Marcy K. Uyenoyama | Scholars@Duke

Marcy K. Uyenoyama
Professor of Biology

Marcy Uyenoyama studies mechanisms of evolutionary change at the molecular and population levels. Among the questions under study include the prediction and detection of the effects of natural selection on genomic structure. A major area of research addresses the development of maximum-likelihood and Bayesian methods for inferring evolutionary processes from the pattern of molecular variation. Evolutionary processes currently under study include characterization of population structure across genomes.

Current Appointments & Affiliations

Professor of Biology, Biology, Trinity College of Arts & Sciences 2000

Contact Information

130 Science Drive, Room 137, Duke Box 90338, Durham, NC 27708
Duke Box 90338, Durham, NC 27708
marcy@duke.edu (919) 660-7350
http://www.biology.duke.edu/marcylab/

Background
Education, Training, & Certifications
- Ph.D., Stanford University 1978
- B.S., Stanford University 1974
Duke Appointment History
- Professor with Tenure, Biology, Trinity College of Arts & Sciences 1992 - 2000
- Associate Professor with Tenure, Biology, Trinity College of Arts & Sciences 1986 - 1992
- Assistant Professor, Biology, Trinity College of Arts & Sciences 1983 - 1986
Research
Selected Grants
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- Mathematical Population Genetics awarded by National Institutes of Health 1986 - 2014
- Mathematical Population Genetics awarded by National Institutes of Health 1996 - 2005
- Experimental and Theoretical Studies of the Coevolution of Inbreeding Depression awarded by National Science Foundation 1997 - 2001
- Molecular Evolution at Locus of Self-incompatibility in Structured Populations of Solanaceae awarded by National Science Foundation 1998 - 2000
- US/Germany/Japan Trinational Workshop on Molecular Evolution awarded by National Science Foundation 1997 - 1998
- Mathematical Population Genetics awarded by National Institutes of Health 1986 - 1996
- Mathematical Population Genetics awarded by National Institutes of Health 1986 - 1996
- Mathematical Population Genetics awarded by National Institutes of Health 1986 - 1992
- Mathematical Population Genetics awarded by National Institutes of Health 1986 - 1992
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Uyenoyama, Marcy K., Naoki Takebayashi, and Seiji Kumagai. “Allele frequency spectra in structured populations: Novel-allele probabilities under the labelled coalescent.” Theoretical Population Biology 133 (June 2020): 130–40. https://doi.org/10.1016/j.tpb.2020.01.002.
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  - Ramachandran, Sohini, Sarah P. Otto, Marcy Uyenoyama, and Jeremy Van Cleve. “"Any news?" Special issue in honor of Marcus Feldman's 75th birthday.” Theoretical Population Biology 129 (October 2019): 1–3. https://doi.org/10.1016/j.tpb.2019.09.001.
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  - Uyenoyama, Marcy K., Naoki Takebayashi, and Seiji Kumagai. “Inductive determination of allele frequency spectrum probabilities in structured populations.” Theoretical Population Biology 129 (October 2019): 148–59. https://doi.org/10.1016/j.tpb.2018.10.004.
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  - Uyenoyama, Marcy K., and Naoki Takebayashi. “Evolution of the sex ratio and effective number under gynodioecy and androdioecy.” Theoretical Population Biology 118 (December 2017): 27–45. https://doi.org/10.1016/j.tpb.2017.08.003.
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  - Uyenoyama, Marcy, and Naoki Takebayashi. “Evolution of the sex ratio and effective number under gynodioecy and androdioecy,” March 4, 2017. https://doi.org/10.1101/113605.
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  - Redelings, Benjamin D., Seiji Kumagai, Andrey Tatarenkov, Liuyang Wang, Ann K. Sakai, Stephen G. Weller, Theresa M. Culley, John C. Avise, and Marcy K. Uyenoyama. “A Bayesian Approach to Inferring Rates of Selfing and Locus-Specific Mutation.” Genetics 201, no. 3 (November 2015): 1171–88. https://doi.org/10.1534/genetics.115.179093.
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  - Kumagai, Seiji, and Marcy K. Uyenoyama. “Genealogical histories in structured populations.” Theoretical Population Biology 102 (June 2015): 3–15. https://doi.org/10.1016/j.tpb.2015.01.003.
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  - Uyenoyama, Marcy K. “Editor's Report for Volume 28 (2011).” Molecular Biology and Evolution 30, no. 1 (January 2013): 236–37. https://doi.org/10.1093/molbev/mss252.
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  - Uyenoyama, M. K. “Editor's report for volume 27 (2010).” Molecular Biology and Evolution 29, no. 5 (May 1, 2012): 1493–94. https://doi.org/10.1093/molbev/mss099.
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  - Kumagai, Seiji, and Marcy K. Uyenoyama. “A method for computing the exact distribution of speciation times and internode lengths in genealogical histories.” Theoretical Population Biology, 2012.
  - Wolfe, Ken, Marta L. Wayne, Kateryna Makova, Tomoko Y. Steen, Marcy Uyenoyama, and Naoyuki Takahata. “SMBE proposal to the government of Japan.” Molecular Biology and Evolution 29, no. 1 (January 2012): 441. https://doi.org/10.1093/molbev/msr209.
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  - Fusco, Diana, and Marcy K. Uyenoyama. “Sex-specific incompatibility generates locus-specific rates of introgression between species.” Genetics 189, no. 1 (September 2011): 267–88. https://doi.org/10.1534/genetics.111.130732.
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  - Fusco, Diana, and Marcy K. Uyenoyama. “Effects of polymorphism for locally adapted genes on rates of neutral introgression in structured populations.” Theoretical Population Biology 80, no. 2 (September 2011): 121–31. https://doi.org/10.1016/j.tpb.2011.06.003.
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  - Uyenoyama, M. K. “Molecular Biology and Evolution: Editor's report.” Molecular Biology and Evolution 27, no. 12 (December 1, 2010): 2890–91. https://doi.org/10.1093/molbev/msq285.
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  - Uyenoyama, M. K. “Editorial: MBE Editor's Report.” Molecular Biology and Evolution 27, no. 3 (March 1, 2010): 742–43. https://doi.org/10.1093/molbev/msp229.
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  - Dutheil, Julien Y., Ganesh Ganapathy, Asger Hobolth, Thomas Mailund, Marcy K. Uyenoyama, and Mikkel H. Schierup. “Ancestral population genomics: the coalescent hidden Markov model approach.” Genetics 183, no. 1 (September 2009): 259–74. https://doi.org/10.1534/genetics.109.103010.
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  - Ganapathy, Ganeshkumar, and Marcy K. Uyenoyama. “Site frequency spectra from genomic SNP surveys.” Theoretical Population Biology 75, no. 4 (June 2009): 346–54. https://doi.org/10.1016/j.tpb.2009.04.003.
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  - Hobolth, Asger, Marcy K. Uyenoyama, and Carsten Wiuf. “Importance sampling for the infinite sites model.” Statistical Applications in Genetics and Molecular Biology 7, no. 1 (January 2008): Article32. https://doi.org/10.2202/1544-6115.1400.
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  - Leman, Scotland C., Marcy K. Uyenoyama, Michael Lavine, and Yuguo Chen. “The evolutionary forest algorithm.” Bioinformatics (Oxford, England) 23, no. 15 (August 2007): 1962–68. https://doi.org/10.1093/bioinformatics/btm264.
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  - Leman, Scotland C., Yuguo Chen, Jason E. Stajich, Mohamed A. F. Noor, and Marcy K. Uyenoyama. “Likelihoods from summary statistics: recent divergence between species.” Genetics 171, no. 3 (November 2005): 1419–36. https://doi.org/10.1534/genetics.104.040402.
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  - Newbigin, Ed, and Marcy K. Uyenoyama. “The evolutionary dynamics of self-incompatibility systems.” Trends in Genetics : Tig 21, no. 9 (September 2005): 500–505. https://doi.org/10.1016/j.tig.2005.07.003.
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  - Uyenoyama, Marcy K. “Evolution under tight linkage to mating type.” The New Phytologist 165, no. 1 (January 2005): 63–70. https://doi.org/10.1111/j.1469-8137.2004.01246.x.
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  - Vallejo-Marín, Mario, and Marcy K. Uyenoyama. “On the evolutionary costs of self-incompatibility: incomplete reproductive compensation due to pollen limitation.” Evolution; International Journal of Organic Evolution 58, no. 9 (September 2004): 1924–35. https://doi.org/10.1111/j.0014-3820.2004.tb00480.x.
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  - Takebayashi, Naoki, Ed Newbigin, and Marcy K. Uyenoyama. “Maximum-likelihood estimation of rates of recombination within mating-type regions.” Genetics 167, no. 4 (August 2004): 2097–2109. https://doi.org/10.1534/genetics.103.021535.
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  - Uyenoyama, Marcy K., and Naoki Takebayashi. “A simple method for computing exact probabilities of mutation numbers.” Theoretical Population Biology 65, no. 3 (May 2004): 271–84. https://doi.org/10.1016/j.tpb.2003.12.001.
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  - Takebayashi, Naoki, Philip B. Brewer, Ed Newbigin, and Marcy K. Uyenoyama. “Patterns of variation within self-incompatibility loci.” Molecular Biology and Evolution 20, no. 11 (November 2003): 1778–94. https://doi.org/10.1093/molbev/msg209.
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  - Uyenoyama, Marcy K. “Genealogy-dependent variation in viability among self-incompatibility genotypes.” Theoretical Population Biology 63, no. 4 (June 2003): 281–93. https://doi.org/10.1016/s0040-5809(03)00020-0.
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  - Uyenoyama, M. K., Y. Zhang, and E. Newbigin. “On the origin of self-incompatibility haplotypes: transition through self-compatible intermediates.” Genetics 157, no. 4 (April 2001): 1805–17.
  - Uyenoyama, M. K. “Mutational origin of new mating type specificities in flowering plants.” Genes & Genetic Systems 75, no. 6 (December 2000): 305–11. https://doi.org/10.1266/ggs.75.305.
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  - Uyenoyama, M. K. “Evolutionary dynamics of self-incompatibility alleles in Brassica.” Genetics 156, no. 1 (September 2000): 351–59.
  - Uyenoyama, M. K., and E. Newbigin. “Evolutionary dynamics of dual-specificity self-incompatibility alleles.” The Plant Cell 12, no. 3 (March 2000): 310–12. https://doi.org/10.1105/tpc.12.3.310.
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  - Uyenoyama, M. K. “A prospectus for new developments in the evolutionary theory of self-incompatibility.” Annals of Botany 85, no. SUPPL. A (January 1, 2000): 247–52. https://doi.org/10.1006/anbo.1999.1040.
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  - Uyenoyama, M. K. “Evolutionary dynamics of self-incompatibility systems in flowering plants.” J. Reprod. Dev. 46 (2000): 35–36.
  - Uyenoyama, M. K. “Genealogical structure among alleles regulating self-incompatibility in natural populations of flowering plants.” Genetics 147, no. 3 (November 1997): 1389–1400.
  - Richman, A. D., M. K. Uyenoyama, and J. R. Kohn. “Allelic diversity and gene genealogy at the self-incompatibility locus in the Solanaceae.” Science (New York, N.Y.) 273, no. 5279 (August 1996): 1212–16. https://doi.org/10.1126/science.273.5279.1212.
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  - Richman, A. D., M. K. Uyenoyama, and J. R. Kohn. “S-allele diversity in a natural population of Physalis crassifolia (Solanaceae) (ground cherry) assessed by RT-PCR.” Heredity 76 (May 1, 1996).
  - Richman, A. D., M. K. Uyenoyama, and J. R. Kohn. “S-allele diversity in a natural population of Physalis crassifolia (Solanaceae) (ground cherry) assessed by RT-PCR.” Heredity 76 ( Pt 5) (May 1996): 497–505. https://doi.org/10.1038/hdy.1996.72.
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  - Richman, A. D., T. H. Kao, S. W. Schaeffer, and M. K. Uyenoyama. “S-allele sequence diversity in natural populations of Solanum carolinense (Horsenettle).” Heredity 75 ( Pt 4) (October 1995): 405–15. https://doi.org/10.1038/hdy.1995.153.
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  - Uyenoyama, M. K. “A generalized least-squares estimate for the origin of sporophytic self-incompatibility.” Genetics 139, no. 2 (February 1995): 975–92.
  - Thrall, P. H., A. Biere, and M. K. Uyenoyama. “Frequency-dependent disease transmission and the dynamics of the Silene-ustilago host-pathogen system.” American Naturalist 145, no. 1 (January 1, 1995): 43–62. https://doi.org/10.1086/285727.
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  - Uyenoyama, M. K., and D. M. Waller. “Coevolution of self-fertilization and inbreeding depression. III. Homozygous lethal mutations at multiple loci.” Theoretical Population Biology 40, no. 2 (October 1991): 173–210. https://doi.org/10.1016/0040-5809(91)90052-h.
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  - Uyenoyama, M. K., and D. M. Waller. “Coevolution of self-fertilization and inbreeding depression. I. Mutation-selection balance at one and two loci.” Theoretical Population Biology 40, no. 1 (August 1991): 14–46. https://doi.org/10.1016/0040-5809(91)90045-h.
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  - Uyenoyama, M. K., and D. M. Waller. “Coevolution of self-fertilization and inbreeding depression. II. Symmetric overdominance in viability.” Theoretical Population Biology 40, no. 1 (August 1991): 47–77. https://doi.org/10.1016/0040-5809(91)90046-i.
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  - Uyenoyama, M. K. “On the evolution of genetic incompatibility systems. VI. A three-locus modifier model for the origin of gametophytic self-incompatibility.” Genetics 128, no. 2 (June 1991): 453–69.
  - Bengtsson, B. O., and M. K. Uyenoyama. “Evolution of the segregation ratio: modification of gene conversion and meiotic drive.” Theoretical Population Biology 38, no. 2 (October 1990): 192–218. https://doi.org/10.1016/0040-5809(90)90010-s.
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  - Uyenoyama, M. K. “On the evolution of genetic incompatibility systems. V. Origin of sporophytic self-incompatibility in response to overdominance in viability.” Theoretical Population Biology 36, no. 3 (December 1989): 339–65. https://doi.org/10.1016/0040-5809(89)90038-5.
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  - Uyenoyama, M. K., and B. O. Bengtsson. “On the origin of meiotic reproduction: a genetic modifier model.” Genetics 123, no. 4 (December 1989): 873–85.
  - Uyenoyama, M. K. “Coevolution of the major histocompatibility complex and the t-complex in the mouse. II. Modification of response to sharing of histocompatibility antigens.” Genetics 121, no. 1 (January 1989): 153–61.
  - Uyenoyama, M. K. “Coevolution of the major histocompatibility complex and the t-complex in the mouse. I. Generation and maintenance of high complementarity associations.” Genetics 121, no. 1 (January 1989): 139–51.
  - Uyenoyama, M. K. “On the evolution of genetic incompatibility systems. IV. Modification of response to an existing antigen polymorphism under partial selfing.” Theoretical Population Biology 34, no. 3 (December 1988): 347–77. https://doi.org/10.1016/0040-5809(88)90028-7.
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  - Uyenoyama, M. K. “On the evolution of genetic incompatibility systems. III. Introduction of weak gametophytic self-incompatibility under partial inbreeding.” Theoretical Population Biology 34, no. 1 (August 1988): 47–91. https://doi.org/10.1016/0040-5809(88)90035-4.
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  - Uyenoyama, M. K. “On the evolution of genetic incompatibility systems. II. Initial increase of strong gametophytic self-incompatibility under partial selfing and half-sib mating.” American Naturalist 131, no. 5 (January 1, 1988): 700–722. https://doi.org/10.1086/284814.
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  - Uyenoyama, Marcy K. “INBREEDING AND THE COST OF MEIOSIS: THE EVOLUTION OF SELFING IN POPULATIONS PRACTICING BIPARENTAL INBREEDING.” Evolution; International Journal of Organic Evolution 40, no. 2 (March 1986): 388–404. https://doi.org/10.1111/j.1558-5646.1986.tb00479.x.
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  - Uyenoyama, M. K. “Quantitative models of hybrid dysgenesis: rapid evolution under transposition, extrachromosomal inheritance, and fertility selection.” Theoretical Population Biology 27, no. 2 (April 1985): 176–201. https://doi.org/10.1016/0040-5809(85)90009-7.
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  - Uyenoyama, M. K. “On the evolution of parthenogenesis. II. Inbreeding and the cost of meiosis.” Evolution 39, no. 6 (January 1, 1985): 1194–1206. https://doi.org/10.1111/j.1558-5646.1985.tb05686.x.
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  - Uyenoyama, Marcy K. “Inbreeding and the Evolution of Altruism Under Kin Selection: Effects on Relatedness and Group Structure.” Evolution 38, no. 4 (July 1984): 778–778. https://doi.org/10.2307/2408389.
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  - UYENOYAMA, M. K. “ON THE EVOLUTION OF PARTHENOGENESIS - A GENETIC REPRESENTATION OF THE COST OF MEIOSIS.” Evolution 38, no. 1 (1984): 87–102. https://doi.org/10.2307/2408549.
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  - Uyenoyama, M. K., and B. O. Bengtsson. “Towards a genetic theory for the evolution of the sex ratio. III. Parental and sibling control of brood investment ratio under partial sib-mating.” Theoretical Population Biology 22, no. 1 (August 1982): 43–68. https://doi.org/10.1016/0040-5809(82)90035-1.
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  - Uyenoyama, M. K., and M. Feldman. “Population genetic theory of kin selection. II. The multiplicative model.” American Naturalist 120, no. 5 (January 1, 1982): 614–27. https://doi.org/10.1086/284016.
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  - Uyenoyama, Marcy K. “The genetics of altruism.” Ethology and Sociobiology 3, no. 1 (January 1982): 47–48. https://doi.org/10.1016/0162-3095(82)90031-0.
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  - Uyenoyama, M. K., M. W. Feldman, and L. D. Mueller. “Population genetic theory of kin selection: Multiple alleles at one locus.” Proceedings of the National Academy of Sciences of the United States of America 78, no. 8 (August 1981): 5036–40. https://doi.org/10.1073/pnas.78.8.5036.
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  - Uyenoyama, M. K., and B. O. Bengtsson. “Towards a genetic theory for the evolution of the sex ratio II. Haplodiploid and diploid models with sibling and parental control of the brood sex ratio and brood size.” Theoretical Population Biology 20, no. 1 (January 1, 1981): 57–79. https://doi.org/10.1016/0040-5809(81)90003-4.
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  - Uyenoyama, M. K., and M. W. Feldman. “On relatedness and adaptive topography in kin selection.” Theoretical Population Biology 19, no. 1 (January 1, 1981): 87–123. https://doi.org/10.1016/0040-5809(81)90036-8.
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  - Uyenoyama, M., and M. W. Feldman. “Theories of kin and group selection: a population genetics perspective.” Theoretical Population Biology 17, no. 3 (June 1980): 380–414. https://doi.org/10.1016/0040-5809(80)90033-7.
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  - Uyenoyama, M. K., and B. O. Bengtsson. “Towards a genetic theory for the evolution of the sex ratio.” Genetics 93, no. 3 (November 1979): 721–36.
  - Uyenoyama, M. K. “Evolution of altruism under group selection in large and small populations in fluctuating environments.” Theoretical Population Biology 15, no. 1 (January 1, 1979): 58–85. https://doi.org/10.1016/0040-5809(79)90027-3.
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  - Uyenoyama, M., M. W. Feldman, and L. L. Cavalli-Sforza. “Evolutionary effects of contagious and familial transmission.” Proceedings of the National Academy of Sciences of the United States of America 76, no. 1 (January 1979): 420–24. https://doi.org/10.1073/pnas.76.1.420.
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  - Uyenoyama, M. K., and M. W. Feldman. “The genetics of sex ratio distortion by cytoplasmic infection under maternal and contagious transmission: an epidemiological study.” Theoretical Population Biology 14, no. 3 (December 1978): 471–97. https://doi.org/10.1016/0040-5809(78)90019-9.
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  - Redelings, Benjamin D., Seiji Kumagai, Liuyang Wang, Andrey Tatarenkov, Ann K. Sakai, Stephen G. Weller, Theresa M. Culley, John C. Avise, and Marcy K. Uyenoyama. “Bayesian co-estimation of selfing rate and locus-specific mutation rates for a partially selfing population,” n.d.
    Open Access Copy Link to Item
- Book Sections
  - Vallejo-Marín, M., and M. K. Uyenoyama. “On the evolutionary modification of self-incompatibility: Implications of partial clonality for allelic diversity and genealogical structure.” In Self-Incompatibility in Flowering Plants: Evolution, Diversity, and Mechanisms, 53–71, 2008. https://doi.org/10.1007/978-3-540-68486-2_3.
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Education, Training, & Certifications

Duke Appointment History

Selected Grants

Selected Publications

Academic Articles

Book Sections

Recent Courses

Presentations & Appearances

Service to the Profession