Positive selection at high temperature reduces gene transcription in the bacteriophage ϕX174

<p>Abstract</p> <p>Background</p> <p>Gene regulation plays a central role in the adaptation of organisms to their environments. There are many molecular components to gene regulation, and it is often difficult to determine both the genetic basis of adaptation and the evolutionary forces that influence regulation. In multiple evolution experiments with the bacteriophage ϕX174, adaptive substitutions in <it>cis</it>-acting regulatory sequences sweep through the phage population as the result of strong positive selection at high temperatures that are non-permissive for laboratory-adapted phage. For one <it>cis</it>-regulatory region, we investigate the individual effects of four adaptive substitutions on transcript levels and fitness for phage growing on three hosts at two temperatures.</p> <p>Results</p> <p>The effect of the four individual substitutions on transcript levels is to down-regulate gene expression, regardless of temperature or host. To ascertain the conditions under which these substitutions are adaptive, fitness was measured by a variety of methods for several bacterial hosts growing at two temperatures, the control temperature of 37°C and the selective temperature of 42°C. Time to lysis and doublings per hour indicate that the four substitutions individually improve fitness over the ancestral strain at high temperature independent of the bacterial host in which the fitness was measured. Competition assays between the ancestral strain and either of two mutant strains indicate that both mutants out-compete the ancestor at high temperature, but the relative frequencies of each phage remain the same at the control temperature.</p> <p>Conclusions</p> <p>Our results strongly suggest that gene transcription plays an important role in influencing fitness in the bacteriophage ϕX174, and different point mutations in a single <it>cis</it>-regulatory region provided the genetic basis for this role in adaptation to high temperature. We speculate that the adaptive nature of these substitutions is due to the physiology of the host at high temperature or the need to maintain particular ratios of phage proteins during capsid assembly. Our investigation of regulatory evolution contributes to interpreting genome-level assessments of regulatory variation, as well as to understanding the molecular basis of adaptation.</p

Aging in a Long-Lived Clonal Tree

Using genetic estimates of clone age in trembling aspen, this study demonstrates a significant decline in male sexual fitness with increasing age, showing that long-lived clonal organisms are vulnerable to aging

The cost of longevity: loss of sexual function in natural clones of Populus tremuloides

Most clonal plants exhibit a modular structure at multiple levels. At the level of the organs, they are characterized by functional modules, such as, internodes, leaves, branches. At the level of the genetic individual (clone or genet), they possess independent evolutionary and physiological units (ramets). These evolutionary units arise through the widespread phenomenon of clonal reproduction, achieved in a variety of ways including rhizomes, stolons, bulbils, or lateral roots. The focus of this study was Populus tremuloides, trembling aspen, a dioecious tree that reproduces sexually by seed and asexually through lateral roots. Local forest patches in western populations of Populus tremuloides consisted largely of multiple genotypes. Multi-clonal patches were dominated by a single genotype, and in one population (Riske Creek) we found several patches (five out of 17) consisting of a single genotype. A second consequence of modularity is that during the repeated cycle of ramet birth, development and death, somatic mutations have the opportunity to occur. Eventually, the clone becomes a mosaic of mutant and non-mutant cell lineages. We found that neutral somatic mutations accumulated across 14 microsatellite loci at a rate of between 10^-6 and 10^-5 per locus per year. We suggest that neutral genetic divergence, under a star phylogeny model of clonal growth, is an alternative way to estimate clone age. Previous estimates of clone age couple the mean growth rate per year of shoots with the area covered by the clone. This assumes a positive linear relationship between clone age and clone size. We found, however, no repeatable pattern across our populations in terms of the relationship of either shape or size to the number of somatic changes. A final consequence of modularity is that during clonal growth, natural selection is relaxed for traits involving sexual function. This means that mutations deleterious to sexual function can accumulate, reducing the overall sexual fitness of a clone. We coupled neutral genetic divergence within clones with pollen fitness data to infer the rate and effect of mildly deleterious mutations. Mutations reduced relative sexual fitness in clonal aspen populations by about 0.12x10^-3 to 1.01x10^-3 per year. Furthermore, the decline in sexual function with clone age is evidence that clonal organisms are vulnerable to the effects of senescence.Medicine, Faculty ofMedical Genetics, Department ofGraduat

Spatial genetic structure in mountain hemlock (Tsuga mertensiana)

The spatial distribution of related and unrelated alleles at a geographic, population, or local scale can unravel the relative roles of random genetic drift, mutation, and natural selection in the maintenance of genetic variation. Characterizing spatial and temporal patterns of genetic variation, and the underlying mechanisms, is central to understanding evolutionary and ecological processes like speciation, succession, and the spread and maintenance of a species. Equally important, is knowing how these patterns of variability change with physical scale and how the same processes differentially affect distinct spatial scales. The first part of this study examines mating systems, level of genetic diversity and the distribution of that genetic variation within and among populations of mountain hemlock {Tsuga mertensiana) across British Columbia. The second half of the thesis examines the effects of fragmentation on the demographic structure at the local scale, that is, within a single old growth stand of mountain hemlock. Levels of genetic diversity, inbreeding and isolation by distance are also examined in the natural regeneration surrounding the clearcut. Genetic diversity, mating system and the evolutionary history of 19 populations of mountain hemlock {Tsuga mertensiana) within British Columbia were inferred from genetic variation at 19 allozyme loci. Within populations, 32% of the loci were polymorphic and expected heterozygosity was 0.087 overall populations, which is approximately half the heterozygosity found in other conifers. Outcrossing rates did not significantly differ from 100%. Overall, populations of mountain hemlock across British Columbia showed moderate differentiation (Gst =0.077). Island populations showed considerably more differentation (Gst =0.095) than mainland populations (Gst =0.058), and an isolation-by-distance analysis suggested gene flow was not restricted. For the populations in southwestern British Columbia, there was a significant positive correlation between average expected heterozygosity and elevation, while expected heterozygosity was negatively correlated with latitude. The low genetic diversity suggests that during a northward post-glacial range expansion, more northerly mountain hemlock populations suffered a loss in genetic variation due to this migration. In an old growth mountain hemlock population in southern British Columbia, genetic diversity and relatedness were examined using two microsatellite loci. Levels of inbreeding were found to be significantly different from zero, and increased exponentially to an asymptote as mean diameter increased. High levels of inbreeding may have resulted from family clustering, the presence of null alleles, and spatial or temporal Wahlund effects. The difference in inbreeding levels between trees established before and after fragmentation may be suggestive of a temporal shift in breeding system. Seedlings from the 0-2cm diameter class (postfragmentation) were found to have the highest genetic diversity and lowest levels of inbreeding. Seedlings and adults also differed in their allelic distribution suggesting that seedlings were not simply a subset of the neighbouring adult gene pool. The 1976 clearcut of 43.3 ha surrounding the old growth patch may have substantially altered the density of trees causing a change in wind currents, subsequently enhancing gene flow. Significant relatedness was detected among adult trees 5m apart and in the clearcut between seedlings 2m apart. Both natural regeneration and adult trees exhibited significant isolation by distance when pairwise estimates of relatedness were plotted as a function of increasing pairwise distance. The local genetic structure in mountain hemlock can be attributed to limited seed dispersal, seedling recruitment over a long period of time and long distance founding events.Forestry, Faculty ofGraduat

Data from: Can clone size serve as a proxy for clone age? An exploration using microsatellite divergence in Populus tremuloides

No description availabl

Data from: Can clone size serve as a proxy for clone age? An exploration using microsatellite divergence in Populus tremuloides

In long-lived clonal plant species, the overall size of a clone has previously been used to estimate clone age. The size of a clone, however, might be largely determined by physical or biotic interactions, obscuring the relationship between clone size and age. Here, we use the accumulation of mutations at 14 microsatellite loci to estimate clone age in trembling aspen, Populus tremuloides, from southwestern Canada. We show that the observed patterns of genetic divergence are consistent with a model of clonal growth, allowing us to use pairwise genetic divergence as an estimator of clone age. In the populations studied, clone size did not exhibit a significant relationship with microsatellite divergence, indicating that clone size is not a good proxy for clone age

RR_SizeData

See README_SIZEDATA Fil

Riske_Creek_sizedata

See the README_SIZEDATA fil

SSR_Data_11905036MEC-08-0315.R1

This data was collected in two geographical locations: Riske Creek, British Columbia and Waterton Lakes National Park, Alberta. The data represent 14 microsatellite loci. See Ally et al. 2008 for a description of the SSRs. Any loci that did not amplify are indicated with an question mark