Mutational Dynamics of Microsatellites

Bhargava, Atul; Fuentes, Francisco

doi:10.1007/s12033-009-9230-4

Cited by 166 publications

(171 citation statements)

References 210 publications

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“…In all simulations, mutation rate was fixed at

5 \times 10^{- 4}

, a value that is thought to be common at microsatellite loci in vertebrates (Bhargava and Fuentes, 2010), and base population size was fixed at 2 N = 2000. The performance of the directional migration method was assessed by calculating relative migration rates derived from both D and

G_{st}

.…”

Section: Methodsmentioning

confidence: 99%

Directional genetic differentiation and relative migration

Sundqvist

Keenan

Zackrisson

et al. 2016

Ecology and Evolution

244

235

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Understanding the population structure and patterns of gene flow within species is of fundamental importance to the study of evolution. In the fields of population and evolutionary genetics, measures of genetic differentiation are commonly used to gather this information. One potential caveat is that these measures assume gene flow to be symmetric. However, asymmetric gene flow is common in nature, especially in systems driven by physical processes such as wind or water currents. As information about levels of asymmetric gene flow among populations is essential for the correct interpretation of the distribution of contemporary genetic diversity within species, this should not be overlooked. To obtain information on asymmetric migration patterns from genetic data, complex models based on maximum‐likelihood or Bayesian approaches generally need to be employed, often at great computational cost. Here, a new simpler and more efficient approach for understanding gene flow patterns is presented. This approach allows the estimation of directional components of genetic divergence between pairs of populations at low computational effort, using any of the classical or modern measures of genetic differentiation. These directional measures of genetic differentiation can further be used to calculate directional relative migration and to detect asymmetries in gene flow patterns. This can be done in a user‐friendly web application called divMigrate‐online introduced in this study. Using simulated data sets with known gene flow regimes, we demonstrate that the method is capable of resolving complex migration patterns under a range of study designs.

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“…In all simulations, mutation rate was fixed at

5 \times 10^{- 4}

G_{st}

.…”

Section: Methodsmentioning

confidence: 99%

Directional genetic differentiation and relative migration

Sundqvist

Keenan

Zackrisson

et al. 2016

Ecology and Evolution

244

235

View full text Add to dashboard Cite

show abstract

“…Although microsatellite mutations often involve insertion or deletion of one repeat length, larger insertions and deletions were common in the loci analysed in lesser kestrels and house wrens. Mutation types are known to vary considerably by locus [13], and by species for a given locus, possibly because multiple mechanisms cause mutation in microsatellites including replication slippage, mismatch repair and recombination [16].…”

Section: Discussionmentioning

confidence: 99%

Evidence for heterozygote instability in microsatellite loci in house wrens

Masters

Johnson

et al. 2010

Biol. Lett.

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Microsatellite loci have high mutation rates and high levels of allelic variation, but the factors influencing their mutation rate are not well understood. The proposal that heterozygosity may increase mutation rates has profound implications for understanding the evolution of microsatellite loci, but currently has limited empirical support. We examined 20 microsatellite mutations identified in an analysis of 12 260 meiotic events across three loci in two populations of a songbird, the house wren (Troglodytes aedon). We found that for an allele of a given length, mutation was significantly more likely when there was a relatively large difference in size between the allele and its homologue (i.e. a large 'allele span'). Our results support the proposal of heterozygote instability at microsatellite loci.

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“…Unlike those phenotype-based characterizations, molecular marker-based evaluations of genetic diversity are more accurate since the molecular markers are not affected by environmental factors. Simple sequence repeats (SSR) or microsatellites is one of the markers widely distributed throughout the nuclear genome of eukaryotes (Bhargava & Fuentes, 2010). SSR marker is highly polymorphic and often use as genetic markers for population genetic analysis (Guichoux et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Population Structure of IRRDB 1981 and Wickham Rubber Germplasm Based on EST-SSR

et al. 2017

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The accession of the IRDB 1981 (PN'81) population is a newly introduced and an important rubber tree germplasm while the Wickham clone is a commercial variety one. The objectives of this study were to assess the genetic diversity and the population structure of PN'81 populations and the Wickham clones using 15 EST-SSR loci. Results of the analysis showed that the evaluated SSR primers yielded polymorphic markers. The gSSR 268 primer pairs yielded the most informative markers while HBE 280 primers generated the lowest ones. Results of the genetic diversity analysis supported that the PN'81 population belonged to a single large natural population of rubber trees while the Wickham clones belonged to a different group than that of PN'81. The population structure analysis of the rubber accessions was also in agreement with the results of the genetic diversity analysis. The experiment also indicated that PN'81 populations would be useful for future rubber breeding in Indonesia, especially as the sources of parent clones for rubber tree hybridization programs and rubber tree genetic resource conservation.

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Mutational Dynamics of Microsatellites

Cited by 166 publications

References 210 publications

Directional genetic differentiation and relative migration

Directional genetic differentiation and relative migration

Evidence for heterozygote instability in microsatellite loci in house wrens

Genetic Diversity and Population Structure of IRRDB 1981 and Wickham Rubber Germplasm Based on EST-SSR

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