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DNA Loci (dna + locus)
Kinds of DNA Loci Selected AbstractsAmplifying Nuclear and Mitochondrial DNA from African Elephant Ivory: a Tool for Monitoring the Ivory TradeCONSERVATION BIOLOGY, Issue 6 2003KENINE E. COMSTOCK cacería furtiva; elefante africano; Loxodonta africana; marfil; microsatélites Abstract: The ability to extract DNA from ivory provides the basis for genetically tracking the origin of poached ivory and thus has important implications for elephant conservation and management. We describe a method to isolate and amplify both genomic and mitochondrial DNA from African elephant ivory that requires very small amounts of ivory taken from any location on the tusk. We pulverized ivory and isolated DNA with a modified QIAamp kit. Ivory as old as 10 to 20 years, stored at ambient conditions, was amenable to DNA isolation with this method. The isolated DNA was robustly amplified at 16 elephant microsatellite loci and two mitochondrial DNA loci. This method has important applications for the forensic analysis of poached African elephant ivory. It enables determination of where stronger antipoaching efforts are needed and provides the basis for monitoring the extent of the trade as well as the consequences of future international trade decisions. Resumen: La habilidad para extraer ADN del marfil proporciona la base para rastrear genéticamente el origen de marfil furtivo y por tanto tiene implicaciones importantes para la conservación y el manejo de elefantes. Describimos un método para aislar y amplificar ADN genómico y mitocondrial de marfil de elefante africano que requiere de cantidades muy pequeñas de marfil tomadas de cualquier parte del colmillo. Pulverizamos el marfil y aislamos el ADN con un equipo QIAamp modificado. Con este método, fue posible aislar el ADN de marfil de 10 a 20 años, conservado en condiciones ambientales. El ADN aislado fue amplificado robustamente en 16 loci microsatélite y dos loci de ADN mitocondrial. Este método tiene aplicaciones importantes para el análisis forense de marfil de elefantes africanos cazados furtivamente. Permite la identificación de sitios donde se requieren mayores esfuerzos para combatir la cacería furtiva y proporciona la base para monitorear la extensión del comercio así como las consecuencias de decisiones futuras de comercio internacional. [source] Effects of environmental pollution on microsatellite DNA diversity in wood mouse (Apodemus sylvaticus) populationsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 11 2005Veerle Berckmoes Abstract Ten microsatellite DNA loci were surveyed to investigate the effects of heavy metal pollution on the genetic diversity and population genetic structure of seven wood mouse (Apodemus sylvaticus) populations along a heavy metal pollution gradient away from a nonferrous smelter in the south of Antwerp (Flanders, Belgium). Analysis of soil heavy metal concentrations showed that soil Ag, As, Cd, Cu, and Pb decreased with increasing distance from the smelter. Genetic analyses revealed high levels of genetic variation in all populations, but populations from the most polluted sites in the gradient did not differ from those of less-polluted sites in terms of mean observed and expected heterozygosity level and mean allelic richness. No correlation was found between measures of genetic diversity and the degree of heavy metal pollution. However, an analysis of molecular variance and a neighbor-joining tree suggested a contamination-related pattern of genetic structuring between the most polluted and less polluted sites. Pairwise FST values indicated that populations were significantly genetically differentiated, and assignment tests and direct estimates of recent migration rates suggested restricted gene flow among populations. Additionally, genetic differentiation increased significantly with geographical distance, which is consistent with an isolation-by-distance model. We conclude that, at least for our microsatellite DNA markers, genetic diversity in the studied wood mouse populations is not affected greatly by the heavy metal pollution. [source] Evidence for genetic differentiation between the molecular forms M and S within the Forest chromosomal form of Anopheles gambiae in an area of sympatryINSECT MOLECULAR BIOLOGY, Issue 1 2002C. Wondji Abstract We studied genetic variation at ten microsatellite DNA loci in Anopheles gambiae populations from the Forest chromosomal form collected in four villages in Cameroon (Central Africa). Both recently described M and S molecular forms occur in sympatry in this area. Geographic differentiation within form was low (Fst < 0.017) despite geographical distance between collection sites ranging from 35 to 350 km. However, higher (Fst > 0.035) and statistically significant levels of genetic differentiation were observed between forms, being the highest between sympatric M and S populations collected within the same village. Results were consistent across all loci spread throughout the genome, therefore reflecting a genome-wide pattern. Considering previous findings of strong assortative mating within forms and general lack of hybrids in areas of sympatry, we propose that there is now sufficient direct and indirect evidence to consider both M and S molecular forms of An. gambiae as distinct species that have probably speciated recently. [source] Speciation chronology of rockhopper penguins inferred from molecular, geological and palaeoceanographic dataJOURNAL OF BIOGEOGRAPHY, Issue 4 2009Marc De Dinechin Abstract Aim, The Southern Ocean is split into several biogeographical provinces between convergence zones that separate watermasses of different temperatures. Recent molecular phylogenies have uncovered a strong phylogeographic structure among rockhopper penguin populations, Eudyptes chrysocome sensu lato, from different biogeographical provinces. These studies suggested a reclassification as three species in two major clades, corresponding, respectively, to warm, subtropical and cold sub-Antarctic watermasses rather than to geographic proximity. Such a phylogeographic pattern, also observed in plants, invertebrates and fishes of the Southern Ocean, suggests that past changes in the positions of watermasses may have affected the evolutionary history of penguins. We calculated divergence times among various rockhopper penguin clades and calibrated these data with palaeomagmatic and palaeoceanographic events to generate a speciation chronology in rockhopper penguins. Location, Southern Ocean. Methods, Divergence times between populations were calculated using five distinct mitochondrial DNA loci, and assuming a molecular clock model as implemented in mdiv. The molecular evolution rate of rockhopper penguins was calibrated using the radiochronological age of St Paul Island and Amsterdam Island in the southern Indian Ocean. Separations within other clades were correlated with palaeoceanographic data using this calibrated rate. Results, The split between the Atlantic and Indian populations of rockhopper penguins was dated as 0.25 Ma, using the date of emergence of St Paul and Amsterdam islands, and the divergence between sub-Antarctic and subtropical rockhopper penguins was dated as c. 0.9 Ma (i.e. during the mid-Pleistocene transition, a major change in the Earth's climate cycles). Main conclusions, The mid-Pleistocene transition is known to have caused a major southward shift in watermasses in the Southern Ocean, thus changing the environment around the northernmost rockhopper penguin breeding sites. This ecological isolation of northernmost populations may have caused vicariant speciation, splitting the species into two major clades. After the emergence of St Paul and Amsterdam islands in the subtropical Indian Ocean 0.25 Ma, these islands were colonized by penguins from the subtropical Atlantic, 6000 km away, rather than by penguins from the sub-Antarctic Indian Ocean, 5000 km closer. [source] Parallel evolution of larval morphology and habitat in the snail-killing fly genus TetanoceraJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 5 2006E. G. CHAPMAN Abstract In this study, we sequenced one nuclear and three mitochondrial DNA loci to construct a robust estimate of phylogeny for all available species of Tetanocera. Character optimizations suggested that aquatic habitat was the ancestral condition for Tetanocera larvae, and that there were at least three parallel transitions to terrestrial habitat, with one reversal. Maximum likelihood analyses of character state transformations showed significant correlations between habitat transitions and changes in four larval morphological characteristics (cuticular pigmentation and three characters associated with the posterior spiracular disc). We provide evidence that phylogenetic niche conservatism has been responsible for the maintenance of aquatic-associated larval morphological character states, and that concerted convergence and/or gene linkage was responsible for parallel morphological changes that were derived in conjunction with habitat transitions. These habitat,morphology associations were consistent with the action of natural selection in facilitating the morphological changes that occurred during parallel aquatic to terrestrial habitat transitions in Tetanocera. [source] Host selection by Anopheles arabiensis and An. quadriannulatus feeding on cattle in ZimbabweMEDICAL AND VETERINARY ENTOMOLOGY, Issue 2 2002A. Prior Abstract In the Zambezi valley, mosquito females of the Anopheles gambiae Giles complex (Diptera: Culicidae) were collected from a hut containing pairs of cattle distinguishable by known DNA markers. DNA was extracted from the blood-fed mosquito abdomens and primer sets for ungulate and mosquito DNA loci were used to identify the mosquito sibling species and individual host source(s) of their bloodmeals. The 67 mosquitoes comprised a mixture of An. arabiensis Patton (31%) and An. quadriannulatus Theobald (69%). DNA from one or both of the cattle present in the hut was detected in 91% of samples. When the hut contained an adult and a calf, the percentage of bloodmeals from the adult, the calf and adult + calf were 58%, 27% and 15%, respectively; the trend towards meals from the adult host was consistent but not always significant. When the pair of cattle comprised two adults of roughly equal size and age, then mosquitoes generally showed no significant bias towards feeding from one individual. There was no significant difference in the pattern of host selection made by An. arabiensis and An. quadriannulatus but the former had a significantly higher percentage (20%) of mixed meals than An. quadriannulatus (9%). These two members of the An. gambiae complex appear to be less selective in their choice of cattle hosts compared to day-active Diptera such as tsetse and Stomoxys, possibly because the hosts are generally asleep when Anopheles are active and there is therefore less selective pressure to adapt to host defensive behaviour. The slight bias of Anopheles towards older and/or larger cattle may be related to the host's larger surface area. [source] Genetic effective size, Ne, tracks density in a small freshwater cyprinid, Pecos bluntnose shiner (Notropis simus pecosensis)MOLECULAR ECOLOGY, Issue 14 2010MEGAN J. OSBORNE Abstract Genetic monitoring tracks changes in measures of diversity including allelic richness, heterozygosity and genetic effective size over time, and has emerged as an important tool for understanding evolutionary consequences of population management. One proposed application of genetic monitoring has been to estimate abundance and its trajectory through time. Here, genetic monitoring was conducted across five consecutive year for the Pecos bluntnose shiner, a federally threatened minnow. Temporal changes in allele frequencies at seven microsatellite DNA loci were used to estimate variance effective size (NeV) across adjacent years in the time series. Likewise, effective size was computed using the linkage disequilibrium method (NeD) for each sample. Estimates of Ne were then compared to estimates of adult fish density obtained from traditional demographic monitoring. For Pecos bluntnose shiner, density (catch-per-unit-effort), NeV and NeD were positively associated across this time series. Results for Pecos bluntnose shiner were compared to a related and ecologically similar species, the Rio Grande silvery minnow. In this species, density and NeV were negatively associated, which suggested decoupling of abundance and effective size trajectories. Conversely, density and NeD were positively associated. For Rio Grande silvery minnow, discrepancies among estimates of Ne and their relationships with adult fish density could be related to effects of high variance in reproductive success in the wild and/or effects of supplementation of the wild population with captive-bred and reared fish. The efficacy of Ne as a predictor of density and abundance may depend on intrinsic population dynamics of the species and how these dynamics are influenced by the landscape features, management protocols and other factors. [source] Influence of habitat discontinuity, geographical distance, and oceanography on fine-scale population genetic structure of copper rockfish (Sebastes caurinus)MOLECULAR ECOLOGY, Issue 13 2008M. L. JOHANSSON Abstract The copper rockfish is a benthic, nonmigratory, temperate rocky reef marine species with pelagic larvae and juveniles. A previous range-wide study of the population-genetic structure of copper rockfish revealed a pattern consistent with isolation-by-distance. This could arise from an intrinsically limited dispersal capability in the species or from regularly,spaced extrinsic barriers that restrict gene flow (offshore jets that advect larvae offshore and/or habitat patchiness). Tissue samples were collected along the West Coast of the contiguous USA between Neah Bay, WA and San Diego, CA, with dense sampling along Oregon. At the whole-coast scale (~2200 km), significant population subdivision (FST = 0.0042), and a significant correlation between genetic and geographical distance were observed based on 11 microsatellite DNA loci. Population divergence was also significant among Oregon collections (~450 km, FST = 0.001). Hierarchical amova identified a weak but significant 130-km habitat break as a possible barrier to gene flow within Oregon, across which we estimated that dispersal (Nem) is half that of the coast-wide average. However, individual-based Bayesian analyses failed to identify more than a single population along the Oregon coast. In addition, no correlation between pairwise population genetic and geographical distances was detected at this scale. The offshore jet at Cape Blanco was not a significant barrier to gene flow in this species. These findings are consistent with low larval dispersal distances calculated in previous studies on this species, support a mesoscale dispersal model, and highlight the importance of continuity of habitat and adult population size in maintaining gene flow. [source] Social kin associations and genetic structuring of striped dolphin populations (Stenella coeruleoalba) in the Mediterranean SeaMOLECULAR ECOLOGY, Issue 14 2007STEFANIA GASPARI Abstract We investigated hierarchical patterns of genetic subdivision, and assessed kinship within and between social groups of striped dolphins (Stenella coeruleoalba) in the Tyrrhenian Sea. A total of 165 samples were analysed at eight microsatellite DNA loci, including outgroup samples from the Adriatic, Scotland and Spain for population-level comparisons. We found population genetic structure within the Mediterranean basin, including small but significant differentiation between the Adriatic and Tyrrhenian Seas (FST = 0.0047, P = 0.008), and between putative ,inshore' and ,offshore' (FST = 0.0217, P = 0.005) populations in the Tyrrhenian Sea. Assessment of kinship within and among 12 association groups showed higher average kinship for females within than between groups, and smaller groups showed higher average kinship. Comparisons of relatedness for both sexes showed a significant difference between males and females, with females more likely to associate with adult kin. Together these data emphasize the importance of the social cohesion of kin in small groups to the structuring of striped dolphin populations in this environment. [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] Contrasting patterns of mitochondrial and microsatellite population structure in fragmented populations of greater prairie-chickensMOLECULAR ECOLOGY, Issue 12 2003Jeff A. Johnson Abstract Greater prairie-chickens (Tympanuchus cupido pinnatus) were once found throughout the tallgrass prairie of midwestern North America but over the last century these prairies have been lost or fragmented by human land use. As a consequence, many current populations of prairie-chickens have become isolated and small. This fragmentation of populations is expected to lead to reductions in genetic variation as a result of random genetic drift and a decrease in gene flow. As expected, we found that genetic variation at both microsatellite DNA and mitochondrial DNA (mtDNA) markers was reduced in smaller populations, particularly in Wisconsin. There was relatively little range-wide geographical structure (FST) when we examined mtDNA haplotypes but there was a significant positive relationship between genetic (FST) and geographical distance (isolation by distance). In contrast, microsatellite DNA loci revealed significant geographical structure (FST) and a weak effect of isolation by distance throughout the range. These patterns were much stronger when populations with reduced levels of genetic variability (Wisconsin) were removed from the analyses. This suggests that the effects of genetic drift were stronger than gene flow at microsatellite loci, whereas these forces were in range-wide equilibrium at mtDNA markers. These differences between the two molecular markers may be explained by a larger effective population size (Ne) for mtDNA, which is expected in species such as prairie-chickens that have female-biased dispersal and high levels of polygyny. Our results suggest that historic populations of prairie-chickens were once interconnected by gene flow but current populations are now isolated. Thus, maintaining gene flow may be important for the long-term persistence of prairie-chicken populations. [source] Population structure in two sympatric species of the Lake Tanganyika cichlid tribe Eretmodini: evidence for introgressionMOLECULAR ECOLOGY, Issue 5 2001Lukas Rüber Abstract Patterns of genetic differentiation were analysed and compared in two sympatric species of the endemic Lake Tanganyika cichlid tribe Eretmodini by means of mitochondrial DNA (mtDNA) sequences of the control region and six microsatellite DNA loci. The sample area covers a total of 138 km of mostly uninterrupted rocky shoreline in the Democratic Republic of Congo and includes the entire distribution range of Tanganicodus cf. irsacae that stretches over a distance of 35 km. Both markers detected significant genetic differentiation within and between the two species. T. cf. irsacae contained lower overall genetic variation than Eretmoduscyanostictus, possibly due to its more restricted range of distribution and its smaller effective population sizes. Complete fixation of Tanganicodus mtDNA haplotypes was observed in Eretmodus at two localities, while at two other localities some Tanganicodus individuals possessed Eretmodus mtDNA haplotypes. Taking into account the relatively large average sequence divergence of 6.2% between the two species, as well as the geographical distribution of mtDNA haplotypes in the lake, the observed pattern is more likely to be a consequence of asymmetric introgression than of shared ancestral polymorphism. As there is significant population differentiation between sympatric Tanganicodus and Eretmodus populations, the events of introgressions may have happened after secondary contact, but our data provide no evidence for ongoing gene flow and suggest that both species are reproductively isolated at present time. [source] Population structure of Atlantic salmon (Salmo salar L.): a range-wide perspective from microsatellite DNA variationMOLECULAR ECOLOGY, Issue 4 2001T. L. King Abstract Atlantic salmon (n = 1682) from 27 anadromous river populations and two nonanadromous strains ranging from south-central Maine, USA to northern Spain were genotyped at 12 microsatellite DNA loci. This suite of moderate to highly polymorphic loci revealed 266 alleles (5,37/locus) range-wide. Statistically significant allelic and genotypic heterogeneity was observed across loci between all but one pairwise comparison. Significant isolation by distance was found within and between North American and European populations, indicating reduced gene flow at all geographical scales examined. North American Atlantic salmon populations had fewer alleles, fewer unique alleles (though at a higher frequency) and a shallower phylogenetic structure than European Atlantic salmon populations. We believe these characteristics result from the differing glacial histories of the two continents, as the North American range of Atlantic salmon was glaciated more recently and more uniformly than the European range. Genotypic assignment tests based on maximum-likelihood provided 100% correct classification to continent of origin and averaged nearly 83% correct classification to province of origin across continents. This multilocus method, which may be enhanced with additional polymorphic loci, provides fishery managers the highest degree of correct assignment to management unit of any technique currently available. [source] Quantification of algal endosymbionts (Symbiodinium) in coral tissue using real-time PCRMOLECULAR ECOLOGY RESOURCES, Issue 1 2009J. C. MIEOG Abstract Understanding the flexibility of the endosymbioses between scleractinian corals and single-cell algae of the genus Symbiodinium will provide valuable insights into the future of coral reefs. Here, a real-time polymerase chain reaction (PCR) assay is presented to accurately determine the cell densities of Symbiodinium clades C and D in the scleractinian coral Acropora millepora, which can be extended to other coral,symbiont associations in the future. The assay targets single- to low-copy genes of the actin family of both the coral host and algal symbiont. Symbiont densities are expressed as the ratio of Symbiodinium cells to each host cell (S/H ratio, error within 30%), but can also be normalized to coral surface area. Greater accuracy in estimating ratios of associations involving multiple clades is achieved compared with previous real-time PCR assays based on high-copy ribosomal DNA loci (error within an order of magnitude). Healthy adult A. millepora containing ~1.4 × 106 zooxanthellae per cm2 (as determined by haemocytometer counts) had S/H ratios of c. 0.15, i.e. ~15 symbiont cells per 100 host cells. In severely bleached colonies, this ratio decreased to less than 0.005. Because of its capacity to accurately determine both densities and ratios of multiple symbionts within one sample, the assay will open the door for novel research into the mechanisms of symbiont shuffling and switching. [source] Isolation and characterization of polymorphic microsatellite markers in the red snow crab (Chionoecetes japonicus)MOLECULAR ECOLOGY RESOURCES, Issue 3 2008N. AZUMA Abstract A total of 12 polymorphic microsatellite DNA loci were isolated from the red snow crab, Chionoecetes japonicus (Brachyura: Majidae), one of important fisheries resources in the Far East. The number of alleles observed at each locus ranged from two to 19, with the observed and expected heterozygosities of 0.125,0.875 and 0.156,0.949, respectively, suggesting these loci to be a useful molecular marker for population analysis in this species. Of the 12 loci, seven also were available for genotyping of the snow crab, Chionoecetes opilio, implying these loci as a useful molecular marker in the genus Chionoecetes. [source] PERMANENT GENETIC RESOURCES: Fifteen polymorphic microsatellite DNA loci from Hawaii's Metrosideros polymorpha (Myrtaceae: Myrtales), a model species for ecology and evolutionMOLECULAR ECOLOGY RESOURCES, Issue 2 2008NICHOLAS G. CRAWFORD Abstract We developed 15 polymorphic microsatellite loci from the Hawaiian tree Metrosideros polymorpha. These loci were screened against two varieties from several populations and from 23 individuals from one mid-elevation population on Hawaii Island. Loci were variable with the number of alleles per locus ranging from three to 24. Polymorphic information content ranged from 0.222 to 0.941, and observed heterozygosity ranged from 0.261 to 0.955. [source] PERMANENT GENETIC RESOURCES: Isolation and characterization of microsatellite DNA loci from the southern flounder, Paralichthys lethostigmaMOLECULAR ECOLOGY RESOURCES, Issue 2 2008C. W. SHAO Abstract Paucity of polymorphic molecular markers in southern flounder (Paralichthys lethostigma) has been a major limitation in genetic improvement of this important economic fish. Hence, we constructed a repeat-enriched genomic library from P. lethostigma. A total of 39 new microsatellites were identified, for which 33 primer pairs were designed. After validating and scoring, 10 of these loci were polymorphic in a test population with the range of alleles from two to nine per locus. The observed and expected heterozygosities ranged from 0.2500 to 0.9000 and from 0.4469 to 0.8514, respectively. These polymorphic microsatellites will be useful for genetic diversity analysis and linkage map construction for P. lethostigma. [source] Development of 15 polymorphic microsatellite markers in the Atlantic tarpon (Megalops atlanticus) for capture,recapture studiesMOLECULAR ECOLOGY RESOURCES, Issue 1 2008SEIFU SEYOUM Abstract Fifteen polymorphic microsatellite DNA loci for Atlantic tarpon, Megalops atlanticus, were isolated by using PIMA, a polymerase chain reaction-based technique. The number of alleles at each locus ranged from two to 24 (mean = 7.7) in 65 specimens from Tampa Bay, Florida. Observed and expected heterozygosities ranged from 0.27 to 0.92 (mean = 0.60) and from 0.28 to 0.95 (mean = 0.62), respectively. Genotypes at one locus deviated significantly from Hardy,Weinberg equilibrium. In exact tests for genotypic disequilibrium, there was no evidence of associations between any pair of loci. Overall, loci were well resolved and highly polymorphic, confirming their suitability for DNA fingerprinting applications and other genetic studies. [source] Microsatellite markers for the invasive plant species white sweetclover (Melilotus alba) and yellow sweetclover (Melilotus officinalis)MOLECULAR ECOLOGY RESOURCES, Issue 6 2007L. M. WINTON Abstract We describe specific primers that amplify nine microsatellite DNA loci from Melilotus alba and Melilotus officinalis, both invasive plant species (Fabaceae) throughout North America. Allelic diversity was slightly lower for M. alba than for M. officinalis, as was expected heterozygosity. For both species, heterozygote deficit was observed at several loci. Genotypic diversity was very high for both species; the 29 plant samples of each species all had different multilocus genotypes. These markers will be used to determine the origins of the sweetclover invasion in Alaska and to compare patterns of diversity between subarctic and lower latitude populations. [source] Tetranucleotide, trinucleotide, and dinucleotide loci from the bobcat (Lynx rufus)MOLECULAR ECOLOGY RESOURCES, Issue 2 2005BRANT C. FAIRCLOTH Abstract We describe primers and polymerase chain reaction (PCR) conditions to amplify four dinucleotide, one trinucleotide, and three tetranucleotide microsatellite DNA loci from the bobcat (Lynx rufus). The primers were tested on 22 individuals collected from a population located within southwestern Georgia (USA). The primer pairs developed in this study yielded an average of 7.4 alleles per locus (range four to 10), an average observed heterozygosity of 0.60 (range 0.40 to 0.76), and an average polymorphic information content of 0.70 (range 0.51 to 0.78). [source] Microsatellite DNA markers for the study of Atlantic salmon (Salmo salar) kinship, population structure, and mixed-fishery analysesMOLECULAR ECOLOGY RESOURCES, Issue 1 2005TIM L. KING Abstract Eleven microsatellite DNA loci were identified and characterized for Atlantic salmon (Salmo salar) collected from the Penobscot River, Maine, USA and the River Nith, Scotland, UK. The markers revealed high levels of genetic diversity (seven to 48 alleles per locus), heterozygosity (to 100%), and allelic heterogeneity (all comparisons). Considerable differentiation was observed as the genetic distance (chord) between the two collections was 0.680 and the pairwise FST, 0.12, was highly significant. These findings are consistent with patterns of continental-level differentiation observed previously using an alternate suite of microsatellite loci. Locus-by-locus analyses of molecular variance suggested that most markers were suitable for delineating kinships and population genetic structure. [source] Microsatellite DNA markers for the study of horseshoe crab (Limulus polyphemus) population structureMOLECULAR ECOLOGY RESOURCES, Issue 3 2004TIM L. KING Abstract Twenty-two microsatellite DNA loci were identified and characterized for horseshoe crabs (Limulus polyphemus) collected from two Atlantic coast and one Gulf of Mexico site. These markers revealed a high degree of genetic diversity (8,35 alleles per locus), heterozygosity (25.0% to 100.0%), and allelic heterogeneity (69.8% of comparisons). Considerable regional differentiation was observed as genetic distances (chord) ranged between 0.25 and 0.45, and all FST values (0.014,0.092) were significant. These preliminary findings are consistent with patterns of regional differentiation observed using allozyme variation and contradictory to findings of limited gene flow reported for sequence variation at the mitochondrial DNA COI region. [source] Microsatellite DNA markers for the ground beetle Pterostichus oblongopunctatus F.MOLECULAR ECOLOGY RESOURCES, Issue 1 2004M. Lagisz Abstract Six microsatellite DNA loci were isolated from the ground beetle Pterostichus oblongopunctatus F. (Coleoptera, Carabidae) to study population structure. Each locus was polymorphic, with the number of alleles ranging from three to six. Observed heterozygosity varied between 0.20 and 0.67. All six loci were tested for amplification in the closely related P. quadrifoveolatus and they were shown to be polymorphic. The primers developed were used in multiplex polymerase chain reactions. [source] Isolation, characterization and cross-species amplification of eight microsatellite DNA loci in the migratory locust (Locusta migratoria)MOLECULAR ECOLOGY RESOURCES, Issue 4 2003De-Xing Zhang Abstract Eight polymorphic di- and trinucleotide microsatellite loci suitable for population genetic analysis were developed in Locusta migratoria from a partial phagemid genomic library enriched for microsatellite inserts. The expected heterozygosity at these loci ranges from 0.45 to 0.97, with the observed allele numbers varying between nine and 45. The overall microsatellite cloning efficiency in L. migratoria is 14%, suggesting that in migratory locusts, microsatellite sequences are abundant and should provide a valuable and easily accessible source of nuclear markers for genetic studies. These microsatellite loci were highly Locusta -specific, with only very limited cross-species applicability. [source] Polymorphic tetranucleotide microsatellite DNA loci from the southern dusky salamander (Desmognathus auriculatus)MOLECULAR ECOLOGY RESOURCES, Issue 4 2003Dean A. Croshaw Abstract We describe polymerase chain reaction (PCR) primers and amplification conditions for seven tetranucleotide microsatellite DNA loci isolated from the southern dusky salamander (Desmognathus auriculatus). Primers were tested on 16 individuals from one population in Aiken County, South Carolina. We detected an average of 6.57 alleles per locus, an observed heterozygosity range of 0.44,0.94, and high polymorphic information contents (mean of 0.68). [source] Microsatellite DNA loci from the Diamondback terrapin (Malaclemys terrapin)MOLECULAR ECOLOGY RESOURCES, Issue 2 2003J. Susanne Hauswaldt Abstract We describe polymerase chain recation (PCR) primers and conditions to amplify one dinucleotide and five tetranucleotide microsatellite DNA loci isolated from the Diamondback terrapin (Malaclemys terrapin). The PCR primers were tested on 21 terrapins from Cape Romain, SC, USA. The microsatellite primers developed yielded a high number of alleles (8,14) and high observed heterozygosities (0.57,1.0). [source] Microsatellite DNA loci for Western Hemlock [Tsuga heterophylla (Raf.) Sarg]MOLECULAR ECOLOGY RESOURCES, Issue 3 2002Vindhya Amarasinghe Abstract Polymorphic microsatellite loci were developed for Western Hemlock [Tsuga heterophylla (Raf.) Sarg], a prominent forest tree species in Western North America. Microsatellite-enriched libraries were screened for (CA)n dinucleotide repeats from which 33 positive clones were sequenced. Polymerase chain reaction (PCR) primers for 16 microsatellite loci were prepared and tested against DNA from unrelated Western Hemlock trees. The 12 most informative microsatellite loci are reported here. From four to 22 alleles per locus were observed, with an average expected heterozygousity of 0.799. [source] Genetic structure of seven Mexican indigenous populations based on five polymarker lociAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 1 2003Leonora Buentello-Malo This descriptive study investigates the genetic structure of seven Mexican indigenous populations (Mixteca Alta, Mixteca Baja, Otomies, Purepecha, Nahuas-Guerrero, Nahuas-Xochimilco, and Tzeltales) on the basis of five PCR-based polymorphic DNA loci: LDLR, GYPA, HBGG, D7S8, and GC. Genetic distance and diversity analyses indicate that these Mexican indigenous are similar and that more than 96% of the total gene diversity (HT) can be attributed to individual variation within populations. Mixteca-Alta, Mixteca-Baja, and Nahuas-Xochimilco show indications of higher admixture with European-derived persons. The demonstration of a relative genetic homogeneity of Mexican Indians for the markers studied suggests that this population is suitable for studying disease-marker associations in the search for candidate genes of complex diseases. Am. J. Hum. Biol. 15:23,28, 2003. © 2002 Wiley-Liss, Inc. [source] Variation at 10 protein coding loci in the mbenzele pygmies from the central african republic and a comparison with microsatellite dataAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 1 2002Valentina Coia Ten protein coding loci (6-PGD, A1-AT, ACP1, CaII, ESD, GC, GPX1, Hb,, PGM1, and TF) were analyzed in the Mbenzele Pygmies from the Central African Republic. The frequency data were used to calculate the genetic distances between Mbenzele Pygmies and other African groups. In the principal coordinate plot of FST genetic distances, the Mbenzele cluster together with other Pygmies of the western cluster, the Biaka from C.A.R., Gielli from Cameroon, and Babinga from Congo. By contrast, they are considerably distanced from other Pygmy groups of the eastern cluster (Twa from Rwanda, Mbuti from Zaire). Genetic distances obtained using protein loci were compared with those based on microsatellite loci. The two distance matrices are insignificantly correlated (r = 0.268; one tail probability = 0.332), and the main difference is in the higher genetic affinity between the Mbenzele and Biaka Pygmies observed at the protein level. Although reasons underlying the discrepancy between inter-populational variation at protein and DNA loci are not established with certainty, the comparison suggests that the genetic distance between the Mbenzele and Biaka Pygmies at microsatellite loci could have been shaped by genetic drift. Am. J. Hum. Biol. 14:9,14, 2002.© 2002 Wiley-Liss, Inc. [source] Cultivar preference exhibited by two sympatric and genetically distinct populations of the soybean fungal pathogen Phialophora gregata f.sp. sojaePLANT PATHOLOGY, Issue 2 2005X. Meng Phialophora gregata f.sp. sojae, a soilborne vascular pathogen causing brown stem rot of soybean, has been divided into A and B populations based on variation in the intergenic spacer region of nuclear rDNA (rDNA marker). The A and B populations correlate with defoliating and nondefoliating pathotypes, respectively. In this study, eight additional polymorphic anonymous marker loci (five inter simple sequence repeat loci and three long-primer random amplified polymorphic DNA loci) were identified and applied to a total of 189 isolates. Alleles of these eight loci were invariant within, but different between the A and B populations, providing further evidence that the rDNA marker identifies genetically distinct populations. The two populations were sympatric, residing not only in the same field, but also in the same plants under field conditions. Representative strains of the two populations, when used individually in inoculations, infected both resistant cv. Bell and susceptible cv. Sturdy. However, when the same representatives of the two populations were mixed in a 1 : 1 ratio and used as a mixed inoculum in a competitive bioassay, differential cultivar preference was revealed using PCR detection of populations in infected plants. Population A was detected significantly more often (18 out of 24 plants) in the susceptible cv. Sturdy, whereas population B was detected significantly more often (17 out of 24 plants) in the resistant cv. Bell, corroborating earlier field studies. This is the first controlled experiment to demonstrate a differential host preference of P. gregata f.sp. sojae toward different cultivars of the same host species. Unification of terminologies used in P. gregata f.sp. sojae is discussed. [source] | |||||||||||||||||||||||||