About

Marcy K. Uyenoyama studies mechanisms of evolutionary change at the molecular and population levels. Her research includes the prediction and detection of the effects of natural selection on genomic structure. A major area of her work involves the development of maximum-likelihood and Bayesian methods for inferring evolutionary processes from the pattern of molecular variation. Her current research addresses the characterization of population structure across genomes. She has been a Professor of Biology at Duke University since 2000, with her academic background including a Ph.D. from Stanford University in 1978 and a B.S. from Stanford University in 1974. Her contributions include studies on neutral genetic diversity in mixed mating systems, joint identity among loci under mutation and inbreeding, and the conceptual understanding of Wright's Hierarchical F-Statistics. She has also been involved in bioinformatics and computational biology training programs and has received multiple grants from the National Institutes of Health for her research in mathematical population genetics.

Research topics

• Biology
• Evolutionary biology
• Computer Science
• Demography
• Statistics
• Genetics
• Mathematics
• Art history

Selected publications

• Joint identity among loci under mutation and regular inbreeding

  Theoretical Population Biology · 2024 · 5 citations

  1st authorCorresponding
  • Biology
  • Genetics
  • Evolutionary biology
  PublisherOA PDFDOI

• Neutral Genetic Diversity in Mixed Mating Systems

  Genes · 2024-12-20

  articleOpen access1st authorCorresponding

  BACKGROUND/OBJECTIVES: Systems of reproduction differ with respect to the magnitude of neutral genetic diversity maintained in a population. In particular, the partitioning of reproductive organisms into mating types and regular inbreeding have long been recognized as key factors that influence effective population number. Here, a range of reproductive systems are compared with respect to the maintenance of neutral genetic diversity. This study addresses full gonochorism, full hermaphroditism, androdioecy (male and hermaphroditic reproductives), and gynodioecy (female and hermaphroditic reproductives). METHODS: Coalescence theory is used to determine the level of diversity maintained under each mating system considered. RESULTS: For each mating system, the nature of the dependence of the level of neutral diversity on inbreeding depression, sex-specific viability, and other factors is described. In particular, the models account for the effects of sex-specific viability on the evolutionarily stable sex ratio and the collective contribution of each mating type (sex) to the offspring generation. CONCLUSIONS: Within the context of conservation biology, population genetic and quantitative genetic theory has addressed the determination of the target minimum effective population size. In contrast, this study proposes and explores a summary statistic (a ratio of effective numbers) as a means of characterizing the context in which evolution occurs.

  PublisherOA PDFDOI

• Wright’s Hierarchical <i>F</i>-Statistics

  Molecular Biology and Evolution · 2024 · 5 citations

  1st authorCorresponding
  • Biology
  • Statistics
  • Evolutionary biology

  This perspective article offers a meditation on FST and other quantities developed by Sewall Wright to describe the population structure, defined as any departure from reproduction through random union of gametes. Concepts related to the F-statistics draw from studies of the partitioning of variation, identity coefficients, and diversity measures. Relationships between the first two approaches have recently been clarified and unified. This essay addresses the third pillar of the discussion: Nei's GST and related measures. A hierarchy of probabilities of identity-by-state provides a description of the relationships among levels of a structured population with respect to genetic diversity. Explicit expressions for the identity-by-state probabilities are determined for models of structured populations undergoing regular inbreeding and recurrent mutation. Levels of genetic diversity within and between subpopulations reflect mutation as well as migration. Accordingly, indices of the population structure are inherently locus-specific, contrary to the intentions of Wright. Some implications of this locus-specificity are explored.

  PublisherDOI

• Neutral genetic diversity in mixed mating systems

  bioRxiv (Cold Spring Harbor Laboratory) · 2022-08-13

  preprintOpen access1st authorCorresponding

  ABSTRACT Systems of reproduction differ with respect to the magnitude of neutral genetic diversity maintained in a population. In particular, the partitioning of reproductives into mating types and regular inbreeding have long been recognized as key factors that influence effective population number. Here, a range of reproductive systems (full gonochorism, full hermaphroditism, androdioecy, and gynodioecy) are compared with respect to the maintenance of neutral genetic diversity. The analysis assumes anisogamy, with reproduction limited by the availability of large gametes (ova or seeds) but not small gametes (sperm or pollen). Levels of neutral genetic diversity respond to the relative proportions of gonochores and hermaphrodites in different ways under androdioecy versus gynodioecy. The manner in which effective number, sex-specific viability differences, and the evolving quantitative trait of the population influence the level of neutral genetic diversity is described across the systems of reproduction studied.

  PublisherOA PDFDOI

• Allele frequency spectra in structured populations: Novel-allele probabilities under the labelled coalescent

  Theoretical Population Biology · 2020 · 2 citations

  1st authorCorresponding
  • Computer Science
  • Mathematics
  • Statistics
  PublisherOA PDFDOI

• “Any news?” Special issue in honor of Marcus Feldman’s 75th birthday

  Theoretical Population Biology · 2019-10-01 · 2 citations

  editorial
  PublisherDOI

• Allele frequency spectra in structured populations: Novel-allele probabilities under the labelled coalescent

  bioRxiv (Cold Spring Harbor Laboratory) · 2019-12-26

  preprintOpen access1st authorCorresponding

  ABSTRACT We address the effect of population structure on key properties of the Ewens sampling formula. We use our previously-introduced inductive method for determining exact allele frequency spectrum (AFS) probabilities under the infinite-allele model of mutation and population structure for samples of arbitrary size. Fundamental to the sampling distribution is the novel-allele probability, the probability that given the pattern of variation in the present sample, the next gene sampled belongs to an as-yet-unobserved allelic class. Unlike the case for panmictic populations, the novel-allele probability depends on the AFS of the present sample. We derive a recursion that directly provides the marginal novel-allele probability across AFSs, obviating the need first to determine the probability of each AFS. Our explorations suggest that the marginal novel-allele probability tends to be greater for initial samples comprising fewer alleles and for sampling configurations in which the next-observed gene derives from a deme different from that of the majority of the present sample. Comparison to the efficient importance sampling proposals developed by De Iorio and Griffiths and colleagues indicates that their approximation for the novel-allele probability generally agrees with the true marginal, although it may tend to overestimate the marginal in cases in which the novel-allele probability is high and migration rates are low.

  PublisherOA PDFDOI

• Inductive determination of allele frequency spectrum probabilities in structured populations

  Theoretical Population Biology · 2019-01-11 · 10 citations

  article1st authorCorresponding
  PublisherDOI

• Inductive determination of allele frequency spectrum probabilities in structured populations

  bioRxiv (Cold Spring Harbor Laboratory) · 2018-10-26

  preprintOpen access1st authorCorresponding

  ABSTRACT We present a method for inductively determining exact allele frequency spectrum (AFS) probabilities for samples derived from a population comprising two demes under the infinite-allele model of mutation. This method builds on a labeled coalescent argument to extend the Ewens sampling formula (ESF) to structured populations. A key departure from the panmictic case is that the AFS conditioned on the number of alleles in the sample is no longer independent of the scaled mutation rate ( θ ). In particular, biallelic site frequency spectra, widely-used in explorations of genome-wide patterns of variation, depend on the mutation rate in structured populations. Variation in the rate of substitution across loci and through time may contribute to apparent distortions of site frequency spectra exhibited by samples derived from structured populations.

  PublisherOA PDFDOI

• Evolution of the sex ratio and effective number under gynodioecy and androdioecy

  Theoretical Population Biology · 2017-09-11 · 4 citations

  articleOpen access1st authorCorresponding
  PublisherOA PDFDOI

Recent grants

• NIH Grant R01HD017925

  NIH · $34k · 1986

• NIH Grant R01GM037841

  NIH · $3.1M · 2014

Frequent coauthors

• Jody Hey

  474 shared

• John M. Archibald

  Dalhousie University

  473 shared

• Elizabeth Raffaele

  Dalhousie University

  470 shared

• George R. Golding

  Public Health Agency of Canada

  470 shared

• Howard Ochman

  The University of Texas at Austin

  469 shared

• Richard C Lewontin

  469 shared

• Masatoshi Nei

  Temple University

  469 shared

• Walter M. Fitch

  469 shared