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Allele Numbers (allele + number)
Selected AbstractsMicrosatellite markers for the polygamous termite Nasutitermes corniger (Isoptera: Termitidae)MOLECULAR ECOLOGY RESOURCES, Issue 2 2007LYNN ATKINSON Abstract We developed eight highly variable microsatellite markers for the termite Nasutitermes corniger. Allele number per locus ranged from nine to 34, and expected heterozygosity from 0.45 to 0.94, in samples from seven sites in the former canal zone of Panama. The utility of these markers was assessed for five congeners varying in phylogenetic distance to N. corniger. The markers will be useful for fine-scale examination of population and colony genetic structure in N. corniger and other closely related species. [source] Genetic analysis of ratmouth barbell (Ptychidio jordani Myers) from different geographic sub-populations in the Pearl River Basin using microsatellite markersJOURNAL OF APPLIED ICHTHYOLOGY, Issue 2 2009X.-P. Zhu Summary Thirteen polymorphic microsatellite markers were used to study the genetic variation of Ptychidio jordani sampled from the three sites of Liuzhou, Guiping and Yunan in the Pearl River Basin with the help of local fishers. Allele numbers ranged from 2 to 19 and fragment sizes ranged from 108 to 288. Average polymorphism information content (PIC), average observed heterozygosity (Ho) and average expected heterozygosity (He) were 0.439917, 0.4147 and 0.4986, respectively, which indicate a comparatively high level of genetic diversity. The coefficient of genetic differentiation (Gst) between the two sub-populations ranged from 0.0074 to 0.0156, which shows little differentiation between sub-populations. amova analysis also offered evidence of weak differentiation with 0.53% variation between sub-populations, 99.47% variation within sub-populations and the Fst = 0.00531. The morphological variation among geographic sub-populations might result from different habitats. The correlation between genotype and morphological characters was analyzed and a significant correlation found between the genotype of microsatellite locus Hlj038 and the ratio of body depth and body length. The results suggest a possible linkage between this locus and these morphological characters. [source] Bioinformatic mining of EST-SSR loci in the Pacific oyster, Crassostrea gigasANIMAL GENETICS, Issue 3 2008Y. Wang Summary A set of expressed sequence tag-simple sequence repeat (EST-SSR) markers of the Pacific oyster, Crassostrea gigas, was developed through bioinformatic mining of the GenBank public database. As of June 30, 2007, a total of 5132 EST sequences from GenBank were downloaded and screened for di-, tri- and tetra-nucleotide repeats, with criteria set at a minimum of 5, 4 and 4 repeats for the three categories of SSRs respectively. Seventeen polymorphic microsatellite markers were characterized. Allele numbers ranged from 3 to 10, and the observed and expected heterozygosity values varied from 0.125 to 0.770 and from 0.113 to 0.732 respectively. Eleven loci were at Hardy,Weinberg equilibrium (HWE); the other six loci showed significant departure from HWE (P < 0.01), suggesting possible presence of null alleles. Pairwise check of linkage disequilibrium (LD) indicated that 11 of 136 pairs of loci showed significant LD (P < 0.01), likely due to HWE present in single markers. Cross-species amplification was examined for five other Crassostrea species and reasonable results were obtained, promising usefulness of these markers in oyster genetics. [source] Microsatellites assessment of Chinese sturgeon (Acipenser sinensis Gray) genetic variabilityJOURNAL OF APPLIED ICHTHYOLOGY, Issue 1 2005N. Zhao Summary Four microsatellites were used to examine the genetic variability of the spawning stocks of Chinese sturgeon, Acipenser sinensis, from the Yangtze River sampled over a 3-year period (1999,2001). Within 60 individuals, a total of 28 alleles were detected over four polymorphic microsatellite loci. The number of alleles per locus ranged from 4 to 15, with an average allele number of 7. The number of genotypes per locus ranged from 6 to 41. The genetic diversity of four microsatellite loci varied from 0.34 to 0.67, with an average value of 0.54. For the four microsatellite loci, the deviation from the Hardy,Weinberg equilibrium was mainly due to null alleles. The mean number of alleles per locus and the mean heterozygosity were lower than the average values known for anadromous fishes. Fish were clustered according to their microsatellite characteristics using an unsupervised ,Artificial Neural Networks' method entitled ,Self-organizing Map'. The results revealed no significant genetic differentiation considering genetic distance among samples collected during different years. Lack of heterogeneity among different annual groups of spawning stocks was explained by the complex age structure (from 8 to 27 years for males and 12 to 35 years for females) of Chinese sturgeon, leading to formulate an hypothesis about the maintenance of genetic diversity and stability in long-lived animals. [source] Major histocompatibility complex variability in the clonal Amazon molly, Poecilia formosa: is copy number less important than genotype?MOLECULAR ECOLOGY, Issue 6 2009K. P. LAMPERT Abstract The evolution of sex is still a major unsolved puzzle in biology. One of the most promising theoretical models to answer this question is the Red Queen hypothesis. The Red Queen hypothesis proposes a fast adaptation of pathogens to common genotypes and therefore a negative frequency-dependent selection against common genotypes. Clonal organisms should be especially endangered when co-occurring with closely related sexual species. In this context, major histocompatibility (MHC) genes have been discussed to be auspicious candidates that could provide the genetic basis on which selection for immune competence could act. In this study, we investigated MHC variability in a clonal teleost fish: the Amazon molly, Poecilia formosa. The Amazon molly is an ideal candidate to test the Red Queen hypothesis as it is a clonal species but co-occurs with a closely related sexual species and should therefore be especially susceptible to pathogen infection. We found that allele numbers did in general not differ between sexual and clonal ,species' but that genotypic variability is reduced in the clonally reproducing fish, especially in the polyploids. We conclude that in clonal organisms, genotype frequency might be more important for immune competence than MHC allele number. Amazon mollies and their co-occurring parental species clearly fulfil a prerequisite of the Red Queen hypothesis and should therefore provide an ideal system to experimentally test this basic principle probably underlying the evolution of sex. [source] Limited effect of anthropogenic habitat fragmentation on molecular diversity in a rain forest skink, Gnypetoscincus queenslandiaeMOLECULAR ECOLOGY, Issue 2 2004Joanna Sumner Abstract To examine the effects of recent habitat fragmentation, we assayed genetic diversity in a rain forest endemic lizard, the prickly forest skink (Gnypetoscincus queenslandiae), from seven forest fragments and five sites in continuous forest on the Atherton tableland of northeastern Queensland, Australia. The rain forest in this region was fragmented by logging and clearing for dairy farms in the early 1900s and most forest fragments studied have been isolated for 50,80 years or nine to 12 skink generations. We genotyped 411 individuals at nine microsatellite DNA loci and found fewer alleles per locus in prickly forest skinks from small rain forest fragments and a lower ratio of allele number to allele size range in forest fragments than in continuous forest, indicative of a decrease in effective population size. In contrast, and as expected for populations with small neighbourhood sizes, neither heterozygosity nor variance in allele size differed between fragments and sites in continuous forests. Considering measures of among population differentiation, there was no increase in FST among fragments and a significant isolation by distance pattern was identified across all 12 sites. However, the relationship between genetic (FST) and geographical distance was significantly stronger for continuous forest sites than for fragments, consistent with disruption of gene flow among the latter. The observed changes in genetic diversity within and among populations are small, but in the direction predicted by the theory of genetic erosion in recently fragmented populations. The results also illustrate the inherent difficulty in detecting genetic consequences of recent habitat fragmentation, even in genetically variable species, and especially when effective population size and dispersal rates are low. [source] Isolation of polymorphic DNA microsatellites in the common sole Solea vulgarisMOLECULAR ECOLOGY RESOURCES, Issue 1 2006FLAVIO GAROIA Abstract A microsatellite-enriched genomic library was obtained from the common sole, Solea vulgaris, and seven polymorphic dinucleotide markers were successfully optimized. These markers showed levels of expected heterozygosity ranging from 0.55 to 0.83 and allele number ranging from eight to 12. Three of these markers were also found to successfully amplify in the closely related Solea senegalensis and can be employed to define population genetic structure of the two Solea species and for inferring stock origins. [source] Microsatellites from Clarias batrachus and their polymorphism in seven additional catfish speciesMOLECULAR ECOLOGY RESOURCES, Issue 3 2003G. H. Yue Abstract We isolated 18 novel microsatellite loci from the walking catfish (Clarias batrachus), and examined their cross-amplification in seven additional catfish species from three families. Sixteen of the 18 microsatellites were polymorphic in the source species (allele number: 2,10/locus and expected heterozygosity: 0.30,0.87). Moreover, nine of these 18 primer pairs cross-amplified specific and polymorphic products from the genome of at least six of the seven other catfish species tested. However, the success rate of cross-species amplification varied from locus to locus, indicating that cross-species amplification of microsatellites is locus-dependent. [source] Estimation of gene frequency and heterozygosity from pooled samplesMOLECULAR ECOLOGY RESOURCES, Issue 3 2002K. Ritland Abstract Pooling of DNA samples can significantly reduce the effort of population studies with DNA markers. I present a statistical model and numerical method for estimating gene frequency when pooled DNA is assayed for the presence/absence of alleles. Analytical and Monte-Carlo methods examined estimation variance and bias, and hence optimal pool size, under a triangular allele frequency distribution. For gene frequency of rarer alleles, the optimal number of pooled individuals is approximately the inverse of the gene frequency. For heterozygosity, the optimal pool is approximately half the allele number; this results in pools containing, on average, 60% of possible alleles. [source] Fluctuation in self-perceived stress and increased risk of flare in patients with lupus nephritis carrying the serotonin receptor 1A ,1019 G alleleARTHRITIS & RHEUMATISM, Issue 10 2006Daniel J. Birmingham Objective Stress is believed to be a risk factor for systemic lupus erythematosus (SLE) flare. Two serotonin-related gene polymorphisms, the serotonin receptor 1A (5-HT1A) polymorphism at ,1019C>G and the serotonin transporter LS polymorphism, have been reported to affect stress-related behaviors. The purpose of this study was to assess the relationship between self-perceived stress (SPS), variability in SPS, and the 2 serotonin-related gene polymorphisms as risk factors for SLE flare. Methods Seventy-seven SLE patients (50 with lupus nephritis) were evaluated every 2 months (mean ± SD total followup 18.5 ± 8.5 months), and patients recorded their daily SPS levels (0,10 scale). Values for mean SPS and coefficient of variation (CV) for SPS were calculated from the 60-day block of daily measurements between study visits. Serotonin-related gene polymorphism genotypes were determined by polymerase chain reaction,based methods. Results Of the 77 patients, 53 experienced 80 flares of SLE (32 renal flares) based on prespecified criteria. Multivariate analysis revealed that whereas neither the serotonin-related gene polymorphisms nor the mean SPS was predictive of an SLE flare, an increased CV for SPS was predictive (P = 0.0031). Interaction between the CV for SPS and the 5-HT1A ,1019C>G polymorphism was also found to be a predictor of SLE flare (P = 0.0039). Subset analysis revealed that only in lupus nephritis patients were increasing CVs for SPS (P = 0.0002) and the interaction between CVs for SPS and 5-HT1A (P < 0.0001) predictive of a flare. Odds ratio curves demonstrated that the predictive effect of increasing CVs for SPS required the presence of the 5-HT1A ,1019 G allele, but appeared to be independent of the G allele number. Conclusion Fluctuation in the level of SPS is a risk factor for the onset of flare in SLE patients with major renal manifestations when it occurs on the background of a stress-related susceptibility gene (the 5-HT1A ,1019 G allele). [source] Effectiveness of Conservation Targets in Capturing Genetic DiversityCONSERVATION BIOLOGY, Issue 1 2003Maile C. Neel We used empirical data from four rare plant taxa to assess these consequences in terms of how well allele numbers ( all alleles and alleles occurring at a frequency openface>0.05 in any population ) and expected heterozygosity are represented when different numbers of populations are conserved. We determined sampling distributions for these three measures of genetic diversity using Monte Carlo methods. We assessed the proportion of alleles included in the number of populations considered adequate for conservation, needed to capture all alleles, and needed to meet an accepted standard of genetic-diversity conservation of having a 90,95% probability of including all common alleles. We also assessed the number of populations necessary to obtain values of heterozygosity within ±10% of the value obtained from all populations. Numbers of alleles were strongly affected by the number of populations sampled. Heterozygosity was only slightly less sensitive to numbers of populations than were alleles. On average, currently advocated conservation intensities represented 67,83% of all alleles and 85,93% of common alleles. The smallest number of populations to include all alleles ranged from 6 to 17 ( 42,57% ), but <0.2% of 1000 samples of these numbers of populations included them all. It was necessary to conserve 16,29 ( 53,93% ) of the sampled populations to meet the standard for common alleles. Between 20% and 64% of populations were needed to reliably represent species-level heterozygosity. Thus, higher percentages of populations are needed than are currently considered adequate to conserve genetic diversity if populations are selected without genetic data. Resumen: Cualquier acción de conservación que preserve algunas poblaciones y no otras tendrá consecuencias genéticas. Utilizamos datos empíricos de cuatro taxones de plantas raras para evaluar estas consecuencias en términos de lo bien representados que están los números de alelos ( todos los alelos ocurriendo a una frecuencia>0.05 en cualquier población ) y la heterocigosidad esperada cuando se conservan diferentes números de poblaciones. Las distribuciones de muestreo de estas tres medidas de la diversidad genética fueron determinadas utilizando métodos Monte Carlo. Evaluamos la proporción de alelos incluida en números de poblaciones: consideradas adecuadas para la conservación; requeridas para capturar todos los alelos; y las requeridas para alcanzar un estándar de conservación de diversidad genética aceptable del 90,95% de probabilidad de incluir todos los alelos comunes. También evaluamos el número de poblaciones necesarias para obtener valores de heterocigosidad que caigan dentro de ±10% del valor obtenido de todas las poblaciones. Los números de alelos fueron afectados significativamente por el número de poblaciones muestreadas. La heterocigosidad solo fue ligeramente menos sensible a los números de poblaciones de lo que fueron los alelos. Las intensidades de conservación propugnadas actualmente representaron en promedio el 67,83% de todos los alelos y el 85,93% de los alelos comunes. El menor número de poblaciones para incluir a todos los alelos varió de 6 a 17 ( 42,57% ), pero <0.2% de 1000 muestras de esos números de poblaciones los incluyó a todos. Fue necesario conservar de 16 a 29 ( 53,93% ) de las poblaciones muestreadas para alcanzar el estándar para los alelos comunes. Se requirió entre 20% y 64% de las poblaciones para representar la heterocigosidad a nivel de especie confiablemente. Por lo tanto, se requieren mayores porcentajes de poblaciones que los actualmente considerados adecuados para conservar la diversidad genética si las poblaciones son seleccionadas sin datos genéticos. [source] Major histocompatibility complex variability in the clonal Amazon molly, Poecilia formosa: is copy number less important than genotype?MOLECULAR ECOLOGY, Issue 6 2009K. P. LAMPERT Abstract The evolution of sex is still a major unsolved puzzle in biology. One of the most promising theoretical models to answer this question is the Red Queen hypothesis. The Red Queen hypothesis proposes a fast adaptation of pathogens to common genotypes and therefore a negative frequency-dependent selection against common genotypes. Clonal organisms should be especially endangered when co-occurring with closely related sexual species. In this context, major histocompatibility (MHC) genes have been discussed to be auspicious candidates that could provide the genetic basis on which selection for immune competence could act. In this study, we investigated MHC variability in a clonal teleost fish: the Amazon molly, Poecilia formosa. The Amazon molly is an ideal candidate to test the Red Queen hypothesis as it is a clonal species but co-occurs with a closely related sexual species and should therefore be especially susceptible to pathogen infection. We found that allele numbers did in general not differ between sexual and clonal ,species' but that genotypic variability is reduced in the clonally reproducing fish, especially in the polyploids. We conclude that in clonal organisms, genotype frequency might be more important for immune competence than MHC allele number. Amazon mollies and their co-occurring parental species clearly fulfil a prerequisite of the Red Queen hypothesis and should therefore provide an ideal system to experimentally test this basic principle probably underlying the evolution of sex. [source] A microsatellite-based estimation of clonal diversity and population subdivision in Zostera marina, a marine flowering plantMOLECULAR ECOLOGY, Issue 2 2000T. B. H. Reusch Abstract We examined the genetic population structure in eelgrass (Zostera marina L.), the dominant seagrass species of the northern hemisphere, over spatial scales from 12 km to 10 000 km using the polymorphism of DNA microsatellites. Twelve populations were genotyped for six loci representing a total of 67 alleles. Populations sampled included the North Sea (four), the Baltic Sea (three), the western Atlantic (two), the eastern Atlantic (one), the Mediterranean Sea (one) and the eastern Pacific (one). Microsatellites revealed substantial genetic variation in a plant group with low allozyme diversity. Average expected heterozygosities per population (monoclonal populations excluded) ranged from 0.32 to 0.61 (mean = 0.48) and allele numbers varied between 3.3 and 6.7 (mean = 4.7). Using the expected frequency of multilocus genotypes within populations, we distinguished ramets from genetic individuals (i.e. equivalent to clones). Differences in clonal diversity among populations varied widely and ranged from maximal diversity (i.e. all ramets with different genotype) to near or total monoclonality (two populations). All multiple sampled ramets were excluded from further analysis of genetic differentiation within and between populations. All but one population were in Hardy,Weinberg equilibrium, indicating that Zostera marina is predominantly outcrossing. From a regression of the pairwise population differentiation with distance, we obtained an effective population size Ne of 2440,5000. The overall genetic differentiation among eelgrass populations, assessed as , (a standardized estimate of Slatkin's RST) was 0.384 (95% CI 0.34,0.44, P < 0.001). Genetic differentiation was weak among three North Sea populations situated 12,42 km distant from one another, suggesting that tidal currents result in an efficient exchange of propagules. In the Baltic and in Nova Scotia, a small but statistically significant fraction of the genetic variance was distributed between populations (, = 0.029,0.053) at scales of 15,35 km. Pairwise genetic differentiation between European populations were correlated with distance between populations up to a distance of 4500 km (linear differentiation-by-distance model, R2 = 0.67). In contrast, both Nova Scotian populations were genetically much closer to North Sea and Baltic populations than expected from their geographical distance (pairwise , = 0.03,0.08, P < 0.01). A biogeographical cluster of Canadian with Baltic/North Sea populations was also supported using a neighbour-joining tree based on Cavalli,Sforza's chord distance. Relatedness between populations may be very different from predictions based on geographical vicinity. [source] Isolation and characterization of microsatellite loci for the European tree frog (Hyla arborea)MOLECULAR ECOLOGY RESOURCES, Issue 5 2008L. BERSET-BRäNDLI Abstract We developed 11 new microsatellite markers for the European tree frog (Hyla arborea), and tested patterns of polymorphism in 54 adults (27 males and 27 females) from two ponds close to Lausanne (Western Switzerland). One marker was sex linked and two pairs displayed linkage disequilibrium. Comparisons of allele numbers with heterozygosity values support a stepwise-mutation model at neutral equilibrium, with mutation rates spanning nearly two orders of magnitude. These markers will prove useful for population genetic studies and fine-scale investigations requiring genetic assignment techniques. [source] Genomic and cDNA microsatellites from apricot (Prunus armeniaca L.)MOLECULAR ECOLOGY RESOURCES, Issue 4 2004L. S. HAGEN Abstract We developed primers for the amplification of 24 polymorphic nuclear microsatellites in apricot (Prunus armeniaca L.). Thirteen loci originated from three genomic libraries enriched for TC, TG and AAG motifs. Eight loci were developed from three fruit EST (Expressed-Sequence-Tag) libraries and three from a leaf cDNA microsatellite-enriched library. There were up to nine alleles per polymorphic locus in 12 different cultivars. No difference in allele numbers were shown between cDNA and genomic-source loci. Mean expected heterozygosity was 0.65 (range: 0.15,0.87). Mendelian segregation was confirmed for all loci. These markers should be helpful for diversity studies, genome mapping and cultivar identification in apricot and related species. [source] Microsatellite loci isolated from the Caribbean coral, Montastraea annularisMOLECULAR ECOLOGY RESOURCES, Issue 1 2004E. G. Severance Abstract We report the isolation and characterization of seven microsatellite loci from the Caribbean reef-building coral, Montastraea annularis. All loci are polymorphic with allele numbers ranging from five to 31 and observed heterozygosities from 0.17 to 0.89. These loci can be used in assessing gene flow patterns and diversity of this stony coral species both for local coral reef management purposes as well as for elucidating population connectivity within the greater Caribbean basin. These markers should also be applicable to other species of Montastraea and for resolving taxonomic relationships within the M. annularis species complex. [source] Novel polymorphic microsatellite markers for the common pandora (Pagellus erythrinus)MOLECULAR ECOLOGY RESOURCES, Issue 4 2003Andreja Ram Abstract Details of six highly polymorphic dinucleotide and one highly polymorphic tetranucleotide microsatellite markers are provided for Pagellus erythrinus. These markers are highly polymorphic, with an expected heterozygosity ranging from 0.713 to 0.959 and allele numbers ranging from seven to 36. These microsatellite markers should help determine population genetic structure and fisheries stocks for management purposes. [source] Allelic Gain and Amplification on the Long Arm of Chromosome 17 in Anaplastic MeningiomasBRAIN PATHOLOGY, Issue 2 2002Rainer Büschges Using comparative genomic hybridization (CGH) we have previously identified amplification at 17q21-qter as a common aberration in anaplastic meningiomas but not in atypical or benign meningiomas (19). To define the amplified genomic region, we analyzed 44 meningeal tumors, including 7 benign meningiomas of World Health Organization (WHO) grade I, 19 atypical meningiomas (WHO grade II) and 18 anaplastic meningiomas (WHO grade III) at 46 chromosome 17 loci (including 42 17q loci). In line with the CGH data we found evidence of increased numbers of alleles on 17q. The incidence rose with malignancy grade, culminating at 61% (11 of 18 cases) in the anaplastic meningioma group. The majority of cases showing increased allele numbers had, on average, low-level allelic gains (relative increase in allele dosage of 2- to 5-fold). Amplification of alleles (defined here as an average relative increase in allele dosage of more than 5 times) was detected in 2 anaplastic meningiomas. The amplification patterns in these tumors defined a number of common regions of amplification/increased allele copy number, the best defined include one between D17S790 and D17S1607 and one between D17S1160 and PS6K. Real-time PCR analysis of the PS6K candidate gene revealed no high-level amplification despite this affecting adjacent loci. Our findings are fundamental for the identification of the gene(s) in 17q22-q23 that is (are) the target(s) for increased copy number in anaplastic meningiomas and possibly other tumor types. [source] | |||||||||||||