Polyandry may mitigate the negative impact of reproductive interference among bumblebees in Japan.

In social hymenopterans, monandry of the queen is an ancestral trait, and polyandry is a derived trait. Polyandry of the queen is the norm in a limited number of lineages, such as honeybees, leaf-cutting ants, Pogonomyrmex ants, and Vespula wasps, which presumably provide fitness advantages for the whole colony. The queen of the introduced bumblebee, Bombus terrestris, is polyandrous in Japan, whereas it is monandrous in native regions. We hypothesize that polyandry can evolve in a process that avoids the negative impacts of reproductive interference caused by interspecific mating and conducted genetic studies of the invasive species B. terrestris and two native subspecies, Bombus hypocrita sapporoensis and Bombus hypocrita hypocrita, in Japan. Our results revealed that although the native queens of B. hypocrita hypocrita allopatric with B. terrestris were strictly monandrous, the native queens of B. hypocrita sapporoensis sympatric with B. terrestris were polyandrous. These results suggested that the queens of native B. hypocrita sapporoensis do not experience negative impacts on interspecific mating from the invasive B. terrestris. We discuss the possibility that reproductive interference is a driving force in selection for multiple mating through an arms race between sympatric species.

Factors contributing to the swimmer puppy syndrome found in Labrador retrievers.

BACKGROUND: Swimmer puppy syndrome is a disease found in neonatal puppies mainly characterized by the inability to stand, but its direct cause is unknown. Since swimmer puppies were observed infrequently but continuously among the Labrador retriever colony at the Hokkaido Guide Dogs for the Blind Association in Japan, based on their birth record and pedigree, factors related to the onset of swimmer puppy syndrome in Labrador retrievers were examined. RESULTS: The total number of offspring over seven years was 436, of which 16 were swimmer puppies. Most of the affected puppies except one recovered steadily. As for the swimmer puppies, the litter size was significantly lower, and the body weights on the 10th and 28th day after delivery were significantly higher than the non-symptomatic puppies. These results suggested that the onset may be related to weight gain in the neonatal stages due to a small litter size. According to the genetic analysis, 26 ancestors common to the affected individuals were confirmed, but the causative individual could not be identified with the inbreeding coefficient. The heritability of the swimmer-puppy onset trait was 0.80, and the heritability for the the 10th-day body-weight trait was equally high at 0.78, both of which strongly suggest genetic involvement. CONCLUSIONS: In this study, the onset of swimmer puppy syndrome in the Labrador retrievers was associated with litter size and early weight gain, and result of study suggests that genetic influence might be involved.

Sampling method for estimating neutral allele frequency in a pedigreed population.

The estimated allele frequency at neutral DNA marker loci is a fundamental parameter for establishing a conservation scheme for a set of livestock breeds. In this study, we propose a novel 'minimum distance (MD) method' for estimating neutral allele frequencies, which minimizes the error by the use of pedigree information. Using computer simulation and actual microsatellite data for a pedigreed cattle population, the performance of the proposed method was compared with that of conventional random sampling (RND). MD manifests a promising superiority to RND, irrespective of the sample size and the depth of pedigree. It is theoretically demonstrated that the error of the estimates depends on both the sample size and the distance of founder allele frequencies between the sampled and the non-sampled individuals. MD samples individuals so as to minimize the latter source of estimation error.

Demographic analysis of breeding structure in Japanese thoroughbred population.

To investigate the breeding structure in the Japanese Thoroughbred population, we applied a demographic analysis to the populations of foals produced from 1978 to 2005. The migration rate estimated from the proportion of foals produced by imported breeding horses was around 40% over the investigated period. After early 1990s, the migration rate through stallions imported from USA sharply increased. The average generation interval was within range of 10.5-11.5 years. The longer generation interval of Thoroughbred was considered to be a reflection of the fact that Thoroughbred horses begin breeding only after completing their performance in races. After the peak of 729 in 1993, the number of sires of foals progressively declined to 358 in 2005. Although the coefficient of variation of the progeny number of sires was within range of 1.0-1.2 until early 1990s, it gradually increased and reached the value of 1.6-1.7 in recent years. The effective number of sires consistently decreased after the peak of 302.6 in 1992, and reached 120-130 in recent years, which is 25-30% of the actual number of sires. In parallel, the demographic estimate of the effective population size declined after early 1990s. The main cause of the observed change in the breeding structure was inferred to be the intensive use of a limited number of stallions for breeding.

Gene dropping analysis of ancestral contributions and allele survival in Japanese thoroughbred population.

Genetic contributions of nine historically important ancestors and allelic diversity in the Japanese Thoroughbred population were examined by applying the gene dropping simulation to the foals produced from 1978 to 2005. Full pedigree records traced to ancestors (base animals) born around 1890 were used for the simulation. Alleles originated from some of the historically important ancestors were found to be at risk of future extinction, although their genetic contributions to the foal population have increased during the last three decades. The proportion of surviving alleles to the total alleles assigned to the base animals was 8.0% in the foal population in 2005, suggesting that a large part of genetic variability contained in the base animals is extinct in the current population.

Interval estimation of the effective population size from heterozygote-excess in SNP markers.

The effective population size N(e) is an important parameter in population genetics and conservation biology. In recent years, there has been great interest in the use of molecular markers to estimate N(e). Although the point estimates from molecular markers in general suffer from a low reliability, the use of single nucleotide polymorphism (SNP) markers over a wide range of genome is expected to remarkably improve the reliability. In this study, expressions were derived for interval estimates of N(e) from one published method, the heterozygote-excess method, when it is applied to SNP markers. The conditional variance theory is applied to the derivation of a confidence interval for N(e) under random union of gametes, monogamy and polygyny. Stochastic simulation shows that the obtained confidence interval is slightly conservative, but fairly useful for practical applications. The result is illustrated with real data on SNP markers in a pig strain.

Maximum avoidance of inbreeding in haplodiploid populations.

Maximum avoidance of inbreeding (MAI) is a mating system, in which mates are as distantly related as possible. Although theoretical aspects and applications of MAI in diploid populations have been studied by many researchers, extension of MAI to haplodiploid populations is an unresolved problem. In this paper, this problem is addressed, and the following conclusions are derived. For a haplodiploid population with a Fibonacci number of females, a set of mating systems (one cycle MAI-hd) to avoid inbreeding to the maximum after one cycle practice of the set can be defined. But unlike MAI in diploid populations, repetition of one cycle MAI-hd cannot be MAI in the global range of generations. Numerical comparison with random mating and circular half-sib mating shows that as in diploid populations, repetition of one cycle MAI-hd in haplodiploid populations attains a lower inbreeding coefficient in early generations at the expense of a higher asymptotic rate of inbreeding.

The complete mitochondrial genome of the bumblebee, Bombus hypocrita sapporensis (Insecta: Hymenoptera: Apidae) from Hokkaido Island, Japan.

The complete is mitochondrial genome of the Japanese bumblebee Bombus hypocrita sapporensis from Hokkaido Island, Japan is analysed using next generation sequencing. The mitochondrial genome of B. h. sapporensis was observed to be a circular molecule of 15,835 bp. The average AT content in the B. h. sapporensis mitochondrial genome was 85.53%. It was predicted to contain 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes, along with one A + T-rich control region. The PCGs had ATA, ATG, or ATT as the initiation codon and were terminated by the typical stop codon TAA, except for Cytb. All the tRNA genes typically formed a cloverleaf secondary structure, except for trnE, trnF, and trnS1. The molecular phylogenetic analysis indicated that the B. h. sapporensis from Hokkaido Island population was most similar to that of the geographically isolated B. h. sapporensis from Rebun Island.

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

In the present report, we describe the complete mitochondrial genome of the common bumblebee, Bombus hypocrita hypocrita, from the Otome Plateau, in Yamanashi Prefecture, Japan. The mitochondrial genome of B. h. hypocrita is a circular molecule of 15,795 bp. It contains 13 protein-coding, 22 tRNA and two rDNA genes. The protein-coding genes had ATA, ATG or ATT as the initiation codon and were terminated by the typical stop codon TAA, except for ND4 and Cytb. All the tRNA genes typically formed a cloverleaf secondary structure, except for trnE and trnS1.

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

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).

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

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.

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

The effective population size, N e, is an important parameter in population genetics and conservation biology. It is, however, difficult to directly estimate N e 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 N eb 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 N eb 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.

Joint effect of selection, linkage and partial inbreeding on additive genetic variance in an infinite population.

Under the inifinitesimal model of gene effects, selection reduces the additive genetic variance by inducing negative linkage disequilibrium among selected genes. If the selected genes are linked, the decay of linkage disequilibrium is delayed, and the reduction of additive genetic variance is enhanced. Inbreeding in an infinite population also alters the additive genetic variance through the generation of positive association among genes within a locus. In the present study, the joint effect of selection, linkage and partial inbreeding (partial selfing or partial full-sib mating) on the additive genetic variance was modeled. The recurrence relations of the additive genetic variance between successive generations and the prediction equation of the asymptotic additive genetic variance were derived. Numerical computation showed that although partially inbred populations initially maintain larger genetic variances, the accumulated effect of selection overrides the effect of inbreeding. Stochastic simulation was carried out to check the precision of prediction, showing that the obtained equations give a satisfactory prediction during initial generations. However, the predicted values always overestimate the simulated values, especially in later generations. Based on these results, possible extensions and perspectives of the assumed model were discussed.

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.