Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila

Inbreeding reveals stronger net selection on Drosophila melanogaster males: implications for mutation load and the fitness of sexual females

Stronger selection on males has the potential to lower the deleterious mutation load of females, reducing the cost of sex. However, few studies have directly quantified the strength of selection for both sexes. As the magnitude of inbreeding depression (ID) is related to the strength of selection, we measured the cost of inbreeding for both males and females in a laboratory population of Drosophila melanogaster. Using a novel technique for inbreeding, we found significant ID for both juvenile viability and adult fitness in both sexes. The genetic variation responsible for this depression in fitness appeared to be recessive for adult fitness (h=0.11) and partially additive for juvenile viability (h=0.29). ID was identical across the sexes in terms of juvenile viability but was significantly more deleterious for males than females as adults, even though female X-chromosome homogamety should predispose them to a higher inbreeding load. We estimated the strength of selection on adult males to be 1.24 greater than on adult females, and this appears to be a consequence of selection arising from competition for mates. Combined with the generally positive intersexual genetic correlation for inbred lines, our results suggest that the mutation load of sexual females could be meaningfully reduced by stronger selection acting on males.

Is the F(ST) a good predictor of extinction?

The organization of neutral genetic variation has long been used as a diagnostic tool to infer demographic properties of populations, and recently it has been shown that this information can also be used to estimate the magnitude of genetic deterioration in small or fragmented populations. A further step of this research is to assess whether neutral genetic indicators can serve to predict and compare the viabilities of endangered species. I use modeling to explore how ecological metapopulation settings are related to neutral genetic indicators (such as the fixation index [F(ST)]), changes in genetic load, and metapopulation viability. The analysis indicates that genetic indicators are generally strongly and consistently correlated with the genetic load, population size and structure, and time of extinction but identifies two potential limitations for their use in viability assessments. First, the regime of environmental perturbations is not accurately reflected by neutral indicators, so that their predictive power may be reduced in variable environments. Second, many species are threatened by recent human-induced changes of their habitat configuration. In most cases, genetic indicators may not have reached their equilibrium value in the altered habitat, which limits their ability to compare species with heterogeneous histories and life-history traits.

Evolutionary dynamics of transposable elements in a small RNA world

Transposable elements (TEs) are selfish elements that cause harmful mutations, contribute to the structure of regulatory networks and shape the architecture of genomes. Natural selection against their harmful effects has long been considered the dominant force limiting their spread. It is now clear that a genome defense system of RNA-mediated silencing also plays a crucial role in limiting TE proliferation. A full understanding of TE evolutionary dynamics must consider how these forces jointly determine their proliferation within genomes. Here I consider these forces from two perspectives - dynamics within populations and evolutionary games within the germline. The analysis of TE dynamics from these two perspectives promises to provide new insight into their role in evolution.

Engineering the genomes of wild insect populations: challenges, and opportunities provided by synthetic Medea selfish genetic elements

Advances in insect transgenesis and our knowledge of insect physiology and genomics are making it possible to create transgenic populations of beneficial or pest insects that express novel traits. There are contexts in which we may want the transgenes responsible for these traits to spread so that all individuals within a wild population carry them, a process known as population replacement. Transgenes of interest are unlikely to confer an overall fitness benefit on those who carry them. Therefore, an essential component of any population replacement strategy is the presence of a drive mechanism that will ensure the spread of linked transgenes. We discuss contexts in which population replacement might be desirable and the requirements a drive system must satisfy to be both effective and safe. We then describe the creation of synthetic Medea elements, the first selfish genetic elements synthesized de novo, with the capability of driving population replacement, in this case in Drosophila. The strategy used to create Drosophila Medea is applicable to a number of other insect species and the Medea system satisfies key requirements for scientific and social acceptance. Finally, we highlight several challenges to implementing population replacement in the wild.

Impacts of mutation effects and population size on mutation rate in asexual populations: a simulation study

Background

In any natural population, mutation is the primary source of genetic variation required for evolutionary novelty and adaptation. Nevertheless, most mutations, especially those with phenotypic effects, are harmful and are consequently removed by natural selection. For this reason, under natural selection, an organism will evolve to a lower mutation rate. Overall, the action of natural selection on mutation rate is related to population size and mutation effects. Although theoretical work has intensively investigated the relationship between natural selection and mutation rate, most of these studies have focused on individual competition within a population, rather than on competition among populations. The aim of the present study was to use computer simulations to investigate how natural selection adjusts mutation rate among asexually reproducing subpopulations with different mutation rates.

Results

The competition results for the different subpopulations showed that a population could evolve to an "optimum" mutation rate during long-term evolution, and that this rate was modulated by both population size and mutation effects. A larger population could evolve to a higher optimum mutation rate than could a smaller population. The optimum mutation rate depended on both the fraction and the effects of beneficial mutations, rather than on the effects of deleterious ones. The optimum mutation rate increased with either the fraction or the effects of beneficial mutations. When strongly favored mutations appeared, the optimum mutation rate was elevated to a much higher level. The competition time among the subpopulations also substantially shortened.

Conclusions

Competition at the population level revealed that the evolution of the mutation rate in asexual populations was determined by both population size and mutation effects. The most striking finding was that beneficial mutations, rather than deleterious mutations, were the leading force that modulated the optimum mutation rate. The initial configuration of the population appeared to have no effect on these conclusions, confirming the robustness of the simulation method developed in the present study. These findings might further explain the lower mutation rates observed in most asexual organisms, as well as the higher mutation rates in some viruses.

Next-generation sequencing as a tool to study microbial evolution

Thanks to their short generation times and large population sizes, microbes evolve rapidly. Evolutionary biologists have exploited this to observe evolution in real time. The falling costs of whole-genome sequencing using next-generation technologies now mean that it is realistic to use this as a tool to study this rapid microbial evolution both in the laboratory and in the wild. Such experiments are being used to accurately estimate the rates of mutation, reveal the genetic targets and dynamics of natural selection, uncover the correlation (or lack thereof) between genetic and phenotypic change, and provide data to test long-standing evolutionary hypotheses. These advances have important implications for our understanding of the within- and between-host evolution of microbial pathogens.

Genetic linkage and natural selection

The prevalence of recombination in eukaryotes poses one of the most puzzling questions in biology. The most compelling general explanation is that recombination facilitates selection by breaking down the negative associations generated by random drift (i.e. Hill-Robertson interference, HRI). I classify the effects of HRI owing to: deleterious mutation, balancing selection and selective sweeps on: neutral diversity, rates of adaptation and the mutation load. These effects are mediated primarily by the density of deleterious mutations and of selective sweeps. Sequence polymorphism and divergence suggest that these rates may be high enough to cause significant interference even in genomic regions of high recombination. However, neither seems able to generate enough variance in fitness to select strongly for high rates of recombination. It is plausible that spatial and temporal fluctuations in selection generate much more fitness variance, and hence selection for recombination, than can be explained by uniformly deleterious mutations or species-wide selective sweeps.

Pervasive horizontal transfer of rolling-circle transposons among animals

Horizontal transfer (HT) of genes is known to be an important mechanism of genetic innovation, especially in prokaryotes. The impact of HT of transposable elements (TEs), however, has only recently begun to receive widespread attention and may be significant due to their mutagenic potential, inherent mobility, and abundance. Helitrons, also known as rolling-circle transposons, are a distinctive subclass of TE with a unique transposition mechanism. Here, we describe the first evidence for the repeated HT of four different families of Helitrons in an unprecedented array of organisms, including mammals, reptiles, fish, invertebrates, and insect viruses. The Helitrons present in these species have a patchy distribution and are closely related (80–98% sequence identity), despite the deep divergence times among hosts. Multiple lines of evidence indicate the extreme conservation of sequence identity is not due to selection, including the highly fragmented nature of the Helitrons identified and the lack of any signatures of selection at the nucleotide level. The presence of horizontally transferred Helitrons in insect viruses, in particular, suggests that this may represent a potential mechanism of transfer in some taxa. Unlike genes, Helitrons that have horizontally transferred into new host genomes can amplify, in some cases reaching up to several hundred copies and representing a substantial fraction of the genome. Because Helitrons are known to frequently capture and amplify gene fragments, HT of this unique group of DNA transposons could lead to horizontal gene transfer and incur dramatic shifts in the trajectory of genome evolution.

Seeing mutations in living cells

BACKGROUND

Evolution depends on mutations: rare errors in the transmission of genetic information. Experimentally, mutations have been found by detecting altered phenotypes or sequencing complete genomes, but most mutations do not have overt phenotypes, and sequencing is expensive and has limited time resolution. The major source of mutations is DNA replication errors. Nearly all mistakes in DNA replication are detected and repaired by the mismatch repair machinery.

RESULTS

We use a functional, fluorescently labeled derivative of one of the key mismatch repair proteins (MutL) to see and count the small fraction of errors in Escherichia coli that does not get repaired and is converted into stable mutations by the next round of DNA replication. Over a 300-fold range, there is a linear relationship between the frequency of fluorescent foci and the genetically measured mutation frequency, and the mean frequency of fluorescent foci agrees well with estimates of the global mutation rate.

CONCLUSION

We describe a method for detecting the majority of genomic mutations emerging in living cells, independently of their potential phenotype. The distribution of emerging mutations per cell is roughly Poisson distributed, suggesting that all the cells in the population have roughly the same mutation rate.

The population genetics of mutations: good, bad and indifferent

Population genetics is fundamental to our understanding of evolution, and mutations are essential raw materials for evolution. In this introduction to more detailed papers that follow, we aim to provide an oversight of the field. We review current knowledge on mutation rates and their harmful and beneficial effects on fitness and then consider theories that predict the fate of individual mutations or the consequences of mutation accumulation for quantitative traits. Many advances in the past built on models that treat the evolution of mutations at each DNA site independently, neglecting linkage of sites on chromosomes and interactions of effects between sites (epistasis). We review work that addresses these limitations, to predict how mutations interfere with each other. An understanding of the population genetics of mutations of individual loci and of traits affected by many loci helps in addressing many fundamental and applied questions: for example, how do organisms adapt to changing environments, how did sex evolve, which DNA sequences are medically important, why do we age, which genetic processes can generate new species or drive endangered species to extinction, and how should policy on levels of potentially harmful mutagens introduced into the environment by humans be determined?

Mutations and quantitative genetic variation: lessons from Drosophila

A central issue in evolutionary quantitative genetics is to understand how genetic variation for quantitative traits is maintained in natural populations. Estimates of genetic variation and of genetic correlations and pleiotropy among multiple traits, inbreeding depression, mutation rates for fitness and quantitative traits and of the strength and nature of selection are all required to evaluate theoretical models of the maintenance of genetic variation. Studies in Drosophila melanogaster have shown that a substantial fraction of segregating variation for fitness-related traits in Drosophila is due to rare deleterious alleles maintained by mutation-selection balance, with a smaller but significant fraction attributable to intermediate frequency alleles maintained by alleles with antagonistic pleiotropic effects, and late-age-specific effects. However, the nature of segregating variation for traits under stabilizing selection is less clear and requires more detailed knowledge of the loci, mutation rates, allelic effects and frequencies of molecular polymorphisms affecting variation in suites of pleiotropically connected traits. Recent studies in D. melanogaster have revealed unexpectedly complex genetic architectures of many quantitative traits, with large numbers of pleiotropic genes and alleles with sex-, environment- and genetic background-specific effects. Future genome wide association analyses of many quantitative traits on a common panel of fully sequenced Drosophila strains will provide much needed empirical data on the molecular genetic basis of quantitative traits.

Genic capture, sex linkage, and the heritability of fitness

Several sexual selection models predict that females will obtain indirect genetic benefits by preferentially mating with males that transmit high-quality genes to their offspring. However, despite widespread observations of additive population genetic variation for fitness as well as for male sexually selected traits, estimated fitness associations between fathers and offspring are often weak. Perhaps more puzzling, the strength of these associations differs drastically between species, leading many researchers to question the relevance of genetic benefits for processes of sexual selection. Here, I show that a species' sex chromosome system can strongly influence the genetic architecture of male and female fitness variation and, consequently, the heritability of fitness between fathers and their offspring. Indirect genetic benefits are reduced, and sexually antagonistic costs are pronounced, in species with X chromosomes relative to species with homomorphic sex chromosomes, environmental sex determination, or Z chromosomes. Data from the sexual selection literature are consistent with predictions of the models, though additional studies will be required to circumvent phylogenetic nonindependence between sex determination systems. This study strongly suggests that inferences about genetic benefits of female choice must be considered within a species-specific genomic context, and it has several implications for the evolution of female preferences as well as the genomic consequences of sex and sexual selection.

The two-mutant problem: clonal interference in evolutionary graph theory

In large asexual populations, clonal interference, whereby different beneficial mutations compete to fix in the population simultaneously, may be the norm. Results extrapolated from the spread of individual mutations in homogeneous backgrounds are found to be misleading in such situations: clonal interference severely inhibits the spread of beneficial mutations. In contrast with results gained in systems with just one mutation striving for fixation at any one time, the spatial structure of the population is found to be an important factor in determining the fixation probability when there are two beneficial mutations.

Regeneration of the variance of metric traits by spontaneous mutation in a Drosophila population

In the C1 population of Drosophila melanogaster of moderate effective size (≈500), which was genetically invariant in its origin, we studied the regeneration by spontaneous mutation of the genetic variance for two metric traits [abdominal (AB) and sternopleural (ST) bristle number] and that of the concealed mutation load for viability, together with their temporal stability, using alternative selection models based on mutational parameters estimated in the C1 genetic background. During generations 381–485 of mutation accumulation (MA), the additive variances of AB and ST approached the levels observed in standing laboratory populations, fluctuating around their expected equilibrium values under neutrality or under relatively weak causal stabilizing selection. This type of selection was required to simultaneously account for the observed additive variance in our population and for those previously reported in natural and laboratory populations, indicating that most mutations affecting bristle traits would only be subjected to weak selective constraints. Although gene action for bristles was essentially additive, transient situations occurred where inbreeding resulted in a depression of the mean and an increase of the additive variance. This was ascribed to the occasional segregation of mutations of large recessive effects. On the other hand, the observed non-lethal inbreeding depression for viability must be explained by the segregation of alleles of considerable and largely recessive deleterious effects, and the corresponding load concealed in the heterozygous condition was found to be temporally stable, as expected from tighter constraints imposed by natural selection.

An analysis of genetic changes during the divergence of Drosophila species

Background

It has been long appreciated that speciation involves changes in body plans and establishes genetic, reproductive, developmental and behavioral incompatibilities between populations. However, little is still known about the genetic components involved in these changes or the sequence and scale of events that lead to the differentiation of species.

Principal Findings

In this paper, we investigated the genetic changes in three closely related species of Drosophila by making pair-wise comparisons of their genomes. We focused our analysis on the modern relatives of the alleles likely to be segregating in pre-historic populations at the time or after the ancestor of D. simulans became separated from the ancestor of D. melanogaster. Some of these genes were previously implicated in the genetics of reproduction and behavior while the biological functions of others are not yet clear.

Conclusions

Together these results identify different classes of genes that might have participated in the beginning of segregation of these species millions of years ago in Africa.

Muller's ratchet and the degeneration of the Drosophila miranda neo-Y chromosome

Since its formation about 1.75 million years ago, the Drosophila miranda neo-Y chromosome has undergone a rapid process of degeneration, having lost approximately half of the genes that it originally contained. Using estimates of mutation rates and selection coefficients for loss-of-function mutations, we show that the high rate of accumulation of these mutations can largely be explained by Muller's ratchet, the process of stochastic loss of the least-loaded mutational class from a finite, nonrecombining population. We show that selection at nonsynonymous coding sites can accelerate the process of gene loss and that this effect varies with the number of genes still present on the degenerating neo-Y chromosome.

Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis

Identical (or more correctly 'monozygotic') twins are widely used to study the contributions of genetics and environment to human disease. A study that focused on three pairs of monozygotic twins, in which one twin had multiple sclerosis and the other did not, has brought the latest techniques of genome sequencing and analysis to this field, and incidentally published the first female human genome sequences. Full sequences were determined for one pair of twins, and for these and the other two pairs the mRNA transcriptome and epigenome sequences of CD4⁺ lymphocytes were determined. The striking result is that no genetic, epigenetic or transcriptome differences were found that explained why one twin had the disease and the other did not. Digging deeper into the data, eQTL (expression quantitative trait locus) mapping revealed tantalizing differences within twin pairs that merit closer examination. And some possible causes can be ruled out. Future work might usefully concentrate on studies of other cell types and epigenetic modifications.

Studies of identical twins are widely used to dissect the contributions of genes and the environment to human diseases. In multiple sclerosis, an autoimmune demyelinating disease, identical twins often show differences. This might suggest that environmental effects are most significant in this case, but genetic and epigenetic differences between identical twins have been described. Here, however, studies of identical twins show no evidence for genetic, epigenetic or transcriptome differences that could explain disease discordance.

Monozygotic or ‘identical’ twins have been widely studied to dissect the relative contributions of genetics and environment in human diseases. In multiple sclerosis (MS), an autoimmune demyelinating disease and common cause of neurodegeneration and disability in young adults, disease discordance in monozygotic twins has been interpreted to indicate environmental importance in its pathogenesis^{1,2,3,4,5,6,7,8}. However, genetic and epigenetic differences between monozygotic twins have been described, challenging the accepted experimental model in disambiguating the effects of nature and nurture^9,10,11,12. Here we report the genome sequences of one MS-discordant monozygotic twin pair, and messenger RNA transcriptome and epigenome sequences of CD4⁺ lymphocytes from three MS-discordant, monozygotic twin pairs. No reproducible differences were detected between co-twins among ∼3.6 million single nucleotide polymorphisms (SNPs) or ∼0.2 million insertion-deletion polymorphisms. Nor were any reproducible differences observed between siblings of the three twin pairs in HLA haplotypes, confirmed MS-susceptibility SNPs, copy number variations, mRNA and genomic SNP and insertion-deletion genotypes, or the expression of ∼19,000 genes in CD4⁺ T cells. Only 2 to 176 differences in the methylation of ∼2 million CpG dinucleotides were detected between siblings of the three twin pairs, in contrast to ∼800 methylation differences between T cells of unrelated individuals and several thousand differences between tissues or between normal and cancerous tissues. In the first systematic effort to estimate sequence variation among monozygotic co-twins, we did not find evidence for genetic, epigenetic or transcriptome differences that explained disease discordance. These are the first, to our knowledge, female, twin and autoimmune disease individual genome sequences reported.

Mutation and the evolution of recombination

Under the classical view, selection depends more or less directly on mutation: standing genetic variance is maintained by a balance between selection and mutation, and adaptation is fuelled by new favourable mutations. Recombination is favoured if it breaks negative associations among selected alleles, which interfere with adaptation. Such associations may be generated by negative epistasis, or by random drift (leading to the Hill-Robertson effect). Both deterministic and stochastic explanations depend primarily on the genomic mutation rate, U. This may be large enough to explain high recombination rates in some organisms, but seems unlikely to be so in general. Random drift is a more general source of negative linkage disequilibria, and can cause selection for recombination even in large populations, through the chance loss of new favourable mutations. The rate of species-wide substitutions is much too low to drive this mechanism, but local fluctuations in selection, combined with gene flow, may suffice. These arguments are illustrated by comparing the interaction between good and bad mutations at unlinked loci under the infinitesimal model.

Measurements of spontaneous rates of mutations in the recent past and the near future

The rate of spontaneous mutation in natural populations is a fundamental parameter for many evolutionary phenomena. Because the rate of mutation is generally low, most of what is currently known about mutation has been obtained through indirect, complex and imprecise methodological approaches. However, in the past few years genome-wide sequencing of closely related individuals has made it possible to estimate the rates of mutation directly at the level of the DNA, avoiding most of the problems associated with using indirect methods. Here, we review the methods used in the past with an emphasis on next generation sequencing, which may soon make the accurate measurement of spontaneous mutation rates a matter of routine.

Darwin and genetics

Darwin's theory of natural selection lacked an adequate account of inheritance, making it logically incomplete. We review the interaction between evolution and genetics, showing how, unlike Mendel, Darwin's lack of a model of the mechanism of inheritance left him unable to interpret his own data that showed Mendelian ratios, even though he shared with Mendel a more mathematical and probabilistic outlook than most biologists of his time. Darwin's own "pangenesis" model provided a mechanism for generating ample variability on which selection could act. It involved, however, the inheritance of characters acquired during an organism's life, which Darwin himself knew could not explain some evolutionary situations. Once the particulate basis of genetics was understood, it was seen to allow variation to be passed intact to new generations, and evolution could then be understood as a process of changes in the frequencies of stable variants. Evolutionary genetics subsequently developed as a central part of biology. Darwinian principles now play a greater role in biology than ever before, which we illustrate with some examples of studies of natural selection that use DNA sequence data and with some recent advances in answering questions first asked by Darwin.

Universal global imprints of genome growth and evolution--equivalent length and cumulative mutation density

Background

Segmental duplication is widely held to be an important mode of genome growth and evolution. Yet how this would affect the global structure of genomes has been little discussed.

Methods/Principal Findings

Here, we show that equivalent length, or , a quantity determined by the variance of fluctuating part of the distribution of the -mer frequencies in a genome, characterizes the latter's global structure. We computed the s of 865 complete chromosomes and found that they have nearly universal but (-dependent) values. The differences among the of a chromosome and those of its coding and non-coding parts were found to be slight.

Conclusions

We verified that these non-trivial results are natural consequences of a genome growth model characterized by random segmental duplication and random point mutation, but not of any model whose dominant growth mechanism is not segmental duplication. Our study also indicates that genomes have a nearly universal cumulative “point” mutation density of about 0.73 mutations per site that is compatible with the relatively low mutation rates of (15)10/site/Mya previously determined by sequence comparison for the human and E. coli genomes.

The role of advantageous mutations in enhancing the evolution of a recombination modifier

Although the evolution of recombination is still a major problem in evolutionary genetics, recent theoretical studies have shown that recombination can evolve by breaking down interference ("Hill-Robertson effects") among multiple loci. This leads to selection on a recombination modifier in a population subject to recurrent deleterious mutation. Here, we use computer simulations to investigate the evolution of a recombination modifier under three different scenarios of recurrent mutation in a finite population: (1) mutations are deleterious only, (2) mutations are advantageous only, and (3) there is a mixture of deleterious and advantageous mutations. We also investigate how linkage disequilibrium, the strength of selection acting on a modifier, and effective population size change under the different scenarios. We observe that adding even a small number of advantageous mutations increases the fixation rate of modifiers that increase recombination, especially if the effects of deleterious mutations are weak. However, the strength of selection on a modifier is less than the summed strengths had there been deleterious mutations only and advantageous mutations only.

Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes

Protein-coding sequences make up only about 1% of the mammalian genome. Much of the remaining 99% has been long assumed to be junk DNA, with little or no functional significance. Here, we show that in hominids, a group with historically low effective population sizes, all classes of noncoding DNA evolve more slowly than ancestral transposable elements and so appear to be subject to significant evolutionary constraints. Under the nearly neutral theory, we expected to see lower levels of selective constraints on most sequence types in hominids than murids, a group that is thought to have a higher effective population size. We found that this is the case for many sequence types examined, the most extreme example being 5'UTRs, for which constraint in hominids is only about one-third that of murids. Surprisingly, however, we observed higher constraints for some sequence types in hominids, notably 4-fold sites, where constraint is more than twice as high as in murids. This implies that more than about one-fifth of mutations at 4-fold sites are effectively selected against in hominids. The higher constraint at 4-fold sites in hominids suggests a more complex protein-coding gene structure than murids and indicates that methods for detecting selection on protein-coding sequences (e.g., using the d(N)/d(S) ratio), with 4-fold sites as a neutral standard, may lead to biased estimates, particularly in hominids. Our constraint estimates imply that 5.4% of nucleotide sites in the human genome are subject to effective negative selection and that there are three times as many constrained sites within noncoding sequences as within protein-coding sequences. Including coding and noncoding sites, we estimate that the genomic deleterious mutation rate U = 4.2. The mutational load predicted under a multiplicative model is therefore about 99% in hominids.

Evidence for pervasive adaptive protein evolution in wild mice

The relative contributions of neutral and adaptive substitutions to molecular evolution has been one of the most controversial issues in evolutionary biology for more than 40 years. The analysis of within-species nucleotide polymorphism and between-species divergence data supports a widespread role for adaptive protein evolution in certain taxa. For example, estimates of the proportion of adaptive amino acid substitutions (alpha) are 50% or more in enteric bacteria and Drosophila. In contrast, recent estimates of alpha for hominids have been at most 13%. Here, we estimate alpha for protein sequences of murid rodents based on nucleotide polymorphism data from multiple genes in a population of the house mouse subspecies Mus musculus castaneus, which inhabits the ancestral range of the Mus species complex and nucleotide divergence between M. m. castaneus and M. famulus or the rat. We estimate that 57% of amino acid substitutions in murids have been driven by positive selection. Hominids, therefore, are exceptional in having low apparent levels of adaptive protein evolution. The high frequency of adaptive amino acid substitutions in wild mice is consistent with their large effective population size, leading to effective natural selection at the molecular level. Effective natural selection also manifests itself as a paucity of effectively neutral nonsynonymous mutations in M. m. castaneus compared to humans.

Rate, molecular spectrum, and consequences of human mutation

Although mutation provides the fuel for phenotypic evolution, it also imposes a substantial burden on fitness through the production of predominantly deleterious alleles, a matter of concern from a human-health perspective. Here, recently established databases on de novo mutations for monogenic disorders are used to estimate the rate and molecular spectrum of spontaneously arising mutations and to derive a number of inferences with respect to eukaryotic genome evolution. Although the human per-generation mutation rate is exceptionally high, on a per-cell division basis, the human germline mutation rate is lower than that recorded for any other species. Comparison with data from other species demonstrates a universal mutational bias toward A/T composition, and leads to the hypothesis that genome-wide nucleotide composition generally evolves to the point at which the power of selection in favor of G/C is approximately balanced by the power of random genetic drift, such that variation in equilibrium genome-wide nucleotide composition is largely defined by variation in mutation biases. Quantification of the hazards associated with introns reveals that mutations at key splice-site residues are a major source of human mortality. Finally, a consideration of the long-term consequences of current human behavior for deleterious-mutation accumulation leads to the conclusion that a substantial reduction in human fitness can be expected over the next few centuries in industrialized societies unless novel means of genetic intervention are developed.

Enhanced fixation and preservation of a newly arisen duplicate gene by masking deleterious loss-of-function mutations

Segmental duplications are enriched within many eukaryote genomes, and their potential consequence is gene duplication. While previous theoretical studies of gene duplication have mainly focused on the gene silencing process after fixation, the process leading to fixation is even more important for segmental duplications, because the majority of duplications would be lost before reaching a significant frequency in a population. Here, by a series of computer simulations, we show that purifying selection against loss-of-function mutations increases the fixation probability of a new duplicate gene, especially when the gene is haplo-insufficient. Theoretically, the probability of simultaneous preservation of both duplicate genes becomes twice the loss-of-function mutation rate (u(c)) when the population size (N), the degree of dominance of mutations (h) and the recombination rate between the duplicate genes (c) are all sufficiently large (Nu(c)>1, h>0.1 and c>u(c)). The preservation probability declines rapidly with h and becomes 0 when h=0 (haplo-sufficiency). We infer that masking deleterious loss-of-function mutations give duplicate genes an immediate selective advantage and, together with effects of increased gene dosage, would predominantly determine the fates of the duplicate genes in the early phase of their evolution.

Spontaneous mutation parameters for Arabidopsis thaliana measured in the wild

Mutations are the ultimate source of genetic diversity and their contributions to evolutionary process depend critically on their rate and their effects on traits, notably fitness. Mutation rate and mutation effect can be measured simultaneously through the use of mutation accumulation lines, and previous mutation accumulation studies measuring these parameters have been performed in laboratory conditions. However, estimation of mutation parameters for fitness in wild populations requires assays in environments where mutations are exposed to natural selection and natural environmental variation. Here we quantify mutation parameters in both the wild and greenhouse environments using 100 25th generation Arabidopsis thaliana mutation accumulation lines. We found significantly greater mutational variance and a higher mutation rate for fitness under field conditions relative to greenhouse conditions. However, our field estimates were low when scaled to natural environmental variation. Many of the mutation accumulation lines have increased fitness, counter to the expectation that nearly all mutations decrease fitness. A high mutation rate and a low mutational contribution to phenotypic variation may explain observed levels of natural genetic variation. Our findings indicate that mutation parameters are not fixed, but are variables whose values may reflect the specific environment in which mutations are tested.

Multiple chicken repeat 1 lineages in the genomes of oestroid flies

Retrotransposons including CR1 (chicken repeat 1) elements are important factors in genome evolution. They also mobilize in a genome in a way that makes them useful for phylogenetic analysis and species identification. This study was designed to identify lineages of CR1 elements in the genomes of forensically important oestroid flies and to further characterize one family, Sbul.CR1B. CR1 fragments from several taxa were amplified, cloned, sequenced and analyzed to identify different lineages of elements. A variety of retrotransposon families were recovered that exhibit similarity to known retrotransposon families. A number of these lineages may have given rise to taxon-specific subfamilies that have been recently active in oestroid fly genomes. One element from Sarcophaga bullata was analyzed in detail to reconstruct a partial Open Reading Frame containing both the reverse transcriptase (RT) and endonuclease (EN) domains. These domains were used to identify conserved amino acid regions in the recovered consensus via comparison to known non-LTR retrotransposons. Phylogenetic analysis of the RT domain revealed the recovered ORF in S. bullata compares favorably with previously documented CR1-like elements. This work will serve as the basis for additional analyses targeted at developing a simple, efficient marker system for the identification of forensically important carrion flies.

The genetics of inbreeding depression

Inbreeding depression - the reduced survival and fertility of offspring of related individuals - occurs in wild animal and plant populations as well as in humans, indicating that genetic variation in fitness traits exists in natural populations. Inbreeding depression is important in the evolution of outcrossing mating systems and, because intercrossing inbred strains improves yield (heterosis), which is important in crop breeding, the genetic basis of these effects has been debated since the early twentieth century. Classical genetic studies and modern molecular evolutionary approaches now suggest that inbreeding depression and heterosis are predominantly caused by the presence of recessive deleterious mutations in populations.

Genomic mutation rates: what high-throughput methods can tell us

High-throughput DNA analyses are increasingly being used to detect rare mutations in moderately sized genomes. These methods have yielded genome mutation rates that are markedly higher than those obtained using pre-genomic strategies. Recent work in a variety of organisms has shown that mutation rate is strongly affected by sequence context and genome position. These observations suggest that high-throughput DNA analyses will ultimately allow researchers to identify trans-acting factors and cis sequences that underlie mutation rate variation. Such work should provide insights on how mutation rate variability can impact genome organization and disease progression.

A genome-wide view of Caenorhabditis elegans base-substitution mutation processes

Knowledge of mutation processes is central to understanding virtually all evolutionary phenomena and the underlying nature of genetic disorders and cancers. However, the limitations of standard molecular mutation detection methods have historically precluded a genome-wide understanding of mutation rates and spectra in the nuclear genomes of multicellular organisms. We applied two high-throughput DNA sequencing technologies to identify and characterize hundreds of spontaneously arising base-substitution mutations in 10 Caenorhabditis elegans mutation-accumulation (MA)-line nuclear genomes. C. elegans mutation rate estimates were similar to previous calculations based on smaller numbers of mutations. Mutations were distributed uniformly within and among chromosomes and were not associated with recombination rate variation in the MA lines, suggesting that intragenomic variation in genetic hitchhiking and/or background selection are primarily responsible for the chromosomal distribution patterns of polymorphic nucleotides in C. elegans natural populations. A strong mutational bias from G/C to A/T nucleotides was detected in the MA lines, implicating oxidative DNA damage as a major endogenous mutagenic force in C. elegans. The observed mutational bias also suggests that the C. elegans nuclear genome cannot be at equilibrium because of mutation alone. Transversions dominate the spectrum of spontaneous mutations observed here, whereas transitions dominate patterns of allegedly neutral polymorphism in natural populations of C. elegans and many other animal species; this observation challenges the assumption that natural patterns of molecular variation in noncoding regions of the nuclear genome accurately reflect underlying mutation processes.

The tempo and mode of evolution of transposable elements as revealed by molecular phylogenies reconstructed from mosquito genomes

Although many mathematical models exist predicting the dynamics of transposable elements (TEs), there is a lack of available empirical data to validate these models and inherent assumptions. Genomes can provide a snapshot of several TE families in a single organism, and these could have their demographics inferred by coalescent analysis, allowing for the testing of theories on TE amplification dynamics. Using the available genomes of the mosquitoes Aedes aegypti and Anopheles gambiae, we indicate that such an approach is feasible. Our analysis follows four steps: (1) mining the two mosquito genomes currently available in search of TE families; (2) fitting, to selected families found in (1), a phylogeny tree under the general time-reversible (GTR) nucleotide substitution model with an uncorrelated lognormal (UCLN) relaxed clock and a nonparametric demographic model; (3) fitting a nonparametric coalescent model to the tree generated in (2); and (4) fitting parametric models motivated by ecological theories to the curve generated in (3).

Asymmetry of genetic variation in fitness-related traits: apparent stabilizing selection on g(max)

The maintenance of genetic variation in traits closely associated with fitness remains a key unresolved issue in evolutionary genetics. One important qualification on the observation of genetic variation in fitness-related traits is that such traits respond asymmetrically to selection, evolving to a greater extent in the direction of lower fitness. Here we test the hypothesis that standing genetic variation in fitness-related traits is principally maintained for unfit phenotypes. Male Drosophila bunnanda vary in mating success (the primary determinant of male fitness) due to female mate choice. We used competitive mating success to partitioning males into two groups: successful (high fitness) and unsuccessful (low fitness). Relative to successful males, unsuccessful males harbored considerably greater levels of additive genetic variation for sexual signaling traits. This genetic asymmetry was detected for a multivariate trait that we demonstrated was not directly under stabilizing sexual selection, leading us to conclude the trait was under apparent stabilizing selection. Consequently, our results suggest genetic variance might be biased toward low fitness even for traits that are not themselves the direct targets of selection. Simple metrics of genetic variance are unlikely to be adequate descriptors of the complex nature of the genetic basis of traits under selection.

Impact of gene copy number variation on anesthesia in Drosophila melanogaster

BACKGROUND

Chromosomal deletions and duplications, which result in halving or doubling of copy number in a block of genes, are an important source of variation between individuals. Phenotypic effects of copy number variation are commonly observed, but effects on sensitivity to volatile anesthetics have not been assessed in any organism.

METHODS

The potency with which halothane depresses the righting reflex of fruit flies was measured in congenic Drosophila strains, each of which was heterozygous for a deletion of average size 400 kb. Over 200 strains were examined, thereby scanning approximately half of the fly genome.

RESULTS

Although the vast majority of deletion heterozygotes were indistinguishable from the control, eight had significantly altered sensitivity to halothane. Genetic tests supported the hypothesis that the change in anesthetic sensitivity was the result of reduction in copy number and not adventitious mutations in the strains. Among the eight outliers, the difference in halothane potency ranged from a 25% increase to a 15% decrease. Changes of similar magnitude but distinctive patterns were found when these lines were tested with enflurane, isoflurane, and sevoflurane.

CONCLUSIONS

Variation in gene copy number has a significant impact on anesthetic sensitivity in Drosophila melanogaster. The level of transcription of a few genes must thus be limiting for a normal response to volatiles. Coupling between gene copy and gene expression is universal, and the components of the fly's nervous system are highly conserved; therefore, this work provides a rationale for investigating the clinical impact of copy number variation.

Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines

We inferred the rate and properties of new spontaneous mutations in Drosophila melanogaster by carrying out whole-genome shotgun sequencing-by-synthesis of three mutation accumulation (MA) lines that had been maintained by close inbreeding for an average of 262 generations. We tested for the presence of new mutations by generating alignments of each MA line to the D. melanogaster reference genome sequence and then compared these alignments base by base. We determined empirically that at least five reads at a site within each line are required for accurate single nucleotide mutation calling. We mapped a total of 174 single-nucleotide mutations, giving a single nucleotide mutation rate of 3.5 x 10(-9) per site per generation. There were no false positives in a random sample of 40 of these mutations checked by Sanger sequencing. Variation in the numbers of mutations among the MA lines was small and nonsignificant. Numbers of transition and transversion mutations were 86 and 88, respectively, implying that transition mutation rate is close to 2x the transversion rate. We observed 1.5x as many G or C --> A or T as A or T --> G or C mutations, implying that the G or C --> A or T mutation rate is close to 2x the A or T --> G or C mutation rate. The base composition of the genome is therefore not at an equilibrium determined solely by mutation. The predicted G + C content at mutational equilibrium (33%) is similar to that observed in transposable element remnants. Nearest-neighbor mutational context dependencies are nonsignificant, suggesting that this is a weak phenomenon in Drosophila. We also saw nonsignificant differences in the mutation rate between transcribed and untranscribed regions, implying that any transcription-coupled repair process is weak. Of seven short indel mutations confirmed, six were deletions, consistent with the deletion bias that is thought to exist in Drosophila.

Low frequency of mutations with strongly deleterious but nonlethal fitness effects

Most experimentally detectable effects of mutations in cellular organisms are either lethal or mildly deleterious. A possible explanation for the paucity of strongly detrimental but nonlethal mutations is that the processes constituting cellular metabolism are either essential or largely redundant. Alternatively, the partition between lethal and inconspicuous mutations exists within important biological processes. To test this, we measured maximum growth rates of yeast strains each carrying the deletion of a single gene in one of 38 protein complexes. We also used relevant data from previous high-throughput phenotypic studies of the yeast gene-deletion collection. The complexes typified well-defined sets of genes engaged in a common process. Within virtually all essential complexes there were two clear modes of phenotypic effects, that is the cessation of growth or slowdown of growth by a few percent. This uniformity is striking given that complexes differ extensively in function, size, and proportion of essential proteins. The pattern of bimodality is observed both under optimal and suboptimal environmental conditions. The generic paucity of strong effects and abundance of small ones relates to the feasibility of analyses of quantitative traits and epidemiological surveys, irrespective of the particular element of metabolism under study.

Patterns of intraspecific DNA variation in the Daphnia nuclear genome

Understanding nucleotide variation in natural populations has been a subject of great interest for decades. However, many taxonomic groups, especially those with atypical life history attributes remain unstudied, and Drosophila is the only arthropod genus for which DNA polymorphism data are presently abundant. As a result of the recent release of the complete genome sequence and a wide variety of new genomic resources, the Daphnia system is quickly becoming a promising new avenue for expanding our knowledge of nucleotide variation in natural populations. Here, we examine nucleotide variation in six protein-coding loci for Daphnia pulex and its congeners with particular emphasis on D. pulicaria, the closest extant relative of D. pulex. Levels of synonymous intraspecific variation, pi(s), averaged 0.0136 for species in the Daphnia genus, and are slightly lower than most prior estimates in invertebrates. Tests of neutrality indicated that segregating variation conforms to neutral model expectations for the loci that we examined in most species, while K(a)/K(s) ratios revealed strong purifying selection. Using a full maximum-likelihood coalescent-based method, the ratio of the recombination rate to the mutation rate (c/u), averaged 0.5255 for species of the Daphnia genus. Lastly, a divergence population-genetics approach was used to investigate gene flow and divergence between D. pulex and D. pulicaria.

Nucleotide polymorphism and within-gene recombination in Daphnia magna and D. pulex, two cyclical parthenogens

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.

Evolution of the Caenorhabditis elegans genome

A fundamental problem in genome biology is to elucidate the evolutionary forces responsible for generating nonrandom patterns of genome organization. As the first metazoan to benefit from full-genome sequencing, Caenorhabditis elegans has been at the forefront of research in this area. Studies of genomic patterns, and their evolutionary underpinnings, continue to be augmented by the recent push to obtain additional full-genome sequences of related Caenorhabditis taxa. In the near future, we expect to see major advances with the onset of whole-genome resequencing of multiple wild individuals of the same species. In this review, we synthesize many of the important insights to date in our understanding of genome organization and function that derive from the evolutionary principles made explicit by theoretical population genetics and molecular evolution and highlight fertile areas for future research on unanswered questions in C. elegans genome evolution. We call attention to the need for C. elegans researchers to generate and critically assess nonadaptive hypotheses for genomic and developmental patterns, in addition to adaptive scenarios. We also emphasize the potential importance of evolution in the gonochoristic (female and male) ancestors of the androdioecious (hermaphrodite and male) C. elegans as the source for many of its genomic and developmental patterns.

Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes

A genome-wide comparison of transposable elements reveals evidence for unexpectedly high rates of horizontal transfer between three species of Drosophila

Background

Horizontal transfer (HT) could play an important role in the long-term persistence of transposable elements (TEs) because it provides them with the possibility to avoid the checking effects of host-silencing mechanisms and natural selection, which would eventually drive their elimination from the genome. However, despite the increasing evidence for HT of TEs, its rate of occurrence among the TE pools of model eukaryotic organisms is still unknown.

Results

We have extracted and compared the nucleotide sequences of all potentially functional autonomous TEs present in the genomes of Drosophila melanogaster, D. simulans and D. yakuba - 1,436 insertions classified into 141 distinct families - and show that a large fraction of the families found in two or more species display levels of genetic divergence and within-species diversity that are significantly lower than expected by assuming copy-number equilibrium and vertical transmission, and consistent with a recent origin by HT. Long terminal repeat (LTR) retrotransposons form nearly 90% of the HT cases detected. HT footprints are also frequent among DNA transposons (40% of families compared) but rare among non-LTR retroelements (6%). Our results suggest a genomic rate of 0.04 HT events per family per million years between the three species studied, as well as significant variation between major classes of elements.

Conclusions

The genome-wide patterns of sequence diversity of the active autonomous TEs in the genomes of D. melanogaster, D. simulans and D. yakuba suggest that one-third of the TE families originated by recent HT between these species. This result emphasizes the important role of horizontal transmission in the natural history of Drosophila TEs.