The mutation process ultimately defines the genetic features of all populations and, hence, has a bearing on a wide range of issues involving evolutionary genetics, inheritance, and genetic disorders, including the predisposition to cancer. Nevertheless, formidable technical barriers have constrained our understanding of the rate at which mutations arise and the molecular spectrum of their effects. Here, we report on the use of complete-genome sequencing in the characterization of spontaneously arising mutations in the yeast Saccharomyces cerevisiae. Our results confirm some findings previously obtained by indirect methods but also yield numerous unexpected findings, in particular a very high rate of point mutation and skewed distribution of base-substitution types in the mitochondrion, a very high rate of segmental duplication and deletion in the nuclear genome, and substantial deviations in the mutational profile among various model organisms.chromosomal instability ͉ mitochondrion ͉ mutation rate ͉ mutational spectrum ͉ Saccharomyces cerevisiae D espite its relevance to every aspect of genetics and evolution, our understanding of the mutation process and its bearing on organismal fitness remains quite limited (1-4). Owing to the technical difficulties in directly observing very low-frequency events, most estimates of the per-nucleotide mutation rate are derived either from surveys of visible mutations at reporter loci (to enhance the detectability of mutations) or from nucleotide-sequence comparisons of silent sites in distantly related species (to magnify the accumulation of mutations). Neither approach is without problems, the first requiring assumptions about the fraction of mutations with observable phenotypic effects and the second relying on assumptions about interspecific divergence times, generation lengths, and neutrality of the monitored nucleotide sites.Long-term mutation-accumulation (MA) experiments, whereby replicate lines are taken through regular bottlenecks to minimize the efficiency of selection, have proven to be highly valuable resources for procuring spontaneous mutations in an essentially unbiased fashion (5-8). However, brute-force sequencing of PCR-amplified products constrains the number of mutations that can be detected in a reasonable amount of time. Here, we demonstrate the feasibility of whole-genome sequencing as a means to assay the complete spectrum of mutational effects in a moderately sized eukaryotic genome.Our analyses are based on an examination of parallel MA lines of a key model system, the yeast Saccharomyces cerevisiae. The initially isogenic lines were passed through 200 single-cell bottlenecks on a 3-to 4-day cycle of clonal growth for a total of Ϸ4,800 cell divisions per line [see supporting information (SI) Text]. Although there is some opportunity for the selective elimination of deleterious mutations during daily clonal amplification, this effect is quite small under the imposed bottlenecking procedure. For mutations with a relative selective disadvantage of s ϭ ...

Speciation involves the origin of trait differences that limit or prevent gene exchange and ultimately results in daughter populations that form monophyletic or exclusive genetic groups. However, for recently diverged populations or species between which reproductive isolation is often incomplete, gene genealogies will be discordant, and most regions of the genome will display nonexclusive genealogical patterns. In these situations, genome regions for which one or both species are exclusive groups may mark the footprint of recent selective sweeps. Alternatively, such regions may include or be closely linked to ''speciation genes,'' genes involved in reproductive isolation. Therefore, comparisons of gene genealogies allow inferences about the genetic architectures of both reproductive isolation and adaptation. Contrasting genealogical relationships in sexually isolated pheromone strains of the European corn borer moth (Ostrinia nubilalis) demonstrate the relevance of this approach. Genealogies for five gene regions are discordant, and only one molecular marker, the sex-linked gene Tpi, has evidence for pheromone strain exclusivity. Tpi maps to a position on the sex chromosome that is indistinguishable from a major factor (Pdd) affecting differences in postdiapause development time. The major factor (Resp) determining male behavioral response to pheromone is also sex-linked, but maps 20 -30 cM away. Exclusivity at Tpi may be a consequence of these linkage relationships because evidence from phenotypic variation in natural populations implicates both Pdd and Resp as candidates for genes involved in recent sweeps and͞or reproductive isolation between strains.genealogy ͉ genetic linkage map ͉ introgression ͉ selective sweep ͉ speciation

Of 12 potential reproductive isolating barriers between closely related Z-and E-pheromone strains of the

The E and Z pheromone strains of the European corn borer (ECB) provide an exceptional model system for examining the genetic basis of sexual isolation. Differences at two major genes account for variation in female pheromone production and male behavioral response, components of the pheromone communication system known to be important for mate recognition and mate choice. Strains of ECB are morphologically indistinguishable, and surveys of allozyme and DNA sequence variation have revealed significant allele frequency differences at only a single sex-linked locus, Tpi. Here we present a detailed genetic linkage map of ECB using AFLP and microsatellite markers and map the factors responsible for pheromone production (Pher) and male response (Resp). Our map covers 1697 cM and identifies all 31 linkage groups in ECB. Both Resp and Tpi map to the Z (sex) chromosome, but the distance between these markers (Ͼ20 cM) argues against the hypothesis that patterns of variation at Tpi are explained by tight linkage to this "speciation gene." However, we show, through analysis of marker density, that Tpi is located in a region of low recombination and suggest that a second Z-linked reproductive barrier could be responsible for the origin and/or persistence of differentiation at Tpi.

Thomas Hunt Morgan and colleagues identified variation in gene copy number in Drosophila in the 1920s and 1930s and linked such variation to phenotypic differences [Bridges CB (1936) Science 83:210]. Yet the extent of variation in the number of chromosomes, chromosomal regions, or gene copies, and the importance of this variation within species, remain poorly understood. Here, we focus on copy-number variation in Drosophila melanogaster. We characterize copy-number polymorphism (CNP) across genomic regions, and we contrast patterns to infer the evolutionary processes acting on this variation. Copy-number variation in D. melanogaster is nonrandomly distributed, presumably because of a mutational bias produced by tandem repeats or other mechanisms. Comparisons of coding and noncoding CNPs, however, reveal a strong effect of purifying selection in the removal of structural variation from functionally constrained regions. Most patterns of CNP in D. melanogaster suggest that negative selection and mutational biases are the primary agents responsible for shaping structural variation.centrality ͉ copy-number variation ͉ deletion ͉ duplication ͉ gene expression C opy-number polymorphism (CNP) has a dramatic impact on phenotypic variation within species. In humans, copyvariable regions account for Ͼ15% of the total detected genetic variation in gene expression (1), and some genes contributing to disease are contained within known duplication and deletion polymorphisms (2). In addition to its role in generating trait variation within species, CNP represents the raw material for gene family expansion and gene duplication between species. This raw material has apparently had a major role in evolution because 30-65% of genes in sequenced eukaryotes have been duplicated (3). On a larger scale, differences in the number, orientation, and distribution of chromosome segments are the most distinguishing features characterizing divergence in genome architecture between species. As in the case of gene duplication, the population genetic processes regulating CNP (and other variation) within species drive these exceptional differences in genome architecture (4).Although there is ample incentive to uncover the properties and dynamics of CNP, other than in humans little is known about copy-number variation in natural populations. Open questions remain about how much CNP exists in species' genomes. The observation that two unrelated healthy individuals can differ from one another in copy number across their genome raises uncertainty about the existence of an archetypal number of copies for any particular gene. Related to issues of the extent of CNP are differences in the type of CNP that can be found. Namely, the frequency, degree of dominance, and size of CNPs are largely unknown, as are differences between duplication and deletion polymorphisms. Equally important are the locations, chromosomal properties, and DNA sequence composition of CNPs. Finally, of all of the major issues surrounding CNPs, our knowledge of the evolutionary impli...

Many temperate insects take advantage of longer growing seasons at lower latitudes by increasing their generation number or voltinism. In some insects, development time abruptly decreases when additional generations are fit into the season. Consequently, latitudinal 'sawtooth' clines associated with shifts in voltinism are seen for phenotypes correlated with development time, like body size. However, latitudinal variation in voltinism has not been linked to genetic variation at specific loci. Here, we show a pattern in allele frequency among voltinism ecotypes of the European corn borer moth (Ostrinia nubilalis) that is reminiscent of a sawtooth cline. We characterized 145 autosomal and sex-linked SNPs and found that period, a circadian gene that is genetically linked to a major QTL determining variation in post-diapause development time, shows cyclical variation between voltinism ecotypes. Allele frequencies at an unlinked circadian clock gene cryptochrome1 were correlated with period. These results suggest that selection on development time to 'fit' complete life cycles into a latitudinally varying growing season produces oscillations in alleles associated with voltinism, primarily through changes at loci underlying the duration of transitions between diapause and other life history phases. Correlations among clock loci suggest possible coupling between the circadian clock and the circannual rhythms for synchronizing seasonal life history. We anticipate that latitudinal oscillations in allele frequency will represent signatures of adaptation to seasonal environments in other insects and may be critical to understanding the ecological and evolutionary consequences of variable environments, including response to global climate change.

Short-read sequencing techniques provide the opportunity to capture genome-wide sequence data in a single experiment. A current challenge is to identify questions that shallow-depth genomic data can address successfully and to develop corresponding analytical methods that are statistically sound. Here, we apply the Roche/454 platform to survey natural variation in strains of Drosophila melanogaster from an African (n = 3) and a North American (n = 6) population. Reads were aligned to the reference D. melanogaster genomic assembly, single nucleotide polymorphisms were identified, and nucleotide variation was quantified genome wide. Simulations and empirical results suggest that nucleotide diversity can be accurately estimated from sparse data with as little as 0.2× coverage per line. The unbiased genomic sampling provided by random short-read sequencing also allows insight into distributions of transposable elements and copy number polymorphisms found within populations and demonstrates that short-read sequencing methods provide an efficient means to quantify variation in genome organization and content. Continued development of methods for statistical inference of shallow-depth genome-wide sequencing data will allow such sparse, partial data sets to become the norm in the emerging field of population genomics.

Host plant use and availability were determined in early nymphal and adult-stage Schistocerca emarginata (=lineata) (Orthoptera: Acrididae) populations at six localities in Texas, USA. Early instar nymphal populations were feeding almost exclusively on either Ptelea trifoliata (Rutaceae) or Rubus trivialis (Rosaceae). This study represents the first demonstration of a geographic structure of host plant specificity in a polyphagous grasshopper. Recognizing this geographic structure required investigations of both developmental and geographical variation in host plant use. Nymphal diet breadths were significantly less than adult diet breadths at four of six localities and smaller overall when pooled nymphal and adult diet breadths were compared among sites. Neither restricted nymphal mobility nor host plant availability accounted for the observed differences in host plant use between developmental stages and among localities. Evidence suggests that the differences in host use among populations are due to host-plant-associated genetic differentiation.