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Allelic Variation (allelic + variation)
Selected AbstractsEvidence for extensive genetic differentiation among populations of the malaria vector Anopheles arabiensis in Eastern AfricaINSECT MOLECULAR BIOLOGY, Issue 4 2000M. J. Donnelly Abstract We describe the geographical population structure of the malaria vector Anopheles arabiensis in Eastern Africa. Allelic variation at eight microsatellite loci was scored in samples from nine localities along a 4500 km transect from Sudan to Mozambique. Highly significant differences in genotype frequencies were found between all populations separated by more than 200 km. Populations within Malawi separated by 191 km were indistinguishable, as were those within Sudan separated by 134 km. FST and ,ST gave significant estimates of isolation by distance. These data, lead us to conclude that there are extensive barriers to gene flow in this region. The high estimates of Nm (9.4 from FST and 5.2 from ,ST) indicate recent range expansion in this species rather than extensive contemporary gene flow. [source] Association of 5-HTT gene polymorphism, platelet MAO activity, and drive for thinness in a population-based sample of adolescent girlsINTERNATIONAL JOURNAL OF EATING DISORDERS, Issue 5 2008Kirsti Akkermann MSc Abstract Objective: Several lines of evidence suggest that alterations in serotonergic activity contribute to the pathophysiology of abnormal eating behaviors. Since platelet monoamine oxidase (MAO) activity and the 5-HT transporter gene promoter polymorphism (5-HTTLPR) have been associated with eating disorders, the knowledge from a population-based sample may provide useful information which changes in 5-HT function observed in eating disorders represent trait vs. state effects. Method: The sample was based on both cohorts of the Estonian Children Personality, Behavior and Health Study (ECPBHS). The current study was conducted during the second follow-up where altogether 82% from the original sample was recruited. EDI-2 subscales,Drive for Thinness and Bulimia,were used to determine eating attitudes and behaviors. Platelet MAO activity was measured and the participants were genotyped for the 5-HTTLPR. Results: Allelic variation of 5-HTTLPR or platelet MAO activity were not independently associated with drive for thinness or binge eating, but girls homozygous for the 5-HTTLPR long allele and with high platelet MAO activity, both considered indicators of a higher capacity 5-HT system, exhibited higher scores of drive for thinness. Conclusion: The results suggest that drive for thinness is the highest in girls with the presence of two markers of higher serotonergic capacity. © 2008 by Wiley Periodicals, Inc. Int J Eat Disord 2008 [source] Fine-scale phylogeographical analysis of Mediterranean Anacamptis palustris (Orchidaceae) populations based on chloroplast minisatellite and microsatellite variationMOLECULAR ECOLOGY, Issue 10 2003S. Cozzolino Abstract The phylogeographical history of the rare marsh orchid Anacamptis palustris (Orchidaceae) was reconstructed using highly polymorphic chloroplast minisatellite and microsatellite loci. Allelic variation at chloroplast microsatellite loci was due to length variation in poly(A/T) repeats and was informative on a regional scale, but was not sufficient to unravel relationships among populations on a local geographical scale. The minisatellite locus, however, was found to be highly variable. Nine distinct repeat types were found and variation in repeat number occurred in five repeat types. The distribution of chloroplast haplotypes, combining microsatellite and minisatellite repeat type variation, provided a clear phylogeographical picture on a large geographical scale, whereas length variation in one highly polymorphic minisatellite repeat type provided fine-scale phylogeographical information. Mediterranean populations could be divided into four main lineages, a western European lineage, a northern and central Italian lineage, a well-isolated southern Italian (Apulian) lineage, and an eastern European lineage. Variation at the most variable minisatellite repeat type N revealed 19 alleles and allowed the study of seed-mediated gene flow and an estimation of the ratio of pollen to seed flow among neighbouring populations. [source] Isolation of nine nuclear microsatellites in the common Mediterranean sea urchin, Paracentrotus lividus (Lamarck)MOLECULAR ECOLOGY RESOURCES, Issue 4 2009I. CALDERÓN Abstract Nine polymorphic microsatellite loci were isolated and characterized for the edible common sea urchin Paracentrotus lividus. Loci were obtained from two genomic libraries enriched with different di-, tri- and tetranucleotides. Most microsatellites obtained were imperfect dinucleotides. Allelic variation was screened for a total of 56 individuals from two populations from North-Western Mediterranean. Microsatellites showed a number of alleles ranging from 13 to 35. Linkage disequilibrium was not detected between any pair of loci, and all loci showed a significant departure from Hardy,Weinberg equilibrium which is not likely to be the result of null alleles, suggesting that demographic features may be acting upon this commercially interesting species. [source] Microsatellite loci for Ponto-Caspian gobies: markers for assessing exotic invasionsMOLECULAR ECOLOGY RESOURCES, Issue 2 2009KEVIN A. FELDHEIM Abstract We developed and tested eight polymorphic microsatellite loci for Ponto-Caspian ,neogobiin' gobies, many of which are invasive in Eurasia and North America, whose study will aid understanding of the population genetics underlying their success. We tested samples from one to two locations from 12 taxa in the recently revised genera Babka, Benthophilus, Mesogobius, Neogobius = Apollonia, Ponticola and Proterorhinus; including the bighead, Caspian, knout, monkey, racer, round, tadpole and tubenose gobies; and taxa from introduced vs. native populations, those diverging between fresh and marine waters, and those differentiated between the Black and Caspian Seas. Populations conformed to Hardy,Weinberg equilibrium expectations, averaging five to 15 alleles per locus and 0.11 to 0.67 mean heterozygosity. Allelic variation significantly differentiated among all taxa and populations. [source] Distribution of fimA genotypes of Porphyromonas gingivalis in subjects with various periodontal conditionsMOLECULAR ORAL MICROBIOLOGY, Issue 4 2004C. G. Missailidis Fimbria encoded by the gene fimA is considered one of the main factors in the colonization of the oral cavity by Porphyromonas gingivalis. Allelic variation in fimA led to the classification of strains of P. gingivalis into six genotypes. The occurrence of P. gingivalis was determined by polymerase chain reaction using 16S rRNA primers in 302 subgingival samples obtained from 102 Brazilian subjects exhibiting different periodontal conditions. Distribution of fimA genotypes was assessed in 146 P. gingivalis positive samples by polymerase chain reaction using primers pairs homologous to the different fimA genes. P. gingivalis was detected in 51 of 57 (89.4%) patients with periodontal attachment loss, in six of 20 gingivitis patients (30.0%) and in two of 25 (8.0%) subjects with a healthy periodontium. Variant type II was the only type detected in 53 sites (39.3%), distributed among 19 periodontitis patients (37.3%) and in one patient with no periodontal destruction. Type Ib was the second most prevalent genotype in periodontitis patients (19.6%). Genotype V was not detected in the studied population. Type IV was the most commonly type found among gingivitis patients, either alone or in combination with other genotypes. Multiple genotypes were detected in nine sites (6.1%). A fimA genotype was not identified in 26 sites (17.8%) of 146 sites positive for P. gingivalis, suggesting that other alleles of fimA not yet sequenced may be prevalent in this population. These data demonstrated that P. gingivalis type II strains followed by type Ib are more prevalent in periodontitis patients from a multiracial population in Brazil, suggesting an increased pathogenic potential of these types. [source] Allelic variation of a BalI polymorphism in the DRD3 gene does not influence susceptibility to bipolar disorder: Results of analysis and meta-analysisAMERICAN JOURNAL OF MEDICAL GENETICS, Issue 4 2001Gareth Elvidge Abstract Bipolar disorder is a major psychiatric illness that has evidence for a significant genetic contribution toward its development. In recent years, the BalI RFLP (restriction fragment length polymorphism) in the dopamine D3 receptor gene has been examined as a possible susceptibility factor for both schizophrenia and bipolar disorder. While analysis in schizophrenia has produced examples of increased homozygosity in patients, less encouraging results have been found for bipolar disorder. Recently, however, a family-based association study has found a significant excess of allele 1 and allele 1,containing genotypes in transmitted alleles to bipolar probands over nontransmitted controls. In a large bipolar case control sample (n,=,454), we have been unable to replicate the family-based association study (chi-square,=,0.137, P,=,0.71, 1 df) or detect an effect similar to the positive homozygosity findings in schizophrenia (chi-square,=,0.463, P,=,0.50, 1 df). A meta-analysis of previous association studies also revealed no difference in allele distributions between bipolar patients and controls for this polymorphism in ethnically homogeneous samples (odds ratio, OR,,=,1.04; P,=,0.60; 95% confidence interval, CI,,=,0.89,1.20). In view of this evidence, we conclude that variation at the BalI RFLP is not an important factor influencing the susceptibility to bipolar disorder. It remains possible, however, that other sequence variations within the DRD3 gene could play a role. © 2001 Wiley-Liss, Inc. [source] The normal population distribution of PRNP codon 129 polymorphismACTA NEUROLOGICA SCANDINAVICA, Issue 5 2003M. H. Nurmi Objectives , The common prion protein gene (PRNP) codon 129 polymorphism modifies the susceptibility to and the phenotype of prion diseases. However, no truly representative normal population-based data, or data stratified according to age or gender are available on the distribution of this polymorphism. Material and methods , Allelic variation of codon 129 in three Finnish populations representing different age groups, and among Finnish, British and Irish blood donors were examined. Results , The PRNP codon 129 genotype distribution in the total Finnish sample was 49% for methionine,methionine (MM), 42% for methionine,valine (MV) and 9% for valine,valine (VV), for the UK blood donors 42% for MM, 47% for MV and 11% for VV, and for the Irish blood donors 34% for MM, 56% for MV, and 10% for VV. Conclusions , The genotype frequencies were almost identical in all three Finnish populations of different ages, with no gender differences, and did not differ from corresponding figures for the Finnish blood donors. However, the PRNP codon 129 genotype distribution in Finland differed significantly from that of the British and the Irish blood donors and the previously published blood donor data on other Western Europeans and Americans. [source] Mutagenic induction of double-podding trait in different genotypes of chickpea and their characterization by STMS markerPLANT BREEDING, Issue 1 2010H. Ali With 1 figure and 2 tables Abstract A gene that confers double-podding in chickpea is considered to be important for breeding higher yielding cultivars. Double-podded mutants were produced from five desi- and four kabuli-type chickpea genotypes through induced mutations and stabilty was checked up to M13 generation. Desi-type produced higher number of mutants as compared with kabuli-type. The inheritance studies in induced mutants of six genotypes showed that the double-podded trait was governed by single recessive gene. Different genotypes and their double-podded mutants were also characterized through sequence-tagged microsatellite site marker, TA-80. Allelic variations were found in single-podded genotypes and eight different alleles were identified, while for double-poddedness no allelic variants were found in all the analysed mutants. Addition of bases in the double-podded mutants showed that there might be involvement of transposable elements in the production of double-podded mutants through mutagens. [source] Association of DRD4 polymorphism with severity of oppositional defiant disorder, separation anxiety disorder and repetitive behaviors in children with autism spectrum disorderEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 6 2010Kenneth D. Gadow Abstract The objective was to examine whether a common polymorphism in the dopamine D4 receptor gene (DRD4) might be a potential biomarker for behavioral variation within the autism spectrum disorder clinical phenotype. Children (N = 66) were evaluated with a validated mother- and teacher-completed DSM-IV-referenced rating scale. Partial eta-squared (,p2) was used to gauge the magnitude of group differences: 0.01,0.06 = small, 0.06,0.14 = moderate and > 0.14 = large. Children who were 7-repeat allele carriers had more severe oppositional defiant disorder behaviors according to mothers' (,p2 = 0.10) and teachers' (,p2 = 0.06) ratings than noncarriers, but the latter was marginally significant (P = 0.07). Children who were 7-repeat allele carriers also obtained more severe maternal ratings of tics (,p2 = 0.07) and obsessions,compulsions (,p2 = 0.08). Findings for maternal ratings of separation anxiety were marginally significant (P = 0.08, ,p2 = 0.05). Analyses of combined DRD4 and dopamine transporter gene (DAT1) genotypes approached significance (P = 0.05) for teachers' ratings of oppositional behavior and mothers' ratings of tics. DRD4 allelic variation may be a prognostic biomarker for challenging behaviors in children with autism spectrum disorder, but these exploratory findings remain tentative pending replication with larger independent samples. [source] Short rare MUC6 minisatellites-5 alleles influence susceptibility to gastric carcinoma by regulating gene,HUMAN MUTATION, Issue 8 2010Jeong-Ah Kwon Abstract The human MUC6 gene, which is reported to be expressed in the stomach and gall bladder, is clustered on chromosome 11p15.5 with other secreted mucins. In this study, the genomic structure of MUC6 has been analyzed and five VNTR (minisatellites; MS1,MS5) were identified. These minisatellites were analyzed in genomic DNA extracted from 1,103 controls, 470 gastric cancer patients, and multigenerational families. Five novel minisatellites were found to be polymorphic and transmitted through meiosis by Mendelian inheritance in families. We evaluated allelic variation in these minisatellites to determine if such variation affected the susceptibility to gastric cancer. A significant association (odds ratio [OR]=7.08) between short rare MUC6,MS5 alleles and relative risks were observed for gastric cancer (95% confidence interval [CI], 1.43,35.19; P=0.005). To investigate the function of minisatellite alleles of MUC6,MS5, we examined the effects on gene expression from luciferase reporters when inserted with minisatellites. Interestingly, when the shortest allele (7TR) was inserted in the promoter, the expression level decreased over 20-fold (P<0.001) in normal and cancer cell lines. Furthermore, the cancer-specific rare allele (TR8) also showed decreased expression levels in cancer cells. Therefore, we suggest that the short rare MUC6,MS5 alleles may be related to cancer development by the regulation of MUC6 expression. Hum Mutat 31:1,8, 2010. © 2010 Wiley-Liss, Inc. [source] Mining an Ostrinia nubilalis midgut expressed sequence tag (EST) library for candidate genes and single nucleotide polymorphisms (SNPs)INSECT MOLECULAR BIOLOGY, Issue 6 2008B. S. Coates Abstract Genes expressed in lepidopteran midgut tissues are involved in digestion and Bacillus thuringiensis (Bt) toxin resistance traits. Five hundred and thirty five unique transcripts were annotated from 1745 high quality O. nubilalis larval midgut expressed sequence tags (ESTs). Full-length cDNA sequence of 12 putative serine proteinase genes and 3 partial O. nubilalis aminopeptidase N protein genes, apn1, apn3, and apn4, were obtained, and genes may have roles in plant feeding and Bt toxin resistance traits of Ostrinia larvae. The EST library was not normalized and insert frequencies reflect transcript levels under the initial treatment conditions and redundancy of inserts from highly expressed transcripts allowed prediction of putative single nucleotide polymorphisms (SNPs). Ten di-, tri- or tetranucleotide repeat unit microsatellite loci were identified, and minisatellite repeats were observed within the C-termini of two encoded serine proteinases. Molecular markers showed polymorphism at 28 SNP loci and one microsatellite locus, and Mendelian inheritance indicated that markers were applicable to genome mapping applications. This O. nubilalis larval midgut EST collection is a resource for gene discovery, expression information, and allelic variation for use in genetic marker development. [source] Interaction of host and viral risk factors for development of cervical carcinoma in situINTERNATIONAL JOURNAL OF CANCER, Issue 4 2005Anna H. Beskow Abstract Infection by oncogenic human papillomavirus (HPV) is a necessary but not sufficient cause of cervical carcinoma. Several host genetic and viral factors have been reported to increase the risk of carcinoma development given an HPV infection. In our study, we have analysed the contribution of HPV 16 E6 sequence subtype and allelic variation at human leukocyte antigen (HLA) class II loci to the risk of developing cervical carcinoma in situ. Non-European-like HPV 16 E6 sequence subtypes were not found to be associated with an increased risk of cervical carcinoma, as compared to European-like variants. However, an association was found between the HPV 16 E6 L83V variant and the DR*04-DQ*03 haplotype. This association has been observed in several independent studies and shows that both the host HLA class II genotype and viral subtype will affect the risk of an infection progressing into cervical carcinoma. © 2005 Wiley-Liss, Inc. [source] MICA-STR, HLA-B haplotypic diversity and linkage disequilibrium in the Hunan Han population of southern ChinaINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 4 2006W. Tian Summary Major histocompatibility complex (MHC) class I chain-related gene A (MICA) is located 46 kb centromeric to HLA-B and encodes a stress-inducible protein. MICA allelic variation is thought to be associated with disease susceptibility and immune response to transplants. This study was aimed to investigate the haplotypic diversity and linkage disequilibrium between human leukocyte antigen (HLA)-B and (GCT)n short tandem repeat in exon 5 of MICA gene (MICA-STR) in a southern Chinese Han population. Fifty-eight randomly selected nuclear families with 183 members including 85 unrelated parental samples were collected in Hunan province, southern China. HLA-B generic typing was performed by polymerase chain reaction,sequence-specific priming (PCR,SSP), and samples showing novel HLA-B-MICA-STR linkage were further typed for HLA-B allelic variation by high-resolution PCR,SSP. MICA-STR allelic variation and MICA gene deletion (MICA*Del) were detected by fluorescent PCR,size sequencing and PCR,SSP. Haplotype was determined through family segregation analysis. Statistical analysis was applied to the data of the 85 unrelated parental samples. Nineteen HLA-B specificities and seven MICA-STR allelic variants were observed in 85 unrelated parental samples, the most predominant of which were HLA-B*46, -B60, -B*13, and -B*15, and MICA*A5, MICA*A5.1 and MICA*A4, respectively. Genotype distributions of HLA-B, MICA-STR loci were consistent with Hardy,Weinberg proportions. The HLA-B-MICA-STR haplotypic phases of all 85 unrelated parental samples were unambiguously assigned, which contained 30 kinds of HLA-B, MICA-STR haplotypic combinations, nine of them have not been reported in the literature. Significant positive linkage disequilibria between certain HLA-B and MICA-STR alleles, including HLA-B*13 and MICA*A4, HLA-B*38 and MICA*A9, HLA-B*58 and MICA*A9, HLA-B*46 and MICA*A5, HLA-B*51 and MICA*A6, HLA-B*52 and MICA*A6, and HLA-B60 and MICA*A5.1, were observed. HLA-B*48 was linked to MICA*A5, MICA*A5.1 and MICA*Del. HLA-B*5801-MICA*A10 linkage was found in a family. Our data indicated a high degree of haplotypic diversity and strong linkage disequilibrium between MICA-STR and HLA-B in a southern Chinese Han population, the data will inform future studies on anthropology, donor,recipient HLA matching in clinical transplantation and HLA-linked disease association. [source] Diversity in five goat populations of the Lombardy Alps: comparison of estimates obtained from morphometric traits and molecular markersJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 3 2001P. Crepaldi Phenotypic and genetic variability were studied within and between the goat populations of Bionda dell'Adamello, Frisa, Orobica, Verzaschese and Val di Livo. These are populations reared for most of the year on pastures of the Lombardy Alps, numbering a minimum of 1000 and a maximum of 8000 individuals per breed. The first four are standardized breeds of recent formation; at present they are supported by the European Union measures for the conservation of rare breeds. On the basis of its visible genetic profile the Val di Livo goat may be classified as a primary population. Phenotypic variability was estimated on the basis of six somatic measurements on 60,140 adult goats per breed, whereas genetic variation was measured on the basis of 201 AFLP loci. The partition of the total molecular variation into the within and between breed components indicates that the majority of the molecular variability is conserved within populations, whereas only 8.8% can be attributed to between population variation. Morphometric and molecular marker data produced unrelated distance values and different topology of UPGMA clusters. It may be hypothesized that the morphometric originality of the Val di Livo goat is mostly determined by environmental factors and selection pressure rather than by different origin and genome evolution. Conversely Orobica seems to have diverged from the other breeds at the genome level, which may be explained by an undocumented Southern Italian origin. An objective evaluation of conservation priorities may in the near future be based on the integrated use of molecular markers and of information on quantitative traits and allelic variation with adaptive relevance. Diversité dans cinq populations de chèvres des Alpes lombardes: comparaisons entre estmations obtenues par des mesures somatiques et par des marqueurs moléculaires On a etudié la variabilité phénotypique et génétique entre et parmi les populations de chèvres Bionda dell'Adamello, Frisa, Orobica, Verzaschese et Val di Livo. Il s'agit de populations qui content entre 1000 et 8000 sujets, elevés pour la plus part de l'année sur les pâturages des Alpes de Lombardie. Les quatre premières, actuellement sauvegardées par des mesures communautaires, sont des races à standard recemment constituées. La chèvre de la Val di Livo peut être rangée parmi les races primaires. La diversité phénotypique a été montrée par un dendrogramme obtenus des distances euclidiennes calculées à partir de six mesures somatiques qui avaient été prises sur 60,140 chèvres adultes pour chaque race. La diversité génétique a été montrée par un dendrogramme bâti sur la matrice des distances de Nei obtenues des 201 marqueurs moléculaires AFLP, produits par 7 combinaisons de primers, sur 30 sujets pour chaque race. La décomposition de la variabilité génétique totale estimée par les données moléculaires a montré que la plus part de la variabilité est conservée parmi la population, tandis que seulement l,8,8% peut être imputé aux différences entre populations. Les données moléculaires et somatiques ont donné lieu à des distances qui ne sont pas corrélées et à des cluster avec une topologie nettement différente. La comparaison entre les deux approches permet d'avancer l'hypothèse que l'originalité somatique de la chèvre de la Val di Livo pourrait être due à des facteurs d'environnement et/ou à la pression de sélection plutôt qu'à des facteurs liés à l'évolution du genome. Au contraire ces derniers seraient responsables de l'originalité génétique de la race Orobica et confirmeraient des témoignages orals non documentés. Un choix objectif des ressources génétiques qui méritent d'être conservées pourra probablement se baser sur l'employ conjoint des marqueurs et de renseignements sur les caractères quantitatifs et sur les variantes alléliques des gènes qui ont une valeur adaptative. Diversität in fünf Ziegenpopulationen der lombardischen Alpen: Vergleich von Schätzungen auf der Basis morphologischer Eigenschaften und molekularer Marker Es wurden die phänotypische und genetische Variabilität innerhalb und zwischen Bionda dell'Adamello, Frisa, Orobica, Verzaschese und Val di Livo Ziegenpopulationen untersucht. Diese Populationen, mit Größen zwischen 1000 und 8000 Tieren, werden den größten Teil des Jahres auf Weiden der lombardischen Alpen gehalten. Die vier erstgenannten Populationen sind erst kürzlich standardisierte Rassen; gegenwärtig werden sie mit EU-Mitteln für die Erhaltung seltener Rassen, unterstützt. Auf der Basis des erkennbaren genetischen Profils muß die Rasse Val di Livo als eine Primärpopulation eingeordnet werden. Phänotypische Variabilität wurde auf der Basis von sechs Körpermaßen an 60,140 ausgewachsenen Ziegen je Rasse geschätzt, die genetische Variation wurde auf der Basis von 201 AFLP-Loci gemessen. Die Aufteilung der gesamten molekularen Varianz in Varianzkomponenten innerhalb und zwischen Populationen zeigt, daß der größte Teil der molekularen Variabilität innerhalb der Populationen auftritt, und nur 8,8% der Gesamtvarianz auf die Varianz zwischen den Populationen entfällt. Morphologische und molekulare Marker erzeugten unabhängige Distanzwerte und unterschiedliche upgma-Cluster. Es kann die Hypothese aufgestellt werden, daß die morphologische Einzigartigkeit der Val di Livo Ziege stärker auf Umwelteffekte und Selektionsdruck als auf eine unterschiedliche Herkunft oder genomische Evolution zurückzuführen ist. Dagegen scheint Orobica auf Genomebene von den anderen Rassen abzuweichen, was durch einen nicht dokumentierten süditalienischen Ursprung erklärt werden könnte. Eine objektive Bewertung von Prioritäten für Konservierungsmaßnahmen dürfte in Zukunft auf einen integrierten Gebrauch molekularer Marker, Informationen über quantitative Merkmale sowie der genetischen Variation bezüglich der Adaptationsfähigkeit basieren. [source] Genetic variation in organisms with sexual and asexual reproductionJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 2 2003B. O. Bengtsson Abstract The genetic variation in a partially asexual organism is investigated by two models suited for different time scales. Only selectively neutral variation is considered. Model 1 shows, by the use of a coalescence argument, that three sexually derived individuals per generation are sufficient to give a population the same pattern of allelic variation as found in fully sexually reproducing organisms. With less than one sexual event every third generation, the characteristic pattern expected for asexual organisms appear, with strong allelic divergence between the gene copies in individuals. At intermediary levels of sexuality, a complex situation reigns. The pair-wise allelic divergence under partial sexuality exceeds, however, always the corresponding value under full sexuality. These results apply to large populations with stable reproductive systems. In a more general framework, Model 2 shows that a small number of sexual individuals per generation is sufficient to make an apparently asexual population highly genotypically variable. The time scale in terms of generations needed to produce this effect is given by the population size and the inverse of the rate of sexuality. [source] Adaptive evolution of lateral plates in three-spined stickleback Gasterosteus aculeatus: a case study in functional analysis of natural variationJOURNAL OF FISH BIOLOGY, Issue 2 2010R. D. H. Barrett The three-spined stickleback Gasterosteus aculeatus is a model species for studying questions in ecology and evolution. The rapid diversification of G. aculeatus in post-glacial freshwater environments, combined with recently developed molecular tools, provides a unique opportunity to study the functional basis of fitness variation in natural populations. In derived freshwater populations, a number of morphological traits have diverged in parallel from the marine ancestral state, including the number of lateral armour plates. Evolution of reduced armour in freshwater populations is due to positive selection from both abiotic and biotic mechanisms. The major effect gene (ectodysplasin-A or Eda), along with several minor effect genetic regions, has recently been shown to control lateral plate variation. Field experiments have further determined the fitness consequences of allelic variation at the major effect locus. This work helps elucidate the mechanisms connecting genetic variation with phenotypic variation and fitness in the wild, a synthesis that should be applicable to many other phenotypic traits and species of fishes. [source] When can ecological speciation be detected with neutral loci?MOLECULAR ECOLOGY, Issue 11 2010XAVIER THIBERT-PLANTE Abstract It is not yet clear under what conditions empirical studies can reliably detect progress toward ecological speciation through the analysis of allelic variation at neutral loci. We use a simulation approach to investigate the range of parameter space under which such detection is, and is not, likely. We specifically test for the conditions under which divergent natural selection can cause a ,generalized barrier to gene flow' that is present across the genome. Our individual-based numerical simulations focus on how population divergence at neutral loci varies in relation to recombination rate with a selected locus, divergent selection on that locus, migration rate and population size. We specifically test whether genetic differences at neutral markers are greater between populations in different environments than between populations in similar environments. We find that this expected signature of ecological speciation can be detected under part of the parameter space, most consistently when divergent selection is strong and migration is intermediate. By contrast, the expected signature of ecological speciation is not reliably detected when divergent selection is weak or migration is low or high. These findings provide insights into the strengths and weaknesses of using neutral markers to infer ecological speciation in natural systems. [source] INVITED REVIEW: Using genome scans of DNA polymorphism to infer adaptive population divergenceMOLECULAR ECOLOGY, Issue 3 2005JAY F. STORZ Abstract Elucidating the genetic basis of adaptive population divergence is a goal of central importance in evolutionary biology. In principle, it should be possible to identify chromosomal regions involved in adaptive divergence by screening genome-wide patterns of DNA polymorphism to detect the locus-specific signature of positive directional selection. In the case of spatially separated populations that inhabit different environments or sympatric populations that exploit different ecological niches, it is possible to identify loci that underlie divergently selected traits by comparing relative levels of differentiation among large numbers of unlinked markers. In this review I first address the question of whether diversifying selection on polygenic traits can be expected to produce predictable patterns of allelic variation at the underlying quantitative trait loci (QTL), and whether the locus-specific effects of selection can be reliably detected against the genome-wide backdrop of stochastic variability. I then review different approaches that have been developed to identify loci involved in adaptive population divergence and I discuss the relative merits of model-based approaches that rely on assumptions about population structure vs. model-free approaches that are based on empirical distributions of summary statistics. Finally, I consider the evolutionary and functional insights that might be gained by conducting genome scans for loci involved in adaptive population divergence. [source] SHORT COMMUNICATION: Do farmers reduce genetic diversity when they domesticate tropical trees?MOLECULAR ECOLOGY, Issue 2 2005A case study from Amazonia Abstract Agroforestry ecosystems may be an important resource for conservation and sustainable use of tropical trees, but little is known of the genetic diversity they contain. Inga edulis, a widespread indigenous fruit tree in South America, is used as a model to assess the maintenance of genetic diversity in five planted vs. five natural stands in the Peruvian Amazon. Analysis of five SSR (simple sequence repeat) loci indicated lower allelic variation in planted stands [mean corrected allelic richness 31.3 (planted) and 39.3 (natural), P = 0.009]. Concerns regarding genetic erosion in planted Amazonian tree stands appear valid, although allelic variation on-farm is still relatively high. [source] Genetic variation within and among fragmented populations of lesser prairie-chickens (Tympanuchus pallidicinctus)MOLECULAR ECOLOGY, Issue 3 2003Ronald A. Van Den Bussche Abstract As a result of recurrent droughts and anthropogenic factors, the range of the lesser prairie-chicken (Tympanuchus pallidicinctus) has contracted by 92% and the population has been reduced by approximately 97% in the past century, resulting in the smallest population size and most restricted geographical distribution of any North American grouse. We examined genetic variation through DNA sequence analysis of 478 base pairs of the mitochondrial genome and by assaying allelic variation at five microsatellite loci from lesser prairie-chickens collected on 20 leks in western Oklahoma and east-central New Mexico. Traditional population genetic analyses indicate that lesser prairie-chickens maintain high levels of genetic variation at both nuclear and mitochondrial loci. Although some genetic structuring among lesser prairie-chicken leks was detected within Oklahoma and New Mexico for both nuclear and mitochondrial loci, high levels of differentiation were detected between Oklahoma and New Mexico populations. Nested-clade analysis of mitochondrial haplotypes revealed that both historic and contemporary processes have influenced patterns of haplotype distributions and that historic processes have most likely led to the level of differentiation found between the Oklahoma and New Mexico populations. [source] Polymorphic microsatellite markers for the symbiotic fungi cultivated by leaf cutter ants (Attini, Formicidae)MOLECULAR ECOLOGY RESOURCES, Issue 5 2009JARROD J. SCOTT Abstract We developed 23 polymorphic microsatellite markers for the symbiotic fungi cultivated by leaf cutter ants, then assessed allelic variation in North American leafcutter-fungus populations (Mexico, Cuba, USA). Polyploidy was indicated by 21 of the 23 loci, consistent with the multinucleate nature of leafcutter fungi. Microsatellite fingerprinting can now assess fungal genetic variation within leafcutter nests to test for monoculture of the cultivated fungi. [source] PRIMER NOTE: Isolation and characterization of polymorphic microsatellite markers for the endangered Korean freshwater fish Hemibarbus mylodonMOLECULAR ECOLOGY RESOURCES, Issue 3 2007WOO-JIN KIM Abstract Korean barbel, Hemibarbus mylodon, is an endangered freshwater species endemic to Korea. In order to undertake a conservation program for this species in Korea, it is essential to evaluate its genetic diversity and population structure. For this purpose, we developed 10 polymorphic microsatellite markers and examined their allelic variation using a total of 60 wild individuals collected from three different localities. The number of alleles per locus ranged from three to 26. The expected and observed heterozygosities per locus ranged from 0.19 to 0.94 and from 0.20 to 0.98, respectively. Significant departures from Hardy,Weinberg equilibrium expectations occurred in four loci. These markers will be useful for the assessment of genetic diversity for this species. [source] Characterization of microsatellite loci in Spartina species (Poaceae)MOLECULAR ECOLOGY RESOURCES, Issue 1 2004Michael J. Blum Abstract The cordgrasses in the genus Spartina have become model organisms for studying biological invasions from both ecological and genetic perspectives. Here we characterize 11 disomic loci in Spartina alterniflora that show promise for population studies and for studying hybridization events between S. alterniflora and S. foliosa. Comparisons among invasive and native S. alterniflora populations showed that levels of allelic variation are lower in invasive populations. In addition, nearly all loci that amplified in S. foliosa populations and in a swarm of S. alterniflora×foliosa hybrids were polymorphic. We also found that several loci amplified successfully in other Spartina species. [source] Eleven microsatellite markers in Nasonia, Ashmead 1904 (Hymenoptera; Pteromalidae)MOLECULAR ECOLOGY RESOURCES, Issue 1 2004Christof Pietsch Abstract We designed primer sequences for 11 microsatellite markers in the jewel wasp Nasonia vitripennis. Most loci could be cross-amplified in Nasonia longicornis and Nasonia giraulti, which make them amenable for linkage analysis in hybrid crosses. Eight loci were assigned to specific chromosomes. Additionally, 10 loci showed allelic variation in a Nasonia vitripennis field population. The observed number of alleles in this population ranged from two to seven, with observed heterozygosities from 0.0750 to 0.4750. [source] Isolation and characterization of 43 microsatellite DNA markers for guppy (Poecilia reticulata)MOLECULAR ECOLOGY RESOURCES, Issue 4 2003T. Watanabe Abstract Thirty-nine polymorphic microsatellite DNA markers were isolated from the guppy (Poecilia reticulata) genomic library. All of the loci showed moderate allelic variation ranging from two to seven alleles, with observed heterozygosities from 0.000 to 0.938. The microsatellite DNA markers isolated will be available for use in analysis of quantitative trait loci in breeding programmes and for population genetic studies on experimental fish. [source] PCR primers for microsatellite loci in the desert tortoise (Gopherus agassizii, Testudinidae)MOLECULAR ECOLOGY RESOURCES, Issue 4 2003Taylor Edwards Abstract The desert tortoise, Gopherus agassizii, is a threatened species native to the North American desert southwest and is recognized as having distinct Mojave and Sonoran populations. We identified six polymorphic microsatellite loci in the desert tortoise. All six loci were polymorphic in Sonoran samples. Five of the loci were variable in Mojave samples with varying degrees of amplification success. Two of the loci exhibited low allelic variation (2,3 alleles) while four were highly variable (8,27 alleles). [source] Isolation and characterization of microsatellite loci in the Bang's leaf-nosed bat Hipposideros turpisMOLECULAR ECOLOGY RESOURCES, Issue 4 2002Lazaro M. Echenique-Diaz Abstract The Bang's leaf-nose bat, Hipposideros turpis, is an endangered cave-dwelling species inhabiting the southwesternmost islands of Japan. We isolated six dinucleotide microsatellite markers from the partial genomic library of the bat, and examined their allelic variation using a sample (N = 33) from the largest colony in Japan. All the loci showed a moderate allelic variation ranging from two to eight alleles, with the observed heterozygosities from 0.33 to 0.73, and conformed to Hardy,Weinberg expectations. The present microsatellite markers will be useful in assessing population genetic structure and gene flow among populations of this species. [source] Evolution of mutation rates in bacteriaMOLECULAR MICROBIOLOGY, Issue 4 2006Erick Denamur Summary Evolutionary success of bacteria relies on the constant fine-tuning of their mutation rates, which optimizes their adaptability to constantly changing environmental conditions. When adaptation is limited by the mutation supply rate, under some conditions, natural selection favours increased mutation rates by acting on allelic variation of the genetic systems that control fidelity of DNA replication and repair. Mutator alleles are carried to high frequency through hitchhiking with the adaptive mutations they generate. However, when fitness gain no longer counterbalances the fitness loss due to continuous generation of deleterious mutations, natural selection favours reduction of mutation rates. Selection and counter-selection of high mutation rates depends on many factors: the number of mutations required for adaptation, the strength of mutator alleles, bacterial population size, competition with other strains, migration, and spatial and temporal environmental heterogeneity. Such modulations of mutation rates may also play a role in the evolution of antibiotic resistance. [source] Differential binding to and biofilm formation on, HEp-2 cells by Salmonella enterica Serovar Typhimurium is dependent upon allelic variation in the fimH gene of the fim gene clusterMOLECULAR MICROBIOLOGY, Issue 5 2002Jennifer D. Boddicker Summary Type 1 fimbria-mediated adherence to HEp-2 cells by two strains of Salmonella enterica serovar Typhimurium was found to be different. Although both strains exhibited a strong mannose-sensitive haemagglutination reaction with guinea pig erythrocytes, characteristic of the expression of type 1 fimbriae, only one of the strains adhered in large numbers to HEp-2 cells. Characterization of the fimH genes, encoding the fimbrial adhesins, indicated two allelic variants. Using fimH mutants of the two strains it was possible to demonstrate that binding to HEp-2 cells was associated with the presence of one of the alleles regardless of the host strain. Therefore, this differential binding was not a function of the type I fimbrial shaft or the presence of other types of fimbriae produced by one strain but not the other. These observations may explain the differences in HEp-2 binding by type 1 fimbriate strains of Salmonella previously reported by several groups. Also, our studies demonstrate that the FimH adhesin can influence the efficiency of biofilm formation on HEp-2 cells using once-flow-through continuous culture conditions. The formation of biofilms on eukaryotic cells using this procedure is more likely to represent those conditions found in the intestinal tract than conditions using batch culture techniques to investigate adherence and biofilm formation. Indeed, the increased efficiency of biofilm formation in the murine intestinal tract confirmed the role of one of the fimH alleles in this process. [source] | |||||||||||||||||||||||||||||||