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Global relationships in fluctuation and response in adaptive evolution.

ABSTRACT: Cells change their internal state to adapt to environmental changes, and evolve in response to the new conditions. The phenotype changes first via adaptation in response to environmental changes, and then through mutational changes in the genomic sequence, followed by selection in evolution. Here, we analysed simulated adaptive evolution using a simple cell model consisting of thousands of intracellular components, and found that the changes in their concentrations by adaptation are proportional to those by evolution across all the components, where the proportion coefficient between the two agreed well with the change in the growth rate of a cell. Furthermore, we demonstrate that the phenotypic variance in concentrations of cellular components due to (non-genetic) noise and to genomic alternations is proportional across all components. This implies that the specific phenotypes that are highly evolvable were already given by non-genetic fluctuations. These global relationships in cellular states were also supported by phenomenological theory based on steady reproduction and transcriptome analysis of laboratory evolution in Escherichia coli. These findings demonstrate that a possible evolutionary change in phenotypic state is highly restricted. Our results provide a basis for the development of a quantitative theory of plasticity and robustness in phenotypic evolution.

SUBMITTER: Furusawa C

PROVIDER: S-EPMC4535414 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature

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Global relationships in fluctuation and response in adaptive evolution.

Furusawa Chikara C Kaneko Kunihiko K

Journal of the Royal Society, Interface 20150801 109

Cells change their internal state to adapt to environmental changes, and evolve in response to the new conditions. The phenotype changes first via adaptation in response to environmental changes, and then through mutational changes in the genomic sequence, followed by selection in evolution. Here, we analysed simulated adaptive evolution using a simple cell model consisting of thousands of intracellular components, and found that the changes in their concentrations by adaptation are proportional ...[more]

PMID: 26202686

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Project description:In general, the chloroplast genomes of angiosperms are considered to be highly conserved and affected little by adaptive evolution. In this study, we tested this hypothesis based on sequence differentiation and adaptive variation in the plastid genomes in the order Dipsacales. We sequenced the plastid genomes of one Adoxaceae species and six Caprifoliaceae species, and together with seven previously released Dipsacales chloroplasts, we determined the sequence variations, evolutionary divergence of the plastid genomes, and phylogeny of Dipsacales species. The chloroplast genomes of Adoxaceae species ranged in size from 157,074 bp (Sinadoxa corydalifolia) to 158,305 bp (Sambucus williamsii), and the plastid genomes of Caprifoliaceae varied from 154,732 bp (Lonicera fragrantissima var. lancifolia) to 156,874 bp (Weigela florida). The differences in the number of genes in Caprifoliaceae and Adoxaceae species were largely due to the expansion and contraction of inverted repeat regions. In addition, we found that the number of dispersed repeats (Adoxaceae = 37; Caprifoliaceae = 384) was much higher than that of tandem repeats (Adoxaceae = 34; Caprifoliaceae = 291) in Dipsacales species. Interestingly, we determined 19 genes with positive selection sites, including three genes encoding ATP protein subunits (atpA, atpB, and atpI), four genes for ribosome protein small subunits (rps3, rps7, rps14, and rps15), four genes for photosystem protein subunits (psaA, psaJ, psbC, and pabK), two genes for ribosome protein large subunits (rpl22 and rpl32), and the clpP, infA, matK, rbcL, ycf1, and ycf2 genes. These gene regions may have played key roles in the adaptation of Dipsacales to diverse environments. In addition, phylogenetic analysis based on the plastid genomes strongly supported the division of 14 Dipsacales species into two previously recognized sections. The diversification of Adoxaceae and Caprifoliaceae was dated to the late Cretaceous and Tertiary periods. The availability of these chloroplast genomes provides useful genetic information for studying taxonomy, phylogeny, and species evolution in Dipsacales.

Dataset Information

Global relationships in fluctuation and response in adaptive evolution.

Publications

Global relationships in fluctuation and response in adaptive evolution.

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