Biology subjects

Uyenoyama, M. K.

Publications and source records attributed to Uyenoyama, M. K..

3 recordsLinked to original sources

bioRxiv2022

Neutral genetic diversity in mixed mating systems

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.

evolutionary biology↗

bioRxiv2019

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

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.

evolutionary biology↗

bioRxiv2018

Inductive determination of allele frequency spectrum probabilities in structured populations

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 ({theta}). 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.

evolutionary biology↗