Publications of Marcy K Uyenoyama :chronological combined listing:
%% Books
@book{fds17906,
Author = {R. S. Singh and M. K. Uyenoyama},
Title = {The Evolution of Population Biology},
Publisher = {Cambridge University Press},
Year = {2004},
Key = {fds17906}
}
%% Papers Published
@article{fds159868,
Author = {Ganeshkumar Ganapathy and Marcy K. Uyenoyama},
Title = {Site frequency spectra from genomic SNP surveys},
Journal = {Theor. Popul. Biology},
Volume = {75},
Pages = {346-354},
Year = {2009},
Abstract = {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 differences among sampling distributions on
goodness of fit analyses of site frequency spectra
constructed from single nucleotide polymorphisms.
Conditioning on the observation of exactly two alleles in a
random sample results in a site frequency spectrum that is
independent of the scaled rate of neutral substitution
(theta). Other sampling distributions, including
conditioning on a single mutational event in the sample
genealogy or randomly selecting a single mutation from a
genealogy with multiple mutations, have distinct site
frequency spectra that show highly significant departures
from the predictions of the biallelic model. Some aspects of
data filtering may contribute to significant departures of
site frequency spectra from expectation, apart from any
violation of the standard neutral model.},
Key = {fds159868}
}
@article{fds159869,
Author = {Dutheil, J. Y. and G. Ganapathy and A. Hobolth and T. Mailund and M. K.
Uyenoyama and M. H. Schierup},
Title = {Ancestral population genomics: The coalescent Hidden Markov
Model approach},
Journal = {Genetics},
Year = {2009},
Abstract = {With incomplete lineage sorting (ILS), the genealogy of
closely related species diers along their genomes. The
amount of ILS depends on population parameters such as the
ancestral eective population sizes and the recombination
rate, but also on the number of generations between
speciation events. We use a hidden Markov model parametrized
according to coalescent theory in order to infer the
genealogy along a four-species genome alignment of closely
related species, and estimate population parameters. We
analyze a basic, panmictic demographic model and study its
properties using an extensive set of coalescent simulations.
We assess the eect of the model assumptions, and
demonstrate that the Markov property provides a good
approximation to the ancestral recombination graph. Using a
too restricted set of possible genealogies, necessary to
reduce the computational load, can bias parameter estimates.
We propose a simple correction for this bias, and suggest
directions for future extensions of the model. We show that
the patterns of ILS along a sequence alignment can be
recovered e ciently together with the ancestral
recombination rate. Finally, we introduce an extension of
the basic model that allows for mutation rate heterogeneity,
and reanalyze Human-Chimpanzee-Gorilla-Orangutan alignments
using the new models. We expect that this framework will
prove useful for population genomics and provide exciting
insights into genome evolution.},
Key = {fds159869}
}
@article{fds154183,
Author = {Asger Hobolth and Marcy K. Uyenoyama and Carsten
Wiuf},
Title = {Importance sampling for the infinite sites
model},
Journal = {Statistical Applications in Genetics and Molecular
Biology},
Volume = {7},
Pages = {Article 32},
Year = {2008},
Abstract = {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 this paper, we discuss importance
sampling for the infinite sites model. The infinite sites
assumption is attractive because it constraints the number
of possible genealogies, thereby allowing for the analysis
of larger data sets. We recall the Griffiths-Tavaré and
Stephens-Donnelly proposals and emphasize the relation
between the latter proposal and exact sampling from the
infinite alleles model. We also introduce a new proposal
that takes knowledge of the ancestral state into account.
The new proposal is derived from a new result on exact
sampling from a single site. The methods are illustrated on
simulated data sets and the data considered in Griffiths and
Tavaré (1994).},
Key = {fds154183}
}
@article{fds140912,
Author = {S. C. Leman and M. K. Uyenoyama and M. Lavine and Y.
Chen},
Title = {The evolutionary forest algorithm},
Journal = {Bioinformatics},
Volume = {23},
Pages = {1962-1968},
Year = {2007},
Key = {fds140912}
}
@article{fds30743,
Author = {M.K. Uyenoyama},
Title = {Evolution under tight linkage to mating type},
Journal = {New Phytologist},
Volume = {165},
Pages = {63-70},
Year = {2005},
Key = {fds30743}
}
@article{fds44481,
Author = {E. Newbigin and M. K. Uyenoyama},
Title = {The evolutionary dynamics of self-incompatibility
systems},
Journal = {Trends in Genetics},
Volume = {21},
Pages = {500-505},
Year = {2005},
Key = {fds44481}
}
@article{fds44482,
Author = {S. C. Leman, and Y. Chen, and J. E. Stajich, and M. A. F.
Noor, and M.K. Uyenoyama},
Title = {Likelihoods from summary statistics: Recent divergence
between species},
Journal = {Genetics},
Volume = {171},
Pages = {1419-1436},
Year = {2005},
Key = {fds44482}
}
@inbook{fds17903,
Author = {M.K. Uyenoyama and N. Takebayashi},
Title = {Genus-specific diversification of mating
types},
Pages = {254-271},
Booktitle = {The Evolution of Population Biology},
Publisher = {Cambridge University Press},
Editor = {R. S. Singh and M. K. Uyenoyama},
Year = {2004},
Key = {fds17903}
}
@article{fds26865,
Author = {Takebayashi, N. and E. Newbigin and M.K. Uyenoyama},
Title = {Maximum likelihood estimation of rates of recombination
within mating-type regions},
Journal = {Genetics},
Volume = {167},
Pages = {2097-2109},
Year = {2004},
Key = {fds26865}
}
@article{fds26866,
Author = {M. Vallejo-Marin and M.K. Uyenoyama},
Title = {On the evolutionary costs of self-incompatibility:
Incomplete reproductive compensation due to pollen
limitation},
Journal = {Evolution},
Volume = {58},
Pages = {1924-1935},
Year = {2004},
Key = {fds26866}
}
@article{fds26864,
Author = {M.K. Uyenoyama and N. Takebayashi},
Title = {A simple method for computing exact probabilities of
mutation numbers},
Journal = {Theoretical Population Biology},
Volume = {65},
Pages = {271-284},
Year = {2004},
Key = {fds26864}
}
@article{fds17904,
Author = {M.K. Uyenoyama},
Title = {Genealogy-dependent variation in viability among
self-incompatibility genotypes},
Journal = {Theoretical Population Biology},
Volume = {63},
Pages = {281-293},
Year = {2003},
Key = {fds17904}
}
@article{fds17905,
Author = {N. Takebayashi and P. Brewer and E. Newbigin and M.K.
Uyenoyama},
Title = {Patterns of variation within self-incompatibility
loci},
Journal = {Molecular Biology and Evolution},
Volume = {20},
Pages = {1778-1794},
Year = {2003},
Key = {fds17905}
}
@article{fds17943,
Author = {M.K. Uyenoyama},
Title = {Outbreeding},
Booktitle = {Encyclopedia of Genetics},
Publisher = {Academic Press, London},
Editor = {S. Brenner and J. Miller},
Year = {2001},
Key = {fds17943}
}
@article{fds17944,
Author = {M.K. Uyenoyama and Y Zhang and E Newbigin},
Title = {On the origin of self-incompatibility haplotypes: Transition
through self-compatible intermediates},
Journal = {Genetics},
Volume = {157},
Pages = {1805-1817},
Year = {2001},
Key = {fds17944}
}
@inbook{fds17940,
Author = {M.K. Uyenoyama},
Title = {The evolution of breeding systems},
Series = {pp.300-316},
Booktitle = {Evolutionary Genetics from Molecules to Morphology},
Publisher = {Cambridge University Press, New York},
Editor = {RS Singh and C Krimbas},
Year = {2000},
Key = {fds17940}
}
@article{fds17945,
Author = {M.K. Uyenoyama},
Title = {Mutational origin of new mating type specificities in
flowering plants},
Journal = {Genes Genet. Syst.},
Volume = {75},
Pages = {305-311},
Year = {2000},
Key = {fds17945}
}
@article{fds17946,
Author = {M.K. Uyenoyama},
Title = {Evolutionary dynamics of self-incompatibility alleles in
Brassica},
Journal = {Genetics},
Volume = {156},
Pages = {351-359},
Year = {2000},
Key = {fds17946}
}
@article{fds17947,
Author = {M.K. Uyenoyama},
Title = {A Prospectus for new developments in the evolutionary theory
of self-incompatibility},
Journal = {Ann. Botany},
Volume = {85a},
Pages = {247-252},
Year = {2000},
Key = {fds17947}
}
@article{fds17948,
Author = {M.K. Uyenoyama and E. Newbigin},
Title = {Evolutionary dynamics of dual-specificity
self-incompatibility alleles},
Journal = {Plant Cell},
Volume = {12},
Pages = {310-312},
Year = {2000},
Key = {fds17948}
}
@article{fds17949,
Author = {M.K. Uyenoyama},
Title = {Evolutionary dynamics of self-incompatibility systems in
flowering plants},
Journal = {J. Reprod. Dev.},
Volume = {46},
Pages = {35-36},
Year = {2000},
Key = {fds17949}
}
%% Papers Accepted
@article{fds154185,
Author = {Ganeshkumar Ganapathy and Marcy K. Uyenoyama},
Title = {Site frequency spectra from genomic SNP surveys},
Journal = {Theoretical Population Biology},
Year = {2008},
Key = {fds154185}
}
%% Book Chapter
@article{fds140985,
Author = {Mario Vallejo-Marin and Marcy K. Uyenoyama},
Title = {On the evolutionary modi fication of self-incompatibility:
Implications of partial clonality for allelic diversity and
genealogical structure},
Pages = {53-71},
Booktitle = {Self-Incompatibility in Flowering Plants: Evolution,
Diversity and Mechanisms},
Publisher = {Springer-Verlag},
Address = {Tiergartenstr. 17, 69121 Heidelberg, Germany},
Editor = {Vernonica Franklin-Tong},
Year = {2008},
Abstract = {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 plants express some
level of clonal reproduction, and phylogenetic analyses
suggest that clonality evolves in a correlated fashion with
SI in Solanum (Solanaceae). Here, we use a diffusion
approximation to explore the effects on the evolutionary
dynamics of SI of vegetative propagation with SI restricted
to reproduction through seed. While clonality reduces the
strength of frequency-dependent selection maintaining
S-allele diversity, much of the great depth typical of
S-allele genealogies is preserved. Our results suggest that
clonality can play an important role in the evolution of SI
systems, and may afford insight into unexplained features of
allele genealogies in the Solanaceae.},
Key = {fds140985}
}
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