Tetsuro Nomura

Estimation of effective number of breeders from molecular coancestry of single cohort sample

The effective population size, Ne, is an important parameter in population genetics and conservation biology. It is, however, difficult to directly estimate Ne from demographic data in many wild species. Alternatively, the use of genetic data has received much attention in recent years. In the present study, I propose a new method for estimating the effective number of breeders Neb from a parameter of allele sharing (molecular coancestry) among sampled progeny. The bias and confidence interval of the new estimator are compared with those from a published method, i.e. the heterozygote‐excess method, using computer simulation. Two population models are simulated; the noninbred population that consists of noninbred and nonrelated parents and the inbred population that is composed of inbred and related parents. Both methods give essentially unbiased estimates of Neb when applied to the noninbred population. In the inbred population, the proposed method gives a downward biased estimate, but the confidence interval is remarkably narrowed compared with that in the noninbred population. Estimate from the heterozygote‐excess method is nearly unbiased in the inbred population, but suffers from a larger confidence interval. By combining the estimates from the two methods as a harmonic mean, the reliability is remarkably improved.

Effective size of populations with heritable variation in fitness

The effective size of monogamous populations with heritable variation in fitness is formulated, and the expression obtained is compared with a published equation. It is shown that the published equation for dioecious populations is inappropriate for most animal and human populations, because the derivation is implicitly based on the assumption that zygotes are produced by random union of gametes, each from conceptual male and female gametic pools. A convenient equation for practical use is proposed, and the application is illustrated with the estimation of the effective size of a rural human community in Japan.

Reduction of inbreeding in commercial females by rotational mating with several sire lines

A mating system to reduce the inbreeding of commercial females in the lower level was examined theoretically, assuming a hierarchical breed structure, in which favorable genes are accumulated in the upper level by artificial selection and the achieved genetic progress is transferred to the lower level through migration of males. The mating system examined was rotational mating with several closed sire lines in the upper level. Using the group coancestry theory, we derived recurrence equations for the inbreeding coefficient of the commercial females. The asymptotic inbreeding coefficient was also derived. Numerical computations showed that the critical factor for determining the inbreeding is the number of sire lines, and that the size of each sire line has a marginal effect. If four or five sire lines were available, rotational mating was found to be quite an effective system to reduce the short- and long-term inbreeding of the commercial females, irrespective of the effective size of each sire line. Oscillation of the inbreeding coefficient under rotational mating with initially related sire lines could be minimized by avoiding the consecutive use of highly related lines. Extensions and perspectives of the system are discussed in relation to practical application.

Effective Population Size Under Random Mating With a Finite Number of Matings

RANDOM union of gametes (RUG) is the null model central to theoretical population genetics. In this model, all male and female parents contribute their gametes equally to male and female gametic pools, respectively. Zygotes (offspring) are produced by random union of gametes, each from the male and

On the methods for predicting the effective size of populations under selection.

Inconsistencies between equations for the effective population size under selection obtained by two different approaches are explained. In one approach, the effective population size is predicted from the drift in the frequency of a neutral allele, accounting for the accumulation of selective advantage over generations. The second approach is based on the rate of inbreeding, using the concept of long-term genetic contributions. It is shown that the long-term genetic contribution approach leads to an identical result to the drift approach, if the effect of mates on the long-term genetic contributions is correctly accounted for.

The complete mitochondrial genome of the Japanese honeybee, Apis cerana japonica (Insecta: Hymenoptera: Apidae)

Abstract In this study, we analyzed the complete mitochondrial genome of the Japanese honeybee Apis cerana japonica. The mitochondrial genome of A. c. japonica is a circular molecule of 15 917 bp and is similar to that of A. c. cerana. It contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one A + T-rich control region. All protein-coding genes are initiated by ATT and ATG codons and are terminated by the typical stop codon TAA or TAG, except for the start codon of ATP8 which ends with C. All tRNA genes typically form a cloverleaf secondary structure, except for tRNA-Ser (AGN).

A simulation study on variation in response to selection and population size required for selection programmes.

SUMMARY To obtain a simple formula for predicting variation in selection response, the drift variance of selection response has been approximated by that under random selection. Using computer simulation, the validity of this approximation was examined under various combinations of population size, heritability, and proportion selected. It was shown that the approximation gives a good prediction when the heritability of the selected trait is low, but produces a serious error when applied to a trait with high heritability. However, when the approximation was used for the prediction of coefficient of variation of selection response, a satisfactory prediction was obtained in all cases studied. Although this predictor includes a coincidental factor, it may be used as a criterion for determining the population size required for selection programmes. ZUSAMMENFASSUNG: Simulationsuntersuchung über Selektionserfolg und notwendige Populationsgrößen für Selektions-programme Zur Schätzung der Variabilität von Selektionserfolgen wurde die Driftvarianz durch die bei Zufallspaarung erwartete approximiert. Die Gültigkeit dieser Approximation wurde an verschiedenen Kombinationen von Populationsgröße, Heritabilität und Remontierungsprozentsat überprüft. Die Approximation ergibt gute Schätzwerte bei geringer Heritabilität, aber erhebliche Fehler bei hoher. Allerdings konnte der Variationskoeffizient des Selektionserfolges in allen Fällen zufriedenstellend geschätzt werden. Obwohl dies auf Über-bzw. Unterschätzung von Zähler wie Nenner zurückzuführen ist, kann es als Kriterium zur Bestimmung der bei Selektionsprogrammen notwendigen Populationsgröße verwendet werden.

Methods for minimizing the loss of genetic diversity in conserved populations with overlapping generations

Minimization of the average coancestry in a population has been theoretically proven to be the most efficient method to preserve genetic diversity. In the present study, based on a population genetic model, two methods to minimize the average coancestry in populations with overlapping generations were developed. For a given parental coancestry structure, the first method (OG) minimizes the average coancestry in the next generation, and the second method (LT) is designed to minimize the long-term accumulation of coancestry. The efficiencies of the two methods were examined by stochastic simulation. Compared to random choice of parents, the annual effective population sizes under the two proposed methods increased 2–3 folds. The difference among the two methods was small in a population with short generation interval. For populations with long generation intervals, the OG method showed a slightly larger annual effective size in an initial few years. However, in the subsequent years, the LT method gave a 5–15% larger annual effective size than the OG method. From these results, it is suggested that the LT method would be preferred to the OG method in most practical situations.

Complete mitochondrial genome of the Japanese bumblebee, Bombus hypocrita sapporensis (Insecta: Hymenoptera: Apidae)

Abstract In the present study, we describe the complete mitochondrial genome of the bumblebee, Bombus hypocrita sapporensis from the Rebun Island, in Hokkaido, Japan. The mitochondrial genome of B. hypocrita sapporensis includes a circular molecule of 15 700 bp. It contains 13 protein-coding genes, 22 tRNA genes, two rDNA genes and an A + T-rich control region. All protein-coding genes are initiated by ATA, ATG, and ATT codons and are terminated by the typical stop codon TAA or T, except for ND4L, which ends with TA. All tRNA genes typically form a cloverleaf secondary structure.

Effective population size for a sex-linked locus in populations under selection

The problem of selection in the prediction of effective population size for a sex-linked locus was addressed in terms of the cumulative effect of selection on change in frequency of a sex-linked neutral gene. To express the cumulative effect of selection, a transition matrix approach was used. It was found that the terms accounting for the cumulative change in gene frequency show different expressions, depending on the gametic pathways. This dependency is due to the fact that the heterogametic sex transmits a sex-linked gene only to offspring of the homogametic sex, whereas the homogametic sex transmits to offspring of both sexes. Monte Carlo simulation was carried out to check the obtained prediction equation. The result showed that there is a good agreement between observed and predicted effective sizes.