Analysis of Microsatellite DNA Polymorphisms in Rockfish Sebastes thompsoni and Application to Population Genetics Studies

Population differentiation and relationships among 6 natural rockfish populations collected from northern coastal seas around Japan were assayed using microsatellite DNA loci. Seven loci examined were polymorphic in all populations. The number of alleles per locus ranged from 6.7 to 9.3, and the average of observed and expected heterozygosity ranged from 0.63 to 0.68, and from 0.66 to 0.69, respectively. The observed genotype frequencies at each locus were almost in agreement with Hardy-Weinberg expectations with two exceptions (P < .05). The allele frequencies of 16 population pairs were significantly different (P < .05). Genetic distance (D _A ) between 6 populations ranged from 0.03 to 0.08. According to a neighbor-joining tree generated from the D _A values, the 6 populations fell into 3 clusters. These clusters were correlated with the geographical positions of each population; larval dispersions due to water current were also found to have an effect on these results. Received May 2, 2000; accepted July 17, 2000.     

Isolation and Characterization of Twelve Microsatellite Loci for Rockfish (Sebastes)

We describe the first microsatellites for rockfishes in the diverse genus Sebastes. Clones containing microsatellites were isolated from the genomic library of a quillback rockfish, Sebastes maliger. Twelve microsatellites are characterized; six of these are polymorphic in quillback rockfish, and eight are polymorphic in at least one rockfish species on which they were tested. The number of alleles per variable locus ranged from 4 to 15 and averaged 6.8. The expected heterozygosities ranged from 0.38 to 0.79 and averaged 0.60 in these loci. These loci should prove valuable in studies examining species identification, population genetics, hybridization, paternity, kinship, and microsatellite evolution. Received September 8, 1998; accepted November 23, 1998.     

Population Dynamics Inferred from Temporal Variation at Microsatellite Loci in the Selfing Snail Bulinus Truncatus

We analyzed short-term forces acting on the genetics of subdivided populations based on a temporal survey of the microsatellite variability in the hermaphrodite freshwater snail Bulinus truncatus. This species inhabits temporary habitats, has a short generation time and exhibits variable rates of selfing. We studied the variability over three sampling dates in 12 Sahelian populations (1161 individuals). Classical genetic parameters (estimators of H(o), H(e), f, selfing rate and Fst) showed limited change over time whereas important temporal changes of allelic frequencies were detected for 10 of the ponds studied. These variations are not easily explained by selection, sampling drift and genetic drift alone and may be due to periodic migration. Indeed the habitats occupied by the populations studied are subject to large temporal fluctuations owing to annual cycles of drought and flood. In such ponds our results support a demographic model of population expansions and contractions under which available habitats, after the rainy season, are colonized by individuals originating from a smaller number of refuges (areas that never dry out in the deepest parts of the ponds). In contrast, selfing appeared to be an important force affecting the genetic structure in permanent ponds.     

Genetic Evidence of Postglacial Population Expansion in Puget Sound Rockfish (Sebastes emphaeus)

Several rockfish species (genus Sebastes) along the northeastern Pacific Ocean have rapidly declined in abundance owing in part to overfishing. A striking exception is the dwarf-like Puget Sound rockfish Sebastes emphaeus, whose densities have increased by several orders of magnitude over the last several decades. To describe their genetic structure, we sequenced 395 bp from the mitochondrial control region of 128 S. emphaeus adults from 5 locations spanning approximately 120 km of the Northwest Straits of Washington state. We detected no significant genetic differentiation among these populations and substantial genetic variation within populations, a pattern that may indicate high levels of ongoing gene flow. Preliminary data from 2 microsatellite loci are also consistent with panmixia. The mtDNA sequences also suggest that Puget Sound rockfish populations have expanded substantially since the retreat of Pleistocene glaciers made habitat in Puget Sound region available approximately 12,000 years ago.     

Genetic Population Structure of Chum Salmon in the Pacific Rim Inferred from Mitochondrial DNA Sequence Variation

We examined the genetic population structure of chum salmon, Oncorhynchus keta, in the Pacific Rim using mitochondrial (mt) DNA analysis. Nucleotide sequence analysis of about 500 bp in the variable portion of the 5′ end of the mtDNA control region revealed 20 variable nucleotide sites, which defined 30 haplotypes of three genealogical clades (A, B, and C), in more than 2,100 individuals of 48 populations from Japan (16), Korea (1), Russia (10), and North America (21 from Alaska, British Columbia, and Washington). The observed haplotypes were mostly associated with geographic regions, in that clade A and C haplotypes characterized Asian populations and clade B haplotypes distinguished North American populations. The haplotype diversity was highest in the Japanese populations, suggesting a greater genetic variation in the populations of Japan than those of Russia and North America. The analysis of molecular variance and contingency χ² tests demonstrated strong structuring among the three geographic groups of populations and weak to moderate structuring within Japanese and North American populations. These results suggest that the observed geographic pattern might be influenced primarily by historic expansions or colonizations and secondarily by low or restricted gene flow between local groups within regions. In addition to the analysis of population structure, mtDNA data may be useful for constructing a baseline for stock identification of mixed populations of high seas chum salmon.     

Genetic Variation and Structure in Natural Populations of a Medicinal Vegetable,Satureja bachtiarica,Inferred from Microsatellite Markers Developed Using Next-Generation Sequencing

Plant Molecular Biology Reporter - Satureja bachtiarica Bunge (Lamiaceae) is a medicinal plant native to Iran which is widely used in traditional medicine, as a spice and as a vegetable....     

Subtle Population Genetic Structure in Yelloweye Rockfish (Sebastes ruberrimus) Is Consistent with a Major Oceanographic Division in British Columbia,Canada

The boundaries between oceanographic domains often function as dispersal barriers for many temperate marine species with a dispersive pelagic larval phase. Yelloweye rockfish (Sebastes ruberrimus, YR) are widely distributed across the northeastern Pacific Ocean, inhabiting coastal rocky reefs from the Aleutian Islands in Alaska through southern California. This species exhibits an extended pelagic larval duration and has the capacity for long distance larval transport. We assayed 2,862 YR individuals from 13 general areas in the northeast Pacific Ocean for allelic variation at nine microsatellite loci. Bayesian model-based clustering analyses grouped individuals from the Strait of Georgia (SG) into a distinct genetic cluster, while individuals from outer coastal water locations (OCLs) were partitioned equally across two genetic clusters, including the cluster associated with the SG fish. Pairwise F_ST values were consistently an order of magnitude higher for comparisons between the SG and OCLs than they were for all OCL-OCL comparisons (∼0.016 vs. ∼0.001). This same pattern was observed across two time points when individuals were binned into an “old” and “young” group according to birth year (old: ∼0.020 vs. 0.0003; young: ∼0.020 vs. ∼0.004). Additionally, mean allelic richness was markedly lower within the SG compared to the OCLs (8.00 vs. 10.54–11.77). These results indicate that the Strait of Georgia “deep-basin” estuary oceanographic domain acts as a dispersal barrier from the outer coastal waters via the Juan de Fuca Strait. Alternatively, selection against maladapted dispersers across this oceanographic transition may underlie the observed genetic differentiation between the Georgia basin and the outer coastal waters, and further work is needed to confirm the SG-OCL divide acts as a barrier to larval dispersal.     

Occurrence and Molecular Identification of Microcotyle sebastis Isolated from Fish Farms of the Korean Rockfish,Sebastes schlegelii

Microcotyle sebastis is a gill monogenean ectoparasite that causes serious problems in the mariculture of the Korean rockfish, Sebastes schlegelii. In this study, we isolated the parasite from fish farms along the coasts of Tongyeong, South Korea in 2016, and characterized its infection, morphology and molecular phylogeny. The prevalence of M. sebastis infection during the study period ranged from 46.7% to 96.7%, and the mean intensity was 2.3 to 31.4 ind./fish, indicating that the fish was constantly exposed to parasitic infections throughout the year. Morphological observations under light and scanning electron microscopes of the M. sebastis isolates in this study showed the typical characteristics of the anterior prohaptor and posterior opisthaptor of monogenean parasites. In phylogenetic trees reconstructed using the nuclear 28S ribosomal RNA gene and the mitochondrial cytochrome c oxidase I gene (cox1), they consistently clustered together with their congeneric species, and showed the closest phylogenetic relationships to M. caudata and M. kasago in the cox1 tree.     

Timing of Parturition, Planktonic Duration, and Settlement Patterns of the Black Rockfish, Sebastes inermis

The microstructure of otoliths was used to examine the relationship among timing of parturition, duration of planktonic stage, and temporal patterns of settlement in young-of-the-year (YOY) Sebastes inermis collected during the settlement seasons of 1998–2001 in a seagrass bed at the northwestern coast of Japan. Parturition occurred in winter, predominantly around the new and full moons, and parturition dates were distributed mainly from early January to late February. In the 4 years YOY S. inermis settled into distinctive groups at early spring, synchronized mainly to a semi-lunar cycle at new and full moon phases; except for 1998, in which settlement occurred around the first and third quarter moons. In all years settlers extruded earlier in the parturition season encompassed the first settlement groups that appeared in the bed and vice versa. Planktonic period ranged from 53 to 113 days, and its mean values varied significantly among settlement groups and years. Mean size at settlement showed less variability among settled groups and between years (range: 18–26mm total length), which suggested an ideal size for settling and active migration. On the basis of our findings we discuss the extent to which the 'tidal control', 'settlement linkage', and 'competent size' hypotheses explain the temporal pattern of settlement.     

利用AIMs分析亚洲9个绵羊群体的群体结构

祖先信息标记(ancestry informative makers,AIMs)可用来分析群体的遗传结构.本研究利用Illumina Ovine SNP50芯片上的SNP位点,在云南乌骨绵羊和其他8个亚洲绵羊群体中以Rosenberg等定义的Informativeness统计量为筛选方法,选取Informativeness值最高的前20、50、100、500个SNP位点与相应数目的随机SNP位点分别用来推断群体的遗传结构.通过主成分分析和用fast STRUCURE推断祖先成分的方法,评价AIMs在推断亚洲绵羊群体遗传结构中的作用.研究显示,利用筛选到的高信息含量标记AIMs,可减少群体结构研究中需要的SNP位点数目.前50个AIMs可有效地将绵羊群体分为4个大类,这与利用全基因组SNPs分析得到的群体结构是一致的,即乌骨绵羊群体blackbone单独为一类、西藏群体changthangi和tibetan归为一类,孟加拉的banglandeshi、banglandeshi Garole群体和印度的Indian Garole群体归为一个类群,其余三个群体(印度尼西亚sumatran、garut群体和印度的deccani群体)近似归为一类.这4大类群在AIMs上存在显著的分化,利用这些位点信息可以为研究群体特征和进化关系提供线索.     

The Ecological and Population Characteristics of the Acadian Redfish Sebastes fasciatus Storer, 1856 (Scorpaeniformes: Sebastidae) Inferred from Analysis of its Parasite Community Composition

Russian Journal of Marine Biology - The results of a study of the composition, ecology, and formation of parasite communities in the Acadian redfish Sebastes fasciatus Storer, 1856 are considered...     

Microsatellite Analysis of Genetic Variation and Population Subdivision for the Black Muntjac, Muntiacus crinifrons

The black muntjac (Muntiacus crinifrons) is a rare deer found only in a restricted region in east China. Recent studies of mitochondrial DNA diversity have shown a markedly low level of nucleotide diversity for the species, and the Suichang population was genetically differentiated from the two other populations, in Huangshan and Tianmushan mountains. In this study, we extended the analysis of genetic diversity and population subdivision for the black muntjac using data from 11 highly polymorphic nuclear DNA microsatellite loci. Contrary to the results based on mtDNA data, the microsatellite loci revealed that the black muntjac retained a rather high nuclear genetic diversity (overall average H (E) = 0.78). Nevertheless, both types of markers supported the idea that the extant black muntjac population is genetically disrupted (overall phi (ST) = 0.16 for mtDNA and overall F (ST) = 0.053 for microsatellite, both P < 0.001). The correlation between genetic differentiation and geographic distance was not significant (Mantel test; P > 0.05), implying that the patterns of genetic differentiation observed in this study might result from recent habitat fragmentation or loss. Based on the results from the mtDNA and nuclear DNA data sets, two management units were defined for the species, Huangshan/Tianmushan and Suichang. We also recommend that a new captive population be established with individuals from the Suichang region as a founder source.     

Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers

Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains.     

Genetic Diversity and Structure of Two Prominent Zebu Cattle Breeds Adapted to the Arid Region of India Inferred from Microsatellite Polymorphism

This study aims to assess the genetic diversity and population structure of two major zebu dairy breeds (Tharparkar and Rathi) adapted to the arid region of Rajasthan state of India. Various variability estimates indicate the existence of sufficient within-breed genetic diversity. Mean estimates of F-statistics are significantly different from zero: F _IS = 0.112 ± 0.029, F _IT = 0.169 ± 0.033, F _ST = 0.065 ± 0.017. The overall positive value of F _IS (0.112) and an F _IT value (0.169) that is more than the F _ST (0.065) indicate departure from random mating. The drift-based estimates reflect a moderate yet significant level of breed differentiation between the Tharparkar and Rathi breeds. The evaluation of an exact test, showing that allele frequencies across all the loci differed significantly, supports the population differentiation. This is paralleled by the outcome of neighbor-joining clustering based on allele-sharing distance measures. The allocation of a high percentage of individuals (95.7%) to their population of origin and correspondence analysis further substantiates the existence of a cohesive genetic structure in both the breeds.     

德宏水牛微卫星标记分析的群体遗传变异

德宏水牛是云南省地方水牛的优良品种之一,为了进一步阐明其群体遗传变异和遗传结构,筛选了分别位于水牛14条染色体上的15对微卫星引物,对德宏水牛81个个体进行了检测分析.共检测到62个等位基因,每个座位等位基因数目从2到6个不等,平均等位基因数为4.13,该水牛群体期望杂合度和多态信息含量分别为0.6520±0.1526和0.5863±0.1789,各座位的遗传分化系数在0～0.0919之间,平均值为0.0202.每个座位的基因流较大,平均12.1502.研究结果表明德宏水牛群体遗传多样性较丰富,亚群间的遗传分化程度低,基因流较大,且很少发生近交.     

基于RAPD标记的丽江云杉遗传多样性及谱系地理

由于青藏高于独特的地理环境,第四纪冰期反复的退缩和扩展对目前该地区生物物种的地理分布及居群结构产生重要的影响。本文对这一地区特有分布物种丽江云杉(Picea likiangnsis)3个变种丽江云杉变种(var. likiangensis)、川西云杉变种(var. rubescens)和林芝云杉变种(var. linzhiensis)共11个种群228个个体进行RAPD分析,研究其遗传多样性及谱系地理。结果表明,该种具有较高的总体遗传多样性,多态位点达85.42%;然而在群体水平上却保持了相对低的多态性,种群间差异不显著,种群平均多态条带百分率为62.31%,Nei’s平均遗传多样性指数(H_E)为0.250,Shannon’s多样性指数(H_pop)从0.267到0.421 1。Nei’s基因多样性(G_ST=0.256)和AMOVE分析(Phi_st=0.236)表明,群体间有较高的遗传分化,群体间基因流有限(N_m=1.453 2),远远低于已报道的其它松科植物。UPGMA聚类分析表明3个形态上分离的变种没有单个聚成一枝,形成单系群。本研究认为,在第四纪冰期丽江云杉这一种在南部可能存在至少3个不同的避难所,北边和西边的居群应该是南方避难所里的居群经过不同的回迁路线而产生的,有可能是由于种内亚种间的反复杂交造成了目前的种群分布模式。     

Microsatellite Markers to Determine Population Genetic Structure in the Golden Anchovy,Coilia dussumieri

Coilia dussumieri (Valenciennes, 1848) commonly called as golden anchovy, constitutes a considerable fishery in the northern part of both the west and east coasts of India. Despite its clear-cut geographic isolation, the species is treated as a unit stock for fishery management purposes. We evaluated 32 microsatellite primer pairs from three closely related species (resource species) belonging to the family Engraulidae through cross-species amplification in C. dussumieri. Successful cross-priming was obtained with 10 loci, which were sequenced for confirmation of repeats. Loci were tested for delineating the genetic stock structure of four populations of C. dussumieri from both the coasts of India. The number of alleles per locus ranged from 8 to 18, with a mean of 12.3. Results of pairwise F _ST indicated genetic stock structuring between the east and west coast populations of India and also validated the utilization of identified microsatellite markers in population genetic structure analysis.     

Genetic Peculiarity of the Yakut Population as Inferred from Autosomal Loci

The autosomal gene pool of Yakuts was analyzed with a panel of polymorphic Alu insertions. The observed allele frequencies were typical for other Asian ethnic groups. Genetic differentiation of three Yakut populations was relatively high, 2%. East Siberian ethnic groups were shown to have a common gene pool and to experience no intense gene flow from other populations. Development of the Yakut gene pool was assumed to involve no substantial genetic effect of neighboring populations. The results fit both autochthonous and southern origin hypotheses.     

Study on Population Genetic Structure in Castanopsis fargesii with Microsatellite Markers

Genetic structure of four populations in Castanopsis fargesii Franch. in Fujian Province was studied with microsatellite (SSR) markers. A high level of genetic variation was detected in the populations of C. fargesii by using SSR with A=9.0, Ne=4.8, He=0.65 and the population differentiation coefficient ( Fst ) was only 0.031. The distributions of alleles of all loci were significantly different among the populations of C. fargesii , and the population differentiation could be found according to the distributions of SSR alleles. Some rare alleles in the populations of C. fargesii were revealed by SSR: Fifteen of 54 alleles appeared in one or two populations with lower frequencies; conservation of these rare alleles is of great importance.