The evolution of low mutation rates in experimental mutator populations of Saccharomyces cerevisiae

Mutation is the source of both beneficial adaptive variation and deleterious genetic load, fueling the opposing selective forces than shape mutation rate evolution. This dichotomy is well illustrated by the evolution of the mutator phenotype, a genome-wide 10- to 100-fold increase in mutation rate. This phenotype has often been observed in clonally expanding populations exposed to novel or frequently changing conditions. Although studies of both experimental and natural populations have shed light on the evolutionary forces that lead to the spread of the mutator allele through a population, significant gaps in our understanding of mutator evolution remain. Here we use an experimental evolution approach to investigate the conditions required for the evolution of a reduction in mutation rate and the mechanisms by which populations tolerate the accumulation of deleterious mutations. We find that after ～6,700 generations, four out of eight experimental mutator lines had evolved a decreased mutation rate. We provide evidence that the accumulation of deleterious mutations leads to selection for reduced mutation rate clones in populations of mutators. Finally, we test the long-term consequences of the mutator phenotype, finding that mutator lines follow different evolutionary trajectories, some of which lead to drug resistance.     

Fitness evolution and the rise of mutator alleles in experimental Escherichia coli populations

We studied the evolution of high mutation rates and the evolution of fitness in three experimental populations of Escherichia coli adapting to a glucose-limited environment. We identified the mutations responsible for the high mutation rates and show that their rate of substitution in all three populations was too rapid to be accounted for simply by genetic drift. In two of the populations, large gains in fitness relative to the ancestor occurred as the mutator alleles rose to fixation, strongly supporting the conclusion that mutator alleles fixed by hitchhiking with beneficial mutations at other loci. In one population, no significant gain in fitness relative to the ancestor occurred in the population as a whole while the mutator allele rose to fixation, but a substantial and significant gain in fitness occurred in the mutator subpopulation as the mutator neared fixation. The spread of the mutator allele from rarity to fixation took >1000 generations in each population. We show that simultaneous adaptive gains in both the mutator and wild-type subpopulations (clonal interference) retarded the mutator fixation in at least one of the populations. We found little evidence that the evolution of high mutation rates accelerated adaptation in these populations.     

Molecular considerations in the evolution of bacterial genes

Summary Synonymous and nonsynonymous substitution rates at the loci encoding glyceraldehyde-3-phosphate dehydrogenase (gap) and outer membrane protein 3A (ompA) were examined in 12 species of enteric bacteria. By examining homologous sequences in species of varying degrees of relatedness and of known phylogenetic relationships, we analyzed the patterns of synonymous and nonsynonymous substitutions within and among these genes. Although both loci accumulate synonymous substitutions at reduced rates due to codon usage bias, portions of thegap andompA reading frames show significant deviation in synonymous substitution rates not attributable to local codon bias. A paucity of synonymous substitutions in portions of theompA gene may reflect selection for a novel mRNA secondary structure. In addition, these studies allow comparisons of homologous protein-coding sequences (gap) in plants, animals, and bacteria, revealing differences in evolutionary constraints on this glycolytic enzyme in these lineages.     

Dynamics of molecular evolution in RNA virus populations depend on sudden versus gradual environmental change

Understanding the dynamics of molecular adaptation is a fundamental goal of evolutionary biology. While adaptation to constant environments has been well characterized, the effects of environmental complexity remain seldom studied. One simple but understudied factor is the rate of environmental change. Here we used experimental evolution with RNA viruses to investigate whether evolutionary dynamics varied based on the rate of environmental turnover. We used whole‐genome next‐generation sequencing to characterize evolutionary dynamics in virus populations adapting to a sudden versus gradual shift onto a novel host cell type. In support of theoretical models, we found that when populations evolved in response to a sudden environmental change, mutations of large beneficial effect tended to fix early, followed by mutations of smaller beneficial effect; as predicted, this pattern broke down in response to a gradual environmental change. Early mutational steps were highly parallel across replicate populations in both treatments. The fixation of single mutations was less common than sweeps of associated “cohorts” of mutations, and this pattern intensified when the environment changed gradually. Additionally, clonal interference appeared stronger in response to a gradual change. Our results suggest that the rate of environmental change is an important determinant of evolutionary dynamics in asexual populations.     

Vertebrate immunity: mutator proteins and their evolution

M.E. Lobashev has brilliantly postulated in 1947 that error-prone repair contribute to mutations in cells. This was shown to be true once the mechanisms of UV mutagenesis in Escherichia coli were deciphered. Induced mutations are generated during error-prone SOS DNA repair with the involvement of inaccurate DNA polymerases belonging to the Y family. Currently, several distinct mutator enzymes participating in spontaneous and induced mutagenesis have been identified. Upon induction of these proteins, mutation rates increase by several orders of magnitude. These proteins regulate the mutation rates in evolution and in ontogeny during immune response. In jawed vertebrates, somatic hypermutagenesis occurs in the variable regions of immunoglobulin genes, leading to affinity maturation of antibodies. The process is initiated by cytidine deamination in DNA to uracil by AID (Activation-Induced Deaminase). Further repair of uracil-containing DNA through proteins that include the Y family DNA polymerases causes mutations, induce gene conversion, and class switch recombination. In jawless vertebrates, the variable lymphocyte receptors (VLR) serve as the primary molecules for adaptive immunity. Generation of mature VLRs most likely depends on agnathan AID-like deaminases. AID and its orthologs in lamprey (PmCDA1 and PMCDA2) belong to the AID/APOBEC family of RNA/DNA editing cytidine deaminases. This family includes enzymes with different functions: APOBEC1 edits RNA, APOBEC3 restricts retroviruses. The functions of APOBEC2 and APOBEC4 have not been yet determined. Here, we report a new member of the AID/APOBEC family, APOBEC5, in the bacterium Xanthomonas oryzae. The widespread presence of RNA/DNA editing deaminases suggests that they are an ancient means of generating genetic diversity.     

Climate change and evolution: disentangling environmental and genetic responses

Rapid climate change is likely to impose strong selection pressures on traits important for fitness, and therefore, microevolution in response to climate-mediated selection is potentially an important mechanism mitigating negative consequences of climate change. We reviewed the empirical evidence for recent microevolutionary responses to climate change in longitudinal studies emphasizing the following three perspectives emerging from the published data. First, although signatures of climate change are clearly visible in many ecological processes, similar examples of microevolutionary responses in literature are in fact very rare. Second, the quality of evidence for microevolutionary responses to climate change is far from satisfactory as the documented responses are often - if not typically - based on nongenetic data. We reinforce the view that it is as important to make the distinction between genetic (evolutionary) and phenotypic (includes a nongenetic, plastic component) responses clear, as it is to understand the relative roles of plasticity and genetics in adaptation to climate change. Third, in order to illustrate the difficulties and their potential ubiquity in detection of microevolution in response to natural selection, we reviewed the quantitative genetic studies on microevolutionary responses to natural selection in the context of long-term studies of vertebrates. The available evidence points to the overall conclusion that many responses perceived as adaptations to changing environmental conditions could be environmentally induced plastic responses rather than microevolutionary adaptations. Hence, clear-cut evidence indicating a significant role for evolutionary adaptation to ongoing climate warming is conspicuously scarce.     

Horizontal transfer of mercury resistance genes in natural bacterial populations

The results of studying the horizontal transfer of mercury resistance determinants in environmental bacterial populations are reviewed. Identical or highly homologous mercury resistance (mer) operons and transposons were found in bacteria of different taxonomic groups from geographically distant regions. Recombinant mer operons and transposons were revealed. The data suggest high frequencies of horizontal transfer and of recombination for mercury resistance determinants. The mechanisms of horizontal gene transfer were elucidated in Gram-negative and Gram-positive bacteria. New transposons were found and analyzed.     

Patterns of change in timing of spring migration in North European songbird populations

From 1976 to 1997 passerines were mist‐netted and ringed on the island of Christiansø, in the Baltic Sea. Here we present analyses of phenological changes (i.e. time of arrival) for 25 species based on the entire populations of mist‐netted songbirds during spring migration. We used two approaches (least square and quantile regression) to test for changes in arrival time of first individuals and three different parts of the songbird populations (i.e. first 5%, 50% and 95% of the total number of trapped individuals corrected for trapping effort). Our results generally confirm earlier spring arrival of migratory passerines with an overall earlier arrival of 0.26 days per year. Changes in the arrival time of first individuals are often the only data available. They are typically analysed on the assumption that they are representative of their respective population. We found a unidirectional, significant change towards earlier arrival for all four measures of arrival timing which seem to support this. However, the four measures of arrival are changing at different rates. First individuals changed arrival time more rapidly than the first 5%, 50% and 95% of the spring total. Such differences are likely to be important for our understanding of population‐dynamic changes in relation to climate change. These differences may also have long‐term evolutionary consequences. Migration distance seems to affect the degree of change in arrival time, but we found no difference between species wintering in different regions of Africa.     

Patterns of change in timing of spring migration in North European songbird populations

From 1976 to 1997 passerines were mist-netted and ringed on the island of Christiansø, in the Baltic Sea. Here we present analyses of phenological changes (i.e. time of arrival) for 25 species based on the entire populations of mist-netted songbirds during spring migration. We used two approaches (least square and quantile regression) to test for changes in arrival time of first individuals and three different parts of the songbird populations (i.e. first 5%, 50% and 95% of the total number of trapped individuals corrected for trapping effort). Our results generally confirm earlier spring arrival of migratory passerines with an overall earlier arrival of 0.26 days per year. Changes in the arrival time of first individuals are often the only data available. They are typically analysed on the assumption that they are representative of their respective population. We found a unidirectional, significant change towards earlier arrival for all four measures of arrival timing which seem to support this. However, the four measures of arrival are changing at different rates. First individuals changed arrival time more rapidly than the first 5%, 50% and 95% of the spring total. Such differences are likely to be important for our understanding of population-dynamic changes in relation to climate change. These differences may also have long-term evolutionary consequences. Migration distance seems to affect the degree of change in arrival time, but we found no difference between species wintering in different regions of Africa.     

Rule-based computing system for microbial interactions and communications: evolution in virtual bacterial populations

We have developed a novel rule-based computing system of microbial interactions and communications, referred to as COSMIC-Rules, for simulating evolutionary processes within populations of virtual bacteria. The model incorporates three levels: the bacterial genome, the bacterial cell and an environment inhabited by such cells. The virtual environment in COSMIC-Rules can contain multiple substances, whose relative toxicity or nutrient status is specified by the genome of the bacterium. Each substance may be distributed uniformly or in a user-defined manner. The organisms in COSMIC-Rules possess individually-defined physical locations, size, cell division status and genomes. Genes and/or gene systems are represented by abstractions that may summate sometimes complex phenotypes. Central to COSMIC-Rules is a simplified representation of bacterial species, each containing a functional genome including, where desired, extrachromosomal elements such as plasmids and/or bacteriophages. A widely applicable computer representation of biological recognition systems based on bit string matching is essential to the model. This representation permits, for example, the modelling of protein-protein interactions, receptor-ligand interactions and DNA-DNA transactions. COSMIC-Rules is intended to inform studies on bacterial adaptation and evolution, and to predict behaviour of populations of pathogenic bacteria and their viruses. The framework is constructed for parallel execution across a large number of machines and efficiently utilises a 64 processor development cluster. It will run on any Grid system and has successfully tested simulations with millions of bacteria, of multiple species and utilising multiple substrates. The model may be used for large-scale simulations where a genealogical record for individual organisms is required.     

Physiological and environmental control of seed germination timing in Mediterranean mountain populations of Gundelia tournefortii

Plant Growth Regulation - Fruit and seed morphology interact with embryo physiology and environmental conditions to control seed germination timing. This interaction plays a pivotal role in...     

Sexual conflict in viscous populations: The effect of the timing of dispersal

In recent years, there has been increasing theoretical and empirical examination of how sexual conflict can arise between males and females. However, much this work has implicitly assumed that interactions take place in panmictic populations with complete dispersal, where interactions are between unrelated individuals. Here, we examine the consequences of limited dispersal and population structure for the evolution of a male phenotype that is associated with the males pre- and post-copulatory reproductive success, using an inclusive-fitness based analysis applied to group-structured populations. We show that: (i) the sex-specific timing of the dispersal phase of the life cycle can drive the evolution of sexual conflict; (ii) the inclusive fitness of a female in this conflict is determined solely by direct (i.e. personal) effects on its own competitive ability. Our analysis is supported by results from individual-based simulations of multi-level selection. Our results support the suggestion that kin selection can influence the evolution of sexual conflict, but reveal that such a role might be more complex than previously appreciated when sex-specific life histories are taken into consideration. We discuss the implications of our results for sexual conflict in various species of insects, but focus primarily on dipteran flies of the family Sepsidae.     

The influence of environmental parameters on the bacterial populations of thermal springs in West Bengal, India

The physico-chemical characteristics and the bacterial populations of three thermal springs in West Bengal have been examined. The springs range in temperature from 42^o C (Saubhagya Kund) to 65^o C (Agni Kur.d). The levels of carbonate and bicarbonate alkalinity, total hardness and the ppm of chloride, phosphate and silicate as well of dissolved oxygen were measured at monthly intervals. Estimates of the bacterial populations were obtained from cultures. Water samples incubated at 37^oC for enumeration of mesophilic microbes, at 50^o C for thermo-tolerant bacteria and at 60^o for strict thermophiles. Tests for coliform organisms were carried out at 37^o C and at 50^o C.
All three springs show seasonal variation in their physico-chemical characteristics and in their bacterial populations. The cooler springs have large populations of mesophilic and thermotolerant bacteria but fewer thermophilic types. In the two hot springs (Saubhagya Kund and Swetganga), the differences of mean bacterial populations observed between 37^o and 50"C and between 50^o and 60^o C are highly significant ( P < 0.01), in the third (Agni Kund) the differences are also significant ( P < 0.01) but the population showed a rising trend with the temperature. Of the biotic and abiotic factors which could be involved in the observed seasonal variation in the bacterial populations, only the fluctuations in the phosphate levels were found to show a significant correlation (0.001 < P < 0.01).     

In search of clinal variation in the period and clock timing genes in Australian Drosophila melanogaster populations

Clinal variation for repeat number in the Thr-Gly region of the period circadian timing gene in Drosophila melanogaster was described in Europe and has subsequently been used as evidence of thermal selection on period alleles. To test for clinal variation in this gene along the east coast of Australia, the period polymorphism was scored on flies from multiple samples collected repeatedly over a 5-year interval, along with variation at another circadian rhythm locus, clock. For period, there was no consistent evidence of clinal variation in the 17 and/or 20 repeat alleles, although when average allele length was examined a weak consistent clinal pattern was detected. For clock there was no evidence of clinal variation in the two most common alleles or in average repeat size. These data are inconsistent with the reported patterns in Europe and suggest that clinal variation in timing genes needs to be re-examined in this region.     

Climate change affects timing and size of populations of an invasive cyanobacterium in temperate regions

Cylindrospermopsis raciborskii, an invasive freshwater cyanobacterium, originated from the tropics but has spread to temperate zones over the last few decades. Its northernmost populations in Europe occur in North German lakes. How such dramatic changes in its biogeography are possible and how its population dynamics in the newly invaded habitats are regulated are still unexplained. We therefore conducted a long-term (1993–2005) study of two German lakes to elucidate the mechanisms behind C. raciborskii population dynamics and to identify the abiotic constraints on its development. Our data revealed that pelagic populations of C. raciborskii thrived for three months during the summer, contributing up to 23% of the total cyanobacteria biovolume. Population sizes varied greatly between years without exhibiting any distinct long-term trends. In the annual lifecycle, C. raciborskii filaments emerged in the pelagic habitat when the temperature rose above 15–17 °C. At that time, mean photosynthetically active radiation in the mixed water column (I _mix) overstepped its maximum. Rates of population net increase were highest at the beginning of the season (0.15–0.28 day⁻¹), declined continuously over time, and were significantly positively correlated with I _mix. This indicates that the onset of the pelagic population is temperature-mediated and that I _mix controls its growth. Since I _mix peaks before the population onset, the time of germination is of crucial importance for successful development. To test this hypothesis, we designed a model to simulate pelagic population size, starting at different dates in the annual cycle. Moving the population onset forward by 30 days resulted in a doubling of the population size. We therefore conclude that an earlier rise in water temperature associated with climate change has promoted the spread of C. raciborskii to the temperate zone. Earlier warming permits earlier germination, thereby shifting the pelagic populations to a phase with higher I _mix, which advances growth and the population establishment.