto (2014) Specialization and generalization in the diversification of phytophagous insects: tests of the musical chairs and oscillation hypotheses. Proceedings of the Royal Society, London B., 281: 20132960.
The Tree of Sex Consortium, D. Bachtrog, J. E. Mank, C. L. Peichel, Kirkpatrick, M., S. P. Otto, T.-L. Ashman, M. W. Hahn, J. Kitano, I. Mayrose, R. Ming, N. Perrin, L. Ross, N. Valenzuela, and J. C. Vamosi (2014) Sex determination: why so many ways of doing it? PLoS Biology, 12(7): e1001899. doi:10.1371/journal.pbio.1001899.
The Tree of Sex Consortium, T.-L. Ashman, D. Bachtrog, H. Blackmon, E. E. Goldberg, M. W. Hahn, Kirkpatrick, M., J. Kitano, J. E. Mank, I. Mayrose, R. Ming, S. P. Otto, C. L. Peichel, M. W. Pennell, N. Perrin, L. Ross, N. Valenzuela, and J. C. Vamosi (2014) Tree of Sex: A database of sexual systems. Scientific Data, 1:140015 doi: 10.1038/sdata.2014.15.
Gerstein, A. C., Kuzmin, A., and S. P. Otto (2014) Loss of heterozygosity facilitates passage through Haldane's sieve. Nature Communications, 5: 3819.
Otto, S. P. (2014) Selective maintenance of recombination between the sex chromosomes. J. Evolutionary Biology, 27: 1431-1442.
Zhan, S. H., L. Glick, C. S. Tsigenopoulos, S. P. Otto, and I. Mayrose (2014) Comparative analysis reveals that polyploidy does not decelerate diversification in fish. J. Evolutionary Biology, 27: 391-403.
Immler, S., and S. P. Otto (2014) Driven apart: the evolution of ploidy differences between the sexes under antagonistic selection. American Naturalist, 183: 96-107.
Uecker, H., S. P. Otto, and J. Hermisson (2014) Evolutionary rescue in structured populations. American Naturalist, 183: E17-E35.
Feldman, M. W., S. P. Otto, and F. B. Christiansen (2013) Gene-culture co-evolution: teaching, learning, and correlations between relatives. Israel J. Ecol. Evol., 59: 72-91 doi: 10.1080/15659801.2013.853435.
Bolnick, D., and S. P. Otto (2013) The magnitude of local adaptation under genotype-dependent dispersal. Ecology and Evolution, 3: 4722- 47.
Otto, S. P. (2013) Evolution of biological systems. In: Losos, J., D. A. Baum, D. Futuyma, H. Hoekstra, R. Lenski, A. Moore, D. Schluter, and M. Whitlock, eds. The Princeton Guide to Evolution. Princeton University Press, pp. 253-260.
Otto, S. P. and M. C. Whitlock (2013) Fixation probabilities and times. Encyclopedia of the Life Sciences. John Wiley & Sons [DOI: 10.1002/9780470015902.a0021130.pub3] (Reprint of Otto and Whitlock, 2002, Encyclopedia of the Human Genome, Nature Publishing Group.)
Hough, J., S. Immler, S. C. H. Barrett, and S. P. Otto (2013) Evolutionary stable sex ratios and mutation load. Evolution, 67: 1915-1925.
Guillaume, F., and S. P. Otto (2012) Gene functional trade-offs and the evolution of pleiotropy. Genetics, 192:1389-1409.
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. [Highlighted in Saccharomyces Genome Database blog.]
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 (2011) 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 (2012) 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.
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: 571-581.
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.

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 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. [Derivations in Mathematica 8.0.]

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.

Op-Eds and Other Media

Wiley, B., McDonald, D. J, and S. P. Otto (2021) An Online Tool to estimate the Vaccination Status of a Group. Blog of the BC COVID-19 Modelling Group

Gonzalez, A., O'Connor, M., and S. P. S. Otto (2021) Harmonizing, co-ordinating scientific initiatives key to filling gaps in knowledge of Canada/s biodiversity. Opinion, Globe and Mail, March 31.

Fitzpatrick, C. L. Alter, S. E., Boughman, J. W., Débarre, F., Edmands, S., Moehring, A., Moyle, L. Otto, S. P., Ronce, O., Rubin, M. J., Sweigart, A. L (2021) The virus evolves: four public health priorities for reducing the evolutionary potential of SARS-CoV-2, BioScience, 71: 319

Otto, S. P., B. Phillips, C. Colijn (2021) Are there COVID variants amongst us? Blog of the BC COVID-19 Modelling Group

Otto, S. P. (2021) Why new COVID-19 variants are on the rise and spreading around the world. The Conversation. (Voici pourquoi les nouveaux variants de la Covid-19 se répandent dans le monde entier)

Tupper, P., Otto, S. P., C. Colijn (2020) Fundamental Limitations of Contact Tracing for COVID-19. Blog of the BC COVID-19 Modelling Group

Otto, S. P. (2020) The tipping point of contact tracing. Blog of the BC COVID-19 Modelling Group

Otto, S. P. (2020) The Impact of Citizen Science. BC's Big Nature Challenge blog of the BC Parks Foundation.

Otto, S. P. (2020) Nature heals us; we need to reciprocate. Blog of the National Environmental Treasure

Otto, S. P., B. Starzomski, J. Whitton, C. Burton, M. Festa-Bianchet (2018) To save endangered species, the federal government needs the provinces' help. Opinion, National Observer, October 24.

Otto, S. P., and B. Starzomski (2018) It's time for B.C. to start legally protecting endangered species. Opinion, The Narwhal, May 23.

Hutchings, J. A., J. Whitton, S. P. Otto, S. Findlay, J. Kerr, and A. Mooers (2017) Recovering the Species at Risk Act. Policy Options, February 14.

Aitken, S., Otto, S. P. and G. Hoberg Climate solutions are within reach. Progress made: But B.C. can't reach its 2020 emissions target unless new policies are introduced." Op-Ed: Vancouver Sun, March 25, 2015.

Otto, S. P. Let scientists share their research knowledge. Commentary, Toronto Star, October 12, 2014.

Jacob, A. L. and 8 others (including Otto, S. P.) Canada needs stronger stand on climate change. Comment, Times Colonist, September 19, 2014.

Potvin, C. and 52 others (including S. P. Otto) The time to face up to climate change is now. Letter to the Editor, The Gazette, September 16, 2014.

Coop, G. and 138 others (including Otto, S. P.) A troublesome inheritance. The New York Times Book Review, August 8, 2014.

Losos, J., S. P. Otto, and M. Pennell. Joseph Felsenstein. (A letter honoring Dr. Felsenstein upon his receiving an honorary lifetime member of the American Society of Naturalists). The American Naturalist 183:iii-iv.

Otto, S. P., S. McKee, and J. Whitton (2013) Saving species at risk starts at the top. Where is our Environment Minister? Letter to the Editor, Globe and Mail, August 14, 2013.

Otto, S. P. and K. Chan (2010) We're losing the battle for diversity of life: B.C. has no law protecting species at risk of extinction, and the laws we do have aren't working. Special to the Vancouver Sun, November 3, 2010, A15.

Otto, S. P. (2006) Women editors: We need more female scientists. Nature (correspondence), 441: 812.

Otto, S. P. and M. C. Whitlock (2003) Problem Solved. Dual-Career Couples: Feature Index. Science Careers.