Scholars@Duke
Marcy K. Uyenoyama

Marcy K. Uyenoyama

Professor of Biology
Biology
marcy@duke.edu
Duke Box 90338, Durham, NC 27708
130 Science Drive, Room 137, Duke Box 90338, Durham, NC 27708

Selected Publications

Joint identity among loci under mutation and regular inbreeding.

Journal Article Theoretical population biology · October 2024 This study describes a compact method for determining joint probabilities of identity-by-state (IBS) within and between loci in populations evolving under genetic drift, crossing-over, mutation, and regular inbreeding (partial self-fertilization). Analogue ... Full text Cite

Wright's Hierarchical F-Statistics.

Journal Article Molecular biology and evolution · May 2024 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 ... Full text Cite

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

Journal Article Theoretical population biology · June 2020 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 ... Full text Open Access Cite

Inductive determination of allele frequency spectrum probabilities in structured populations.

Journal Article Theoretical population biology · October 2019 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 ... Full text Open Access Cite

"Any news?" Special issue in honor of Marcus Feldman's 75th birthday.

Journal Article Theoretical population biology · October 2019 Full text Cite

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

Journal Article Theoretical population biology · December 2017 We address the evolution of effective number of individuals under androdioecy and gynodioecy. We analyze dynamic models of autosomal modifiers of weak effect on sex expression. In our zygote control models, the sex expressed by a zygote depends on its own ... Full text Open Access Cite

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

Journal Article · 2017 We address the evolution of effective number of individuals under androdioecy and gynodioecy. We analyze dynamic models of autosomal modifiers of weak effect on sex expression. In our zygote control models, the sex expressed by a zygote depends on its own ... Full text Cite

A Bayesian Approach to Inferring Rates of Selfing and Locus-Specific Mutation.

Journal Article Genetics · November 2015 We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for inference about repr ... Full text Open Access Link to item Cite

Genealogical histories in structured populations.

Journal Article Theoretical population biology · June 2015 In genealogies of genes sampled from structured populations, lineages coalesce at rates dependent on the states of the lineages. For migration and coalescence events occurring on comparable time scales, for example, only lineages residing in the same deme ... Full text Open Access Cite

Bayesian co-estimation of selfing rate and locus-specific mutation rates for a partially selfing population

Journal Article · January 22, 2015 We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for inference about pure ... Open Access Link to item Cite

Editor's Report for Volume 28 (2011).

Journal Article Molecular biology and evolution · January 2013 Full text Cite

Editor's report for volume 27 (2010)

Journal Article Molecular Biology and Evolution · May 1, 2012 Full text Cite

SMBE proposal to the government of Japan.

Journal Article Molecular biology and evolution · January 2012 Full text Cite

Sex-specific incompatibility generates locus-specific rates of introgression between species.

Journal Article Genetics · September 2011 Disruption of interactions among ensembles of epistatic loci has been shown to contribute to reproductive isolation among various animal and plant species. Under the Bateson-Dobzhansky-Muller model, such interspecific incompatibility arises as a by-product ... Full text Open Access Cite

Effects of polymorphism for locally adapted genes on rates of neutral introgression in structured populations.

Journal Article Theoretical population biology · September 2011 Adaptation to local conditions within demes balanced by migration can maintain polymorphisms for variants that reduce fitness in certain ecological contexts. Here, we address the effects of such polymorphisms on the rate of introgression of neutral marker ... Full text Open Access Cite

Molecular Biology and Evolution: Editor's report

Journal Article Molecular Biology and Evolution · December 1, 2010 Full text Cite

Editorial: MBE Editor's Report

Journal Article Molecular Biology and Evolution · March 1, 2010 Full text Cite

Ancestral population genomics: the coalescent hidden Markov model approach.

Journal Article Genetics · September 2009 With incomplete lineage sorting (ILS), the genealogy of closely related species differs along their genomes. The amount of ILS depends on population parameters such as the ancestral effective population sizes and the recombination rate, but also on the num ... Full text Open Access Cite

Site frequency spectra from genomic SNP surveys.

Journal Article Theoretical population biology · June 2009 Genomic survey data now permit an unprecedented level of sensitivity in the detection of departures from canonical evolutionary models, including expansions in population size and selective sweeps. Here, we examine the effects of seemingly subtle differenc ... Full text Open Access Cite

Editor's Report for 2008

Journal Article Molecular Biology and Evolution · February 1, 2009 Full text Cite

On the evolutionary modification of self-incompatibility: Implications of partial clonality for allelic diversity and genealogical structure

Chapter · January 1, 2008 Experimental investigations of homomorphic self-incompatibility (SI) have revealed an unanticipated level of complexity in its expression, permitting fine regulation over the course of a lifetime or a range of environmental conditions. Many flowering plant ... Full text Open Access Cite

Importance sampling for the infinite sites model.

Journal Article Statistical applications in genetics and molecular biology · January 2008 Importance sampling or Markov Chain Monte Carlo sampling is required for state-of-the-art statistical analysis of population genetics data. The applicability of these sampling-based inference techniques depends crucially on the proposal distribution. In th ... Full text Open Access Cite

The evolutionary forest algorithm.

Journal Article Bioinformatics (Oxford, England) · August 2007 MotivationGene genealogies offer a powerful context for inferences about the evolutionary process based on presently segregating DNA variation. In many cases, it is the distribution of population parameters, marginalized over the effectively infin ... Full text Open Access Cite

Likelihoods from summary statistics: recent divergence between species.

Journal Article Genetics · November 2005 We describe an importance-sampling method for approximating likelihoods of population parameters based on multiple summary statistics. In this first application, we address the demographic history of closely related members of the Drosophila pseudoobscura ... Full text Open Access Cite

The evolutionary dynamics of self-incompatibility systems.

Journal Article Trends in genetics : TIG · September 2005 Self-incompatible flowering plants reject pollen that expresses the same mating specificity as the pistil (female reproductive tract). In most plant families, pollen and pistil mating specificities segregate as a single locus, the S locus. In at least two ... Full text Cite

Evolution under tight linkage to mating type.

Journal Article The New phytologist · January 2005 Recent large-scale sequencing studies of mating type loci in a number of organisms offer insight into the origin and evolution of these genomic regions. Extensive tracts containing genes with a wide diversity of functions typically cosegregate with mating ... Full text Cite

On the evolutionary costs of self-incompatibility: incomplete reproductive compensation due to pollen limitation.

Journal Article Evolution; international journal of organic evolution · September 2004 Pollen limitation affects plants with diverse reproductive systems and ecologies. In self-incompatible (SI) species, pollen limitation may preclude full reproductive compensation for prezygotic rejection of pollen. We present a model designed to explore th ... Full text Cite

Maximum-likelihood estimation of rates of recombination within mating-type regions.

Journal Article Genetics · August 2004 Features common to many mating-type regions include recombination suppression over large genomic tracts and cosegregation of genes of various functions, not necessarily related to reproduction. Model systems for homomorphic self-incompatibility (SI) in flo ... Full text Cite

A simple method for computing exact probabilities of mutation numbers.

Journal Article Theoretical population biology · May 2004 We describe a method for the recursive computation of exact probability distributions for the number of neutral mutations segregating in samples of arbitrary size and configuration. Construction of the recursions requires only characterization of evolution ... Full text Cite

Patterns of variation within self-incompatibility loci.

Journal Article Molecular biology and evolution · November 2003 Diverse self-incompatibility (SI) mechanisms permit flowering plants to inhibit fertilization by pollen that express specificities in common with the pistil. Characteristic of at least two model systems is greatly reduced recombination across large genomic ... Full text Cite

Genealogy-dependent variation in viability among self-incompatibility genotypes.

Journal Article Theoretical population biology · June 2003 Many hermaphroditic plants avoid self-fertilization by rejecting pollen that express genetically determined specificities in common with the pistil. The S-locus, comprising the determinants of pistil and pollen specificity, typically shows extremely high p ... Full text Cite

On the origin of self-incompatibility haplotypes: transition through self-compatible intermediates.

Journal Article Genetics · April 2001 Self-incompatibility (SI) in flowering plants entails the inhibition of fertilization by pollen that express specificities in common with the pistil. In species of the Solanaceae, Rosaceae, and Scrophulariaceae, the inhibiting factor is an extracellular ri ... Full text Cite

Mutational origin of new mating type specificities in flowering plants.

Journal Article Genes & genetic systems · December 2000 Many hermaphroditic plants avoid self-fertilization by rejecting pollen that express genetically-determined specificities in common with the pistil. Self-incompatibility systems typically show extremely high genetic diversity, some maintaining hundreds of ... Full text Cite

Evolutionary dynamics of self-incompatibility alleles in Brassica.

Journal Article Genetics · September 2000 Self-incompatibility in Brassica entails the rejection of pollen grains that express specificities held in common with the seed parent. In Brassica, pollen specificity is encoded at the multipartite S-locus, a complex region comprising many expressed genes ... Full text Cite

A prospectus for new developments in the evolutionary theory of self-incompatibility

Journal Article Annals of Botany · January 1, 2000 Recent advances in the study of the genetic and physiological basis of self-incompatibility have raised novel evolutionary questions. I enumerate basic elements of the classical theory for the evolution of self-incompatibility, describe some evolutionary q ... Full text Cite

Genealogical structure among alleles regulating self-incompatibility in natural populations of flowering plants.

Journal Article Genetics · November 1997 A method is proposed for characterizing the structure of genealogies among alleles that regulate self-incompatibility in flowering plants. Expected distributions of ratios of divergence times among alleles, scaled by functions of allele number, were genera ... Full text Cite

Allelic diversity and gene genealogy at the self-incompatibility locus in the Solanaceae.

Journal Article Science (New York, N.Y.) · August 1996 The self-incompatibility (S) locus of flowering plants offers an example of extreme polymorphism maintained by balancing selection. Estimates of recent and long-term effective population size (Ne) were determined for two solanaceous species by examination ... Full text Cite

S-allele diversity in a natural population of Physalis crassifolia (Solanaceae) (ground cherry) assessed by RT-PCR.

Journal Article Heredity · May 1, 1996 Allelic diversity at the self-incompatibility (S-) locus in the ground cherry, Physalis crassifolia (Solanaceae), was surveyed in a natural population occurring in Deep Canyon, CA, using a molecular assay to determine the genotype of individual plants. A t ... Cite

S-allele diversity in a natural population of Physalis crassifolia (Solanaceae) (ground cherry) assessed by RT-PCR.

Journal Article Heredity · May 1996 Allelic diversity at the self-incompatibility (S-) locus in the ground cherry, Physalis crassifolia (Solanaceae), was surveyed in a natural population occurring in Deep Canyon, CA, using a molecular assay to determine the genotype of individual plants. A t ... Full text Cite

S-allele sequence diversity in natural populations of Solanum carolinense (Horsenettle).

Journal Article Heredity · October 1995 S-allele diversity in Solanum carolinense was surveyed in two natural populations, located in Tennessee and North Carolina, with a molecular assay to determine the genotype of individual plants. A total of 13 different S-alleles were identified and sequenc ... Full text Cite

A generalized least-squares estimate for the origin of sporophytic self-incompatibility.

Journal Article Genetics · February 1995 Analysis of nucleotide sequences that regulate the expression of self-incompatibility in flowering plants affords a direct means of examining classical hypotheses for the origin and evolution of this major feature of mating systems. Departing from the clas ... Full text Cite

Coevolution of self-fertilization and inbreeding depression. III. Homozygous lethal mutations at multiple loci.

Journal Article Theoretical population biology · October 1991 We study the evolution of the rate of self-fertilization in response to deleterious mutations at multiple loci. Although partial selfing induces associations among loci even in the absence of linkage, associations among mutations at different loci are of a ... Full text Cite

Coevolution of self-fertilization and inbreeding depression. I. Mutation-selection balance at one and two loci.

Journal Article Theoretical population biology · August 1991 Simple theories for the evolution of breeding systems suggest that the fate of an allele that modifies the rate of self-fertilization hinges only on the degree to which selfing reduces opportunities for outcrossing ("pollen discounting") and the extent of ... Full text Cite

Coevolution of self-fertilization and inbreeding depression. II. Symmetric overdominance in viability.

Journal Article Theoretical population biology · August 1991 We describe the evolutionary dynamics of a modifier of selfing coevolving with a locus subject to symmetric overdominance in viability under general levels of reduction in pollination success as a consequence of self-fertilization (pollen discounting). Sim ... Full text Cite

On the evolution of genetic incompatibility systems. VI. A three-locus modifier model for the origin of gametophytic self-incompatibility.

Journal Article Genetics · June 1991 Recent genetic analyses have demonstrated that self-incompatibility in flowering plants derives from the coordinated expression of a system of loci. To address the selective mechanisms through which a genetic system of this kind evolves, I present a three- ... Full text Cite

Evolution of the segregation ratio: modification of gene conversion and meiotic drive.

Journal Article Theoretical population biology · October 1990 We compare the evolutionary pressures that direct the modification of gene conversion and meiotic drive at loci subject to purifying and overdominant viability selection. Gene conversion differs from meiotic drive in that modifers do not affect their own s ... Full text Cite

On the evolution of genetic incompatibility systems. V. Origin of sporophytic self-incompatibility in response to overdominance in viability.

Journal Article Theoretical population biology · December 1989 Conditions for the origin of partial sporophytic self-incompatibility (SSI) are obtained from two quantitative models, which differ with respect to the determination of offspring viability. Offspring viability depends solely on the source (self or nonself) ... Full text Cite

On the origin of meiotic reproduction: a genetic modifier model.

Journal Article Genetics · December 1989 We study the conditions under which a rare allele that modifies the relative rates of meiotic reproduction and apomixis increases in a population in which meiotic reproduction entails selfing as well as random outcrossing. A distinct locus, at which mutati ... Full text Cite

Coevolution of the major histocompatibility complex and the t-complex in the mouse. II. Modification of response to sharing of histocompatibility antigens.

Journal Article Genetics · January 1989 Selective pressures imposed by high complementarity associations between the major histocompatibility complex (MHC) and the t-complex on a locus that modifies the expression of prezygotic and postzygotic incompatibility are investigated through the analysi ... Full text Cite

Coevolution of the major histocompatibility complex and the t-complex in the mouse. I. Generation and maintenance of high complementarity associations.

Journal Article Genetics · January 1989 A quantitative model is developed to explore the effects of prezygotic and postzygotic incompatibility on the origin and maintenance of associations between the major histocompatibility complex (MHC) and the t-complex in the mouse. Incompatibility is repre ... Full text Cite

On the evolution of genetic incompatibility systems. IV. Modification of response to an existing antigen polymorphism under partial selfing.

Journal Article Theoretical population biology · December 1988 A 2-locus model of the evolution of self-incompatibility in a population practicing partial selfing is presented. An allele is introduced at a modifier locus which influences the strength of the rejection reaction expressed by the style in response to anti ... Full text Cite

On the evolution of genetic incompatibility systems. III. Introduction of weak gametophytic self-incompatibility under partial inbreeding.

Journal Article Theoretical population biology · August 1988 I explore the proposition that genetic incompatibility systems serve as a means for parents to evaluate and discriminate among their own offspring. Conditions for the initial increase of gametophytic self-incompatibility in a self-compatible population und ... Full text Cite

On the evolution of genetic incompatibility systems. II. Initial increase of strong gametophytic self-incompatibility under partial selfing and half-sib mating

Journal Article American Naturalist · January 1, 1988 This study addresses the origin of gametophytic self-incompatibility in populations undergoing a mixture of random outcrossing, sib mating, and selfing. The effect of the incompatibility system on the genotypic distribution among offspring derived from the ... Full text Cite

Inbreeding and the cost of meiosis: the evolution of selfing in populations practising biparental inbreeding.

Journal Article Evolution · 1986 The effect of biparental inbreeding on the conditions governing the evolution of selfing is examined using recursions in mating-type frequences.-from Author ... Cite

Quantitative models of hybrid dysgenesis: rapid evolution under transposition, extrachromosomal inheritance, and fertility selection.

Journal Article Theoretical population biology · April 1985 A model of the P-M system of hybrid dysgenesis is presented which incorporates single-site transposition of P factors in M cytotype, determination of offspring cytotype by both maternal cytotype and maternal or offspring nuclear genotype, and strong fertil ... Full text Cite

On the evolution of parthenogenesis. II. Inbreeding and the cost of meiosis.

Journal Article Evolution · 1985 Quantitative models of genetic change were analyzed to study the effect of inbreeding on the conditions for the evolution of parthenogenesis. Inbreeding does not greatly change the cost of meiosis in diploids and actually increases it is haplodiploids. Inb ... Cite

INBREEDING AND THE EVOLUTION OF ALTRUISM UNDER KIN SELECTION: EFFECTS ON RELATEDNESS AND GROUP STRUCTURE.

Journal Article Evolution; international journal of organic evolution · July 1984 Full text Cite

Population genetic theory of kin selection. II. The multiplicative model.

Journal Article American Naturalist · January 1, 1982 Analyzes multiplicative kin selection models incorporating fitness functions which involve products of the costs and benefits that are associated with altruistic actions. Multiplicative models exhibit a number of qualitative differences compared to additiv ... Full text Open Access Cite

The genetics of altruism

Journal Article Ethology and Sociobiology · January 1982 Full text Cite

Population genetic theory of kin selection: Multiple alleles at one locus.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · August 1981 Exact population genetic models of one-locus sib-to-sib kin selection with an arbitrary number of alleles are studied. First, a natural additive scaling is established for the genotypic value associated with probabilities of performance of altruism. Two cl ... Full text Open Access Cite

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

Journal Article Theoretical Population Biology · January 1, 1981 Population genetic models involving sister, brother, and father control of the brood sex ratio and brood size in both the haplodiploid and diploid cases are constructed and analyzed. The results are interpreted in light of the verbal theories which predict ... Full text Open Access Cite

On relatedness and adaptive topography in kin selection

Journal Article Theoretical Population Biology · January 1, 1981 Full text Open Access Cite

Theories of kin and group selection: a population genetics perspective.

Journal Article Theoretical population biology · June 1980 Full text Open Access Cite

Towards a genetic theory for the evolution of the sex ratio.

Journal Article Genetics · November 1979 A genetical model is formulated in which the sex ratio in broods and the relative size of broods are determined by the genotype at an autosomal locus. The results also apply to the case in which the sex-ratio locus is sex linked and expressed in the homoga ... Full text Open Access Cite

Evolutionary effects of contagious and familial transmission.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · January 1979 Two models involving non-Mendelian transmission of a discrete valued trait through within- and across-generation contagion are proposed in an investigation of the joint evolution of phenotype and genotype. A single locus with two alleles determines suscept ... Full text Open Access Cite

Evolution of altruism under group selection in large and small populations in fluctuating environments

Journal Article Theoretical Population Biology · January 1, 1979 A continuous, graded form of group selection which does not involve extinction of demes can effectively oppose selection on the individual level against an altruistic allele under fluctuating environments in infinitely large demes among which uniform mixin ... Full text Open Access Cite