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
- Mathematical Population Genetics awarded by National Institutes of Health 1986 - 2014
- Mathematical Population Genetics awarded by National Institutes of Health 1996 - 2005
- (97-0453) 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
- (97-0257) US/Germany/Japan Trinational Workshop on Molecular Evolution awarded by National Science Foundation 1997 - 1998
- (92-0288) Mathematical Population Genetics awarded by National Institutes of Health 1986 - 1996
- (93-0791) Mathematical Population Genetics awarded by National Institutes of Health 1986 - 1996
- (94-0847) Mathematical Population Genetics awarded by National Institutes of Health 1986 - 1996
- (95-0657) Mathematical Population Genetics awarded by National Institutes of Health 1986 - 1996
- (88-0679) Mathematical Population Genetics awarded by National Institutes of Health 1986 - 1992
- (90-0584) Mathematical Population Genetics awarded by National Institutes of Health 1986 - 1992
- (91-0683) Mathematical Population Genetics awarded by National Institutes of Health 1986 - 1992
- (87-0321) Mathematical Population Genetics awarded by National Institutes of Health 1986 - 1989
- (88-0557) Mathematical Population Genetics awarded by National Institutes of Health 1986 - 1989
Publications & Artistic Works
Selected Publications
- Book Sections
  - Vallejo-Marín, M, and Uyenoyama, MK. "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. January 1, 2008. Full Text
- Journal Articles
  - Uyenoyama, MK, and Takebayashi, N. "Evolution of the sex ratio and effective number under gynodioecy and androdioecy." Theoretical population biology 118 (December 2017): 27-45. Full Text
  - Redelings, BD, Kumagai, S, Tatarenkov, A, Wang, L, Sakai, AK, Weller, SG, Culley, TM, Avise, JC, and Uyenoyama, MK. "A Bayesian Approach to Inferring Rates of Selfing and Locus-Specific Mutation." Genetics 201, no. 3 (November 2015): 1171-1188. Full Text
  - Kumagai, S, and Uyenoyama, MK. "Genealogical histories in structured populations." Theoretical population biology 102 (June 2015): 3-15. Full Text
  - Kumagai, S, and Uyenoyama, MK. "Genealogical histories in structured populations." Theoretical Population Biology 102 (June 1, 2015): 3-15. Full Text
  - Uyenoyama, MK. "Editor's Report for Volume 28 (2011)." Mol Biol Evol 30, no. 1 (January 2013): 236-237. Full Text Link to Item
  - Kumagai, S, and Uyenoyama, MK. "A method for computing the exact distribution of speciation times and internode lengths in genealogical histories (Submitted)." Theoretical Population Biology (2012). (Academic Article)
  - Uyenoyama, MK. "Editor's report for volume 27 (2010)." Molecular Biology and Evolution 29, no. 5 (2012): 1493-1494. Full Text
  - Wolfe, K, Wayne, ML, Makova, K, Steen, TY, Uyenoyama, M, and Takahata, N. "SMBE proposal to the government of Japan." Molecular Biology and Evolution 29, no. 1 (2012): 441--. Full Text
  - Fusco, D, and Uyenoyama, MK. "Sex-specific incompatibility generates locus-specific rates of introgression between species." Genetics 189, no. 1 (September 2011): 267-288. Full Text Link to Item
  - Fusco, D, and Uyenoyama, MK. "Effects of polymorphism for locally adapted genes on rates of neutral introgression in structured populations." Theor Popul Biol 80, no. 2 (September 2011): 121-131. Full Text Link to Item
  - Uyenoyama, MK. "Molecular Biology and Evolution: Editor's report." Molecular Biology and Evolution 27, no. 12 (2010): 2890-2891. Full Text
  - Uyenoyama, MK. "Editorial: MBE Editor's Report." Molecular Biology and Evolution 27, no. 3 (2010): 742-743. Full Text
  - Dutheil, JY, Ganapathy, G, Hobolth, A, Mailund, T, Uyenoyama, MK, and Schierup, MH. "Ancestral population genomics: the coalescent hidden Markov model approach." Genetics 183, no. 1 (September 2009): 259-274. Full Text Link to Item
  - Ganapathy, G, and Uyenoyama, MK. "Site frequency spectra from genomic SNP surveys." Theor Popul Biol 75, no. 4 (June 2009): 346-354. Full Text Link to Item
  - Hobolth, A, Uyenoyama, MK, and Wiuf, C. "Importance sampling for the infinite sites model." Stat Appl Genet Mol Biol 7, no. 1 (2008): Article32-. Full Text Link to Item
  - Leman, SC, Uyenoyama, MK, Lavine, M, and Chen, Y. "The evolutionary forest algorithm." Bioinformatics 23, no. 15 (August 1, 2007): 1962-1968. Full Text Link to Item
  - Leman, SC, Chen, Y, Stajich, JE, Noor, MAF, and Uyenoyama, MK. "Likelihoods from summary statistics: recent divergence between species." Genetics 171, no. 3 (November 2005): 1419-1436. Full Text Link to Item
  - Newbigin, E, and Uyenoyama, MK. "The evolutionary dynamics of self-incompatibility systems." Trends Genet 21, no. 9 (September 2005): 500-505. Full Text Link to Item
  - Uyenoyama, MK. "Evolution under tight linkage to mating type." New Phytol 165, no. 1 (January 2005): 63-70. (Review) Full Text Link to Item
  - Vallejo-Marín, M, and Uyenoyama, MK. "On the evolutionary costs of self-incompatibility: incomplete reproductive compensation due to pollen limitation." Evolution 58, no. 9 (September 2004): 1924-1935. Link to Item
  - Takebayashi, N, Newbigin, E, and Uyenoyama, MK. "Maximum-likelihood estimation of rates of recombination within mating-type regions." Genetics 167, no. 4 (August 2004): 2097-2109. Full Text Link to Item
  - Uyenoyama, MK, and Takebayashi, N. "A simple method for computing exact probabilities of mutation numbers." Theor Popul Biol 65, no. 3 (May 2004): 271-284. Full Text Link to Item
  - Takebayashi, N, Brewer, PB, Newbigin, E, and Uyenoyama, MK. "Patterns of variation within self-incompatibility loci." Mol Biol Evol 20, no. 11 (November 2003): 1778-1794. Full Text Link to Item
  - Uyenoyama, MK. "Genealogy-dependent variation in viability among self-incompatibility genotypes." Theor Popul Biol 63, no. 4 (June 2003): 281-293. Link to Item
  - Uyenoyama, MK, Zhang, Y, and Newbigin, E. "On the origin of self-incompatibility haplotypes: transition through self-compatible intermediates." Genetics 157, no. 4 (April 2001): 1805-1817. Link to Item
  - Uyenoyama, MK. "Mutational origin of new mating type specificities in flowering plants." Genes Genet Syst 75, no. 6 (December 2000): 305-311. (Review) Link to Item
  - Uyenoyama, MK. "Evolutionary dynamics of self-incompatibility alleles in Brassica." Genetics 156, no. 1 (September 2000): 351-359. Link to Item
  - Uyenoyama, MK, and Newbigin, E. "Evolutionary dynamics of dual-specificity self-incompatibility alleles." Plant Cell 12, no. 3 (March 2000): 310-312. (Letter) Link to Item
  - Uyenoyama, MK. "A prospectus for new developments in the evolutionary theory of self-incompatibility." Annals of Botany 85, no. SUPPL. A (2000): 247-252.
  - Uyenoyama, MK. "Evolutionary dynamics of self-incompatibility systems in flowering plants." J. Reprod. Dev. 46 (2000): 35-36. (Academic Article)
  - Uyenoyama, MK. "Genealogical structure among alleles regulating self-incompatibility in natural populations of flowering plants." Genetics 147, no. 3 (November 1997): 1389-1400. Link to Item
  - Richman, AD, Uyenoyama, MK, and Kohn, JR. "Allelic diversity and gene genealogy at the self-incompatibility locus in the Solanaceae." Science 273, no. 5279 (August 30, 1996): 1212-1216. Link to Item
  - Richman, AD, Uyenoyama, MK, and Kohn, JR. "S-allele diversity in a natural population of Physalis crassifolia (Solanaceae) (ground cherry) assessed by RT-PCR." Heredity (Edinb) 76 ( Pt 5) (May 1996): 497-505. Link to Item
  - Richman, AD, Uyenoyama, MK, and Kohn, JR. "S-allele diversity in a natural population of Physalis crassifolia (Solanaceae) (ground cherry) assessed by RT-PCR." Heredity 76 (1996): Pt 5/--.
  - Richman, AD, Kao, TH, Schaeffer, SW, and Uyenoyama, MK. "S-allele sequence diversity in natural populations of Solanum carolinense (Horsenettle)." Heredity (Edinb) 75 ( Pt 4) (October 1995): 405-415. Link to Item
  - Uyenoyama, MK. "A generalized least-squares estimate for the origin of sporophytic self-incompatibility." Genetics 139, no. 2 (February 1995): 975-992. Link to Item
  - Thrall, PH, Biere, A, and Uyenoyama, MK. "Frequency-dependent disease transmission and the dynamics of the Silene-ustilago host-pathogen system." American Naturalist 145, no. 1 (1995): 43-62. Full Text
  - Uyenoyama, MK, and Waller, DM. "Coevolution of self-fertilization and inbreeding depression. III. Homozygous lethal mutations at multiple loci." Theor Popul Biol 40, no. 2 (October 1991): 173-210. (Review) Link to Item
  - Uyenoyama, MK, and Waller, DM. "Coevolution of self-fertilization and inbreeding depression. I. Mutation-selection balance at one and two loci." Theor Popul Biol 40, no. 1 (August 1991): 14-46. Link to Item
  - Uyenoyama, MK, and Waller, DM. "Coevolution of self-fertilization and inbreeding depression. II. Symmetric overdominance in viability." Theor Popul Biol 40, no. 1 (August 1991): 47-77. Link to Item
  - Uyenoyama, MK. "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): 453-469. (Review) Link to Item
  - Bengtsson, BO, and Uyenoyama, MK. "Evolution of the segregation ratio: modification of gene conversion and meiotic drive." Theor Popul Biol 38, no. 2 (October 1990): 192-218. Link to Item
  - Uyenoyama, MK, and Bengtsson, BO. "On the origin of meiotic reproduction: a genetic modifier model." Genetics 123, no. 4 (December 1989): 873-885. Link to Item
  - Uyenoyama, MK. "On the evolution of genetic incompatibility systems. V. Origin of sporophytic self-incompatibility in response to overdominance in viability." Theor Popul Biol 36, no. 3 (December 1989): 339-365. Link to Item
  - Uyenoyama, MK. "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): 153-161. Link to Item
  - Uyenoyama, MK. "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): 139-151. Link to Item
  - Uyenoyama, MK. "On the evolution of genetic incompatibility systems. IV. Modification of response to an existing antigen polymorphism under partial selfing." Theor Popul Biol 34, no. 3 (December 1988): 347-377. Link to Item
  - Uyenoyama, MK. "On the evolution of genetic incompatibility systems. III. Introduction of weak gametophytic self-incompatibility under partial inbreeding." Theor Popul Biol 34, no. 1 (August 1988): 47-91. Link to Item
  - Uyenoyama, MK. "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 (1988): 700-722.
  - Uyenoyama, MK. "Inbreeding and the cost of meiosis: the evolution of selfing in populations practising biparental inbreeding." Evolution 40, no. 2 (1986): 388-404.
  - Uyenoyama, MK. "Quantitative models of hybrid dysgenesis: rapid evolution under transposition, extrachromosomal inheritance, and fertility selection." Theor Popul Biol 27, no. 2 (April 1985): 176-201. Link to Item
  - Uyenoyama, MK. "On the evolution of parthenogenesis. II. Inbreeding and the cost of meiosis." Evolution 39, no. 6 (1985): 1194-1206.
  - UYENOYAMA, MK. "ON THE EVOLUTION OF PARTHENOGENESIS - A GENETIC REPRESENTATION OF THE COST OF MEIOSIS." EVOLUTION 38, no. 1 (1984): 87-102. Full Text Link to Item
  - UYENOYAMA, MK. "INBREEDING AND THE EVOLUTION OF ALTRUISM UNDER KIN SELECTION - EFFECTS ON RELATEDNESS AND GROUP-STRUCTURE." EVOLUTION 38, no. 4 (1984): 778-795. Full Text Link to Item
  - Uyenoyama, MK, and Bengtsson, BO. "Towards a genetic theory for the evolution of the sex ratio. III. Parental and sibling control of brood investment ratio under partial sib-mating." Theor Popul Biol 22, no. 1 (August 1982): 43-68. Link to Item
  - UYENOYAMA, MK. "THE GENETICS OF ALTRUISM - BOORMAN,SA, LEVITT,PR." ETHOLOGY AND SOCIOBIOLOGY 3, no. 1 (1982): 47-48. Full Text Link to Item
  - Uyenoyama, MK, and Feldman, M. "Population genetic theory of kin selection. II. The multiplicative model." American Naturalist 120, no. 5 (1982): 614-627. Full Text
  - Uyenoyama, MK, Feldman, MW, and Mueller, LD. "Population genetic theory of kin selection: Multiple alleles at one locus." Proc Natl Acad Sci U S A 78, no. 8 (August 1981): 5036-5040. Link to Item
  - Uyenoyama, MK, Feldman, MW, and Mueller, LD. "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 I (1981): 5036-5040.
  - Uyenoyama, MK, and Bengtsson, BO. "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 (1981): 57-79.
  - Uyenoyama, MK, and Feldman, MW. "On relatedness and adaptive topography in kin selection." Theoretical Population Biology 19, no. 1 (1981): 87-123.
  - Uyenoyama, M, and Feldman, MW. "Theories of kin and group selection: A population genetics perspective." Theoretical Population Biology 17, no. 3 (1980): 380-414.
  - Uyenoyama, MK, and Bengtsson, BO. "Towards a genetic theory for the evolution of the sex ratio." Genetics 93, no. 3 (November 1979): 721-736. Link to Item
  - Uyenoyama, M, Feldman, MW, and Cavalli-Sforza, LL. "Evolutionary effects of contagious and familial transmission." Proceedings of the National Academy of Sciences of the United States of America 76, no. 1 (1979): 420-424.
  - Uyenoyama, MK. "Evolution of altruism under group selection in large and small populations in fluctuating environments." Theoretical Population Biology 15, no. 1 (1979): 58-85.
  - Uyenoyama, MK, and Feldman, MW. "The genetics of sex ratio distortion by cytoplasmic infection under maternal and contagious transmission: an epidemiological study." Theor Popul Biol 14, no. 3 (December 1978): 471-497. Link to Item
  - Redelings, BD, Kumagai, S, Wang, L, Tatarenkov, A, Sakai, AK, Weller, SG, Culley, TM, Avise, JC, and Uyenoyama, MK. "Bayesian co-estimation of selfing rate and locus-specific mutation rates for a partially selfing population." Open Access Copy Link to Item
Teaching & Mentoring
Recent Courses
- BIOLOGY 250: Population Genetics 2018
- BIOLOGY 293: Research Independent Study 2018
- BIOLOGY 493: Research Independent Study 2018
- BIOLOGY 660: Evolution from a Coalescence Perspective 2018
- BIOLOGY 650: Molecular Population Genetics 2016
- BIOLOGY 791T: Tutorial 2016
- BIOLOGY 792: Research 2016
Scholarly, Clinical, & Service Activities
Presentations & Appearances
Service to the Profession

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Education, Training, & Certifications

Duke Appointment History

Selected Grants

Selected Publications

Book Sections

Journal Articles

Recent Courses

Presentations & Appearances

Service to the Profession