Knowledge of the genome-wide rate and spectrum of mutations is necessary to understand the origin of disease and the genetic variation driving all evolutionary processes. Here, we provide a genome-wide analysis of the rate and spectrum of mutations obtained in two Daphnia pulex genotypes via separate mutation-accumulation (MA) experiments. Unlike most MA studies that utilize haploid, homozygous, or self-fertilizing lines, D. pulex can be propagated ameiotically while maintaining a naturally heterozygous, diploid genome, allowing the capture of the full spectrum of genomic changes that arise in a heterozygous state. While base-substitution mutation rates are similar to those in other multicellular eukaryotes (about 4 × 10 −9 per site per generation), we find that the rates of large-scale (>100 kb) de novo copy-number variants (CNVs) are significantly elevated relative to those seen in previous MA studies. The heterozygosity maintained in this experiment allowed for estimates of gene-conversion processes. While most of the conversion tract lengths we report are similar to those generated by meiotic processes, we also find larger tract lengths that are indicative of mitotic processes. Comparison of MA lines to natural isolates reveals that a majority of large-scale CNVs in natural populations are removed by purifying selection. The mutations observed here share similarities with disease-causing, complex, large-scale CNVs, thereby demonstrating that MA studies in D. pulex serve as a system for studying the processes leading to such alterations.

Despite the enormous theoretical attention given to the evolutionary consequences of sexual reproduction, the validity of the key assumptions on which the theory depends rarely has been evaluated. It is often argued that a reduced ability to purge deleterious mutations condemns asexual lineages to an early extinction. However, most well characterized asexual lineages fail to exhibit the high levels of neutral allelic divergence expected in the absence of recombination. With purely descriptive data, it is difficult to evaluate whether this pattern is a consequence of the rapid demise of asexual lineages, an unusual degree of mutational stability, or recombination. Here, we show in mutation-accumulation lines of asexual Daphnia that the rate of loss of nucleotide heterozygosity by ameiotic recombination is substantially greater than the rate of introduction of new variation by mutation. This suggests that the evolutionary potential of asexual diploid species is not only a matter of mutation accumulation and reduced efficiency of selection, but it underscores the limited utility of using neutral allelic divergence as an indicator of ancient asexuality.allelic divergence ͉ loss of heterozygosity ͉ mutation accumulation I t has long been assumed that the absence of meiosis reduces rates of homologous recombination to evolutionarily unimportant levels in asexual eukaryotes. The resultant reduction in the efficiency of natural selection is expected to magnify the rate of deleterious mutation accumulation and reduce the rate of fixation of adaptive mutations, condemning asexual species to an early extinction (1-4). Yet, despite this bleak theoretical forecast, some lineages, including the bdelloid rotifers (5), oribatid mites (6), and darwinulid ostracods (7,8), dispensed with sexual reproduction long ago, and the majority of animal phyla have some obligately asexual species (9).A substantial body of theory has been developed to account for the evolutionary persistence of asexual species (or lack thereof), but only a few large-scale empirical surveys have been undertaken to characterize the molecular genetic consequences of asexual reproduction (e.g., refs. 10 and 11). It has been suggested that the absence of meiosis in asexual lineages causes the two alleles at any given locus to become progressively more divergent given that within-individual recombination (gene conversion and/or crossing over) and chromosomal deletions occur at negligible levels (5, 12, 13). However, with the exception of the bdelloid rotifers, most closely studied asexual lineages fail to exhibit high levels of neutral allelic divergence (e.g., refs. 5 and 14-16). These observations call attention to other processes that might erode allelic divergence in real biological systems, such as recombination, unusually effective DNA repair, automixis, or clandestine sexual reproduction (e.g., refs. 12-16). Direct experimental observations on the genomic stability of asexual lineages are necessary to shed light on this issue.Although mitotic recombination h...

The evolutionary theory of senescence predicts that high extrinsic mortality in natural populations should select for accelerated reproductive investment and shortened life span. Here, we test the theory with natural populations of the Daphnia pulex-pulicaria species complex, a group of freshwater zooplankton that spans an environmental gradient of habitat permanence. We document substantial genetic variation in demographic life-history traits among parent and hybrid populations of this complex. Populations from temporary ponds have shorter life spans, earlier and faster increases of intrinsic mortality risk, and earlier and steeper declines in fecundity than populations from permanent lakes. We also examine the age-specific contribution to fitness, measured by reproductive value, and to expected lifetime reproduction; these traits decline faster in populations from temporary ponds. Despite having more rapid senescence, pond Daphnia exhibit faster juvenile growth and higher early fitness, measured as population growth rate (r). Among populations within this species complex we observed negative genetic correlations between r and indices of life-history timing, suggesting trade-offs between early- and late-life performance. Our results cannot be explained by a trade-off between survival and fecundity or by nonevolutionary theories of senescence. Instead, our data are consistent with the evolutionary theory of senescence because the genetic variation in life histories we observed is roughly congruent with the temporal scale of environmental change in the field.

Abstract. We know very little about aging (senescence) in natural populations, and even less about plant aging. Demographic aging is identified by an increasing rate of mortality following reproductive maturity. In natural populations, quantifying aging is often confounded because changes in mortality may be influenced by both short-and long-term environmental fluctuations as well as age-dependent changes in performance. Plants can be easily marked and monitored longitudinally in natural populations yet the age-dependent dynamics of mortality are not known. This study was designed to determine whether a plant species, Plantago lanceolata, shows demographic aging in its natural environment. A large, multiple-cohort design was used to separate age-independent and age-dependent processes. Seven years of results show environmental influences on mortality as evidenced by synchronous changes in mortality across four cohorts over time. Age-dependent mortality was found through an age-by-environment interaction when the oldest cohorts had significantly higher mortality relative to the younger cohorts during times of stress. Neither size nor quantity of reproduction could explain this variation in mortality across cohorts. These results demonstrate demographic senescence in a natural population of plants.