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Microsatellites are continuing to increase in popularity for genetic studies. A major drawback, however, is they often need to be isolated de novo. The traditional method (shotgun cloning) generally results in thousands of recombinant clones, which are then screened by Southern hybridization. Results are typically around 2% positive for mammals, but less than 0.4% for birds. Shotgun cloning is therefore generally not an effective method for isolating microsatellites from avian genomes. Several alternative methods have been developed, but the decision as to which method to use is often arbitrary. Here we present results for two microsatellite isolation techniques from four avian species. 相似文献
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CHRISTINE REBER FUNK REGULA SCHMID‐HEMPEL PAUL SCHMID‐HEMPEL 《Molecular ecology resources》2006,6(1):83-86
We report the details and characteristics of a total of 44 novel microsatelllite loci for Bombus spp. Most of them are highly polymorphic in Bombus terrestris, and a high degree of polymorphism is also found where these primers have been tested in 10 other bumblebee species. These markers will therefore be useful for the genetic study of this group. 相似文献
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Novel sixgill shark (Hexanchus griseus) microsatellite loci were developed and tested on five shark species. A suite of microsatellite loci previously developed for lemon sharks (Negaprion brevirostris) was also tested. Data on 15 microsatellites are presented including primer sequences, number of alleles (a), observed (HO) and expected heterozygosities (HE), and FIS values for sixgill sharks (a = 10–69, HO = 0.24–1.00, HE = 0.76–0.96 and FIS = –0.21–0.60), sevengill sharks (Notorynchus cepedianus) (a = 6–40, HO = 0.20–0.73, HE = 0.59–0.94 and FIS = –0.47–0.58), Pacific spiny dogfish (Squalus acanthias) (a = 3–13, HO = 0.00–0.96, HE = 0.24–0.93 and FIS =–0.52–1.00), angle sharks (Squatina californica) (a = 1–4, HO = 0.00–1.00, HE = 0.60–1.00 and FIS =–1.00–0.25), and leopard sharks (Triakis semifasciata) (a = 3–16, HO = 0.20–1.00, HE = 0.53–0.92 and FIS = –0.57–1.00). A final suite of 14 microsatellites (13 developed from sixgill sharks and one from lemon sharks) were found to be polymorphic and conform to Hardy–Weinberg equilibrium within sixgill sharks. 相似文献
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K. M. MILLER K. H. KAUKINEN K. LABEREE K. J. SUPERNAULT 《Molecular ecology resources》2004,4(4):722-724
Strongylocentrotus franciscanus is a keystone marine herbivore in the Pacific North West of North America, that is commercially harvested for its roe in wild fisheries and is under development as an aquaculture species. We report the development of 11 novel, highly polymorphic di‐ and trinucleotide loci for use in population studies of this species. In a survey of over 200 individuals from three coastal sites in British Columbia, observed heterozygosities of the loci ranged from 0.39 to 0.85 and an average of 26 alleles per locus were resolved. Seven of the 11 microsatellite loci were in Hardy–Weinburg equiulibruim (HWE). 相似文献
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Cherrie's tanager (Ramphocelus costaricensis) is a common woodland bird of the Pacific lowlands of Costa Rica. Males and females have sexually dimorphic plumage and are socially monogamous. As part of a study of sexual selection in this species, we characterized six species‐specific polymorphic microsatellite loci and one cross‐species locus that works well in Cherrie's tanager to ascertain parentage. 相似文献
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Nine novel microsatellite loci were isolated from Oplegnathus fasciatus by screening an enriched genomic library using nonradioactive PCR (polymerase chain reaction) techniques. All loci were found to be polymorphic with an average of 8.1 alleles per locus (range 3–15). The mean observed and expected heterozygosities were 0.71 (range 0.40–1.00) and 0.74 (range 0.50–0.90), respectively. Two loci showed significant Hardy–Weinberg disequilibrium at the P < 0.05 level. The high variabilities revealed in this study suggest that these microsatellite loci should provide useful markers for genetic variation monitoring of O. fasciatus. 相似文献
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We describe 19 polymorphic microsatellite loci for the bamboo rat Rhizomus sinensis. When tested with 20 samples from a single population, these loci exhibited a mean of 4.5 alleles per locus and a mean expected heterozygosity of 0.612. All loci were in Hardy-Weinberg equilibrium and no evidence for linkage disequilibrium was detected between any loci. These loci will be useful for studying population genetic diversity and differentiation in the Chinese bamboo rat. 相似文献
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We report the isolation and characterization of polymorphic microsatellite loci for the Siberian flying squirrel Pteromys volans. The seven most useful loci had between six and 11 alleles and expected heterozygosities ranging from 0.477 to 0.866. We also tested the utility of these loci in other squirrel species, northern flying squirrels (Glaucomys sabrinus and G. volans) and the common red squirrel (Sciurus vulgaris). Three of the Siberian flying squirrel loci were polymorphic in other squirrel species, suggesting a limited potential for cross‐species use. 相似文献
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Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis 总被引:1,自引:0,他引:1
Homoplasy has recently attracted the attention of population geneticists, as a consequence of the popularity of highly variable stepwise mutating markers such as microsatellites. Microsatellite alleles generally refer to DNA fragments of different size (electromorphs). Electromorphs are identical in state (i.e. have identical size), but are not necessarily identical by descent due to convergent mutation(s). Homoplasy occurring at microsatellites is thus referred to as size homoplasy. Using new analytical developments and computer simulations, we first evaluate the effect of the mutation rate, the mutation model, the effective population size and the time of divergence between populations on size homoplasy at the within and between population levels. We then review the few experimental studies that used various molecular techniques to detect size homoplasious events at some microsatellite loci. The relationship between this molecularly accessible size homoplasy size and the actual amount of size homoplasy is not trivial, the former being considerably influenced by the molecular structure of microsatellite core sequences. In a third section, we show that homoplasy at microsatellite electromorphs does not represent a significant problem for many types of population genetics analyses realized by molecular ecologists, the large amount of variability at microsatellite loci often compensating for their homoplasious evolution. The situations where size homoplasy may be more problematic involve high mutation rates and large population sizes together with strong allele size constraints. 相似文献
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Reticulitermes termites have such a cryptic life style and complex colony structure that polymorphic microsatellite markers are desired to investigate their population and colony structures. We successfully isolated seven microsatellite loci in R. speratus , the Japanese subterranean termite, five of which were polymorphic. These polymorphic loci had 2–8 alleles per locus and their observed heterozygosities ranged from 0.059 to 0.438. These five loci were also polymorphic in R . kanmonensis , distributed sympatrically with R. speratus in the Kanmon Region, western Japan; the number of alleles per locus was 2–5, and observed heterozygosity was 0.176–0.625. 相似文献
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We report the isolation and characterization of eight microsatellite loci from the scleractinian coral, Acropora nobilis. The microsatellite loci were obtained using compound SSR primers or an enrichment protocol. All the loci were polymorphic with four to eight alleles per locus and observed heterozygosities ranging from 0.22 to 0.76. Some of the primers developed for the two congeners, Acropora palmata and Acropora millepora were applicable to A. nobilis. These loci are useful for studying the connectivity among A. nobilis populations in Okinawa, southern Japan. 相似文献
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Vogler AJ Keys CE Allender C Bailey I Girard J Pearson T Smith KL Wagner DM Keim P 《Mutation research》2007,616(1-2):145-158
VNTRs are able to discriminate among closely related isolates of recently emerged clonal pathogens, including Yersinia pestis the etiologic agent of plague, because of their great diversity. Diversity is driven largely by mutation but little is known about VNTR mutation rates, factors affecting mutation rates, or the mutational mechanisms. The molecular epidemiological utility of VNTRs will be greatly enhanced when this foundational knowledge is available. Here, we measure mutation rates for 43 VNTR loci in Y. pestis using an in vitro generated population encompassing approximately 96,000 generations. We estimate the combined 43-locus rate and individual rates for 14 loci. A comparison of Y. pestis and Escherichia coli O157:H7 VNTR mutation rates and products revealed a similar relationship between diversity and mutation rate in these two species. Likewise, the relationship between repeat copy number and mutation rate is nearly identical between these species, suggesting a generalized relationship that may be applicable to other species. The single- versus multiple-repeat mutation ratios and the insertion versus deletion mutation ratios were also similar, providing support for a general model for the mutations associated with VNTRs. Finally, we use two small sets of Y. pestis isolates to show how this general model and our estimated mutation rates can be used to compare alternate phylogenies, and to evaluate the significance of genotype matches, near-matches, and mismatches found in empirical comparisons with a reference database. 相似文献
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We isolated 20 trinucleotide microsatellites from two African tree species: Sorindeia madagascariensis (nine microsatellites) and Leptonychia usambarensis (11 microsatellites). Number of alleles ranged from three to seven in Sorindeia and two to 10 in Leptonychia. Observed heterozygosity ranged from 0.025 to 0.829 for Sorindeia and from 0.226 to 0.933 for Leptonychia. Two loci from each species departed from Hardy-Weinberg equilibrium. These microsatellite markers will be used to study how forest fragmentation affects pollination and seed dispersal processes of these tree species. 相似文献
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The first microsatellite primers are described for the mayfly family Baetidae (order Ephemeroptera). Seven polymorphic loci were isolated and characterized for the species Baetis rhodani from two enriched genomic libraries. A total of 183 individuals were genotyped using these loci. Allelic diversity was high for all loci, and observed heterozygosities ranged between 0.382 and 0.772. A heterozygote deficiency was detected in some loci, suggesting the presence of ‘null’ alleles. 相似文献
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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). 相似文献
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Feldheim KA Willink P Brown JE Murphy DJ Neilson ME Stepien CA 《Molecular ecology resources》2009,9(2):639-644
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. 相似文献