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Evolution maintains organismal fitness by preserving genomic information. This is widely assumed to involve conservation of specific genomic loci among species. Many genomic encodings are now recognized to integrate small contributions from multiple genomic positions into quantitative dispersed codes, but the evolutionary dynamics of such codes are still poorly understood. Here we show that in yeast, sequences that quantitatively affect nucleosome occupancy evolve under compensatory dynamics that maintain heterogeneous levels of A+T content through spatially coupled A/T-losing and A/T-gaining substitutions. Evolutionary modeling combined with data on yeast polymorphisms supports the idea that these substitution dynamics are a consequence of weak selection. This shows that compensatory evolution, so far believed to affect specific groups of epistatically linked loci like paired RNA bases, is a widespread phenomenon in the yeast genome, affecting the majority of intergenic sequences in it. The model thus derived suggests that compensation is inevitable when evolution conserves quantitative and dispersed genomic functions.


Purifying selection is a major force in conserving genomic features. It pushes deleterious mutations to extinction while conserving the specific DNA sequence. Here we show that a large proportion of the yeast genome evolves under compensatory dynamics that conserve genomic properties while modifying the genomic sequence. Such compensatory evolution conserves the local G+C content of the genome, which influences nucleosome organization. Since purifying selection is too weak to eliminate every weakly deleterious mutation in nucleosome bound or unbound sequences, the local G+C content is frequently stabilized by compensatory G+C gaining and G+C losing mutations in proximal loci. Theoretical analysis shows that compensatory evolution is inevitable when natural selection is weak and the genomic feature is distributed over many loci. These results imply that sequence conservation may not always be equated with overall selection. They demonstrate that cycles of weakly deleterious substitutions followed by positive selection for corrective mutations, which were so far studied mostly in RNA coding genes, are observed broadly and profoundly affect genome evolution.

An important assumption underlying our evolutionary analysis above is that the evolutionary regime operating in regions that are occupied (or unoccupied) by nucleosomes in the extant S. cerevisiae genome has been the same since the divergence of S. cerevisiae from S. paradoxus. Violations of this assumption can potentially affect our substitution rate estimations. For example, if nucleosome occupancy is determined by the genomic sequence, but is not under selection, nucleosomes may drift freely following substitutions spontaneously generating new A+T rich hotspots. Following that, we may enrich for substitutions that increase A+T content in extant low occupancy sequences by assuming nucleosome organization were conserved. To verify that such a scenario has not significantly affected our analysis of TSS-proximal substitution rates, we inferred the G+C content in the common ancestor of S. cerevisiae and S. paradoxus, for 10 ranges of S. cerevisiae nucleosome occupancy levels, and compared it to the extant G+C content (Fig 2D). We found that the G+C content at all levels of nucleosome occupancy did not change significantly during evolution in the S. cerevisiae lineage. Sequences proximal to TSSs therefore conserve their regional G+C content (at least on average). Consequently, the different rates of substitutions in high and low nucleosome occupancy loci do not represent net divergence in the sequence features that correlates with nucleosome occupancy. This is further confirmed by recent comparative analysis of nucleosome organization in S. cerevisiae and S. paradoxus, which revealed only limited divergence in nucleosome positioning for these species [37], [38]. The highly non symmetric substitution dynamics observed at different levels of nucleosome occupancy must therefore be explained by means of a stationary evolutionary process that conserves the underlying nucleosome-associated encoding.

We studied here a model of evolution as manipulating sequences in a complex fitness landscape that combines contributions from multiple coupled loci into a single dispersed encoding. As shown by theoretical and empirical analysis of the model, when selection on each individual locus is weak, purifying selection is incapable of completely purging mutations that are only slightly deleterious and these are continuously challenging the overall optimality of the sequence. This suboptimality is compensated effectively by adaptive evolution at multiple other loci that participate in the dispersed encoding. In contrast to other cases of compensatory evolution (proteins [41] or RNA molecules [8]-[10], [42]), the encodings we studied here provide ample direct ways to correct a slightly deleterious substitution, thereby increasing the rate of compensation. Our study builds on earlier work on codon bias [43], [44], but uses the global and experimentally characterized sequence classes at high and low nucleosomes occupancy loci to establish compensatory evolution as a major driving force in evolution under multi-site selection. This type of evolutionary dynamics may be generalized to other dispersed functional encodings [45], [46] including complex regulatory switches that typically involve a large number of TF binding sites of variable factors and specificities. The remarkably global nature of the compensatory effect we observed in yeast, which cause a measurable global increase in the substitution rate of specific mutations, supports the notion of an evolutionary process that conserves function without a strict requirement to conserve sequence. It is tempting to speculate that such a process may allow genomes to maintain diversity and continuously search the sequence space, without significantly compromising their existing regulatory circuits. Furthermore, this process may reduce, through compensation, the mutational load [47] resulting from the use of multiple loci to encode regulatory functions.

Members of the 12th Flying Training Wing Maintenance Directorate wash a T-38 Talon Feb. 2 at the new wash rack inside Hangar 42 at Joint Base San Antonio-Randolph. The 14-member corrosion control team now has its own indoor wash rack in Hangar 42 with benefits that include washes unimpeded by weather conditions and an environmentally friendly water-recycling system that conserves water, saving the Air Force $174,000 per year.

Rudy Olivarez, 12th Flying Training Wing Maintenance Directorate, rinses a T-38 Talon Feb. 2 at the new wash rack inside Hangar 42 at Joint Base San Antonio-Randolph. The water-recycling system conserves water and prevents contaminants from entering the San Antonio River Authority wastewater system.

A museum is a not-for-profit, permanent institution in the service of society that researches, collects, conserves, interprets and exhibits tangible and intangible heritage. Open to the public, accessible and inclusive, museums foster diversity and sustainability. They operate and communicate ethically, professionally and with the participation of communities, offering varied experiences for education, enjoyment, reflection and knowledge sharing.

The traditional method used in producing our conserve results in a soft set texture. Enhanced fresh fruit flavor is favored over a firmer set. These conserves have a very low sugar content and no commercial pectin. Please refrigerate after opening.

Before the advent of the refrigerator, the French preserved their fruit in sugar, calling these preserves a "confiture," according to Douciers Etoiles. But even with the development of food preservation technology, these confitures remained. The proof is in the pudding; we have entire aisles in our grocery stores dedicated to fruit jellies, jams, butters, and conserves. But why are there distinct terms that all seem to represent the exact same thing: a gelatinous, macerated fruit preserved in sugar and acid? Well, there are slight differences between these varieties of fruit spreads.

This means that every jam is a type of conserve, but not every conserve is a jam. If you've ever had a triple-berry jam, that is technically a conserve because it contains more than one fruit. Then, there is also hot pepper jelly, which is more of a pepper conserve because it contains a medley of vegetables rather than one. Some people even add nuts or herbs to their conserves, which can make excellent sweet and savory spreads. While the distinction between a jam and a conserve is rooted in specificity, the difference between a jam and a jelly is more about the cooking technique and finishing texture. But that's a conversation for another time. 041b061a72

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