The Rate and Spectrum of Microsatellite Mutation in <i>Caenorhabditis elegans</i> and <i>Daphnia pulex</i>

Seyfert, Amanda L.; Cristescu, Melania E.; Frisse, Linda A.; Schaack, Sarah; Thomas, W. Kelley; Lynch, Michael

doi:10.1534/genetics.107.081927

Cited by 72 publications

(84 citation statements)

References 86 publications

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“…Among the different factors, the motif repeat number of the microsatellite was found to be significantly correlated to the number of new alleles in G 15 . This result is consistent with mutation studies that suggest that longer microsatellites are more unstable (Wierdl et al 1997) and have higher mutation rates (Rubinsztein et al 1995;Schug et al 1998;Seyfert et al 2008). In this study, we found no evidence that the motif of the microsatellite locus, its degree of perfection, its chromosomal location, or its genome (A, B, D) position had an effect on the microsatellite diversity, but we had little power to detect weak effects.…”

Section: Mutation Rate Estimatorssupporting

confidence: 91%

“…As far as we know, four kinds of approaches have been used to estimate mutation rates in a wide range of species. They can be described according to the timescale they consider: a short timescale when using (i) pedigree-based (or parent-offspring) estimation [in humans (Weber and Wong 1993;Heyer et al 1997;Whittaker et al 2003), in birds (Brohede et al 2002(Brohede et al , 2004Beck et al 2003), 1 and in Gastropoda (Gow et al 2005)] or (ii) mutationaccumulation lines [in maize (Vigouroux et al 2002), in wheat (Thuillet et al 2002), in Drosophila Vazquez et al 2000), in Caenorhabditis elegans (Denver et al 2004;Seyfert et al 2008), and in Dictyostelium discoideum (McConnell et al 2007)], and a long timescale with (iii) interspecies comparison scaling divergence time with fossil data [human/chimp (Webster et al 2002;Sainudiin et al 2004;Kayser et al 2006)] or (iv) within-species allele-frequency distribution [in wheat (Chakraborty et al 1997;Thuilletet al 2004), in humans (Xu et al 2005), and in Arabidopsis thaliana (Symonds and Lloyd 2003)]. Short timescale approaches (pedigree or accumulation lines) are expected to be less biased since they rely on the direct observation of neo-mutations but to reach a sufficient accuracy they need larger sample sizes to allow for the detection of rather rare events.…”

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confidence: 99%

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Experimental Estimation of Mutation Rates in a Wheat Population With a Gene Genealogy Approach

et al. 2008

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Microsatellite markers are extensively used to evaluate genetic diversity in natural or experimental evolving populations. Their high degree of polymorphism reflects their high mutation rates. Estimates of the mutation rates are therefore necessary when characterizing diversity in populations. As a complement to the classical experimental designs, we propose to use experimental populations, where the initial state is entirely known and some intermediate states have been thoroughly surveyed, thus providing a short timescale estimation together with a large number of cumulated meioses. In this article, we derived four original gene genealogy-based methods to assess mutation rates with limited bias due to relevant model assumptions incorporating the initial state, the number of new alleles, and the genetic effective population size. We studied the evolution of genetic diversity at 21 microsatellite markers, after 15 generations in an experimental wheat population. Compared to the parents, 23 new alleles were found in generation 15 at 9 of the 21 loci studied. We provide evidence that they arose by mutation. Corresponding estimates of the mutation rates ranged from 0 to 4.97 3 10 À3 per generation (i.e., year). Sequences of several alleles revealed that length polymorphism was only due to variation in the core of the microsatellite. Among different microsatellite characteristics, both the motif repeat number and an independent estimation of the Nei diversity were correlated with the novel diversity. Despite a reduced genetic effective size, global diversity at microsatellite markers increased in this population, suggesting that microsatellite diversity should be used with caution as an indicator in biodiversity conservation issues. B ECAUSE microsatellite markers (tandemly repeated DNA motifs of 1-6 bp in length) are highly polymorphic and since they are distributed across the whole genome (Wu and Tanksley 1993;Plaschke et al. 1995;Pejic et al. 1998), they constitute a powerful tool to assess the level of genetic differentiation within and among experimental or natural populations at different generations. The high degree of polymorphism at microsatellite markers is directly related to their underlying mutation rates, which can be explained by two mutational mechanisms: polymerase slippage during DNA replication and unequal crossing over during recombinationbut not excluding SNP mutations at a lower rate. These two mechanisms involve changes in the number of motif repeats. Understanding the evolutionary properties of microsatellites is hence necessary for correctly interpreting diversity data when studying populations across generations and/or populations that have spatially diverged (Ellegren 2004).An increasing number of studies have been devoted to the estimation of mutation rates at microsatellite loci (e.g., Schug et al. 1998;Symonds and Lloyd 2003;Denver et al. 2004;Thuillet et al. 2004), which reveal a far more complex scheme for microsatellite evolution than previously stated (Schlö tterer 2000;Elleg...

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Section: Mutation Rate Estimatorssupporting

confidence: 91%

mentioning

confidence: 99%

Experimental Estimation of Mutation Rates in a Wheat Population With a Gene Genealogy Approach

et al. 2008

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“…Although this expression ignores the possibility of loss of heterozygosity by back mutations, this assumption appears reasonable for moderate timescales given that most microsatellite mutations in Daphnia involve multiple-step changes and that almost all single-step changes involve single-repeat insertions to the exclusion of deletions (Seyfert et al 2008). Results from long-term mutation-accumulation experiments indicate that, for the loci involved in this study, average u ¼ 7.1 (2.6) 3 10…”

Section: Phylogenetic Distribution Of Meiosis Suppressionmentioning

confidence: 82%

“…/allele/generation (Seyfert et al 2008) and that the average rate of loss of heterozygosity by gene conversion (c) ¼ 1.2 (0.6) 3 10 À4 /allele/generation (Omilian et al 2006).…”

Section: à5mentioning

confidence: 99%

Localization of the Genetic Determinants of Meiosis Suppression in Daphnia pulex

et al. 2008

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Although $1 in 10,000 animal species is capable of parthenogenetic reproduction, the evolutionary causes and consequences of such transitions remain uncertain. The microcrustacean Daphnia pulex provides a potentially powerful tool for investigating these issues because lineages that are obligately asexual in terms of female function can nevertheless transmit meiosis-suppressing genes to sexual populations via haploid sperm produced by environmentally induced males. The application of association mapping to a wide geographic collection of D. pulex clones suggests that sex-limited meiosis suppression in D. pulex has spread westward from a northeastern glacial refugium, conveyed by a dominant epistatic interaction among the products of at least four unlinked loci, with one entire chromosome being inherited through males in a nearly nonrecombining fashion. With the enormous set of genomic tools now available for D. pulex, these results set the stage for the determination of the functional underpinnings of the conversion of meiosis to a mitotic-like mode of inheritance.

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“…The mutation rate in Daphnia is not yet known, but, at least for microsatellites, it appears to be similar to that of Caenorhabditis elegans and D. melanogaster (Seyfert et al 2008). We thus used the average genomic mutation rate À6 cM/bp per sexual generation, or r % 7.5 3 10 À7 per generation (sexual and asexual generations combined, assuming one sexual generation per 10 asexual ones).…”

Section: Stratification Of Samplesmentioning

confidence: 99%

Nucleotide Polymorphism and Within-Gene Recombination in Daphnia magna and D. pulex, Two Cyclical Parthenogens

et al. 2009

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Theory predicts that partially asexual organisms may make the ''best of both worlds'': for the most part, they avoid the costs of sexual reproduction, while still benefiting from an enhanced efficiency of selection compared to obligately asexual organisms. There is, however, little empirical data on partially asexual organisms to test this prediction. Here we examine patterns of nucleotide diversity at eight nuclear loci in continentwide samples of two species of cyclically parthenogenetic Daphnia to assess the effect of partial asexual reproduction on effective population size and amount of recombination. Both species have high nucleotide diversities and show abundant evidence for recombination, yielding large estimates of effective population sizes (300,000-600,000). This suggests that selection will act efficiently even on mutations with small selection coefficients. Divergence between the two species is less than one-tenth of previous estimates, which were derived using a mitochondrial molecular clock. As the two species investigated are among the most distantly related species of the genus, this suggests that the genus Daphnia may be considerably younger than previously thought. Daphnia has recently received increased attention because it is being developed as a model organism for ecological and evolutionary genomics. Our results confirm the attractiveness of Daphnia as a model organism, because the high nucleotide diversity and low linkage disequilibrium suggest that fine-scale mapping of genes affecting phenotypes through association studies should be feasible.

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The Rate and Spectrum of Microsatellite Mutation in Caenorhabditis elegans and Daphnia pulex

Cited by 72 publications

References 86 publications

Experimental Estimation of Mutation Rates in a Wheat Population With a Gene Genealogy Approach

Experimental Estimation of Mutation Rates in a Wheat Population With a Gene Genealogy Approach

Localization of the Genetic Determinants of Meiosis Suppression in Daphnia pulex

Nucleotide Polymorphism and Within-Gene Recombination in Daphnia magna and D. pulex, Two Cyclical Parthenogens

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