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394 results for “Microsatellite data”
Drakaea glyptodon nuclear microsatellite and chloroplast haplotype data
<p class="CxSpFirst">Many orchids are characterized by small, patchily distributed populations. Resolving how they persist is important for understanding the ecology of this hyper-diverse family, many members of which are of conservation concern. <span>Ten</span> populations of the common terrestrial orchid <i>Drakaea glyptodon</i> from Southwest Australia were genotyped with ten nuclear and five chloroplast SSR markers. Levels and partitioning of genetic variation, and effective population sizes (<i>N</i><sub>e</sub>), were estimated. Spatial genetic structure of nuclear diversity, together with chloroplast data, are used to infer the effective number of seed parents per population. We found high genetic diversity, <i>N</i><sub>e</sub> values that generally exceed predictions based on the number of flowering individuals, and moderate levels of gene flow. Two populations were founded by < 5 colonists suggesting some populations are colonized by few seeds, with growth largely resulting from <i>in situ</i> recruitment. A value of 3.65 for <i>m</i><sub>p </sub>/<i>m</i><sub>s</sub> indicates that pollinators play a greater role than seed in introducing genetic diversity to populations via gene flow. Our results highlight that <i>D. glyptodon</i> is highly effective at persisting in patchily distributed populations. However, it is important to examine how insights from this common, widespread species transfer to species that are rare and/or occur in fragmented landscapes.</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>
Orchis nuclear microsatellite data
<p><b>Premise of the study </b>The genetic structure of hybrid zones provides an insight into the potential for gene flow to occur between plant taxa. Four closely related European orchid species (<i>Orchis anthropophora</i>, <i>O. militaris</i>, <i>O. purpurea</i> and <i>O. simia</i>) hybridize when they co-occur. We aimed to characterize patterns of hybridization in <i>O. militaris – O. purpurea</i>, <i>O. purpurea – O. simia</i> and <i>O. anthropophora – O. simia</i> hybrid zones using molecular and morphological data.</p> <p><b>Methods </b>We used 11 newly isolated nuclear microsatellites to genotype 695 individuals collected from seven hybrid zones and six allopatric parental populations in France. Geometric morphometric analysis was conducted using 15 labellum landmarks to capture the main aspects of petal shape.</p> <p><b>Key Results </b>Backcrossing was asymmetric towards <i>O. militaris</i> in multiple <i>O. militaris – O. purpurea</i> hybrid zones. Hybrids in <i>O. purpurea – O. simia</i> and <i>O. anthropophora – O. simia</i> hybrid zones were largely limited to F1 and F2 generations, but further admixture had occurred. These patterns were reflected in labellum geometric morphometric data which correlated strongly with nuclear microsatellite data in all three species combinations.</p> <p><b>Conclusions </b>The co-existence of parental and admixed individuals in these <i>Orchis</i> hybrid zones implies they are likely to be tension zones being maintained by a balance between gene flow into the hybrid zone and selection acting against admixed individuals. The pattern of admixture in the three species combinations suggests intrinsic selection acting on the hybrids is weaker in more closely related taxa.</p>
Field data and microsatellite genotypes of Cercidiphyllum japonicum
<p>Field data and genotypes at five microsatellite loci of 281 <i>Cercidiphyllum japonicum </i>adults of a population distributed over a ca. 80 ha along a stream and 755 <i>C. japonicum </i>current-year seedlings sampled at approximate center of the populatoin. The population is located in Iwanazawa Forest Reserve (43°13′N, 142°34′E), University of Tokyo Hokkaido Forest, in central Hokkaido, Japan.</p>
Microsatellite data set
<p>Microsatellite data set for article RADICAL TEMPORAL SHIFT IN THE GENETIC COMPOSITION OF NEW ENGLAND CHICORY POPULATIONS published in Journal of Ecology.</p>
RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results
<p>Microsatellites have been a workhorse of evolutionary genetic studies for decades and are still commonly in use for estimating signatures of genetic diversity at the population and species level across a multitude of taxa. Yet, the very high mutation rate of these loci is a double-edged sword, conferring great sensitivity at shallow levels of analysis (e.g., paternity analysis) but yielding considerable uncertainty for deeper evolutionary comparisons. For the present study, we used reduced representation genome-wide data (RADseq) to test for patterns of interspecific hybridization previously characterized using microsatellite data in a contact zone between two closely related mouse lemur species in Madagascar (<em>Microcebus murinus</em> and <em>M</em>. <em>griseorufus</em>). We revisit this system by examining populations in, near, and far from the contact zone, including many of the same individuals that had previously been identified as hybrids with microsatellite data. Surprisingly, we find no evidence for admixed nuclear ancestry. Instead, re-analyses of microsatellite data and simulations suggest that previously inferred hybrids were false positives and that the program NewHybrids can be particularly sensitive to erroneously inferring hybrid ancestry. Combined with results from coalescent-based analyses and evidence for local syntopic co-occurrence, we conclude that the two mouse lemur species are in fact completely reproductively isolated, thus providing a cautionary tale for the inference of interspecific hybridization with microsatellite data.</p>
Supplementary material 2 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Component data at the four successive thresholds used to illustrate Figure 5: Explanation note: Component data are used to illustrate the structure of the subset of Bactrocera carambolae and Bactrocera dorsalis populations. The highest Betweenness-centrality is highlighted in blue.
Supplementary material 1 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Component data at the five successive thresholds used to illustrate Figure 4: Explanation note: Component data are used to illustrate the structure of the subset of Bactrocera carambolae populations. The Highest Betweenness-centrality is highlighted in blue.
Supplementary material 4 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Comparisons among three different the individual admixture plots: Explanation note: Comparisons among the individual admixture plots of 289 individuals, for K = 3, considering correlated allele frequency, uncorrelated allele frequency, and missing data as recessive homozygotes for the null alleles, respectively.
Supplementary material 3 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Component data at the four successive thresholds used to illustrate Figure 6: Explanation note: Component data are used to illustrate the structure of the subset of the Salaya5 strain and wild populations. The highest Betweenness-centrality is highlighted in blue.
Microsatellite data on Scomber colias in NW Africa
<p><span><em><span>Scomber colias</span></em></span><span><span> is an ecologically and economically valuable species, which is targeted by industrial and artisanal fisheries throughout its geographical distribution. Some 1,169 fish were collected by trawl onboard the R.V. “Dr. Fridtjof Nansen” in the coastal waters stretching from </span></span><span>Morocco (~28°N) to Namibia (~22°S) </span><span><span>and genotyped at a suite of 8 microsatellite loci. None of the statistical procedures utilized managed to detect any significant population structure. Likewise, no marker was depicted to deviate from neutral expectations.</span></span></p> <p><span><span> </span></span><span><span>Information is available at https://imr.brage.unit.no/imr-xmlui/handle/11250/3072605</span></span><span><span> and provided in excel file called <strong><em>Scomber colias</em>_microsatellite raw data.xlx</strong>, which contains three spreadsheets:</span></span></p> <p><span><span><span>1.<span> </span></span></span></span><span><span>Geographic coordinates for each of the sampling sites that were merged into larger samples for genetic analysis.</span></span></p> <p><span><span><span>2.<span> </span></span></span></span><span><span>Raw data for microsatellite genotypes</span></span></p> <p><span><span><span>3.<span> </span></span></span></span><span><span>Microsatellites data in GenAlEx format ready for exportation in different file formats.</span></span></p>
Microsatellite data for Prosopis species sampled from different non-native populations in Kenya and Ethiopia
<p>Microsatellite data for seven loci and 711 individuals of <em>P. juliflora</em> and <em>P. pallida</em> sampled from non-native populations from Kenya and Ethiopia.</p>
Genotype data of 14 nuclear microsatellite loci for 18 Quercus chenii populations in China
<p>This dataset includes genotype data of 14 nuclear microsatellite loci for 419 individuals of Quercus chenii from 18 natural populations in China.</p>
FIGURE 1. STRUCTURE analysis using microsatellite data shows that Sphagnum incundum form a separate genetic group from S. subnitens and S in Sphagnum incundum a new species in Sphagnum subg. Acutifolia (Sphagnaceae) from boreal and arctic regions of North America
FIGURE 1. STRUCTURE analysis using microsatellite data shows that Sphagnum incundum form a separate genetic group from S. subnitens and S. subfulvum. Sphagnum flavicomans seems to be a mixture of the recognized genetic groups. The upper panel shows data separated in two genetic groups, the middel panel shows the data separated in three genetic groups, and the lower one show the data separated in four genetic groups.
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: Stabilising selection on microsatellite allele length at arginine vasopressin 1a receptor and oxytocin receptor loci
The loci arginine vasopressin receptor 1a (avpr1a) and oxytocin receptor (oxtr) have evolutionarily conserved roles in vertebrate social and sexual behavior. Allelic variation at a microsatellite locus in the 5' regulatory region of these genes is associated with fitness in the bank vole Myodes glareolus. Given the low frequency of long and short alleles at these microsatellite loci in wild bank voles, we used breeding trials to determine whether selection acts against long and short alleles. Female bank voles with intermediate length avpr1a alleles had the highest probability of breeding, while male voles whose avpr1a alleles were very different in length had reduced probability of breeding. Moreover, there was a significant interaction between male and female oxtr genotypes, where potential breeding pairs with dissimilar length alleles had reduced probability of breeding. These data show how genetic variation at microsatellite loci associated with avpr1a and oxtr is associated with fitness, and highlight complex patterns of selection at these loci. More widely, these data show how stabilising selection might act on allele length frequency distributions at gene-associated microsatellite loci.
Data from: Microsatellite evidence for obligate autogamy, but abundant genetic variation in the herbaceous monocarp Lobelia inflata (Campanulaceae)
Although high levels of self-fertilization (>85%) are not uncommon in nature, organisms reproducing entirely through selfing are extremely rare. Predominant selfers are expected to have low genetic diversity because genetic variation is distributed among rather than within lineages, and is readily lost through genetic drift. We examined genetic diversity at 22 microsatellite loci in 105 individuals from a population of the semelparous herb Lobelia inflata L., and found (1) no evidence of heterozygosity through outcrossing, yet (2) high rates of genetic polymorphism (2-4 alleles per locus). Furthermore, this genetic variation among lineages was associated with phenotypic traits (e.g. flower colour, size at first flower). Coupled with previous work characterizing the fitness consequences of reproductive timing, our results suggest that temporal genotype-by-environment interaction may maintain genetic variation and, because genetic variation occurs only among lineages, this simple system offers a unique opportunity for future tests of this mechanism.
Data from: Skin swabbing of amphibian larvae yields sufficient DNA for efficient sequencing and reliable microsatellite genotyping
Skin swabbing, a minimally invasive DNA sampling method recently developed on adult amphibians, was tested on larvae of fire salamanders (Salamandra salamandra). The quality and quantity of the sampled DNA was evaluated by (i) measuring DNA concentration in DNA extracts, (ii) sequencing part of the mtDNA cytochrome b gene (692 bp) and (iii) genotyping eight polymorphic nuclear microsatellite loci. The multiple-tubes approach was used for calculating allelic dropout (ADO) and false allele (FA) rates to evaluate the reliability of the genotypes. DNA extracts from tissue samples of road-killed individuals were included in the study as positive controls. Our results showed that skin swabs of fire salamander larvae can provide DNA in sufficient quantity and quality, as sequencing was successful and no allelic dropouts or false alleles were detected. This method, tested for the first time on amphibian larvae, has proven to be an efficient and reliable alternative to the controversial tail fin clipping procedure.
Data from: Can clone size serve as a proxy for clone age? An exploration using microsatellite divergence in Populus tremuloides
In long-lived clonal plant species, the overall size of a clone has previously been used to estimate clone age. The size of a clone, however, might be largely determined by physical or biotic interactions, obscuring the relationship between clone size and age. Here, we use the accumulation of mutations at 14 microsatellite loci to estimate clone age in trembling aspen, Populus tremuloides, from southwestern Canada. We show that the observed patterns of genetic divergence are consistent with a model of clonal growth, allowing us to use pairwise genetic divergence as an estimator of clone age. In the populations studied, clone size did not exhibit a significant relationship with microsatellite divergence, indicating that clone size is not a good proxy for clone age.
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.
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