Genetic divergence and relationships among smelts of the genus Osmerus from the Russian waters

Smelts of the genus Osmerus, O. eperlanus and O. mordax dentes, inhabiting the basins of the Atlantic, Arctic, and Pacific oceans were investigated using RFLP analysis of the mitochondrial DNA segments A8/A6/COIII/ND3 and ND3/ND4, and sequencing of the cytb and COI genes (mtDNA), and intron 1 of the rpS7 gene (nDNA). A total of 14 samples from the populations from most part of the Russian range were examined. The mean values of haplotype and nucleotide diversity constituted 0.5997 +/- 0.11264 and 0.003201 for O. m. dentex, and 0.3086 +/- 0.09892 and 0.000431 for O. eperlanus, respectively. The high level of interspecific diversity (12.94%) along with the low level of intraspercific diversity (0.049% for O. m. dentex, and 0.001% for O. eperlanus was observed. The dendrograms (UPGMA, NJ, MP, and BA) constructed using the data of RFLP analysis of mtDNA, along with the sequencing data of mitochondrial and nuclear genes were congruent. The representatives of O. eperlanus and O. m. dentex formed steady clusters in accordance with their species affiliation, albeit without subdivision into local populations depending on their geographic locality.     

Genetic individualization of sable (Martes zibellina L. 1758) using microsatellites

Genetic individualization based on non-invasive sampling is crucial for estimating the numbers of individuals in endangered mammalian populations. In sable (Martes zibellina)-poaching cases, identifying the number of animals involved is critical for determining the penalty. In addition, investigating animal numbers for wild sable populations requires genetic individualization when collecting several samples in neighboring regions. Microsatellites have been demonstrated to be reliable markers for individual identification. Thirty-three microsatellite loci derived from Mustelidae were selected to develop a genetic individualization method for sable. Three reference populations containing 54 unrelated sables were used to calculate allele number, allelic frequencies, and the polymorphic information content of each locus. The data were subsequently used to assess the validity of a combination of twelve loci for sable individualization. We defined twelve polymorphic loci that were easy to be amplified and genotyped. Four significant deviations from Hardy-Weinberg equilibrium were observed among the 12?loci in the three populations. The match probability of an individual from the reference populations with a random individual based on the 12?loci was 1.37?×?10^?13. Using the combination of the twelve loci provides sufficient power to individualize sables considering the levels of microsatellite polymorphism observed. These loci were successfully applied to a case of sable poaching and provided valid evidence to determine the penalty. The genetic individualization of sable based on these loci might also be useful to investigate the numbers of animals in wild populations.     

Genetic analysis of twelve X-chromosomal STRs in Japanese and Chinese populations

We investigated the genetic markers of twelve X-STR loci in 670 healthy, unrelated Japanese (438 men and 232 women) from Tokyo and 488 Chinese (263 men and 225 women) from Shenyang, using the Investigator Argus X-12 kit. Allele and haplotype analyses of twelve X-STRs clustered into four linkage groups indicated that they are highly informative for forensic applications in Japanese and Chinese populations. Hardy–Weinberg equilibrium tests demonstrated no significant deviations in the two populations. Among the four closely linked X-STR trios, some haplotype unique to Japanese or Chinese population were detected. Haplotype diversity for each linkage group ranged from 0.9861 to 0.9968, showing high values in each of the study populations. The genetic distances between populations based on the 12 X-STR loci and the phylogenetic tree revealed long genetic distances between Asian and Caucasian populations and between Asian and African population (Moroccan). These results suggest that the twelve X-STR loci will contribute to forensic casework in Japanese and Chinese populations.     

青鱼野生与养殖群体遗传变异的微卫星分析

研究利用自主开发的12个微卫星标记, 对来自于长江水系4个野生群体(湖北石首、湖南湘江、江苏邗江、浙江嘉兴)和1个养殖群体(江苏吴江)青鱼(Mylopharyngodon piceus)进行遗传多样性和遗传结构分析。遗传多样性分析结果显示这12个位点多态信息含量(PIC)介于0.660—0.923, 表明这12个位点均具有高度多态性(PIC>0.5)。5个群体的平均等位基因数(N_a)介于7.917—11.667, 平均有效等位基因数(N_e)介于4.837—6.035; 平均观测杂合度介于0.713—0.861; 平均期望杂合度介于0.749—0.819; 平均多态信息含量介于0.711—0.788, 表明这5个群体均具有较高的遗传多样性。遗传距离分析结果表明4个野生群体之间遗传距离较近, 养殖群体与这4个野生群体遗传距离均较远。UPGMA系统进化树显示, 湘江群体和石首群体首先聚为一支, 然后与邗江群体和嘉兴群体聚为一支, 最后与吴江养殖群体聚为一支。这12个微卫星位点具有较为丰富的遗传多样性特征, 可以用于青鱼不同群体的种质资源的评估和遗传多样性的分析。     

Microsatellite markers for the diploid basidiomycete fungus Armillaria mellea

We isolated and characterized 12 microsatellite markers for two North American populations (California, Pennsylvania) of Armillaria mellea, a fungal pathogen responsible for Armillaria root disease of numerous woody plants. Allele frequency ranged from two to nine alleles per locus, and gene diversity ranged from 0.05 to 0.86. Of the 12 loci, eight loci were polymorphic in the California and Pennsylvania populations, and showed no evidence of heterozygote deficiencies or severe linkage disequilibrium. Our results suggest that we have isolated and characterized variable loci to estimate genotypic diversity, gene flow and migration, and to determine population structure of North American A. mellea.     

Microsatellite diversity among the primitive tribes of India

The present study was undertaken to determine the extent of diversity at 12 microsatellite short tandem repeat (STR) loci in seven primitive tribal populations of India with diverse linguistic and geographic backgrounds. DNA samples of 160 unrelated individuals were analyzed for 12 STR loci by multiplex polymerase chain reaction (PCR). Gene diversity analysis suggested that the average heterozygosity was uniformly high ( >0.7) in these groups and varied from 0.705 to 0.794. The Hardy-Weinberg equilibrium analysis revealed that these populations were in genetic equilibrium at almost all the loci. The overall G(ST) value was high (G(ST) = 0.051; range between 0.026 and 0.098 among the loci), reflecting the degree of differentiation/heterogeneity of seven populations studied for these loci. The cluster analysis and multidimensional scaling of genetic distances reveal two broad clusters of populations, besides Moolu Kurumba maintaining their distinct genetic identity vis-à-vis other populations. The genetic affinity for the three tribes of the Indo-European family could be explained based on geography and Language but not for the four Dravidian tribes as reflected by the NJT and MDS plots. For the overall data, the insignificant MANTEL correlations between genetic, linguistic and geographic distances suggest that the genetic variation among these tribes is not patterned along geographic and/or linguistic lines.     

Development of microsatellite markers for the endangered Neotropical tree species Tibouchina papyrus (Melastomataceae)

We isolated and characterized 12 microsatellite loci for Tibouchina papyrus (Melastomataceae), an endangered species with narrow and disjunct range, endemics to a few localities in "cerrado rupestre" from Central Brazil. These microsatellites were obtained by sequencing of a genomic shotgun library for primer design. Leaves from 96 individuals collected in the three known local populations were genotyped using the 12 primers designed to analyze the polymorphisms at each locus. The number of alleles per locus ranged from one to six; two loci were monomorphic. Among the polymorphic loci, expected heterozygosities ranged from 0.161 to 0.714. Combined paternity exclusion probability was 0.957 and combined genetic identity (0.051) was high for studies on parentage. Tibouchina papyrus is a rare and endemic tree species of outcrop quartzite and sandstone soils, with highly isolated populations, which may have lead to the low degree of polymorphism that we detected. Also, motifs of most loci are larger than dinucleotide, which typically display lower levels of polymorphism.     

Genetic differentiation among common and selected hatchery populations of flounder: Evidence from RAPD markers

Randomly amplified polymorphism DNA (RAPD) analysis was performed in order to evaluate one common population and two selected hatchery populations of flounder Paralichthys olivaceus. A total of 90 individuals belonging to three populations were screened using 12 different RAPD primers. A total of 71 loci were produced in the three studied populations, and 43.5%, 42.4% and 42.2% of these loci were polymorphic over all the genotypes tested in common, susceptible and resistant populations, respectively. The number of loci detected by single primers ranged from four to eight. The average heterozygosites of common, susceptible and resistant populations were 0.112, 0.103 and 0.111, respectively. Compared with the common population, the two selected hatchery populations, susceptible and resistant, showed some genetic differences including a smaller number of loci, a smaller number of polymorphic loci, a smaller number of genotypes and a smaller Shannon index. The present study confirmed that it is important to detect the genetic variability of the selected hatchery population for the conservation of natural flounder resources.     

梨小食心虫微卫星标记的扩增稳定性及多态性分析

【目的】筛选适合我国梨小食心虫Grapholita molesta种群遗传学研究的微卫星位点,并依据所筛选的微卫星位点进行梨小食心虫地理种群的遗传多样性分析。【方法】利用欧洲梨小食心虫和苹果蠹蛾Cydia pomonella种群中已报道的11个微卫星位点, 分析各位点在我国12个种群257头梨小食心虫样本中的扩增稳定性,再进行其多态性分析,筛选适合的位点,然后进行种群遗传多态性分析。【结果】在分析的11个微卫星位点中, 位点Gm01, Gm03, Gm04和Cyd15无法稳定扩增; 位点Gm05扩增成功率较低, 位点Gm07遗传多态性较低; 而位点Gm02, Gm06, Gm08, Gm09和Gm10等扩增效果稳定且遗传多态性丰富。这5个稳定扩增的微卫星位点平均等位基因数量（N_A）为7.417~12.500, 平均观察杂合度（H_o）为0.366~0.655, 平均期望杂合度（H_e）为0.642~0.846, 多态信息含量（PIC）为0.800~0.935。【结论】本研究成功筛选出位点Gm02, Gm06, Gm08, Gm09和Gm10等5个微卫星位点。基于这5个微卫星位点标记的结果显示, 山东和陕西不同梨小食心虫地理种群均具有丰富的遗传多样性。 这5个位点可以适用于我国梨小食心虫种群的进一步遗传分析研究。     

High levels of allozyme variation within populations and low allozyme divergence within and among species of Hemerocallis (Liliaceae)

Thirty populations from five species of Hemerocallis in Korea were analyzed by starch gel electrophoresis to measure genetic diversity and to determine genetic population structure and the amount of genetic divergence within and between species at 12 isozyme loci. In addition, Moran's I spatial autocorrelation statistics were used to examine the spatial distribution of allozyme polymorphisms in populations of H. thunbergii and H. hakuunensis. Populations of five Korean species maintain high levels of genetic variation and little differentiation among populations and species. Mean expected heterozygosities range from 0.165 in H. hongdoensis, an island endemic, to 0.265 in H. taeanensis, and a total of 81 alleles across the 12 loci were detected in the five species. G(ST) values for each of the five species were low, ranging from 0.051 in H. taeanensis to 0.078 in H. hakuunensis. Mean intraspecific Nei's genetic identities (I) between populations of the five species were all above 0.97. However, a considerable level of heterozygote deficiencies within populations was detected, ranging from 0.242 to 0.411 measured as F(IS) statistics. This deficiencies may be due to inbreeding, limited pollen and seed dispersal, or from the pooling of subpopulations that differ in allele frequencies. A small spatial scale population substructuring (<12 m) was found in H. thunbergii and H. hakuunensis. A group of populations from each of the five previously designated Hemerocallis species (based on their morphology, ecology, and phenology) agrees with our allozyme data, though pairwise comparisons among species had high I values (from 0.862, H. middendorffii vs. H. hongdoensis, to 0.969, H. thunbergii vs. H. taeanensis). This is attributed to the presence of the same high-frequency alleles in different species at seven loci. In addition, no "diagnostic allele" that appears in all populations of one species, but is absent in other species, was detected at the 12 isozyme loci. These all suggest that species of Hemerocallis in Korea may have recently derived from an ancestor or progenitor harboring high levels of genetic diversity.     

The distribution of individual heterozygosity in natural populations

Estimation of the distribution of the level of individual heterozygosity within natural populations is explored with both Monte-Carlo simulation studies and data from natural populations. Simulations indicate that heterozygosities estimated from as few as a dozen randomly chosen loci may, to some degree, reflect (r = 0.35) heterozygosity determined by 100 independent loci. The shape of the expected distribution of heterozygosity is heavily dependent upon levels of heterozygosity at the loci. Complete genetic data for 12 loci from 997 Fundulus heteroclitus are used to describe the distributions of heterozygosity for different localities, for age classes and for sexes. The distributions deviate from normality. Distributions from different localities are not different, but the distributions are heterogeneous among age classes at one of two localities and are heterogeneous between the sexes.     

Characterisation of 12 microsatellite loci in the Vietnamese commercial clam <Emphasis Type="Italic">Lutraria rhynchaena</Emphasis> Jonas 1844 (Heterodonta: Bivalvia: Mactridae) through next-generation sequencing

The marine clam Lutraria rhynchaena is gaining popularity as an aquaculture species in Asia. Lutraria populations are present in the wild throughout Vietnam and several stocks have been established and translocated for breeding and aquaculture grow-out purposes. In this study, we demonstrate the feasibility of utilising Illumina next-generation sequencing technology to streamline the identification and genotyping of microsatellite loci from this clam species. Based on an initial partial genome scan, 48 microsatellite markers with similar melting temperatures were identified and characterised. The 12 most suitable polymorphic loci were then genotyped using 51 individuals from a population in Quang Ninh Province, North Vietnam. Genetic variation was low (mean number of alleles per locus = 2.6; mean expected heterozygosity = 0.41). Two loci showed significant deviation from Hardy–Weinberg equilibrium (HWE) and the presence of null alleles, but there was no evidence of linkage disequilibrium among loci. Three additional populations were screened (n = 7–36) to test the geographic utility of the 12 loci, which revealed 100 % successful genotyping in two populations from central Vietnam (Nha Trang). However, a second population from north Vietnam (Co To) could not be successfully genotyped and morphological evidence and mitochondrial variation suggests that this population represents a cryptic species of Lutraria. Comparisons of the Qang Ninh and Nha Trang populations, excluding the 2 loci out of HWE, revealed statistically significant allelic variation at 4 loci. We reported the first microsatellite loci set for the marine clam Lutraria rhynchaena and demonstrated its potential in differentiating clam populations. Additionally, a cryptic species population of Lutraria rhynchaena was identified during initial loci development, underscoring the overlooked diversity of marine clam species in Vietnam and the need to genetically characterise population representatives prior to microsatellite development. The rapid identification and validation of microsatellite loci using next-generation sequencing technology warrant its integration into future microsatellite loci development for key aquaculture species in Vietnam and more generally, aquaculture countries in the South East Asia region.     

Twelve microsatellite loci for lake trout (Salvelinus namaycush)

We describe 12 microsatellite loci isolated from lake trout (Salvelinus namaycush). The number of alleles at these loci ranged from two to 11 with an average of 5.3 alleles per locus. The expected heterozygosity ranged from 0.29 to 0.76, with an average of 0.68. Accidental (or illegal) introductions of lake trout into watersheds are decimating native trout populations in the northern Rocky Mountains, and these loci will be useful for identifying the source of these introductions and for estimating the number of founding individuals.     

Polymorphic microsatellite loci for population studies of the Japanese scallop,Patinopecten yessoensis

Fifteen microsatellite loci were developed to examine the population structure of Japanese scallop, Patinopecten yessoensis. These markers were tested in samples from two geographically distant populations: the Sakhalin Island (Russia) and Dalian City (China). The mean numbers of alleles, observed and expected heterozygosities between the two populations were summarized by locus, but none of them show significant divergence between the two populations. Most loci conformed to Hardy–Weinberg expectation with the exception of loci HLJX‐06, HLJX‐12, HLJX‐13 and HLJX‐28, which had heterozygote deficits.     

菲律宾蛤仔EST-SSRs标记开发及不同地理群体遗传多样性

利用13对微卫星引物对大连、莆田、青岛3个地理群体蛤仔遗传多样性进行了检测。结果表明:13个基因座共检测到154个等位基因,每个座位检测到的等位基因数在2-7个之间,平均有效等位基因数为2.7657;3个群体平均观测杂合度分别为0.4387、0.4194、0.2383,平均期望杂合度分别为0.6488、0.6484、0.5526;群体间的遗传多样性差异不显著(P＞0.05)。NJ聚类结果显示大连和莆田群体的蛤仔亲缘关系较近,二者与青岛群体关系较远。3个群体均有不同程度的偏离Hardy-Weinberg平衡现象,表明各群体基因频率和基因型频率的稳定性相对较低。本研究所获得的微卫星标记的多态信息含量(PIC)>0.5,说明这些微卫星位点的多样性较高,可为下一步遗传图谱构建研究提供参考。     

A genetic affinity analysis of human populations

Genetic affinity of human populations based on allele frequency data was studied from two viewpoints. (1) The effect of the number of polymorphic loci on the reconstruction of a phylogenetic tree of human populations was empirically investigated. Genetic affinity trees were constructed based on data for 1–12 polymorphic loci, by using the neighbor-joining method. Geographical clustering of populations gradually appeared when the number of loci was increased. A new classification and terminology of higher order human population clusters is proposed based on these and other studies. (2) A new method of estimating the absolute divergence time of two populations is proposed, which is based on a diffusion equation that describes random genetic drift.     

Polymorphisms in Blood Proteins of Bos indicus and Bos taurus Cattle Breeds of Cameroon and Nigeria, and Description of New Albumin Variants

Polymorphisms in the five blood protein loci albumin (ALB), carbonic anhydrase (CA II), vitamin D binding protein (GC), haemoglobin (HBB), and transferrin (TF) were investigated in 520 individuals from 12 cattle populations (Bos indicus and Bos taurus) in Cameroon and Nigeria by isoelectric focusing with carrier ampholytes in ultrathin polyacrylamide gels (PAG-IEF) and by linear gradient polyacrylamide gel electrophoresis (PAGE). While all loci in nine populations were polymorphic with up to six alleles at the ALB and TF loci: the Namchi population showed monomorphism at the CA II locus and Muturu at the ALB, CA II, and HBB loci. There was a clear distinction between Bos indicus and Bos taurus breeds at the ALB locus with ALBB predominating in indicine and ALBA predominating in taurtine breeds. CA IIS, GCA, and HBBA were the most commonly occurring alleles in all populations. Two variants not described before were demonstrated by PAG-IEF at the ALB locus and named ALBJ and ALBK. Mean effective number of alleles as measure of intrabreed diversity was higher in zebu populations (2.040-2.288) as compared to taurine breeds (1.349-1.836). Significant deviations from Hardy-Weinberg equilibrium occurred in some populations at the HBB and TF loci. More haplotypes of ALB/GC occurred in the zebu than taurine breeds. ALBAGCA predominated in the taurine populations and ALBBGCA in the indicine populations. Influence of zebu genes on the Namchi and N'Dama taurine breeds was detected at the ALB, CA II, HBB, and TF loci, and estimated at 61.5% and 5.7%, respectively. The high resolution of PAG-IEF in screening for polymorphisms within diversity studies was demonstrated.     

Isolation and characterization of polymorphic microsatellite loci from Tetratheca ericifolia (Elaeocarpaceae)

We identified 11 informative microsatellite loci in Tetratheca ericifolia from an (AG)_n‐enriched library. Using these loci on 32 individuals from two populations (16 individuals from each), we detected an average of 11.3 alleles per locus (range of five to 21, average expected heterozygosity of 0.728), of which 56% were unique to one population or the other. All loci were amplifiable in seven to 12 of a further 12 species of Tetratheca under the same reaction conditions. The markers will be useful tools for evolutionary studies of this Australian endemic group.     

Isolation and characterization of macaroni penguin (Eudyptes chrysolophus) microsatellite loci and their utility in other penguin species (Spheniscidae, AVES)

We report the characterization of 25 microsatellite loci isolated from the macaroni penguin (Eudyptes chrysolophus). Thirteen loci were arranged into four multiplex sets for future genetic studies of macaroni penguin populations. All 25 loci were tested separately in each of four other penguin species [Adélie penguin (Pygoscelis adeliae), chinstrap penguin (Pygoscelis antarctica), gentoo penguin (Pygoscelis papua) and king penguin (Aptenodytes patagonicus)]. Between eight and 12 loci were polymorphic per species. These loci are expected to be useful for studies of population genetic structure in a range of penguin species.     

Genetic diversity and differentiation between the two remaining populations of the critically endangered Mediterranean monk seal

The Mediterranean monk seal Monachus monachus , is a critically-endangered species of which only two populations, separated by c . 4000 km, remain: the eastern Mediterranean (150–300 individuals) and the Atlantic/western Sahara populations (100–130 individuals). We measured current levels of nuclear genetic variation at 24 microsatellite loci in 12 seals from the eastern Mediterranean and 98 seals from the western Sahara population and assessed differences between them. In both populations, genetic variation was found to be low, with mean allelic richness for the loci polymorphic in the species of 2.09 and 1.96, respectively. For most loci, the observed allele frequency distributions in both populations were discontinuous and the size ranges similar. The eastern Mediterranean population had 14 private alleles and the western Sahara had 18, but with a much larger sample size. Highly significant differences in allele frequencies between the two populations were found for 14 out of 17 loci. F _ST between the two populations was 0.578 and the estimated number of migrants per generation was 0.046, both clearly indicating substantial genetic differentiation. From a conservation perspective, these results suggest that each population may act as a source for introducing additional genetic variation into the other population.