As one of the few cellular traits that can be quantified across the tree of life, DNA-replication fidelity provides an excellent platform for understanding fundamental evolutionary processes. Furthermore, because mutation is the ultimate source of all genetic variation, clarifying why mutation rates vary is crucial for understanding all areas of biology. A potentially revealing hypothesis for mutation-rate evolution is that natural selection primarily operates to improve replication fidelity, with the ultimate limits to what can be achieved set by the power of random genetic drift. This drift-barrier hypothesis is consistent with comparative measures of mutation rates, provides a simple explanation for the existence of error-prone polymerases and yields a formal counter-argument to the view that selection fine-tunes gene-specific mutation rates.

Mutation dictates the tempo and mode of evolution, and like all traits, the mutation rate is subject to evolutionary modification. Here, we report refined estimates of the mutation rate for a prokaryote with an exceptionally small genome and for a unicellular eukaryote with a large genome. Combined with prior results, these estimates provide the basis for a potentially unifying explanation for the wide range in mutation rates that exists among organisms. Natural selection appears to reduce the mutation rate of a species to a level that scales negatively with both the effective population size (N e ), which imposes a drift barrier to the evolution of molecular refinements, and the genomic content of coding DNA, which is proportional to the target size for deleterious mutations. As a consequence of an expansion in genome size, some microbial eukaryotes with large N e appear to have evolved mutation rates that are lower than those known to occur in prokaryotes, but multicellular eukaryotes have experienced elevations in the genome-wide deleterious mutation rate because of substantial reductions in N e .random genetic drift | replication fidelity M utation is the ultimate source of variation for all evolutionary processes, but like all other traits, the mutation rate itself is subject to evolutionary modification. Unfortunately, because the fidelity of DNA replication and repair is typically very high, mutation-rate estimation is a laborious process, and few comprehensive studies have been performed. However, three phylogenetically general patterns have been suggested. First, for nearly every taxon for which mutations have been cataloged, there is an elevated rate of mutation from G/C to A/T bases relative to the opposite direction (1-3), the only exceptions being derived from indirect polymorphism studies in a few high-GC prokaryotes (3). Second, there is a strong relationship between the mutation rate per nucleotide site per generation (u) and total genome size (4), although the direction of scaling differs dramatically between microbes and multicellular eukaryotes. Third, there appears to be an overall deletion bias in prokaryotes (5, 6), but an overall insertion bias in most eukaryotes because of a predominance of mobile-element activity (7).Summarizing all studies up to 1990, Drake (8) concluded that u varies inversely with genome size (G) in microbes, such that the total genome-wide mutation rate (the product uG) is an approximate constant 0.003 across taxa. This pattern was derived from data on just three microbes (the bacterium Escherichia coli, the budding yeast Saccharomyces cerevisiae, and the filamentous fungus Neurospora crassa) and three bacteriophage. Subsequent observations continue to uphold the inverse relationship postulated by "Drake's rule" for prokaryotes and DNA viruses, but because of the narrow range of prokaryotic genome sizes, the significance remains borderline unless bacteriophage are included (4).In contrast, when such an analysis is restricted to eukaryotes (ranging from yeast to inver...

Despite much theoretical work, the molecular-genetic causes and evolutionary consequences of asexuality remain largely undetermined. Asexual animal species are rare, evolutionarily short-lived, and thought to suffer mutational meltdown as a result of lack of recombination. Whole-genome analysis of 11 sexual and 11 asexual genotypes of Daphnia pulex indicates that current asexual lineages are in fact very young, exhibit no signs of purifying selection against accumulating mutations, and have extremely high rates of gene conversion and deletion. The reconstruction of chromosomal haplotypes in regions containing SNP markers associated with asexuality (chromosomes VIII and IX) indicates that introgression from a sister species, Daphnia pulicaria, underlies the origin of the asexual phenotype. Silent-site divergence of the shared chromosomal haplotypes of asexuals indicates that the spread of asexuality is as recent as 1,250 y, although the origin of the meiosissuppressing element or elements could be substantially older. In addition, using previous estimates of the gene conversion rate from Daphnia mutation accumulation lines, we are able to age each asexual lineage. Although asexual lineages originate from wide crosses that introduce elevated individual heterozygosities on clone foundation, they also appear to be constrained by the inbreeding-like effect of loss of heterozygosity that accrues as gene conversion and hemizygous deletion expose preexisting recessive deleterious alleles of asexuals, limiting their evolutionary longevity. Our study implies that the buildup of newly introduced deleterious mutations (i.e., Muller's ratchet) may not be the dominant force imperiling nonrecombining populations of D. pulex, as previously proposed.evolution of sex | parthenogenesis O bligately asexual lineages are thought to suffer from elevated deleterious mutation accumulation resulting from permanent linkage at selected sites, which reduces the efficiency of selection against newly arising deleterious alleles (1-5). However, although substantial theory suggests that the diminished ability to purge new deleterious mutations will constrain the longevity of asexual populations (6-8), little is known about the genetic mechanisms responsible for a shift in reproductive mode, the consequences of asexuality for genome evolution, or the fate of asexual lineages in nature. To examine the evolution of asexual genomes, we carried out a population-genomic analysis of an asexual animal, one made interpretable by the inclusion of a parallel set of related sexual genotypes.Although most lineages of the microcrustacean Daphnia pulex are cyclically parthenogenetic, alternating between sexual and asexual phases, obligately asexual lineages have arisen polyphyletically across North America (9-11). The spread of obligate asexuality results from the proliferation of sex-limited, meiosissuppressing genetic elements via males produced by asexual females (11). Unlike their female clone mates, these males are often capable of haploid gamete product...

Despite the general assumption that site-specific mutation rates are independent of the local sequence context, a growing body of evidence suggests otherwise. To further examine context-dependent patterns of mutation, we amassed 5,645 spontaneous mutations in wild- type (WT) and mismatch-repair deficient (MMR(-)) mutation-accumulation (MA) lines of the gram-positive model organism Bacillus subtilis. We then analyzed>7,500 spontaneous base-substitution mutations across B. subtilis, Escherichia coli, and Mesoplasma florum WT and MMR(-) MA lines, finding a context-dependent mutation pattern that is asymmetric around the origin of replication. Different neighboring nucleotides can alter site-specific mutation rates by as much as 75-fold, with sites neighboring G:C base pairs or dimers involving alternating pyrimidine-purine and purine-pyrimidine nucleotides having significantly elevated mutation rates. The influence of context-dependent mutation on genome architecture is strongest in M. florum, consistent with the reduced efficiency of selection in organisms with low effective population size. If not properly accounted for, the disparities arising from patterns of context-dependent mutation can significantly influence interpretations of positive and purifying selection.

Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with .90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino acid sequence identity of 98.8 and .60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with 7000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we observe more proliferation of transposable elements (TEs) and a higher frequency of gained introns in the TCO genome. KEYWORDSgenome annotation effective population size gene number intron mobile elementsThe ultimate goal of comparative genomics is to form a synthesis integrating the fundamental evolutionary forces explaining the variation of genomic architecture across a wide range of phylogenetic lineages. The reduced effective population size (N e ) of eukaryotic species relative to prokaryotic species is hypothesized to be centrally involved in the emergence and distribution of numerous genomic features unique to eukaryotes, and the associated principles should naturally extend to variation among lineages of closely related species (Lynch 2007). However, until recently, it has been difficult to study the impact of reduced N e on the evolution of genomic architecture because of the lack of genomic data from closely related species or populations with disparate population sizes. Moreover, a lack of parallel understanding of other fundamental microevolutionary parameters such as mutation and recombination rates complicates efforts to single out the role of N e (and the associated power of random genetic drift) on genome evolution.Here, we focus on the comparative genomics of two cyclically parthenogenetic Daphnia pulex clones (PA42 and TCO), which come from populations differing substantially in historical N e . The D. pulex species complex consists of a vast array of populations inhabiting hundreds of thousands of ponds and lakes, throughout the northern temperate zone, most of which (including PA42 and TCO) reproduce by repeated generations of clonal reproduction via unfertilized eggs, punctuated by a phase of sexual reproduction. PA42 was sampled from a woodland vernal pond within Portland Arch Nature Preserve, IN, whereas TCO was derived from a permanent pond in the Siuslaw National Forest, near the Pacific coast in OR. A complex geological history in western OR contributes to the presence of divergent lineages of multiple zooplan...