Measures of Variation at DNA Repeat Loci under a General Stepwise Mutation Model

Polymorphisms at tandem repeat loci are caused by mutations with allele sizes occasionally altered by more than one repeat unit in both forward and backward directions. Such mutational changes may occur with asymmetric probabilities. Therefore, a one-step symmetric stepwise mutation model may not be appropriate for studying the population dynamics at all repeat loci. In this work, we evaluated the expectation and variance of the within-population variance of the allele size distribution in a finite population, and the expected homozygosity at a locus by the coalescence approach under a general stepwise mutation model, where mutational transitions of allele sizes can be arbitrary, including being asymmetric. Under the special cases of symmetric one-step, two-step, and multi-step geometric distributions of mutations, our general results reduce to the corresponding results obtained by earlier investigators. The general results indicate that in a finite population, which has reached a steady state under the (general stepwise) mutation and drift balance, the within-population variance of allele sizes has a simple expectation (i.e., proportional toNν, the product of the mutation rate,ν, and effective population size,N). However, its stochastic variance is a quadratic function of this composite parameter,Nν. Furthermore, this second-order variance does not decay with the number of alleles sampled from a population. Application of this theory to data on allele size distributions in unrelated Caucasians from the CEPH pedigree (obtained from the Genome Data Base) shows that the relationship of the variance and mean of within-population variance of allele sizes at tandem repeat loci, grouped by their chromosomal assignment, has a trend compatible with the theory. However, there is an indication that the second-order variance is generally underestimated. One reason for this departure might be that the CEPH sample may not represent a single homogeneous population that reached equilibrium at all tandem repeat loci.     

Analysis and implications of mutational variation

Variation from new mutations is important for several questions in quantitative genetics. Key parameters are the genomic mutation rate and the distribution of effects of mutations (DEM), which determine the amount of new quantitative variation that arises per generation from mutation (V _M ). Here, we review methods and empirical results concerning mutation accumulation (MA) experiments that have shed light on properties of mutations affecting quantitative traits. Surprisingly, most data on fitness traits from laboratory assays of MA lines indicate that the DEM is platykurtic in form (i.e., substantially less leptokurtic than an exponential distribution), and imply that most variation is produced by mutations of moderate to large effect. This finding contrasts with results from MA or mutagenesis experiments in which mutational changes to the DNA can be assayed directly, which imply that the vast majority of mutations have very small phenotypic effects, and that the distribution has a leptokurtic form. We compare these findings with recent approaches that attempt to infer the DEM for fitness based on comparing the frequency spectra of segregating nucleotide polymorphisms at putatively neutral and selected sites in population samples. When applied to data for humans and Drosophila, these analyses also indicate that the DEM is strongly leptokurtic. However, by combining the resultant estimates of parameters of the DEM with estimates of the mutation rate per nucleotide, the predicted V _M for fitness is only a tiny fraction of V _M observed in MA experiments. This discrepancy can be explained if we postulate that a few deleterious mutations of large effect contribute most of the mutational variation observed in MA experiments and that such mutations segregate at very low frequencies in natural populations, and effectively are never seen in population samples.     

Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs

A number of applications of analysis of human Y-chromosome microsatellite loci to human evolution and forensic science require reliable estimates of the mutation rate and knowledge of the mutational mechanism. We therefore screened a total of 4,999 meioses from father/son pairs with confirmed paternity (probability >/=99. 9%) at 15 Y-chromosomal microsatellite loci and identified 14 mutations. The locus-specific mutation-rate estimates were 0-8. 58x10-3, and the average mutation rate estimates were 3.17x10-3 (95% confidence interval [CI] 1.89-4.94x10-3) across 8 tetranucleotide microsatellites and 2.80x10-3 (95% CI 1.72-4.27x10-3) across all 15 Y-chromosomal microsatellites studied. Our data show a mutational bias toward length increase, on the basis of observation of more repeat gains than losses (10:4). The data are in almost complete agreement with the stepwise-mutation model, with 13 single-repeat changes and 1 double-repeat change. Sequence analysis revealed that all mutations occurred in uninterrupted homogenous arrays of >/=11 repeats. We conclude that mutation rates and characteristics of human Y-chromosomal microsatellites are consistent with those of autosomal microsatellites. This indicates that the general mutational mechanism of microsatellites is independent of recombination.     

Characterization of microsatellites located within the genes of goldfish (Carassius auratus auratus)

The goldfish (Carassius auratus auratus; Cyprinidae) is not only an important ornamental fish species, but also a useful model for biological studies. The sequence of goldfish genes present in the public database was searched for short tandem repeats, and 11 polymorphic microsatellites were detected within eight important genes. Two microsatellites were located in coding regions of the c‐myc and GAP‐43 genes, respectively, whereas the others were mainly located in 5′ and 3′ untranscribed regions of other genes, such as gonadotropin and activin. The average allele number of these microsatellites was 5.5 per locus with a range between 3 and 9. These microsatellites will be useful for ecological and population genetic studies of this species, as well as for the ornamental fish industry.     

Unconstrained evolution in short introns? – An analysis of genome‐wide polymorphism and divergence data from Drosophila

An unconstrained reference sequence facilitates the detection of selection. In Drosophila, sequence variation in short introns seems to be least influenced by selection and dominated by mutation and drift. Here, we test this with genome‐wide sequences using an African population (Malawi) of D. melanogaster and data from the related outgroup species D. simulans, D. sechellia, D. erecta and D. yakuba. The distribution of mutations deviates from equilibrium, and the content of A and T (AT) nucleotides shows an excess of variance among introns. We explain this by a complex mutational pattern: a shift in mutational bias towards AT, leading to a slight nonequilibrium in base composition and context‐dependent mutation rates, with G or C (GC) sites mutating most frequently in AT‐rich introns. By comparing the corresponding allele frequency spectra of AT‐rich vs. GC‐rich introns, we can rule out the influence of directional selection or biased gene conversion on the mutational pattern. Compared with neutral equilibrium expectations, polymorphism spectra show an excess of low frequency and a paucity of intermediate frequency variants, irrespective of the direction of mutation. Combining the information from different outgroups with the polymorphism data and using a generalized linear model, we find evidence for shared ancestral polymorphism between D. melanogaster and D. simulans, D. sechellia, arguing against a bottleneck in D. melanogaster. Generally, we find that short introns can be used as a neutral reference on a genome‐wide level, if the spatially and temporally varying mutational pattern is accounted for.     

Causes of variability in estimates of mutational variance from mutation accumulation experiments

Characteristics of the new phenotypic variation introduced via mutation have broad implications in evolutionary and medical genetics. Standardized estimates of this mutational variance, V_M, span 2 orders of magnitude, but the causes of this remain poorly resolved. We investigated estimate heterogeneity using 2 approaches. First, meta-analyses of ∼150 estimates of standardized V_M from 37 mutation accumulation studies did not support a difference among taxa (which differ in mutation rate) but provided equivocal support for differences among trait types (life history vs morphology, predicted to differ in mutation rate). Notably, several experimental factors were confounded with taxon and trait, and further empirical data are required to resolve their influences. Second, we analyzed morphological data from an experiment in Drosophila serrata to determine the potential for unintentional heterogeneity among environments in which phenotypes were measured (i.e. among laboratories or time points) or transient segregation of mutations within mutation accumulation lines to affect standardized V_M. Approximating the size of an average mutation accumulation experiment, variability among repeated estimates of (accumulated) mutational variance was comparable to variation among published estimates of standardized V_M. This heterogeneity was (partially) attributable to unintended environmental variation or within line segregation of mutations only for wing size, not wing shape traits. We conclude that sampling error contributed substantial variation within this experiment, and infer that it will also contribute substantially to differences among published estimates. We suggest a logistically permissive approach to improve the precision of estimates, and consequently our understanding of the dynamics of mutational variance of quantitative traits.     

Moderately and Highly Polymorphic Microsatellites Provide Discordant Estimates of Population Divergence in Sockeye Salmon, Oncorhynchus nerka

Mutation rate can vary widely among microsatellite loci. This variation may cause discordant single-locus and multi-locus estimates of F_ST, the commonly used measure of population divergence. We use 16 microsatellite and five allozyme loci from 14 sockeye salmon populations to address two questions about the affect of mutation rate on estimates of F_ST: (1) does mutation rate influence F_ST estimates from all microsatellites to a similar degree relative to allozymes?; (2) does the influence of mutation rate on F_ST estimates from microsatellites vary with geographic scale in spatially structured populations? For question one we find that discordant estimates of F_ST among microsatellites as well as between the two marker classes are correlated with mean within-population heterozygosity (H_S) and thus are likely due to differences in mutation rate. Highly polymorphic microsatellites (H_S > 0.84) provide significantly lower estimates of F_ST than moderately polymorphic microsatellites and allozymes (H_S < 0.60). Estimates of F_ST from binned allele frequency data and R_ST provide more accurate measures of population divergence for highly polymorphic but not for moderately polymorphic microsatellites. We conclude it is more important to pool loci of like H_S rather than marker class when estimating F_ST. For question two we find the F_ST values for moderately and highly polymorphic loci, while significantly different, are positively correlated for geographically proximate but not geographically distant population pairs. These results are consistent with expectations from the equilibrium approximation of Wright's infinite island model and confirm that the influence of mutation on estimates of F_ST can vary in spatially structured populations presumably because the rate of migration varies inversely with geographic scale.     

MULLER'S RATCHET AND MUTATIONAL MELTDOWNS

We extend our earlier work on the role of deleterious mutations in the extinction of obligately asexual populations. First, we develop analytical models for mutation accumulation that obviate the need for time-consuming computer simulations in certain ranges of the parameter space. When the number of mutations entering the population each generation is fairly high, the number of mutations per individual and the mean time to extinction can be predicted using classical approaches in quantitative genetics. However, when the mutation rate is very low, a fixation-probability approach is quite effective. Second, we show that an intermediate selection coefficient (s) minimizes the time to extinction. The critical value of s can be quite low, and we discuss the evolutionary implications of this, showing that increased sensitivity to mutation and loss of capacity for DNA repair can be selectively advantageous in asexual organisms. Finally, we consider the consequences of the mutational meltdown for the extinction of mitochondrial lineages in sexual species.     

鲤鱼微卫星突变速率和模式(英文)

利用150个微卫星分子标记在F1代家系的基因型分析过程中,共有27600个等位基因从亲本向子代传递,其中在5个微卫星座位上检测到6个突变的等位基因。对突变的等位基因数目进行统计分析后得出:鲤鱼平均每个世代每个微卫星座位的突变速率为2.53×10-4。在发现突变的5个位点中,经测序发现,突变序列中插入1个以上的重复单元就导致了突变的发生。这些突变表明,鲤鱼的微卫星突变没有遵循严格的渐变突变模型(stepwise mutation model,SMM)。该文关于鲤鱼微卫星突变速率和模式的研究将会对统计鲤鱼有效群体的统计提供有效参数。     

Clustered microsatellite mutations in the pipefish Syngnathus typhle.

Clustered mutations are copies of a mutant allele that enter a population's gene pool together due to replication from a premeiotic germline mutation and distribution to multiple successful gametes of an individual. Although the phenomenon has been studied in Drosophila and noted in a few other species, the topic has received scant attention despite claims of being of major importance to population genetics theory. Here we capitalize upon the reproductive biology of male-pregnant pipefishes to document the occurrence of clustered microsatellite mutations and to estimate their rates and patterns from family data. Among a total of 3195 embryos genetically screened from 110 families, 40% of the 35 detected de novo mutant alleles resided in documented mutational clusters. Most of the microsatellite mutations appeared to involve small-integer changes in repeat copy number, and they arose in approximately equal frequency in paternal and maternal germlines. These findings extend observations on clustered mutations to another organismal group and motivate a broader critique of the mutation cluster phenomenon. They also carry implications for the evolution of microsatellites with respect to mutational models and homoplasy among alleles.     

Rate and pattern of mutation at microsatellite loci in maize

Microsatellites are important tools for plant breeding, genetics, and evolution, but few studies have analyzed their mutation pattern in plants. In this study, we estimated the mutation rate for 142 microsatellite loci in maize (Zea mays subsp. mays) in two different experiments of mutation accumulation. The mutation rate per generation was estimated to be 7.7 x 10(-4) for microsatellites with dinucleotide repeat motifs, with a 95% confidence interval from 5.2 x 10(-4) to 1.1 x 10(-3). For microsatellites with repeat motifs of more than 2 bp in length, no mutations were detected; so we could only estimate the upper 95% confidence limit of 5.1 x 10(-5) for the mutation rate. For dinucleotide repeat microsatellites, we also determined that the variance of change in the number of repeats (sigma(m)2) is 3.2. We sequenced 55 of the 73 observed mutations, and all mutations proved to be changes in the number of repeats in the microsatellite or in mononucleotide tracts flanking the microsatellite. There is a higher probability to mutate to an allele of larger size. There is heterogeneity in the mutation rate among dinucleotide microsatellites and a positive correlation between the number of repeats in the progenitor allele and the mutation rate. The microsatellite-based estimate of the effective population size of maize is more than an order of magnitude less than previously reported values based on nucleotide sequence variation.     

Individual variation in microsatellite mutation rate in barn swallows

The hypermutable nature of some microsatellite loci implies realistic possibilities for the large-scale detection of germline mutations by pedigree analysis. We have developed a model system for mutation analysis by the characterisation of patterns of mutation at three hypervariable microsatellites (two tetranucleotide and one pentanucleotide repeat loci) in barn swallows, all three markers having mutation rates at the percentage level. Here, we study how the mutation rate varies between individual birds of a Spanish population of barn swallows. A total of 53 mutations were identified from 2920 germline transmissions in 90 families with a total of 694 offspring. Mutations were not randomly distributed among individuals (P = 0.020). Attempts to correlate mutation rate with allele size, degree of inbreeding, immunocompetence and male age only revealed a strong effect of allele size. The mean mutation rate differed between colonies of breeding swallows which was probably due to a corresponding variation in allele size between colonies. There was no difference in the mean mutation rate between the Spanish and an Italian population. These results corroborate earlier findings, at the population level, of an allele size effect on the microsatellite mutation rate.     

A high incidence of clustered microsatellite mutations revealed by parent-offspring analysis in the African freshwater snail, <Emphasis Type="BoldItalic">Bulinus forskalii</Emphasis> (Gastropoda,Pulmonata)

Genotyping of 11 microsatellites in 432 offspring from 28 families of the hermaphroditic, freshwater snail Bulinus forskalii detected 10 de novo mutant alleles. This gave an estimated mutation rate of 1.1 × 10^–3 per locus per gamete per generation. There was a trend towards repeat length expansion and, unlike most studies, multi-step mutations predominated, suggesting that the microsatellite mutation process does not conform to a strict stepwise mutation model. Interestingly, the ten mutant alleles appear to have arisen from only six independent germline mutation events within the microsatellite array, with seven of them residing in three mutational clusters. Our results extend observations of clustered microsatellite mutations to another taxonomic group and type of mating system, self-fertile gastropods, and provide compelling evidence of premeiotic germline mutations, a phenomenon that could greatly impact upon our understanding of mutation dynamics but which has received little attention.     

Characteristics of loci and individuals are associated with germline microsatellite mutation rates in lesser kestrels (Falco naumanni)

Although microsatellites are one of the most popular tools in genetic studies, their mutational dynamics and evolution remain unclear. Here, we apply extensive pedigree genotyping to identify and analyze the patterns and factors associated with de novo germline mutations across nine microsatellite loci in a wild population of lesser kestrels (Falco naumanni). A total of 10 germline mutations events were unambiguously identified in four loci, yielding an average mutation rate of 2.96x10(-3). Across loci, mutation rate was positively correlated with locus variability and average allele size. Mutations were primarily compatible with a stepwise mutation model, although not exclusively involved single-step changes. Unexpectedly, we found an excess of maternally transmitted mutations (male-to-female ratio of 0.1). One of the analyzed loci (Fn2.14) resulted hypermutable (mutation rate=0.87%). This locus showed a size-dependent mutation bias, with longer alleles displaying deletions or additions of a small number of repeat than shorter alleles. Mutation probability at Fn2.14 was higher for females and increased with parental (maternal) age but was not associated with individual physical condition, multilocus heterozygosity, allele length or allele span. Overall, our results do not support the male-biased mutation rate described in other organisms and suggest that mutation dynamics at microsatellite loci are a complex process which requires further research.     

Characterization of Demographic Expansions From Pairwise Comparisons of Linked Microsatellite Haplotypes

This work extends the methods of demographic inference based on the distribution of pairwise genetic differences between individuals (mismatch distribution) to the case of linked microsatellite data. Population genetics theory describes the distribution of mutations among a sample of genes under different demographic scenarios. However, the actual number of mutations can rarely be deduced from DNA polymorphisms. The inclusion of mutation models in theoretical predictions can improve the performance of statistical methods. We have developed a maximum-pseudolikelihood estimator for the parameters that characterize a demographic expansion for a series of linked loci evolving under a stepwise mutation model. Those loci would correspond to DNA polymorphisms of linked microsatellites (such as those found on the Y chromosome or the chloroplast genome). The proposed method was evaluated with simulated data sets and with a data set of chloroplast microsatellites that showed signal for demographic expansion in a previous study. The results show that inclusion of a mutational model in the analysis improves the estimates of the age of expansion in the case of older expansions.     

Mutation and evolution of microsatellite loci in Neurospora

The patterns of mutation and evolution at 13 microsatellite loci were studied in the filamentous fungal genus Neurospora. First, a detailed investigation was performed on five microsatellite loci by sequencing each microsatellite, together with its nonrepetitive flanking regions, from a set of 147 individuals from eight species of Neurospora. To elucidate the genealogical relationships among microsatellite alleles, repeat number was mapped onto trees constructed from flanking-sequence data. This approach allowed the potentially convergent microsatellite mutations to be placed in the evolutionary context of the less rapidly evolving flanking regions, revealing the complexities of the mutational processes that have generated the allelic diversity conventionally assessed in population genetic studies. In addition to changes in repeat number, frequent substitution mutations within the microsatellites were detected, as were substitutions and insertion/deletions within the flanking regions. By comparing microsatellite and flanking-sequence divergence, clear evidence of interspecific allele length homoplasy and microsatellite mutational saturation was observed, suggesting that these loci are not appropriate for inferring phylogenetic relationships among species. In contrast, little evidence of intraspecific mutational saturation was observed, confirming the utility of these loci for population-level analyses. Frequency distributions of alleles within species were generally consistent with the stepwise mutational model. By comparing variation within species at the microsatellites and the flanking-sequence, estimated microsatellite mutation rates were approximately 2500 times greater than mutation rates of flanking DNA and were consistent with estimates from yeast and fruit flies. A positive relationship between repeat number and variance in repeat number was significant across three genealogical depths, suggesting that longer microsatellite alleles are more mutable than shorter alleles. To test if the observed patterns of microsatellite variation and mutation could be generalized, an additional eight microsatellite loci were characterized and sequenced from a subset of the same Neurospora individuals.     

Likelihood-based estimation of microsatellite mutation rates

Microsatellites are widely used in genetic analyses, many of which require reliable estimates of microsatellite mutation rates, yet the factors determining mutation rates are uncertain. The most straightforward and conclusive method by which to study mutation is direct observation of allele transmissions in parent-child pairs, and studies of this type suggest a positive, possibly exponential, relationship between mutation rate and allele size, together with a bias toward length increase. Except for microsatellites on the Y chromosome, however, previous analyses have not made full use of available data and may have introduced bias: mutations have been identified only where child genotypes could not be generated by transmission from parents' genotypes, so that the probability that a mutation is detected depends on the distribution of allele lengths and varies with allele length. We introduce a likelihood-based approach that has two key advantages over existing methods. First, we can make formal comparisons between competing models of microsatellite evolution; second, we obtain asymptotically unbiased and efficient parameter estimates. Application to data composed of 118,866 parent-offspring transmissions of AC microsatellites supports the hypothesis that mutation rate increases exponentially with microsatellite length, with a suggestion that contractions become more likely than expansions as length increases. This would lead to a stationary distribution for allele length maintained by mutational balance. There is no evidence that contractions and expansions differ in their step size distributions.     

Mutation rate and pattern of microsatellites in common carp (<Emphasis Type="Italic">Cyprinus carpio</Emphasis> L.)

Microsatellites are popular molecular markers in genetic and evolutionary studies. Their mutational dynamics have been extensively studied in humans and fruit flies, but few data were available in fish. By genotyping 55 individuals of a F1 pedigree, we investigated the mutation rates and patterns of 49 microsatellites in one of the most important fresh water fish species, the common carp (Cyprinus carpio L.). The overall mutation rate of the 49 loci was 5.56×10⁻⁴/locus/generation (95% confidence interval 1.52×10⁻⁴ and 1.63×10⁻³). The change of allele size was between +2 to −5 repeat units, assuming that the mutation allele arose from the parental allele most similar in size to the mutant.     

Development of polymorphic microsatellite loci in the hermaphroditic freshwater snails Drepanotrema surinamense and Drepanotrema depressissimum

We characterized new variable microsatellites in two congeneric species of hermaphroditic freshwater snails (Drepanotrema depressissimum and D. surinamense), as well as conditions for multiplexing and simultaneously genotyping sets of loci. D. depressissimum had high mean gene diversity (> 0.8) and large number of alleles (= 10.9) per population. Most loci and populations were at Hardy–Weinberg equilibrium. The F_ST estimates were low among lesser Antilles populations and larger with a Venezuelan population. Far less diversity was found in D. surinamense with mean number of alleles and gene diversity per population of 2.8 and 0.34, respectively. Very few heterozygous individuals were observed. The most likely explanation is a high selfing rate (> 0.825) in this species. Unsurprisingly, the F_ST estimates among populations were much higher than in D. depressissimum. Cross‐species amplification in three congeneric species was on the whole unsuccessful.     

MUTATIONAL MELTDOWN IN LABORATORY YEAST POPULATIONS

Abstract.— In small or repeatedly bottlenecked populations, mutations are expected to accumulate by genetic drift, causing fitness declines. In mutational meltdown models, such fitness declines further reduce population size, thus accelerating additional mutation accumulation and leading to extinction. Because the rate of mutation accumulation is determined partly by the mutation rate, the risk and rate of meltdown are predicted to increase with increasing mutation rate. We established 12 replicate populations of Saccharomyces cerevisiae from each of two isogenic strains whose genomewide mutation rates differ by approximately two orders of magnitude. Each population was transferred daily by a fixed dilution that resulted in an effective population size near 250. Fitness declines that reduce growth rates were expected to reduce the numbers of cells transferred after dilution, thus reducing population size and leading to mutational meltdown. Through 175 daily transfers and approximately 2900 generations, two extinctions occurred, both in populations with elevated mutation rates. For one of these populations there is direct evidence that extinction resulted from mutational meltdown: Extinction immediately followed a major fitness decline, and it recurred consistently in replicate populations reestablished from a sample frozen after this fitness decline, but not in populations founded from a predecline sample. Wild‐type populations showed no trend to decrease in size and, on average, they increased in fitness.