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Wagner, Andreas

doi:10.1046/j.1420-9101.1999.00008.x

Cited by 75 publications

(5 citation statements)

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“…Generally it is hypothesized, that duplicated genes will not persist over evolutionary time unless sub-, or neofunctionalization results in functional divergence [25-27]. EScaAG1 and EScaAG2 share about 81.7% sequence similarity in the open reading frame and are 75.5% identical when the 5'UTR is included.…”

Section: Discussionmentioning

confidence: 99%

Floral homeotic C function genes repress specific B function genes in the carpel whorl of the basal eudicot California poppy (Eschscholzia californica)

Yellina

Orashakova

Lange

et al. 2010

EvoDevo

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BackgroundThe floral homeotic C function gene AGAMOUS (AG) confers stamen and carpel identity and is involved in the regulation of floral meristem termination in Arabidopsis. Arabidopsis ag mutants show complete homeotic conversions of stamens into petals and carpels into sepals as well as indeterminacy of the floral meristem. Gene function analysis in model core eudicots and the monocots rice and maize suggest a conserved function for AG homologs in angiosperms. At the same time gene phylogenies reveal a complex history of gene duplications and repeated subfunctionalization of paralogs.ResultsEScaAG1 and EScaAG2, duplicate AG homologs in the basal eudicot Eschscholzia californica show a high degree of similarity in sequence and expression, although EScaAG2 expression is lower than EScaAG1 expression. Functional studies employing virus-induced gene silencing (VIGS) demonstrate that knock down of EScaAG1 and 2 function leads to homeotic conversion of stamens into petaloid structures and defects in floral meristem termination. However, carpels are transformed into petaloid organs rather than sepaloid structures. We also show that a reduction of EScaAG1 and EScaAG2 expression leads to significantly increased expression of a subset of floral homeotic B genes.ConclusionsThis work presents expression and functional analysis of the two basal eudicot AG homologs. The reduction of EScaAG1 and 2 functions results in the change of stamen to petal identity and a transformation of the central whorl organ identity from carpel into petal identity. Petal identity requires the presence of the floral homeotic B function and our results show that the expression of a subset of B function genes extends into the central whorl when the C function is reduced. We propose a model for the evolution of B function regulation by C function suggesting that the mode of B function gene regulation found in Eschscholzia is ancestral and the C-independent regulation as found in Arabidopsis is evolutionarily derived.

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Section: Discussionmentioning

confidence: 99%

Floral homeotic C function genes repress specific B function genes in the carpel whorl of the basal eudicot California poppy (Eschscholzia californica)

Yellina

Orashakova

Lange

et al. 2010

EvoDevo

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“…It has been repeatedly emphasized that positive selection is needed for the evolution of new functions by gene duplication (30)(31)(32)(33)(34)(35)(36). However, it is possible that selection is very weak in this case.…”

Section: Three Levels Of Weak Selectionmentioning

confidence: 99%

Near-neutrality in evolution of genes and gene regulation

Ohta

2002

Proc. Natl. Acad. Sci. U.S.A.

306

219

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The nearly neutral theory contends that the interaction of drift and selection is important and occurs at various levels, including synonymous and nonsynonymous substitutions in protein coding regions and sequence turnover of regulatory elements. Recent progress of the theory is reviewed, and the interaction between drift and selection is suggested to differ at these different levels. Weak selective force on synonymous changes is stable, whereas its consequence on nonsynonymous changes depends on environmental factors. Selection on differentiation of regulatory elements is even more dependent on environmental factors than on amino acid changes. Of particular significance is the role of drift in the evolution of gene regulation that directly participates in morphological evolution. The range of near neutrality depends on the effective size of the population that is influenced by selected linked loci. In addition to the effective population size, molecular chaperones such as heat shock protein 90 have significant effects on the range of near neutrality.A lthough the neutral and the nearly neutral theories have now been recognized as realistic models to apply to evolutionary changes of genes and proteins, their significance for morphological evolution is still unsettled (1). During the last several years, ''slightly advantageous'' as well as ''slightly deleterious'' amino acid substitutions have been noted as important (2-4), and the significance of such weakly selected mutations for morphological evolution needs to be reconsidered. In addition, the molecular basis of gene regulation that is essential for development is being elucidated (5-7). In the evolution of gene regulation, interaction of selection and drift has been suggested to be important (8). The purpose of this article is to review such findings and to expand the concept of near-neutrality. Synonymous vs. Nonsynonymous SubstitutionsA most efficient way to find how natural selection has worked is to examine the patterns of synonymous and nonsynonymous substitutions. The McDonald and Kreitman test (9) is most popular, and compares the numbers of nonsynonymous and synonymous substitutions within a population and between closely related species. These authors found that the number of fixed amino acid changes at the Adh locus between Drosophila sibling species is greater than the prediction under the neutral theory, and suggested that the fixed amino acid substitutions were selectively advantageous. Many subsequent studies showed that there were various patterns; i.e., most mitochondria data were characterized by an excess of nonsynonymous withinpopulation (polymorphic) changes, indicating weak negative selection against amino acid changes, whereas nuclear gene data showed more diverse patterns (for a review, see ref. 10).Recent studies along this line are attempts to examine collections of data of many loci. Smith and Eyre-Walker (11) did a statistical analysis using data of Drosophila simulans and Drosophila yakuba. Assuming three distinct classes of nonsy...

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“…However, at least some theoretical treatments show that even gene pairs that are on an evolutionary trajectory of subfunctionalization may retain redundant functions for long periods [12]. Another set of theoretical models predicts that natural selection can favor stable genetic redundancy or partial redundancy under certain conditions, especially in large populations [13,14]. Other formulations allow for simultaneous evolution of subfunctionalization, neofunctionalization, and redundancy in the same genome [15].…”

Section: Introductionmentioning

confidence: 99%

Predicting genome-wide redundancy using machine learning

et al. 2010

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BackgroundGene duplication can lead to genetic redundancy, which masks the function of mutated genes in genetic analyses. Methods to increase sensitivity in identifying genetic redundancy can improve the efficiency of reverse genetics and lend insights into the evolutionary outcomes of gene duplication. Machine learning techniques are well suited to classifying gene family members into redundant and non-redundant gene pairs in model species where sufficient genetic and genomic data is available, such as Arabidopsis thaliana, the test case used here.ResultsMachine learning techniques that combine multiple attributes led to a dramatic improvement in predicting genetic redundancy over single trait classifiers alone, such as BLAST E-values or expression correlation. In withholding analysis, one of the methods used here, Support Vector Machines, was two-fold more precise than single attribute classifiers, reaching a level where the majority of redundant calls were correctly labeled. Using this higher confidence in identifying redundancy, machine learning predicts that about half of all genes in Arabidopsis showed the signature of predicted redundancy with at least one but typically less than three other family members. Interestingly, a large proportion of predicted redundant gene pairs were relatively old duplications (e.g., Ks > 1), suggesting that redundancy is stable over long evolutionary periods.ConclusionsMachine learning predicts that most genes will have a functionally redundant paralog but will exhibit redundancy with relatively few genes within a family. The predictions and gene pair attributes for Arabidopsis provide a new resource for research in genetics and genome evolution. These techniques can now be applied to other organisms.

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Cited by 75 publications

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Floral homeotic C function genes repress specific B function genes in the carpel whorl of the basal eudicot California poppy (Eschscholzia californica)

Floral homeotic C function genes repress specific B function genes in the carpel whorl of the basal eudicot California poppy (Eschscholzia californica)

Near-neutrality in evolution of genes and gene regulation

Predicting genome-wide redundancy using machine learning

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