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Non-invasive DNA genotyping using hair samples has become a common method in population surveys of Asiatic black bears ( Ursus thibetanus) in Japan; however, the accuracy of the genotyping data has rarely been discussed in empirical studies. Therefore, we conducted a large-scale pilot study to examine genotyping accuracy and sought an efficient way of error-checking hair-trapping data. We collected 2,067 hair samples, successfully determined the genotypes of 1,245 samples, and identified 295 individuals. The genotyping data were further divided into 3 subsets of data according to the number of hairs used for DNA extraction in each sample (1-4, 5-9, and ≥10 hairs), and the error rates of allelic dropout and false alleles were estimated for each subset using a maximum likelihood method. The genotyping error rates in the samples with ≥10 hairs were found to be lower than those in the samples with 1-4 and 5-9 hairs. The presence of erroneous genotypes among the identified individuals was further checked using a post hoc goodness-of-fit test that determined the match between the expected and observed frequencies of individual homozygotes at 0-6 loci. The results indicated the presence of erroneous genotypes, possibly as a result of allelic dropout, in the samples. Therefore, for improved accuracy, it is recommended that samples containing ≥10 hairs should be used for genotyping and a post hoc goodness-of-fit test should be performed to exclude erroneous genotypes before proceeding with downstream analysis such as capture-mark-recapture estimation. [ABSTRACT FROM AUTHOR]

The freshwater amphipod Crangonyx floridanus (Amphipoda: Crangonyctidae) is considered to have been recently introduced from North America to Japan, and the recorded sites at which it has been collected now cover nearly all of Japan except for the northern part. In this study, we surveyed further areas outside of its known distribution range, and examined the population genetic structure and the phylogenetic relationships between Japanese and North American populations of this species based on nuclear (18S rRNA) and mitochondrial (COI) DNA sequences. We found that this amphipod has already reached Hokkaido, northernmost Japan, which suggests that it has undergone rapid expansion in a pattern of concentric circles from the central part of Japan. Genetic analysis showed that the Japanese population is genetically homogeneous, in contrast to the genetic diversification of this species seen in North American Crangonyx populations. The process of introducing, establishing, and expanding this amphipod in Japan may be explained as follows. A limited number of individuals from a North American native population were probably inadvertently introduced and established somewhere within the Kanto region. The local population size then increased and its distribution range expanded rapidly across Japan. [ABSTRACT FROM AUTHOR]

Genetic endemism of island organisms and the threat to such organisms provided by artificially introduced genes are aspects of major interest in evolutionary and conservation studies of fishes. In this paper the genetic population structure of the oriental weatherloach, Misgurnus anguillicaudatus, in Sado Island of Japan was elucidated by phylogeographic analysis based on partial mitochondrial control region sequences. The specimens were sampled at 62 sites in Sado Island and 14 sites on the mainland close to the island. We found various haplotypes of different origins, most of which had already been reported from the mainland and other places of Japan. This suggests that the loach has been historically introduced to the island from various regions of Japan. Of the 62 sites on the island, cultured/nonnative individuals were confirmed to have been stocked at eight specific sites for feeding of re-introduced Japanese crested ibis ( Nipponia nippon). By a Mantel test, geographical and genetic distances were not significantly correlated among the local populations in Sado Island. However a significant correlation was found when the eight stocked local populations were excluded from the analysis. This implied that the genetic distribution pattern of the loach on the island has been disturbed by the stocking. In addition, the nucleotide diversity values of stocked local populations were significantly higher than those of other local populations, also a likely outcome of the stocking. In conclusion, the loach on the island likely had their origins in multiple historical introductions and colonizations, where more recent stocking for the ibis has caused further genetic disturbance to their local populations. [ABSTRACT FROM AUTHOR]

The article presents a study which examines if mutualism between aphid-ant Tuberculatus quercicola and Formica yessensis has a mutual effects on the microgeographical genetic population structure of both partner species. The collected aphids and ants from the dunes on the Ishikari Coast in Japan were subjected to microsatellite analysis. Results of the two-way analysis of variance (ANOVA) show a large genetic difference in the spring and summer samples of F. yessensis but not in T. quercicola.

Phylogenetic relationships were inferred for populations of the Ryukyu five-lined skink Plestiodon marginatus, a species showing an extraordinary distribution across the Tokara Tectonic Strait. Phylogenetic analyses of 809 base positions of the mitochondrial 12S and 16S rRNA genes supported collective divergence of the southern Tokara and northern Amami populations, which have been classified as P. m. oshimensis. A population from Nakanoshima, an island of the Tokara Group north of the Tokara Tectonic Strait, has the closest affinity with the Okinawajima population of P. m. marginatus rather than with the geographically closer southern Tokara and northern Amami populations. This result is concordant with that of a recent allozyme study and suggests an origin of the Nakanoshima population through long-distance dispersal from the Okinawa Island Group. Also, our results strongly suggest a closer relationship of a population of P. m. oshimensis from Okinoerabujima, a southern island of the Amami Group, with P. m. marginatus from Okinawajima than with the ''consubspecific'' southern Tokara and northern Amami populations. Both Nakanoshima and Okinoerabujima populations are usually referred to as P. m. oshimensis, and therefore our results indicate nonmonophyly of P. m. oshimensis in the current taxonomic arrangement. [ABSTRACT FROM AUTHOR]

A peculiar relationship exists between population genetics and invasion biology. Introduced populations often suffer a depletion of genetic variation, but they can persist and adapt to new environments. Here, we show that this relationship is observed in bluegill sunfish ( Lepomis macrochirus), an invasive exotic fish in Japan. Genetic analysis using selectively neutral genetic markers reconfirmed that the bluegill introduced into Japan from the United States in 1960 had a single origin with only 15 founders. The analysis also shows that in the process of range expansion, the introduced bluegills experienced severe depletion of genetic diversity due to the founder effect and/or genetic drift. Despite such a decline in genetic diversity, the bluegill populations exhibited a divergent feeding morphology in response to the colonized environments. Such a morphological divergence can facilitate prey exploitation, thereby causing a greater negative impact on native prey resources. Further, in a trophically polymorphic bluegill population in Lake Biwa, physiological characteristics and genetic structures of the intestinal bacterial communities were associated with the difference in diet among the trophic morphs in the host bluegill population. This empirical evidence suggests that despite the severe decline in genetic diversity, the introduced bluegill populations rapidly adapted to the new environment and formed diverse functional relationships with the native bacterial community. Thus, these findings suggest that genetic variation at selectively neutral markers does not always predict adaptability and invasiveness in introduced populations. [ABSTRACT FROM AUTHOR]

We studied the dynamics of hobo elements of Drosophila melanogaster in Japan with the goal of better understanding the invasion and evolution of transposons in natural populations. One hundred and twenty-six isofemale lines and 11 older stocks were tested for the presence and genetic phenotype of hobo elements. The oldest H strain, containing complete and deleted hobo elements, is Hikone-H (1957), but Hikone-R (1952) has no hobo-homologous sequences. The findings suggest that the hobo element invaded Japanese populations in the mid-1950s, at about the same time as the P element invasion in Japan. This chronology is consistent with the hypothesis of a recent worldwide hobo element invasion into D. melanogaster in the mid-1950s. In recently collected populations, H° strains (low hobo activity and high repression potency) are predominant, whereas H+ strains (high hobo activity and high repression potency) are predominant in the Sakishima Islands, the most southwestern islands of the Japanese archipelago. H′ strains (high hobo activity and low repression potency) were first found in limited island populations. Japanese populations have not only full-size hobo elements and 1.5 kb Th elements but also characteristic deletion derivatives (1.6 and 1.8 kb XhoI fragments) that we have named Jh elements. These results are consistent with transgenic experiments with complete hobo elements, in which populations evolved to H+ or H° via H′, and in which 1.8 kb fragments appeared. We conclude that hobo elements invaded the central region of Japan, spread to the far islands, and that the invasion is currently at an intermediate, nonequilibrium stage.Heredity (2006) 96, 426–433. doi:10.1038/sj.hdy.6800816; published online 26 April 2006 [ABSTRACT FROM AUTHOR]

Abstract: We examined the genotypic diversity of the large population of Heliopora coerulea, discovered recently in Ooura Bay, northern Okinawa Main Island Japan, together with another large population in Shiraho Reef, also in southwest Japan, using 9 polymorphic microsatellite markers. From each population, 40 samples were systematically collected along 2 transect lines with 4-m intervals. Surprisingly, all 40 samples from Ooura Bay were mono-genotypic, implying that the huge coral structure (30m×80m) originated from a single larva. Conversely, the 40 samples collected from the Shiraho Reef site all had different genotypes; measurements of genetic diversity, H E and H O , were 0.075–0.975 and 0.064–0.655, respectively. At least four factors are considered to make such a huge H. coerulea population with a single genotype in Ooura Bay, (1) origin of single larva or fragment (2) a genetic bottleneck, (3) post settlement selection, and (4) frequent asexual propagation. [Copyright &y& Elsevier]