Biomedical subjects

Shuichi Kitada

Publications and source records attributed to Shuichi Kitada.

3 recordsLinked to original sources

PubMed2006

An integrated-likelihood method for estimating genetic differentiation between populations.

The aim of this article is to develop an integrated-likelihood (IL) approach to estimate the genetic differentiation between populations. The conventional maximum-likelihood (ML) and pseudolikelihood (PL) methods that use sample counts of alleles may cause severe underestimations of FST, which means overestimations of theta=4Nm, when the number of sampling localities is small. To reduce such bias in the estimation of genetic differentiation, we propose an IL method in which the mean allele frequencies over populations are regarded as nuisance parameters and are eliminated by integration. To maximize the IL function, we have developed two algorithms, a Monte Carlo EM algorithm and a Laplace approximation. Our simulation studies show that the method proposed here outperforms the conventional ML and PL methods in terms of unbiasedness and precision. The IL method was applied to real data for Pacific herring and African elephants.

Algorithms↗

PubMed2006

Simultaneous estimation of mixing rates and genetic drift under successive sampling of genetic markers with application to the mud crab (Scylla paramamosain) in Japan.

In stock enhancement programs, it is important to assess mixing rates of released individuals in stocks. For this purpose, genetic stock identification has been applied. The allele frequencies in a composite population are expressed as a mixture of the allele frequencies in the natural and released populations. The estimation of mixing rates is possible, under successive sampling from the composite population, on the basis of temporal changes in allele frequencies. The allele frequencies in the natural population may be estimated from those of the composite population in the preceding year. However, it should be noted that these frequencies can vary between generations due to genetic drift. In this article, we develop a new method for simultaneous estimation of mixing rates and genetic drift in a stock enhancement program. Numerical simulation shows that our procedure estimates the mixing rate with little bias. Although the genetic drift is underestimated when the amount of information is small, reduction of the bias is possible by analyzing multiple unlinked loci. The method was applied to real data on mud crab stocking, and the result showed a yearly variation in the mixing rate.

Animals↗

PubMed2004

Simultaneous detection of linkage disequilibrium and genetic differentiation of subdivided populations.

We propose a new method for simultaneously detecting linkage disequilibrium and genetic structure in subdivided populations. Taking subpopulation structure into account with a hierarchical model, we estimate the magnitude of genetic differentiation and linkage disequilibrium in a metapopulation on the basis of geographical samples, rather than decompose a population into a finite number of random-mating subpopulations. We assume that Hardy-Weinberg equilibrium is satisfied in each locality, but do not assume independence between marker loci. Linkage states remain unknown. Genetic differentiation and linkage disequilibrium are expressed as hyperparameters describing the prior distribution of genotypes or haplotypes. We estimate related parameters by maximizing marginal-likelihood functions and detect linkage equilibrium or disequilibrium by the Akaike information criterion. Our empirical Bayesian model analyzes genotype and haplotype frequencies regardless of haploid or diploid data, so it can be applied to most commonly used genetic markers. The performance of our procedure is examined via numerical simulations in comparison with classical procedures. Finally, we analyze isozyme data of ayu, a severely exploited fish species, and single-nucleotide polymorphisms in human ALDH2.

Animals↗