Genetic Structure of Japanese Scallop Population in Hokkaido, Analyzed by Mitochondrial Haplotype Distribution

To examine the genetic structure of Japanese scallop populations (Mizuhopecten yessoensis) in Hokkaido prefecture, Japan, and compare it with those in the Aomori prefecture, we applied a method for lineage analysis based on sequence variation in a mitochondrial DNA segment (NcR2). After showing that there was a low probability of doubly uniparental inheritance of mitochondrial DNA in the scallop, we sequenced the NcR2 regions of 914 individuals from 15 populations (13 in Hokkaido and 2 in Aomori). In total, 103 different haplotypes were detected. Results of homogeneity tests for pairwise populations and the fixation indices indicated that significant heterogeneity (P < 0.0005) and structuring (pairwise fixation index F_ST = 0.1606–0.4444, P = 0.0000; fixation index among groups F_CT = 0.1549, P = 0.0078) could be inferred between the Hokkaido and Aomori groups, but not among populations within the groups. Moreover, heterogeneity of the haplotype distribution between populations of the 1980s and 1990s or 2000s at the 4 culturing areas was not observed (P > 0.05), and the haplotype diversity between them was not significant (P = 0.05), suggesting that the culture operations had not imparted a significant effect on the genetic structure during these periods.     

利用17个微卫星标记分析鳙鱼的遗传多样性

选用本实验室克隆的17个鳙鱼微卫星分子标记分析四川泸州和江西鄱阳湖的两个种群鳙鱼的遗传多样性及种质特性,计算和统计了杂合度、多态信息含量（PIC）、有效等位基因数、等位基因频率、遗传距离、遗传相似系数、Hardy-Weinberg平衡偏离指数等方面内容。结果表明：选择使用17个微卫星标记,其中有4个为单态标记,13个为多态标记。江西和四川鳙鱼群体每个微卫星位点的平均等位基因数分别为3.325及3.882,平均有效等位基因数分别为3.531及2.676,多态位点百分率分别为82.4及70.5, 17个微卫星标记共有等位基因71个,多态微卫星位点的PIC在0.114~0.960之间变动,平均为0.417 ,两群体位点平均观测杂合度为0.385和0.452,平均期望杂合度为0.360和0.422,两个群体间的遗传相似系数为0.897,群体间的遗传距离为0.109。     

Molecular and genetic characterization of the allelic variants of Du215, Du281, Du323, and Du47G microsatellite loci in parthenogenetic lizard <Emphasis Type="Italic">Darevskia armeniaca</Emphasis> (Lacertidae)

A key issue in the study of unisexual (parthenogenetic) vertebrate species is the determination of their genetic and clonal diversity. In pursuing this aim, various markers of nuclear and mitochondrial genomes can be used. The most effective genetic markers include microsatellite DNA, characterized by high variability. The development and characterization of such markers is a necessary step in the genetic studies of parthenogenetic species. In the present study, using locus-specific PCR, for the first time, an analysis of allelic polymorphism of four microsatellite loci is performed in the populations of parthenogenetic species Darevskia armeniaca. In the studied populations, allelic variants of each locus are identified, and the nucleotide sequences of each allele are determined. It is demonstrated that allele differences are associated with the variation in the structure of microsatellite clusters and single nucleotide substitutions at fixed distances in flanking DNA regions. Structural allele variations form haplotype markers that are specific to each allele and are inherited from their parental bisexual species. It is established which of the parental alleles of each locus were inherited by the parthenogenetic species. The characteristics of the distribution and frequency of the alleles of microsatellite loci in the populations of D. armeniaca determining specific features of each population are obtained. The observed heterozygosity of the populations at the studied loci and the mutation rates in genome regions, as well as Nei’s genetic distances between the studied populations, are determined, and the phylogenetic relationships between them are established.     

Genetic structure of the clonal herb Tanakaea radicans (Saxifragaceae) at multiple spatial scales,revealed by nuclear and mitochondrial microsatellite markers

The genus Tanakaea is a plant genus that consists of one or two evergreen herbaceous species in Japan and China. As rithophytic plant species occur on shaded rocks, the populations are usually isolated and sporadically found in disjunct areas. To evaluate the genetic structure of the species at multiple spatial scales, 10 nuclear and mitochondrial microsatellite markers were developed. The novel markers showed high genetic variations (two to 15 alleles and H_e from 0.400 to 0.894). Clonal samples were identified with the probability of identity of 9.0E‐8. When evaluated with 11 populations in Japan, significant genetic differentiation between regional population groups was detected (F_ST = 0.313 between Shikoku and Honshu islands), suggesting they have long been isolated from each other. Overall, these markers will be useful for population genetic research to investigate clonal structure and genetic diversity and levels of genetic differentiation between the geographically isolated populations.     

Genetic structure in the marbled rockfish (Sebastiscus marmoratus) across most of the distribution in the northwestern Pacific

The marbled rockfish (Sebastiscus marmoratus) is an important species that is widely distributed across the marginal seas of the northwestern Pacific. Several kinds of DNA markers, such as amplified fragment length polymorphisms (AFLP), mitochondrial DNA (mtDNA) and single nucleotide polymorphisms (SNPs), have been used to assess the population genetic characteristics of this species in previous studies. However, there have been no genetic profiling studies to cover the entire distribution. Here, six highly polymorphic microsatellite markers were applied to 18 populations across a spatially large area (from the Sea of Japan in the north to the South China Sea in the south). The results showed that the whole population exhibits high, stable genetic diversity, low relatedness and large effective population size. There was very weak genetic differentiation overall and no isolation by distance occurred among the populations, which may be attributed to significant contemporary gene flow, each generation. The above results may lead us to infer that the recent S. marmoratus population structure could be considered as one large integrated population. The present study will be beneficial to population conservation and fisheries management of S. marmoratus and will lead to better insights into the genetic characteristics of other species that belong to the Sebastidae family.     

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

China is regarded as one of the domestication cen-ters for chickens and archaeological studies provided evidence of chicken domestication in northern Chinaas early as 6000 BC[1]. At present, China has the larg-est chicken population in the world, represen…     

Isolation and characterization of new microsatellite markers from the Japanese scallop (<Emphasis Type="Italic">Patinopecten yessoensis</Emphasis>)

Twenty polymorphic microsatellite loci were isolated from the Japanese scallop (Patinopecten yessoensis) using a method of hybridizing twice. The genetic diversity was analyzed by these microsatellite markers in field specimens from Zhangzidao Island in Liaoning Province, China. Observed heterozygosity (H _o), expected heterozygosity (H _e), number of effective alleles (N _e), and polymorphism information contents (PIC) were calculated. The heterozygote deficiency or excess was detected by the fixation index (Fis). The Hardy–Weinberg equilibrium was tested by possibilities (P _HWE) using chi-square test. Results indicate that the average of allele numbers was 6.0. The mean values of the parameters H _o, H _e, N _e, and PIC were 0.7921, 0.7076, 4.4347, and 0.6684, respectively. Only 4 of 20 microsatellite markers showed heterozygote deficiency including loci FJ262370, FJ262381, FJ262384, and FJ262400. The P _HWE value indicates the wild population deviated somewhat from the Hardy–Weinberg equilibrium. These newly isolated markers increase the available molecular resources of the Japanese scallop.     

Population structure of the invasive forest pathogen Hymenoscyphus pseudoalbidus

Understanding the genetic diversity and structure of invasive pathogens in source and in introduced areas is crucial to the revelation of hidden biological features of an organism, to the reconstruction of the course of invasions and to the establishment of effective control measures. Hymenoscyphus pseudoalbidus (anamorph: Chalara fraxinea) is an invasive and highly destructive fungal pathogen found on common ash Fraxinus excelsior in Europe and is native to East Asia. To gain insights into its dispersal mechanisms and history of invasion, we used microsatellite markers and characterized the genetic structure and diversity of H. pseudoalbidus populations at three spatial levels: (i) between Europe and Japan, (ii) in Europe and (iii) at the epidemic's front in Switzerland. Phylogenetic and network analysis demonstrated that individuals from both regions are conspecific. However, populations from Japan harboured a higher genetic diversity and were genetically differentiated from European ones. No evident population structure was found among the 1208 European strains using Bayesian and multivariate clustering analysis. Only the distribution of genetic diversity in space, pairwise population differentiation (G_ST) and the spatial analysis of principal components revealed a faint geographical pattern around Europe. A significant allele deficiency in most European populations pointed to a recent genetic bottleneck, whereas no pattern of isolation by distance was found. Our data suggest that H. pseudoalbidus was introduced just once by at least two individuals. The potential source region of H. pseudoalbidus is vast, and further investigations are required for a more accurate localization of the source population.     

The genetic structure of endangered indigenous populations of the amago salmon, <Emphasis Type="Italic">Oncorhynchus</Emphasis><Emphasis Type="Italic">masou</Emphasis><Emphasis Type="Italic">ishikawae</Emphasis>, in Japan

The amago salmon, Oncorhynchus masou ishikawae, is an endemic subspecies of O. masou in Japan. Owing to the extensive stocking of hatchery fish throughout Japan, indigenous populations of O. m. ishikawae are now on the verge of extinction. We examined the genetic effects of stocking hatchery fish on wild populations in the River Koza, Japan, using microsatellite and mitochondrial DNA (mtDNA) markers. For mtDNA, haplotype mt1, which is common in wild populations, was present exclusively in isolated wild populations assumed to be unaffected by previous stocking, while it was never observed in hatchery fish. Genetic diversity was much higher in wild populations in the stocked area, which shared many mtDNA haplotypes with hatchery fish, than in isolated wild populations with haplotype mt1. Pairwise F _ST estimates based on microsatellites showed significant differentiation among the isolated populations with many microsatellite loci monomorphic. Significant deviation from Hardy–Weinberg equilibrium was observed in wild populations in the area subject to stocking, where a Bayesian-based assignment test showed a high level of introgression with hatchery fish. These results suggest that wild populations with haplotype mt1, which became isolated through anthropogenic environmental change in the 1950–1960s, represent indigenous populations of O. m. ishikawae in the River Koza. They have low genetic diversity, most likely caused by genetic bottlenecks following damming and environmental deterioration, while stocking of hatchery fish over the past 30 years apparently had a large impact on the genetic structure of wild populations in the main channel of the River Koza.     

Strong genetic isolation despite wide distribution in a commercially exploited coastal shark

The common smoothhound, Mustelus mustelus, is an epibenthic species targeted by fisheries around the world driven by the increasing demand for shark products. Given the wide-spread occurrence of this species and corresponding lack of molecular data in many areas of said distribution, baseline molecular assessments of this commercially important shark may contribute to finer-scale analyses in areas in which this species is targeted. Therefore, population genetic analyses were conducted along the East Atlantic, from the Mediterranean Sea to the south-east coast of Africa, using microsatellite markers and the mitochondrial control region (mtCR). Overall, M. mustelus displayed low to moderate genetic diversity, with the Mediterranean populations appearing to exhibit the lowest mitochondrial diversity, and the west African populations displaying the lowest nuclear diversity. Microsatellite analysis indicated strong genetic differentiation between the three regions, with finer-scale population structure in each region, without correlation between genetic and geographical distance. For the mtCR sequences, a total of 18 haplotypes were identified, with a high degree of divergence discernable between the regions, largely in accordance with the microsatellite data. The study documents a remarkable level of population isolation across a vast area, suggesting little or no present-day connectivity among extant populations. The findings may serve as an essential baseline for global population management and commercial traceability of this threatened shark.

     

The genetic population structure of lacustrine sockeye salmon, <Emphasis Type="Italic">Oncorhynchus nerka,</Emphasis> in Japan as the endangered species

Lacustrine sockeye salmon (Oncorhynchus nerka) are listed as an endangered species in Japan despite little genetic information on their population structure. In order to clarify the genetic diversity and structure of Japanese populations for evaluating on the bottleneck effect and an endangered species, we analyzed the ND5 region of mitochondrial DNA (mtDNA) and 45 single nucleotide polymorphisms (SNPs) in 640 lacustrine sockeye salmon in Japan and 80 anadromous sockeye salmon in Iliamna Lake of Alaska. The genetic diversity of the Japanese population in both mtDNA and SNPs was significantly less than that of the Iliamna Lake population. Moreover, all Japanese populations had SNP loci deviating from the HWE. In spite of low genetic diversity, the SNP analyses resulted that the Japanese population was significantly divided into three groups. These suggest that Japanese sockeye salmon populations should be protected as an endangered species and genetically disturbed by the hatchery program and transplantations.     

Genetic diversity and structure of the endangered lady's slipper orchid Cypripedium japonicum Thunb. (Orchidaceae) in Japan

Cypripedium japonicum Thunb. (Orchidaceae), once a common perennial herb, is now designated as endangered throughout most of its distribution due to habitat destruction and fragmentation, and the impacts of horticultural collection. We investigated the genetic characteristics of this species for conservation purposes, using microsatellite markers to examine the genetic diversity and structure of 15 native and 5 ex situ populations in Japan. The results imply that although allelic variation is low in Japanese C. japonicum, sexual reproduction by seed, as well as clonal propagation, may occur in some populations. Both native and ex situ populations were found to be genetically differentiated, indicating that some populations may have experienced recent population declines, genetic fragmentation, or bottlenecks. The degree of genetic drift from the putative ancestral population, inferred through STRUCTURE analysis, was more pronounced in northern populations than in southern populations. Some of the ex situ conserved populations exhibited a low degree of differentiation from ancestral native populations. Our results imply that conservation of C. japonicum in Japan is best supported by maintaining individual populations and their unique genetic characteristics.     

Variation in blood proteins and mitochondrial DNA within and between local populations of longtail macaques,Macaca fascicularis on the Island of Java, Indonesia

We examined 31 blood protein loci, and restriction fragment length profiles of a PCR product of mitochondrial DNA containing the D-loop region using five kinds of restriction endonucleases (HaeIII,HinfI,MboII,MspI, andSau3 AI) in order to quantify the level of genetic variation of longtail macaques,Macaca fascicularis. Samples were collected from nine social groups in five localities of West Java, Indonesia. The average heterozygosity per individual was 0.060 and 15.7% of the loci were polymorphic (P_poly) over all populations in the protein analysis. There was no mtDNA haplotype variation within either social groups or local populations. To the contrary, great diversity was observed among local populations. Both nuclear diversity (measured byNei's standard genetic distance) and mitochondrial diversity (measured by sequence divergence) showed a significantly positive correlation with geographic distance. There was no significant correlation between these two genetic markers, however. The genetic structure of the population was evaluated in terms of local inbreeding and temporal changes in allele frequency. Differences between nuclear and mitochondrial data are discussed in relation to gender specific migration and lineage sorting.     

Extensive gene flow over Europe and possible speciation over Eurasia in the ectomycorrhizal basidiomycete Laccaria amethystina complex

Biogeographical patterns and large-scale genetic structure have been little studied in ectomycorrhizal (EM) fungi, despite the ecological and economic importance of EM symbioses. We coupled population genetics and phylogenetic approaches to understand spatial structure in fungal populations on a continental scale. Using nine microsatellite markers, we characterized gene flow among 16 populations of the widespread EM basidiomycete Laccaria amethystina over Europe (i.e. over 2900 km). We also widened our scope to two additional populations from Japan (10(4) km away) and compared them with European populations through microsatellite markers and multilocus phylogenies, using three nuclear genes (NAR, G6PD and ribosomal DNA) and two mitochondrial ribosomal genes. European L. amethystina populations displayed limited differentiation (average F(ST) = 0.041) and very weak isolation by distance (IBD). This panmictic European pattern may result from effective aerial dispersal of spores, high genetic diversity in populations and mutualistic interactions with multiple hosts that all facilitate migration. The multilocus phylogeny based on nuclear genes confirmed that Japanese and European specimens were closely related but clustered on a geographical basis. By using microsatellite markers, we found that Japanese populations were strongly differentiated from the European populations (F(ST) = 0.416), more than expected by extrapolating the European pattern of IBD. Population structure analyses clearly separated the populations into two clusters, i.e. European and Japanese clusters. We discuss the possibility of IBD in a continuous population (considering some evidence for a ring species over the Northern Hemisphere) vs. an allopatric speciation over Eurasia, making L. amethystina a promising model of intercontinental species for future studies.     

Genetic diversity and phylogeography of Daphnia similoides sinensis located in the middle and lower reaches of the Yangtze River

Geographical patterns, climate, and environmental change have important influences on the distribution and spread of aquatic organisms. However, the relationships between the geographical pattern and phylogenetics of Daphnia as well as environmental change are not well known. The genetic diversity and phylogeography of seven D. similoides sinensis populations located in the middle and lower reaches of the Yangtze River were investigated based on the combination of mitochondrial (COI gene) and nuclear (14 microsatellite primers) markers. Based on the mitochondrial gene markers, D. similoides sinensis from the middle and lower reaches of the Yangtze River had one ancestral haplotype and two evolutionary clades. In addition, D. similoides sinensis population deviated from neutral evolution, showing signs of a bottleneck effect followed by population expansion. Based on the microsatellite markers, the seven D. similoides sinensis populations formed three main groups. The dendrogram (NJ/ME) showed that D. similoides sinensis based on the mitochondrial genes marker were obviously clustered two main clades, whereas there were three clades based on the microsatellite markers. Our results suggested that the habitat fragmentation due to the barrier of the dams and sluices promoted the genetic differentiation and phylogeography of D. similoides sinensis populations in the middle and lower reaches of the Yangtze River.     

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

China is rich in chicken genetic resources, and many indigenous breeds can be found throughout the country. Due to poor productive ability, some of them are threatened by the commercial varieties from domestic and foreign breeding companies. In a large-scale investigation into the current status of Chinese poultry genetic resources, 78 indigenous chicken breeds were surveyed and their blood samples collected. The genomes of these chickens were screened using microsatellite analysis. A total of 2740 individuals were genotyped for 27 microsatellite markers on 13 chromosomes. The number of alleles of the 27 markers ranged from 6 to 51 per locus with a mean of 18.74. Heterozygosity (H) values of the 78 chicken breeds were all more than 0.5. The average H value (0.622) and polymorphism information content (PIC, 0.573) of these breeds suggested that the Chinese indigenous chickens possessed more genetic diversity than that reported in many other countries. The fixation coefficients of subpopulations within the total population (F _ST) for the 27 loci varied from 0.065 (LEI0166) to 0.209 (MCW0078), with a mean of 0.106. For all detected microsatellite loci, only one (LEI0194) deviated from Hardy-Weinberg equilibrium (HWE) across all the populations. As genetic drift or non-random mating can occur in small populations, breeds kept on conservation farms such as Langshan chicken generally had lower H values, while those kept on large populations within conservation regions possessed higher polymorphisms. The high genetic diversity in Chinese indigenous breeds is in agreement with great phenotypic variation of these breeds. Using Nei’s genetic distance and the Neighbor-Joining method, the indigenous Chinese chickens were classified into six categories that were generally consistent with their geographic distributions. The molecular information of genetic diversity will play an important role in conservation, supervision, and utilization of the chicken resources.     

Population differentiation in the Pacific white-sided dolphin Lagenorhynchus obliquidens inferred from mitochondrial DNA and microsatellite analyses

We investigated genetic diversity and differentiation of the Pacific white-sided dolphin (Lagenorhynchus obliquidens) in Japanese coastal waters and offshore North Pacific by analyzing mitochondrial DNA and nuclear microsatellite variation. A total of 519 bp of the mitochondrial control region was sequenced and five microsatellite locus were genotyped for 59 individuals. A high level of haplotypic diversity (h=96.1%), moderate level of nucleotide diversity (pi=1.65%) and average expected heterozygosity (HE=0.66-0.76) were within an extent of those reported for other odontocetes. Consistent genetic difference between the samples from Japanese coastal Pacific-Sea of Japan and offshore North Pacific was indicated by analyses of molecular variance (AMOVAs) based on mtDNA and microsatellite variations, comparison of genetic variabilities, and geographical distributions of mtDNA haplotypes and microsatellite alleles. This result suggests that Pacific white-sided dolphins in each of the above two areas belong to different populations between which gene flow has been severely restricted. The low genetic diversity and mtDNA genealogy of the population in Japanese coastal waters suggest that it originated from a small population that colonized the Sea of Japan or that experienced population reduction when this Sea was isolated from the North Pacific during a glacial period in the Late Pleistocene.     

Genetic diversity and biogeography of native and introduced populations of Ulva pertusa (Ulvales,Chlorophyta)

Genetic diversity of native and introduced populations of Ulva pertusa (Ulvales, Chlorophyta) was examined using genetic markers of chloroplast, mitochondria and nuclear non‐coding region sequences. In the preliminary investigations to genetically identify the species for further analyses, U. pertusa was found only from temperate coasts of the more extensive collection sites including tropical coasts suggesting that it is a temperate species and basically not distributed in tropical regions. For chloroplast and mitochondrial sequences, repeating patterns of short tandem repeat sequences and nucleotide substitutions were used to recognize the haplotypes (genetic types). A total of 48 haplotypes based on combinations of chloroplast and mitochondrial haplotypes were recognized in the 244 specimens collected in the presumptive native range (Northeast Asia) and introduced populations (North America, Australia, New Zealand, Chile and Europe). Among them, 46 haplotypes (H1–H8 and H11–H48) were recognized in Northeast Asia, whereas only 1–5 haplotypes were recognized in the other areas. Nuclear microsatellite sequences were also analyzed. The lengths of the PCR products including the nuclear microsatellite region of 234 specimens were determined, and a total of 17 genotypes were recognized. Among them, 14 genotypes were found in Northeast Asia, whereas 1–7 genotypes were recognized in the other areas. Based on the results, the hypothesis that the native range of the species is in Northeast Asia was supported, and the populations outside this range were concluded to be non‐indigenous populations.     

Regional and local spatial genetic structure of Siberian primrose populations in Northern Europe

We have investigated the local and regional scale genetic structure of Siberian primrose (Primula nutans) populations in Northern Europe. The genetic diversity and structure of fifteen populations sampled from the Bothnian Bay in Finland, the Barents Sea in Norway and the White Sea in Russia were assessed using eleven microsatellite markers. We investigated the distribution of genetic variation within and between populations, and studied the local genetic structure using spatial autocorrelation analysis. We found very low genetic and allelic diversity in the Bothnian Bay and Barents Sea populations, and only slightly higher in the White Sea population. The level of genetic differentiation between the regions was very high, whereas differentiation between the populations within the regions was moderate. We found no spatial structuring of populations in any region suggesting efficient dispersal on a local scale. Clonal reproduction seemed to have no effect on genetic structure.     

Application of Microsatellite Markers to Population Genetics Studies of Japanese Flounder Paralichthys olivaceus

We examined population genetic structure by means of microsatellite analysis among 7 Japanese flounder (Paralichthys olivaceus) populations collected from coastal sea areas around Japan. As was expected, all of the 11 microsatellite loci examined were variable in all populations (number of alleles per locus, 15.2–18.2; average of expected heterozygosity, 0.74–0.78). Eleven population pairs in 21 possible pairwise comparisons showed significant genetic heterogeneity associated with allele frequency distributions or fixation index (F _ST ). Modified Cavalli-Sforza chord distance (D _A ) and Nei's standard genetic distance (D _ST ) ranged from 0.051 to 0.090, and from 0.000 to 0.025, respectively. There was evidence that the populations assessed in this study were not drawn from a single panmictic population; however, it appears that Japanese flounder populations around Japan are not well-structured, as an estimate of the fixation index value among the 7 localities was very low (F _ST = 0.0025). Received April 27, 2001; accepted June 27, 2001.