Antagonistic pleiotropy and mutation accumulation contribute to age‐related decline in stress response

As organisms age, the effectiveness of natural selection weakens, leading to age‐related decline in fitness‐related traits. The evolution of age‐related changes associated with senescence is likely influenced by mutation accumulation (MA) and antagonistic pleiotropy (AP). MA predicts that age‐related decline in fitness components is driven by age‐specific sets of alleles, nonnegative genetic correlations within trait across age, and an increase in the coefficient of genetic variance. AP predicts that age‐related decline in a trait is driven by alleles with positive effects on fitness in young individuals and negative effects in old individuals, and is expected to lead to negative genetic correlations within traits across age. We build on these predictions using an association mapping approach to investigate the change in additive effects of SNPs across age and among traits for multiple stress‐response fitness‐related traits, including cold stress with and without acclimation and starvation resistance. We found support for both MA and AP theories of aging in the age‐related decline in stress tolerance. Our study demonstrates that the evolution of age‐related decline in stress tolerance is driven by a combination of alleles that have age‐specific additive effects, consistent with MA, as well as nonindependent and antagonistic genetic architectures characteristic of AP.     

Rate of deleterious mutation and the distribution of its effects on fitness in vesicular stomatitis virus

Despite their importance, the parameters describing the spontaneous deleterious mutation process have not been well described in many organisms. If mutations are important for the evolution of every living organism, their importance becomes critical in the case of RNA-based viruses, in which the frequency of mutation is orders of magnitude larger than in DNA-based organisms. The present work reports minimum estimates of the deleterious mutation rate, as well as the characterization of the distribution of deleterious mutational effects on the total fitness of the vesicular stomatitis virus (VSV). The estimates are based on mutation-accumulation experiments in which selection against deleterious mutations was minimized by recurrently imposing genetic bottlenecks of size one. The estimated deleterious mutation rate was 1.2 mutations per genome and generation, with a mean fitness effect of –0.39% per generation. At the end of the mutation-accumulation experiment, the average reduction in fitness was 38% and the distribution of accumulated deleterious effects was, on average, left-skewed. The magnitude of the skewness depends on the initial fitness of the clone analysed. The implications of our findings for the evolutionary biology of RNA viruses are discussed.     

Heterosis in age‐specific selected populations of a seed beetle: Sex differences in longevity and reproductive behavior

We tested mutation accumulation hypothesis for the evolution of senescence using short‐lived and long‐lived populations of the seed‐feeding beetle, Acanthoscelides obtectus (Say), obtained by selection on early‐ and late‐life for many generations. The expected consequence of the mutation accumulation hypothesis is that in short‐lived populations, where the force of natural selection is the strongest early in life, the late‐life fitness traits should decline due to genetic drift which increases the frequency of mutations with deleterious effects in later adult stages. Since it is unlikely that identical deleterious mutations will increase in several independent populations, hybrid vigor for late‐life fitness is expected in offspring obtained in crosses among populations selected for early‐life fitness traits. We tested longevity of both sexes, female fecundity and male reproductive behavior for hybrid vigor by comparing hybrid and nonhybrid short‐lived populations. Hybrid vigor was confirmed for male virility, mating speed and copulation duration, and longevity of both sexes at late ages. In contrast to males, the results on female fecundity in short‐lived populations did not support mutation accumulation as a genetic mechanism for the evolution of this trait. Contrary to the prediction of this hypothesis, male mating ability indices and female fecundity in long‐lived populations exhibited hybrid vigor at all assayed age classes. We demonstrate that nonhybrid long‐lived populations diverged randomly regarding female and male reproductive fitness, indicating that sexually antagonistic selection, when accompanied with genetic drift for female fecundity and male virility, might be responsible for overriding natural selection in the independently evolving long‐lived populations.     

Ecological genomics—changing perspectives on Darwin’s basic concerns

Ecological Genomics is an interdisciplinary field that seeks to understand the genetic and physiological basis of species interactions for evolutionary inferences. At the 7th annual Ecological Genomics Symposium, November 13–15, 2009, members of the Ecological Genomics program at Kansas State University invited 13 speakers and 56 poster presentations.     

Drift load in populations of small size and low density

According to theory, drift load in randomly mating populations is determined by past population size, because enhanced genetic drift in small populations causes accumulation and fixation of recessive deleterious mutations of small effect. In contrast, segregating load due to mutations of low frequency should decline in smaller populations, at least when mutations are highly recessive and strongly deleterious. Strong local selection generally reduces both types of load. We tested these predictions in 13 isolated, outcrossing populations of Arabidopsis lyrata that varied in population size and plant density. Long-term size was estimated by expected heterozygosity at 20 microsatellite loci. Segregating load was assessed by comparing performance of offspring from selfings versus within-population crosses. Drift load was the heterosis effect created by interpopulation outbreeding. Results showed that segregating load was unrelated to long-term size. However, drift load was significantly higher in populations of small effective size and low density. Drift load was mostly expressed late in development, but started as early as germination and accumulated thereafter. The study largely confirms predictions of theory and illustrates that mutation accumulation can be a threat to natural populations.     

Fitness change in relation to mutation number in spontaneous mutation accumulation lines of Chlamydomonas reinhardtii

Although all genetic variation ultimately stems from mutations, their properties are difficult to study directly. Here, we used multiple mutation accumulation (MA) lines derived from five genetic backgrounds of the green algae Chlamydomonas reinhardtii that have been previously subjected to whole genome sequencing to investigate the relationship between the number of spontaneous mutations and change in fitness from a nonevolved ancestor. MA lines were on average less fit than their ancestors and we detected a significantly negative correlation between the change in fitness and the total number of accumulated mutations in the genome. Likewise, the number of mutations located within coding regions significantly and negatively impacted MA line fitness. We used the fitness data to parameterize a maximum likelihood model to estimate discrete categories of mutational effects, and found that models containing one to two mutational effect categories (one neutral and one deleterious category) fitted the data best. However, the best‐fitting mutational effects models were highly dependent on the genetic background of the ancestral strain.     

Evolution of late-life mortality in Drosophila melanogaster

Abstract.— Aging appears to cease at late ages, when mortality rates roughly plateau in large-scale demographic studies. This anomalous plateau in late-life mortality has been explained theoretically in two ways: (1) as a strictly demographic result of heterogeneity in life-long robustness between individuals within cohorts, and (2) as an evolutionary result of the plateau in the force of natural selection after the end of reproduction. Here we test the latter theory using cohorts of Drosophila melanogaster cultured with different ages of reproduction for many generations. We show in two independent comparisons that populations that evolve with early truncation of reproduction exhibit earlier onset of mortality-rate plateaus, in conformity with evolutionary theory. In addition, we test two population genetic mechanisms that may be involved in the evolution of late-life mortality: mutation accumulation and antagonistic pleiotropy. We test mutation accumulation by crossing genetically divergent, yet demographically identical, populations, testing for hybrid vigor between the hybrid and nonhybrid parental populations. We found no difference between the hybrid and nonhybrid populations in late-life mortality rates, a result that does not support mutation accumulation as a genetic mechanism for late-life mortality, assuming mutations act recessively. Finally, we test antagonistic pleiotropy by returning replicate populations to a much earlier age of last reproduction for a short evolutionary time, testing for a rapid indirect response of late-life mortality rates. The positive results from this test support antagonistic pleiotropy as a genetic mechanism for the evolution of late-life mortality. Together these experiments comprise the first corroborations of the evolutionary theory of late-life mortality.     

Mitochondrial mutations and aging: random drift is insufficient to explain the accumulation of mitochondrial deletion mutants in short‐lived animals

Mitochondrial DNA deletions accumulate over the life course in post‐mitotic cells of many species and may contribute to aging. Often a single mutant expands clonally and finally replaces the wild‐type population of a whole cell. One proposal to explain the driving force behind this accumulation states that random drift alone, without any selection advantage, is sufficient to explain the clonal accumulation of a single mutant. Existing mathematical models show that such a process might indeed work for humans. However, to be a general explanation for the clonal accumulation of mtDNA mutants, it is important to know whether random drift could also explain the accumulation process in short‐lived species like rodents. To clarify this issue, we modelled this process mathematically and performed extensive computer simulations to study how different mutation rates affect accumulation time and the resulting degree of heteroplasmy. We show that random drift works for lifespans of around 100 years, but for short‐lived animals, the resulting degree of heteroplasmy is incompatible with experimental observations.     

The relative effects of mutation accumulation versus inbreeding depression on fitness in experimental populations of the housefly

Loss of fitness due to inbreeding depression in small captive populations of endangered species is widely appreciated. Populations of all sizes may also experience loss in fitness when environmental conditions are ameliorated because deleterious alleles may be rendered neutral and accumulate rapidly. Few data exist, however, to demonstrate loss in fitness due to relaxed selection. Loss of fitness in life‐history traits were compared between LARGE (N_e ≥ 500) and SMALL (N_e = 50) populations of the housefly Musca domestica L that were subjected to curtailed life span at 21 days to remove selection on late‐acting deleterious alleles. During the early part of the life history (≤21 days), the rate of decline in fecundity and progeny production over 24 generations was greater in the small (1.5%) than in the large populations <0.2%), but rate of loss in late‐life fecundity and progeny production (>21 days) was equivalent across populations, consistent with neutral theory, and amounted to 1.7% per generation. This rate of loss due to relaxed selection was equivalent to the rate of loss due to inbreeding in populations with an effective size of 50 individuals. Even if captive populations are kept large to avoid inbreeding, breeding them in benign environments where the forces of natural selection are curtailed may jeopardize the capability of these populations to exist in natural environments within few generations. Zoo Biol 20:145–156, 2001. © 2001 Wiley‐Liss, Inc.     

4个棉花ADF基因的分子鉴定及其差异表达

肌动蛋白解聚合因子(actin-depolymerizing factor, ADF)是一种在真核生物中广泛存在的低分子量的肌动蛋白结合蛋白,它在调控细胞内肌动蛋白纤丝的解聚合和再聚合中起着关键作用。我们在棉纤维cDNA文库中分离克隆了4个ADF基因(cDNAs),分别命名为GhADF2,GhADF3,GhADF4,GhADF5。GhADF2 cDNA 长度为705 bp,编码139个氨基酸;GhADF3 cDNA长度为819 bp,编码139个氨基酸;GhADF4 cDNA长度为804 bp,编码143个氨基酸;GhADF5 cDNA长度为644 bp,编码141个氨基酸。分析表明,GhADF2与GhADF3的氨基酸序列同源性为99%。而且,GhADF2/3与矮牵牛PeADF2之间的氨基酸序列同源性也高达89%。GhADF4与拟南芥AtADF6的亲缘关系较近,二者的氨基酸序列同源性为78%。GhADF5与拟南芥AtADF5的亲缘关系较近,氨基酸序列的同源性为83%。上述结果表明植物ADF基因在进化中具有高度保守性。RT-PCR分析表明,GhADF2在纤维中优势表达,而GhADF5基因则在子叶中表达量最高。另一方面,GhADF3和GhADF4似乎不具有组织特异性或偏爱性表达。同一组织中不同GhADF基因表达量有较大的差异,表明它们可能涉及棉花不同组织生长发育过程的调节。而且,在进化过程中,各ADF同分异构体之间可能发展形成某种功能上的差异性。     

Shared signatures of social stress and aging in peripheral blood mononuclear cell gene expression profiles

Chronic social stress is a predictor of both aging‐related disease and mortality risk. Hence, chronic stress has been hypothesized to directly exacerbate the process of physiological aging. Here, we evaluated this hypothesis at the level of gene regulation. We compared two data sets of genome‐wide gene expression levels in peripheral blood mononuclear cells (PBMCs): one that captured aging effects and another that focused on chronic social stress. Overall, we found that the direction, although not necessarily the magnitude, of significant gene expression changes tends to be shared between the two data sets. This overlap was observable at three levels: (i) individual genes; (ii) general functional categories of genes; and (iii) molecular pathways implicated in aging. However, we also found evidence that heterogeneity in PBMC composition limits the power to detect more extensive similarities, suggesting that our findings reflect an underestimate of the degree to which age and social stress influence gene regulation in parallel. Cell type‐specific data on gene regulation will be important to overcome this limitation in the future studies.     

Resilience to aging in the regeneration‐capable flatworm Macrostomum lignano

Animals show a large variability of lifespan, ranging from short‐lived as Caenorhabditis elegans to immortal as Hydra. A fascinating case is flatworms, in which reversal of aging by regeneration is proposed, yet conclusive evidence for this rejuvenation‐by‐regeneration hypothesis is lacking. We tested this hypothesis by inducing regeneration in the sexual free‐living flatworm Macrostomum lignano. We studied survival, fertility, morphology, and gene expression as a function of age. Here, we report that after regeneration, genes expressed in the germline are upregulated at all ages, but no signs of rejuvenation are observed. Instead, the animal appears to be substantially longer lived than previously appreciated, and genes expressed in stem cells are upregulated with age, while germline genes are downregulated. Remarkably, several genes with known beneficial effects on lifespan when overexpressed in mice and C. elegans are naturally upregulated with age in M. lignano, suggesting that molecular mechanism for offsetting negative consequences of aging has evolved in this animal. We therefore propose that M. lignano represents a novel powerful model for molecular studies of aging attenuation, and the identified aging gene expression patterns provide a valuable resource for further exploration of anti‐aging strategies.     

A dual role of the Wnt signaling pathway during aging in Caenorhabditis elegans

Wnt signaling is a major and highly conserved developmental pathway that guides many important events during embryonic and larval development. In adulthood, misregulation of Wnt signaling has been implicated in tumorigenesis and various age‐related diseases. These effects occur through highly complicated cell‐to‐cell interactions mediated by multiple Wnt‐secreted proteins. While they share a high degree of sequence similarity, their function is highly diversified. Although the role of Wnt ligands during development is well studied, very little is known about the possible actions of Wnt signaling in natural aging. In this study, Caenorhabditis elegans serves, for the first time, as a model system to determine the role of Wnt ligands in aging. Caenorhabditis elegans has five Wnt proteins, mom‐2, egl‐20, lin‐44, cwn‐1, and cwn‐2. We show that all five Wnt ligands are expressed and active past the development stages. The ligand mom‐2/Wnt plays a major detrimental role in longevity, whereas the function of lin‐44/Wnt is beneficial for long life. Interestingly, no evidence was found for Wnt signaling being involved in cellular or oxidative stress responses during aging. Our results suggest that Wnt signaling regulates aging‐intrinsic genetic pathways, opening a new research direction on the role of Wnt signaling in aging and age‐related diseases.     

Molecular evolution and population genetics of duplicated accessory gland protein genes in Drosophila

To investigate the potential importance of gene duplication in D. melanogaster accessory gland protein (Acp) gene evolution we carried out a computational analysis comparing annotated D. melanogaster Acp genes to the entire D. melanogaster genome. We found that two known Acp genes are actually members of small multigene families. Polymorphism and divergence data from these duplicated genes suggest that in at least four cases, protein divergence between D. melanogaster and D. simulans is a result of directional selection. One putative Acp revealed by our computational analysis shows evidence of a recent selective sweep in a non-African population (but not in an African population). These data support the idea that selection on reproduction-related genes may drive divergence of populations within species, and strengthen the conclusion that Acps may often be under directional selection in Drosophila.     

The costs of breed reconstruction from cryopreserved material in mammalian livestock species

The aim of this work was to compare costs, in the horse, cattle, sheep, swine, and rabbit species, for the creation of gene banks for reconstruction of an extinct breed, using different strategies: embryos-only, embryos in combination with semen, and semen-only. Three cost measures were used: time required for population reconstruction, cost for creation of the gene bank, number of years-keeping-female to reach reconstruction. Semen costs were estimated across four scenarios: the presence or absence of a commercial market for semen, purchase of semen donors, and semen extracted from the epididymus. The number of cells were doubled to take into account the creation of two storage sites. The strategy embryos-only required the shortest time to reach reconstruction. With the strategy embryos + semen, time increased with decreasing proportions of embryos. With semen-only, reconstruction time varied from 2 to 21 years. A high variation of costs was observed across species and strategies, from 360 Euros in the rabbit to 1 092 300 in the horse. In all species, the embryos-only strategy was about 10% more expensive than using 90% embryos + semen. Decreasing the percentage of embryos further diminished costs. The number of years-keeping-female ranged across strategies, from 2 in the rabbit, to a maximum of 12 878 in the horse.     

A novel gene mutation that confers abnormal patterns of beta-carotene accumulation in cauliflower (Brassica oleracea var. botrytis)

The Or gene of cauliflower (Brassica oleracea var. botrytis) causes many tissues of the plant to accumulate carotenoids and turn orange, which is suggestive of a perturbation of the normal regulation of carotenogenesis. A series of experiments to explore the cellular basis of the carotenoid accumulation induced by the Or gene was completed. The Or gene causes obvious carotenoid accumulation in weakly or unpigmented tissues such as the curd, pith, leaf bases and shoot meristems, and cryptically in some cells of other organs, including the roots and developing fruits. The dominant carotenoid accumulated is beta-carotene, which can reach levels that are several hundred-fold higher than those in comparable wild-type tissues. The beta-carotene accumulates in plastids mainly as a component of massive, highly ordered sheets. The Or gene does not affect carotenoid composition of leaves, nor does it alter color and chromoplast appearance in flower petals. Interestingly, mRNA from carotenogenic and other isoprenoid biosynthetic genes upstream of the carotenoid pathway was detected both in orange tissues of the mutant, and in comparable unpigmented wild-type tissues. Thus the unpigmented wild-type tissues are likely to be competent to synthesize carotenoids, but this process is suppressed by an unidentified mechanism. Our results suggest that the Or gene may induce carotenoid accumulation by initiating the synthesis of a carotenoid deposition sink in the form of the large carotenoid-sequestering sheets.     

Ultraviolet radiation exposure accelerates the accumulation of the aging-dependent T414G mitochondrial DNA mutation in human skin

The accumulation of mitochondrial DNA (mtDNA) mutations has been proposed as an underlying cause of the aging process. Such mutations are thought to be generated principally through mechanisms involving oxidative stress. Skin is frequently exposed to a potent mutagen in the form of ultraviolet (UV) radiation and mtDNA deletion mutations have previously been shown to accumulate with photoaging. Here we report that the age-related T414G point mutation originally identified in skin fibroblasts from donors over 65 years also accumulates with age in skin tissue. Moreover, there is a significantly greater incidence of this mutation in skin from sun-exposed sites (chi(2)= 6.8, P < 0.01). Identification and quantification of the T414G mutation in dermal skin tissue from 108 donors ranging from 8 to 97 years demonstrated both increased occurrence with photoaging as well as an increase in the proportion of molecules affected. In addition, we have discovered frequent genetic linkage between a common photoaging-associated mtDNA deletion and the T414G mutation. This linkage indicates that mtDNA mutations such as these are unlikely to be distributed equally across the mtDNA population within the skin tissue, increasing their likelihood of exerting focal effects at the cellular level. Taken together, these data significantly contribute to our understanding of the DNA damaging effects of UV exposure and how resultant mutations may ultimately contribute towards premature aging.