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738 results for “Microsatellite”
Data from: Heterozygosity-fitness correlations in zebra finches: microsatellite markers can be better than their reputation
Numerous studies have reported associations between heterozygosity in microsatellite markers and fitness-related traits (heterozygosity-fitness correlations, HFCs). However, it has often been questioned whether HFCs reflect general inbreeding depression, because a small panel of microsatellite markers does not reflect very well an individual's inbreeding coefficient (F) as calculated from a pedigree. Here we challenge this prevailing view. Due to chance events during Mendelian segregation, an individual's realized proportion of the genome that is identical by descent (IBD) may substantially deviate from the pedigree-based expectation (i.e. F). This Mendelian noise may result in a weak correlation between F and multi-locus heterozygosity, but this does not imply that multi-locus heterozygosity is a bad estimator of realized IBD. We examined correlations between 11 fitness-related traits measured in up to 1,192 captive zebra finches and three measures of inbreeding: (1) heterozygosity across 11 microsatellite markers, (2) heterozygosity across 1,359 SNP markers, and (3) F, based on a 5-generation pedigree. All 11 phenotypic traits showed positive relationships with measures of heterozygosity, especially traits that are most closely related to fitness. Remarkably, the small panel of microsatellite markers produced equally strong HFCs as the large panel of SNP markers, and both marker-based approaches produced stronger correlations with phenotypes than the pedigree-based F. We argue that a small panel of microsatellites with high allelic richness may better reflect an individual's realized IBD than previously appreciated, especially in species like the zebra finch, where much of the genome is inherited in large blocks that rarely experience cross-over during meiosis.
Data from: Microsatellite abundance across the Anthozoa and Hydrozoa in the phylum Cnidaria
Background: Microsatellite loci have high mutation rates and thus are indicative of mutational processes within the genome. By concentrating on the symbiotic and aposymbiotic cnidarians, we investigated if microsatellite abundances follow a phylogenetic or ecological pattern. Individuals from eight species were shotgun sequenced using 454 GS-FLX Titanium technology. Sequences from the three available cnidarian genomes (Nematostella vectensis, Hydra magnipapillata and Acropora digitifera) were added to the analysis for a total of eleven species representing two classes, three subclasses and eight orders within the phylum Cnidaria. Results: Trinucleotide and tetranucleotide repeats were the most abundant motifs, followed by hexa- and dinucleotides. Pentanucleotides were the least abundant motif in the data set. Hierarchical clustering and log likelihood ratio tests revealed a weak relationship between phylogeny and microsatellite content. Further, comparisons between cnidaria harboring intracellular dinoflagellates and those that do not, show microsatellite coverage is higher in the latter group. Conclusions: Our results support previous studies that found tri- and tetranucleotides to be the most abundant motifs in invertebrates. Differences in microsatellite coverage and composition between symbiotic and non-symbiotic cnidaria suggest the presence/absence of dinoflagellates might place restrictions on the host genome.
Data from: Rapid development and screening of microsatellite loci for Artibeus lituratus and their utility for six related species within Phyllostomidae
Microsatellites are often the marker of choice for population genetic studies at intermediate spatial and temporal scales. Developing large numbers of markers has traditionally been technically difficult and this has limited our ability to investigate evolutionary phenomena that emerge across short temporal scales. Moreover, few markers tend to successfully amplify across species boundaries. As rapid advancements in high-throughput sequencing make microsatellite development cost and time-effective, new avenues for evolutionary, population genetic, and chromosome linkage mapping research are emerging. We used a published PERL script and second-generation sequencing to rapidly and affordably develop microsatellite loci for a widespread phyllostomid bat, Artibeus lituratus, for which no markers were previously available. We used Roche FLX (Titanium) Genome Sequencing to randomly sequence ~101 Mb (255,065 unique reads) of genomic DNA for A. lituratus, within which we discovered 30100 microsatellite loci. We designed primers for 19395 loci that contained suitable flanking regions. We ordered primers for 96 loci, 90 of which produced a single PCR product in A. lituratus. We genotyped 52 loci, and 45 were polymorphic in A. lituratus. We tested cross-species amplification for 96 loci in six additional phyllostomid species: A. planirostris, A. fimbriatus, A. phaeotis, Enchisthenes hartii, Sturnira lilium, and Carollia perspicillata. Cross-species amplification was successful for at least one species for 87 loci (A. fimbriatus), and in all species at least 66 loci amplified. These markers will facilitate future work on these seven species, but also illustrate the utility of this high-throughput method for development of primers across many species simultaneously.
Data from: Sex, size and timing: sampling design for reliable population genetics analyses using microsatellite data
1. Population genetics is used in a wide variety of fields such as ecology and biodiversity conservation. How estimated genetic characteristics of natural populations can be influenced by the sampling design has been a long-standing concern. Multiple simulation and empirical studies illustrated the influence of both sample size and polymorphism of markers. However, our review of studies on butterfly population genetics indicates no consensus on sample size for the estimation of genetic diversity or differentiation. Furthermore, other aspects of sampling design (sex ratio and timing of sampling) were not addressed and their potential impact on genetic parameter estimates rarely explored. 2. Using a large empirical dataset (with spatial and temporal replicates) collected on a butterfly species, Boloria aquilonaris, as well as simulated datasets reflecting (1) three scenarios of migration-genetic drift equilibrium and (2) one scenario of parameter stabilization after 100,000 generations, we quantified the impacts of three aspects of genetic sampling design (namely sample size, sex ratio, and timing of sampling) on the estimation of allele frequencies and its potential downstream impact on the estimation of genetic parameters. 3. With empirical data, we found that sample size and timing of sampling strongly affected the accuracy of allele frequencies and the downstream analyses, while sex ratio did not. Our results were consistent across spatial and temporal replicates. Also, with simulated data, we showed that the genetic sampling design had limited effect in systems where dispersal outweighs genetic drift, while it can have major consequences on our understanding of the genetic diversity and population differentiation in systems dominated by genetic drift (such as most study systems with conservation concerns). 4. We advocate for careful consideration of all aspects of the sampling design in population genetics studies, i.e. a sufficient number of samples, while ensuring similar sex ratio among sampling locations and collecting with timing appropriate to the question under study. This is particularly important when the study aims at species conservation.
Data from: Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species
Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within groups has been conducted. In this study, we examined microsatellite coverage and motif patterns from 454 shotgun sequences of 154 Eukaryote species from eight distantly related phyla (Cnidaria, Arthropoda, Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and Streptophyta) to test if a consistent phylogenetic pattern emerges from the microsatellite composition of these species. It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.
Data from: Polyploidy and microsatellite variation in the relict tree Prunus lusitanica L.: how effective are refugia in preserving genotypic diversity of clonal taxa?
Refugia are expected to preserve genetic variation of relict taxa, especially in polyploids, because high gene dosages could prevent genetic erosion in small isolated populations. However, other attributes linked to polyploidy, such as asexual reproduction, may strongly limit the levels of genetic variability in relict populations. Here, ploidy levels and patterns of genetic variation at nuclear microsatellite loci were analysed in Prunus lusitanica, a polyploid species with clonal reproduction that is considered a paradigmatic example of a Tertiary relict. Sampling in this study considered a total of 20 populations of three subspecies: mainland lusitanica (Iberian Peninsula and Morocco), and island azorica (Azores) and hixa (Canary Islands and Madeira). Flow cytometry results supported an octoploid genome for lusitanica and hixa, whereas a 16-ploid level was inferred for azorica. Fixed heterozygosity of a few allele variants at most microsatellite loci resulted in levels of allelic diversity much lower than those expected for a high-order polyploid. Islands as a whole did not contain higher levels of genetic variation (allelic or genotypic) than mainland refuges, but island populations displayed more private alleles and higher genotypic diversity in old volcanic areas. Patterns of microsatellite variation were compatible with the occurrence of clonal individuals in all but two island populations, and the incidence of clonality within populations negatively correlated with the estimated timing of colonization. Our results also suggest that gene flow has been very rare among populations, and thus population growth following founder events was apparently mediated by clonality rather than seed recruitment, especially in mainland areas. This study extends to clonal taxa the idea of oceanic islands as important refugia for biodiversity, since the conditions for generation and maintenance of clonal diversity (i.e. occasional events of sexual reproduction, mutation and/or seed immigration) appear to have been more frequent in these enclaves than in mainland areas.
Data from: Mining of expressed sequence tag libraries of cacao for microsatellite markes using five computational tools
Expressed Sequence Tags (ESTs) provide researchers with a quick and inexpensive route for discovering new genes, and data on gene expression and regulation and provide genic markers that help in constructing genome maps. Cacao is an important perennial crop of humid tropics. Cacao EST sequences as available in public domain were downloaded and made into contigs. A total of 769 contigs were made using contigs assembly program pharp. Puative information of contigs were identified using NCBI and ExPASy tools such as BlastX, tblastn.
Data from: Genome-wide identification of microsatellites and transposable elements in the dromedary camel genome using whole genome sequencing data
Transposable elements (TEs) along with simple sequence repeats (SSRs) are prevalent in eukaryotic genome, especially in mammals. Repetitive sequences form approximately one-third of the camelid genomes, so study on this part of genome can be helpful in providing deeper information from the genome and its evolutionary path. Here, in order to improve our understanding regarding the camel genome architecture, the whole genome of the two dromedaries (Yazdi and Trodi camels) was sequenced. Totally, 92- and 84.3-Gb sequence data were obtained and assembled to 137,772 and 149,997 contigs with a N50 length of 54,626 and 54,031 bp in Yazdi and Trodi camels, respectively. Results showed that 30.58% of Yazdi camel genome and 30.50% of Trodi camel genome were covered by TEs. Contrary to the observed results in the genomes of cattle, sheep, horse, and pig, no endogenous retrovirus-K (ERVK) elements were found in the camel genome. Distribution pattern of DNA transposons in the genomes of dromedary, Bactrian, and cattle was similar in contrast with LINE, SINE, and long terminal repeat (LTR) families. Elements like RTE-BovB belonging to LINEs family in cattle and sheep genomes are dramatically higher than genome of dromedary. However, LINE1 (L1) and LINE2 (L2) elements cover higher percentage of LINE family in dromedary genome compared to genome of cattle. Also, 540,133 and 539,409 microsatellites were identified from the assembled contigs of Yazdi and Trodi dromedary camels, respectively. In both samples, di-(393,196) and tri-(65,313) nucleotide repeats contributed to about 42.5% of the microsatellites. The findings of the present study revealed that non-repetitive content of mammalian genomes is approximately similar. Results showed that 9.1 Mb (0.47% of whole assembled genome) of Iranian dromedary's genome length is made up of SSRs. Annotation of repetitive content of Iranian dromedary camel genome revealed that 9,068 and 11,544 genes contain different types of TEs and SSRs, respectively. SSR markers identified in the present study can be used as a valuable resource for genetic diversity investigations and marker-assisted selection (MAS) in camel-breeding programs.
Data from: Challenges in analysis and interpretation of microsatellite data for population genetic studies
Advancing technologies have facilitated the ever-widening application of genetic markers such as microsatellites into new systems and research questions in biology. In light of the data and experience accumulated from several years of using microsatellites, we present here a literature review that synthesizes the limitations of microsatellites in population genetic studies. With a focus on population structure, we review the widely used fixation (FST) statistics and Bayesian clustering algorithms and find that the former can be confusing and problematic for microsatellites and that the latter may be confounded by complex population models and lack power in certain cases. Clustering, multivariate analyses, and diversity-based statistics are increasingly being applied to infer population structure, but in some instances these methods lack formalization with microsatellites. Migration-specific methods perform well only under narrow constraints. We also examine the use of microsatellites for inferring effective population size, changes in population size, and deeper demographic history, and find that these methods are untested and/or highly context-dependent. Overall, each method possesses important weaknesses for use with microsatellites, and there are significant constraints on inferences commonly made using microsatellite markers in the areas of population structure, admixture, and effective population size. To ameliorate and better understand these constraints, researchers are encouraged to analyze simulated datasets both prior to and following data collection and analysis, the latter of which is formalized within the approximate Bayesian computation framework. We also examine trends in the literature and show that microsatellites continue to be widely used, especially in non-human subject areas. This review assists with study design and molecular marker selection, facilitates sound interpretation of microsatellite data while fostering respect for their practical limitations, and identifies lessons that could be applied toward emerging markers and high-throughput technologies in population genetics.
Phylogeographic structure and putative migration pathway of Sogatella furcifera in China based on microsatellite markers
<p>Sequencing data of 12 microsatellite loci from 25 populations of in China.</p>
Lambertia multiflora microsatellite data
<p>The restoration of diverse self-sustaining ecosystems requires re-establishment of functional interactions among species. For plant communities, pollinators are usually essential for pollination, seed set, and seed quality. A common assumption in ecological restoration for plants pollinated by animals is one of "build it and they will come", which is rarely tested. Beyond seed set, there may be negative genetic consequences for seed quality if pollinators and their behaviour do not reflect those in reference populations. Here, we conduct an ecological genetic assessment of seed quality via mating system parameters in <em>Lambertia multiflora</em>(Proteaceae), a species dependent on nectar-feeding birds for pollination. Four populations of <em>L. multiflora</em> in disturbed sites that were rehabilitated following mineral sand mining were compared to four natural reference populations, near Eneabba, Western Australia. In each population, approximately 10 offspring from each of 10 maternal plants were genotyped with 11 highly polymorphic microsatellite markers. From these data, genetic diversity and mating system parameters were assessed and found to be equivalent across all populations. Mean allelic diversity and heterozygosity across loci were very high. All populations were completely outcrossing with no bi-parental inbreeding. Mean correlated paternity, sibship, and effective population size estimates for restored and natural populations were not significantly different and reflected uniformly high paternal diversity and wide outcrossing. Results suggest self-incompatibility, a surprising result given high levels of selfing detected in other lambertias. Equivalent genetic results for restored and natural reference populations indicate successful restitution of bird-pollinator services for <em>L. multiflora</em> in these post-mining rehabilitation sites.</p> <p><em>Synthesis and applications</em>: Reviewing our results with other published studies suggests a resilience of bird-pollinator services in restored plant communities, a finding of broad reassurance to restoration practitioners working in these global south systems where bird pollination is a feature. Our study also highlights the global contribution of ecological genetics to the objective assessment of functional species interactions in ecological restoration, an increasingly important goal of land managers and regulators seeking to improve restoration standards.</p>
Microsatellite data from: Multiple colonizations and genetic differentiation from the mainland populations in insular populations of the perennial herb Solidago virgaurea complex (Asteraceae) on recently formed nearshore oceanic islands
<p><b>Aim: </b>Although the evolution of island endemic plants has long been investigated, the majority of such studies have focused on species with remarkable levels of morphological variation and on islands substantially far from the mainland. Except for a few examples such as the Canary Islands, endemic plants on nearshore oceanic islands have received less attention. In this study, we examined the <i>Solidago virgaurea </i>complex on the Japanese mainland Honshu and the adjacent Izu Islands to investigate the population genetic structure and dynamics in plants endemic to nearshore and recently formed oceanic islands.</p> <p><b>Location: </b>Japanese mainland Honshu and the adjacent Izu Islands</p> <p><b>Taxon: </b><i>Solidago virgaurea</i> (Asteraceae)</p> <p><b>Methods: </b>Sixteen and nine populations of <i>S. virgaurea</i> complex were sampled from the mainland and islands, respectively; phylogeographic and population genetics analyses were performed using plastid DNA and nuclear microsatellite DNA variations.</p> <p><b>Results: </b>Phylogenetically close plastid DNA haplotypes were shared between the mainland and islands, although the populations of <i>S. virgaurea</i> from different islands tended to exhibit phylogenetically distinct haplotypes. Admixture analyses based on nuclear DNA variations revealed distinct genetic structures between the mainland and island populations. Gene flow among islands is restricted but may partially offset genetic drift on each island.</p> <p><b>Main conclusions: </b>The genetic structure observed in this study may not have originated from a single dispersal event and successive expansion but rather from at least three colonization events and subsequent gene flow among island populations. Based on the nuclear DNA variations, the Izu Island populations of <i>S. virgaurea</i> are genetically distinct from the mainland ones. Repeated colonization events may have provided sufficient genetic diversity, which would generally be susceptible to founder effects and exert a driving force for evolutionary adaptation, to these oceanic island populations.</p>
Microsatellite data for 13 populations of Reindeer
<p>Genotypes of 16 microsatellite loci </p>
Zapus hudsonius luteus microsatellite and mtDNA datasets
<p><span>In the face of accelerated warming and drying, habitat specialists of riparian zones could be threatened with genetic erosion if their effective population sizes become small due to loss and fragmentation of habitat. The New Mexico meadow jumping mouse (<em>Zapus hudsonius luteus</em>) is Endangered due to a suite of disturbances to their riparian habitat but the degree of functional connectivity within and among the drainages they occupy is unknown. Using microsatellite and mtDNA, we examined the hypothesis of hydrologically-mediated gene flow (via riparian networks) by assessing structure, diversity, and the possibility of overland dispersal among disconnected watersheds (White Mountains, AZ). Both a priori and de novo structure supported stream-mediated gene flow. However, inferred clusters crossed watershed boundaries, and migration rates and dispersers suggest infrequent use of overland paths at nearby sub-drainages among each watershed. Analysis of mtDNA indicated that this was likely a long-term phenomenon, also suggesting that one of the watersheds (LCR) may have been more historically diverse than its contemporary snapshot (nuDNA). Our analysis led us to suspect fragmentation in its eastern fork, an area most impacted by human development. We conclude that the boundaries of drainages affect the White Mountains population structure but short, cryptic, overland paths among them likely play a role in replenishing genetic diversity. We also report an extension to the species longevity from 2 to 4 years from genetic recaptures during our six-year study period.</span></p>
Microsatellite genotypes for Gambusia marshi
<p>1. The valley of Cuatro Ciénegas in Coahuila, Mexico has the highest degree of local endemism of any habitat in North America. Despite the arid desert climate, the Cuatro Ciénegas basin harbors an extensive system of permanent streams, wetlands, and spring fed pools.</p> <p>2. Microsatellite loci were surveyed to infer genetic diversity and population structure of <i>Gambusia marshi</i>, a poeciliid fish endemic to the desert springs of the Cuatro Ciénegas basin and its outflow the Río Salado de Nadadores in Mexico.</p> <p>3. The Sierra de San Marcos and long-term isolation have played a vital role in shaping the current pattern of phylogeographic structure in<i> G. marshi</i>, and Bayesian clustering analysis revealed four genetic populations within <i>G. marshi</i> as well as a major east-west division of the of the species corresponding to the Sierra de San Marcos.</p> <p>4. Most sample sites exhibited high levels of genetic differentiation, although there is evidence for recent gene flow between some of these locations, presumably facilitated by irrigation canals. Although all populations exhibit genetic differentiation, the population of <i>G. marshi</i> in Poza Anteojo is extremely divergent and should be considered as an independent management unit.</p>
Data from: Isolation and characterization of fifteen polymorphic microsatellite loci for the citrus mealybug, Planococcus citri (Hemiptera: Pseudococcidae), and cross-amplification in two other mealybug species
[No abstract filled]
Data from: Characterization of microsatellite loci for the Gulf Coast waterdog (Necturus beyeri) using paired-end Illumina shotgun sequencing and cross-amplification in other Necturus
[No abstract filled]
Microsatellite genotyping data for habitat-linked genetic structure for white-crowned sparrow (Zonotrichia leucophrys): local factors shape population genetic structure
<p>Ecological, environmental, and geographic factors all influence genetic structure. Species with broad distributions are ideal systems because they cover a range of ecological and environmental conditions allowing us to test which components predict genetic structure. This study presents a novel, broad geographic approach using molecular markers, morphology, and habitat modelling to investigate rangewide and local barriers causing contemporary genetic differentiation within the geographical range of three white-crowned sparrow (<i>Zonotrichia leucophrys</i>) subspecies: <i>Z. l. gambelii, Z. l. oriantha, </i>and <i>Z. l. pugetensis</i>. Three types of genetic markers showed geographic distance between sampling sites, elevation, and ecosystem type are key factors contributing to population genetic structure. Microsatellite markers revealed white-crowned<i> </i>sparrows<i> </i>do not group by subspecies, but instead indicated four groupings at a rangewide scale and two groupings based on coniferous and deciduous ecosystems at a local scale. Our analyses of morphological variation also revealed habitat differences; sparrows from deciduous ecosystems are larger than individuals from coniferous ecosystems based on principal component analyses. Habitat modeling showed isolation by distance was prevalent in describing genetic structure, but isolation by resistance also had a small but significant influence. Not only do these findings have implications concerning the accuracy of subspecies delineations, they also highlight the critical role of local factors such as habitat in shaping contemporary population genetic structure of species with high dispersal ability.</p>
Supplementary material 5 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Table 5 : Data type: Table
Supplementary material 4 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Table 4 : Data type: Table
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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