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135 results for “microsatellite marker”
Data from: Population genetics of overwintering monarch butterflies, Danaus plexippus (Linnaeus), from central Mexico inferred from mitochondrial DNA and microsatellite markers
Population genetic variation and demographic history in Danaus plexippus (L.), from Mexico were assessed based on analyses of mitochondrial cytochrome c oxidase subunit I (COI; 658 bp) and subunit II (COII; 503 bp) gene segments and seven microsatellite loci. The sample of 133 individuals included both migratory monarchs, mainly from four overwintering sites within the Monarch Butterfly Biosphere Reserve (MBBR) in central Mexico (states of Michoacán and México), and a nonmigratory population from Irapuato, Guanajuato. Haplotype (h) and nucleotide (π) diversities were relatively low, averaging 0.466 and 0.00073, respectively, for COI, and 0.629 and 0.00245 for COII. Analysis of molecular variance (AMOVA) of the COI data set, which included additional GenBank sequences from a nonmigratory Costa Rican population, showed significant population structure between Mexican migratory monarchs and nonmigratory monarchs from both Mexico and Costa Rica, suggesting limited gene flow between the two behaviorally distinct groups. Interestingly, while the COI haplotype frequencies of the nonmigratory populations differed from the migratory, they were similar to each other, despite the great physical distance between them. Microsatellite analyses, however, suggested a lack of structure between the two groups, possibly owing to the number of significant deviations from Hardy Weinberg equilibrium resulting from heterzoygote deficiencies found for most of the loci. Estimates of demographic history of the combined migratory MBBR monarch population, based on the mismatch distribution and Bayesian skyline analyses of the concatenated COI and COII data set (n = 89) suggested a population expansion dating to the late Pleistocene (~35,000 to 40,000 years before present) followed by a stable effective female population size (Nef) of about six million over the last 10,000 years.
Data from: A comparative assessment of SNP and microsatellite markers for assigning parentage in a socially monogamous bird
Single-nucleotide polymorphisms (SNPs) are preferred over microsatellite markers in many evolutionary studies, but have only recently been applied to studies of parentage. Evaluations of SNPs and microsatellites for assigning parentage have mostly focused on special cases that require a relatively large number of heterozygous loci, such as species with low genetic diversity or with complex social structures. We developed 120 SNP markers from a transcriptome assembled using RNA-sequencing of a songbird with the most common avian mating system—social monogamy. We compared the effectiveness of 97 novel SNPs and six previously described microsatellites for assigning paternity in the black-throated blue warbler, Setophaga caerulescens. We show that the full panel of 97 SNPs (mean Ho = 0.19) was as powerful for assigning paternity as the panel of multiallelic microsatellites (mean Ho = 0.86). Paternity assignments using the two marker types were in agreement for 92% of the offspring. Filtering individual samples by a 50% call rate and SNPs by a 75% call rate maximized the number of offspring assigned with 95% confidence using SNPs. We also found that the 40 most heterozygous SNPs (mean Ho = 0.37) had similar power to assign paternity as the full panel of 97 SNPs. These findings demonstrate that a relatively small number of variable SNPs can be effective for parentage analyses in a socially monogamous species. We suggest that the development of SNP markers is advantageous for studies that require high-throughput genotyping or that plan to address a range of ecological and evolutionary questions.
Data from: Multilocus microsatellite markers for molecular typing of Candida tropicalis isolates
Background: Candida tropicalis is considered to be the leading pathogen causing nosocomial fungemia and hepatosplenic fungal infections in patients with cancer, particularly those with leukemia. Microsatellite-based typing methods using sets of genetic markers have been developed and reported for population structure analysis of C. albicans, C. glabrata, and C. parapsilosis, but no studies have been published for genetic analysis of C. tropicalis. The objective of this study was to develop new microsatellite loci that have the ability to distinguish among C. tropicalis isolates. Results: DNA sequences containing over 10 bi- or tri-nucleotide repeats were selected from the C. tropicalis genome database. Thirty PCR primers sets specific for the microsatellite loci were designed and tested using eight clinically independent isolates. According to the amplification efficiency, specificity, and observed polymorphisms, eight markers were selected for further population structure analysis and molecular typing. Sixty-five independent C. tropicalis isolates were genotyped using these 8 markers. Based on these analyses, six microsatellite loci were confirmed, although two loci were found to be with unstable flanking areas. The six polymorphic loci displayed 4–22 alleles and 7–27 genotypes. The discriminatory power of the six loci ranged from 0.70 to 0.95. Genotyping results obtained by microsatellite analysis were compared to PCR-fingerprinting and multi-locus sequence typing (MLST). The comparisons showed that microsatellite analysis and MLST had the similar discriminatory power for C. tropicalis, which were more powerful than PCR-fingerprinting. Conclusions: This is the first attempt to develop new microsatellite loci for C. tropicalis. These newly developed markers will be a valuable resource for the differentiation of C. tropicalis isolates. More C. tropicalis isolates will need to be sequenced and analyzed in order to fully show the potential of these newly developed microsatellite markers.
Data from: Multiplexed microsatellite markers for genetic studies of beech
European beech (Fagus sylvatica L.) is one of the economically most important broadleaved tree species in Europe and has become a model for studying climate change effects. Multiplex PCR of microsatellites is a fast and cost-effective technique allowing high throughput genotyping. Here we present the procedure used to develop two multiplex kits (8-plexes) for European beech. We paid particular attention to quality control throughout all steps of the multiplex kits development (null allele detection, error rate measurements, linkage disequilibrium). Preliminary assays suggest that the multiplex kits amplify 16 loci largely devoid of null alleles and allow rapid and cost-effective genotyping of beech with low error rates. The two kits, which differ in their levels of polymorphism, most likely due to marker origin, were also informative in seven other beech species tested.
Data from: Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds
Microsatellite loci are ideal for testing hypotheses relating to genetic segregation at fine spatio-temporal scales. They are also conserved among closely related species, making them potentially useful for clarifying interspecific relationships between recently diverged taxa. However, mutations at primer binding sites may lead to increased nonamplification, or disruptions that may result in decreased polymorphism in nontarget species. Furthermore, high mutation rates and constraints on allele size may also with evolutionary time, promote an increase in convergently evolved allele size classes, biasing measures of interspecific genetic differentiation. Here, we used next-generation sequencing to develop microsatellite markers from a shotgun genome sequence of the sub-Antarctic seabird, the thin-billed prion (Pachyptila belcheri), that we tested for cross-species amplification in other Pachyptila and related sub-Antarctic species. We found that heterozygosity decreased and the proportion of nonamplifying loci increased with phylogenetic distance from the target species. Surprisingly, we found that species trees estimated from interspecific FST provided better approximations of mtDNA relationships among the studied species than those estimated using DC, even though FST was more affected by null alleles. We observed a significantly nonlinear second order polynomial relationship between microsatellite and mtDNA distances. We propose that the loss of linearity with increasing mtDNA distance stems from an increasing proportion of homoplastic allele size classes that are identical in state, but not identical by descent. Therefore, despite high cross-species amplification success and high polymorphism among the closely related Pachyptila species, we caution against the use of microsatellites in phylogenetic inference among distantly related taxa.
Isolation and characterization of twelve polymorphic microsatellite markers in the endangered Hopea hainanensis (Dipterocarpaceae)
<p>Using next-generation sequencing technology, 26 microsatellite markers were developed and genotyped by capillary electrophoresis for <i>Hopea</i> <i>hainanensis</i> Merrill & Chun, an endangered tree species in Hainan Island and northern Vietnam. Twelve markers were found to be polymorphic in this species. Primer transferability was tested with <i>H</i>. <i>chinensis</i> Hand.-Mazz. and <i>H</i>.<i> reticulata</i> Tardieu, in which 3 and 7 microsatellite markers were found to be polymorphic, separately. The 12 polymorphic microsatellite markers could be applied to population genetic studies aimed at <i>H</i>. <i>hainanensis</i> as well as its close relatives, facilitating the conservation and restoration of these endangered but valuable <i>Hopea</i> species.</p>
Microsatellite markers for assessing genetic diversity and kinship relationships in one of the largest South American fur seal (Arctocephalus australis) populations of the Pacific Ocean
<p class="CuerpoAA">The genetic diversity of a population is the foundation of its adaptability to environmental challenges. The South American fur seal is a widely distributed pinniped in the south cone of South America. However, a large gap in the Pacific coast separates two distinct evolutionary units for the species: the Peruvian and the Southern Pacific/Atlantic populations. Throughout the Pacific, one of the main breeding colonies is located in Guafo Island, in the southern Chilean Patagonia. As the closest reproductive population to the isolated Peruvian group, Guafo's colony may potentially facilitate gene flow, contribute with new alleles and increase genetic variability to Peruvian populations', connecting the entire Pacific's distribution of the species. In this study, Guafo's Island South American fur seal population was characterized by the identification and genotyping of species-specific microsatellite markers. As a result, we confirm that Guafo's colony is a diverse group with mild evidence of genetic structure. Although a couple of family groups among seasons were observed, results indicate that half-siblings are rare and suggest that polygyny in this species is more relaxed than previously thought. Additionally, three full-sibling pairs were genetically identified within the 2017 season, which is the first genetic support that describes the presence of twins for the species. These attributes suggest that the colony at Guafo is a panmictic large group, and could serve as a potential genetic source for other isolated populations.</p>
Microsatellite marker data for Chernobyl Daphnia populations
<p>Populations experiencing varying levels of ionising radiation provide an excellent opportunity to study the fundamental drivers of evolution. Radiation can cause mutations, and thus supply genetic variation; it can also selectively remove individuals that are unable to cope with the physiological stresses associated with radiation exposure, or non-selectively cull swathes of the population, reducing genetic variation. Since the nuclear power plant explosion in 1986, the Chernobyl area has experienced a spatially heterogeneous exposure to varying levels of ionising radiation. We sampled <em>Daphnia pulex</em> (a freshwater crustacean) from lakes across the Chernobyl area, genotyped them at ten microsatellite loci, and also calculated the current radiation dose rates. We then investigated whether the pattern of genetic diversity was positively associated with radiation dose rates, consistent with radiation-mediated supply of de novo mutations, or negatively associated with radiation dose rates, as would be expected with strong radiation-mediated selection. We found that measures of genetic diversity, including expected heterozygosity and mean allelic richness (an unbiased indicator of diversity) were significantly higher in lakes that experienced the highest radiation dose rates. This suggests that mutation outweighs selection as the key evolutionary force in populations exposed to high radiation dose rates. We also found significant but weak population structure, indicative of low genetic drift, and clear evidence for isolation by distance between populations. This further suggests gene flow between nearby populations is eroding population structure, and that mutational input in high radiation lakes could, ultimately, supply genetic variation to lower radiation sites.</p>
Data from: Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers
The pen shell, Atrina pectinata, is one of the commercial bivalves in East Asia and thought to be recently affected by anthropogenic pressure (habitat destruction and/or fishing pressure). Information on its population genetic structure is crucial for the conservation of A. pectinata. Considering its long pelagic larval duration and iteroparity with high fecundity, the genetic structure for A. pectinata could be expected to be weak at a fine scale. However, the unusual oceanography in the coasts of China and Korea suggests potential for restricted dispersal of pelagic larvae and geographical differentiation. In addition, environmental changes associated with Pleistocene sea level fluctuations on the East China Sea continental shelf may also have strongly influenced historical population demography and genetic diversity of marine organisms. Here, partial sequences of the mitochondrial Cytochrome c oxidase subunit I (COI) gene and seven microsatellite loci were used to estimate population genetic structure and demographic history of seven samples from Northern China coast and one sample from North Korea coast. Despite high levels of genetic diversity within samples, there was no genetic differentiation among samples from Northern China coast and low but significant genetic differentiation between some of the Chinese samples and the North Korean sample. A late Pleistocene population expansion, probably after the Last Glacial Maximum, was also demonstrated for A. pectinata samples. No recent genetic bottleneck was detected in any of the eight samples. We concluded that both historical recolonization (through population range expansion and demographic expansion in the late Pleistocene) and current gene flow (through larval dispersal) were responsible for the weak level of genetic structure detected in A. pectinata.
Data from: Ex situ conservation of underutilised fruit tree species: establishment of a core collection for Ficus carica L. using microsatellite markers (SSRs)
Ex situ germ plasm collections of woody crops are necessary to ensure the optimal use of plant genetic resources. The fig tree (Ficus carica L.) germ plasm bank, consisting of 229 accessions, is located in Centro de Investigación 'La Orden'. Despite great progress in conservation, ex situ collections face size and organization problems. Core collections obtained from structured samples of bigger collections are a useful tool to improve germ plasm management. In this work, we used simple sequence repeat (SSR) markers to establish a core collection in this underutilised Mediterranean fruit tree species. Four approaches have been carried out (random sampling, maximization, simulated annealing and stepwise clustering) to determine the best method to develop a core collection in this woody plant. The genetic diversity obtained with each subset was compared with that of the complete collection. It was found that the most efficient way to achieve the maximum diversity was the maximization strategy, which, with 30 accessions, recovers all the SSR alleles and does not show significant differences in allele frequency distribution in any of the loci or in the variability parameters (H O, H E) between the whole and core collections. Thus, this core collection, a representative of most fig diversity conserved in the germ plasm bank, could be used as a basis for plant material exchange among researchers and breeders.
Data from: Development of 15 nuclear EST microsatellite markers for the palaeoendemic conifer Pherosphaera hookeriana (Podocarpaceae)
Premise of the study: Nuclear microsatellite markers were developed for population genetic analysis of the threatened palaeoendemic conifer Pherosphaera hookeriana W. Archer (Podocarpaceae). Methods and Results: Fifteen variable loci were identified showing 1 to 13 alleles per population with seven loci displaying over four alleles in all populations and the average number of alleles per locus ranging from 4.8 to 5.93 per population. The observed heterozygosity per locus varied from 0.00 to 0.91 and overall heterozygosity was markedly consistent between populations (from 0.54 to 0.57). All loci also amplified in the endangered congener P. fitzgeraldii but only five of the loci had more than one allele. Conclusions: These 15 loci are the first microsatellite markers developed in the genus Pherosphaera. These loci will be useful for investigating the species' extant genetic diversity and structure, the impact of past environmental change and the significance of asexual reproduction.
Figure 4. Individual multilocus genotype clustering analysis for Podarcis carbonelli. A in Recent evolutionary history of the Iberian endemic lizards Podarcis bocagei (Seoane, 1884) and Podarcis carbonelli Pérez-Mellado, 1981 (Squamata: Lacertidae) revealed by allozyme and microsatellite markers
Figure 4. Individual multilocus genotype clustering analysis for Podarcis carbonelli. A, inferred population structure from the number of clusters (K) = 2 to 5. These plots were obtained from the runs producing the highest values of Ln probability for each value of K, assuming correlated allele frequencies. In these plots, each individual is represented by a column divided into K segments, the size of each corresponding to the individual's estimated membership fraction in each of the K clusters. See Table 1 for locality name abbreviations. B, variation of the value of DK with the number of clusters, following Evanno et al. (2005). C, pie charts representing the mean proportion of membership for K = 4 (chosen by the previous method) for each locality.
Figure 3. Individual multilocus genotype clustering analysis for Podarcis bocagei. A in Recent evolutionary history of the Iberian endemic lizards Podarcis bocagei (Seoane, 1884) and Podarcis carbonelli Pérez-Mellado, 1981 (Squamata: Lacertidae) revealed by allozyme and microsatellite markers
Figure 3. Individual multilocus genotype clustering analysis for Podarcis bocagei. A, inferred population structure from the number of clusters (K) = 2 to 5. These plots were obtained from the runs producing the highest values of Ln probability for each value of K, assuming correlated allele frequencies. In these plots, each individual is represented by a column divided into K segments, the size of each corresponding to the individual's estimated membership fraction in each of the K clusters. See Table 1 for locality name abbreviations. B, variation of the value of DK with the number of clusters, following Evanno et al. (2005). C, pie charts representing the mean proportion of membership for K = 3 and 5 (chosen by the previous method) for each locality.
Figure 2 in Recent evolutionary history of the Iberian endemic lizards Podarcis bocagei (Seoane, 1884) and Podarcis carbonelli Pérez-Mellado, 1981 (Squamata: Lacertidae) revealed by allozyme and microsatellite markers
Figure 2. Synthetic maps showing patterns of geographical variation in allele frequencies across species distribution ranges based on the inversed distance weighted interpolation of the values calculated for each locality of Podarcis bocagei (top) and Podarcis carbonelli (bottom) for the first (A, D), second (B, E), and third (C, F) axes of factorial correspondence analyses. White represents higher and black lower factor score values.
Figure 1 in Recent evolutionary history of the Iberian endemic lizards Podarcis bocagei (Seoane, 1884) and Podarcis carbonelli Pérez-Mellado, 1981 (Squamata: Lacertidae) revealed by allozyme and microsatellite markers
Figure 1. Distribution and localities analysed in this study for Podarcis bocagei (dark grey, circles) and Podarcis carbonelli (light grey, squares) (A), and median-joining networks of mtDNA haplotypes for P. bocagei (B) and P. carbonelli (C) reproduced from Pinho et al., 2007a. Dashed lines indicate the mtDNA groups and corresponding geographical distributions in P. carbonelli. Locality codes and sampling details are given in Table 1. Notice that the distribution shown for P. carbonelli is based on a 20 km buffer of occupied 10 ¥ 10 km UTM (Universal Transverse Mercator) squares and is therefore amplified compared to that in Pinho et al., 2007a. This was necessary in order to visualize geographical patterns of genetic variation (see Material and methods).
Development of microsatellite markers for colony delineation of the invasive Asian subterranean termite in South Florida and Taiwan
<p>Delineating the colony identity of <em>Coptotermes gestroi </em>(Wasmann) is a core issue of colony elimination in the implementation of subterranean termite baiting systems. Invasion history is believed the possible cause of genetic variabilities among colonies. Haplotype network analysis of mitochondrial cytochrome <em>c</em> oxidase subunit II revealed the multiple origins of American <em>C</em>.<em> gestroi</em> from<em> </em>the Philippines and Southeast Asia and the Taiwan population only from the Philippines. We further developed 21 new microsatellite markers for the comparison of genetic variabilities on colony delineation of <em>C</em>.<em> gestroi </em>colonies from South Florida (invaded ~30 years; 3–7 generations) and Taiwan (~110 years; 13–27 generations). The present microsatellite markers with 1–4 alleles per locus have validated the effectiveness of colony delineation for three incipient colonies reared in the laboratory and three field colonies from Taiwan. Genetic admixture of the Floridian <em>C</em>. <em>gestroi</em> probably caused by recent invasion history, multiple invasions, and anthropogenic activities among regions. A possible introduction event likely occurred through human-mediated activities between Fort Lauderdale and Miami. Overall, these new microsatellite markers provide suitable and efficient candidate genetic markers for colony delineation of <em>C</em>. <em>gestroi</em> to consolidate the effectiveness of the colony elimination system in termite management.</p>
Microsatellite marker data for Chernobyl Daphnia populations
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Isolation and characterization of twelve polymorphic microsatellite markers in the endangered Hopea hainanensis (Dipterocarpaceae)
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Data from: Genetic patterns in Neotropical Magnolias (Magnoliaceae) using de novo developed microsatellite markers
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Data from: Mitochondrial and microsatellite DNA markers reveal a Balkanic origin for the highly invasive Horse-Chestnut leaf miner Cameraria ohridella (Lepidoptera, Gracillariidae)
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