On the evolution of scale-free topologies with a gene regulatory network model

A novel approach to generating scale-free network topologies is introduced, based on an existing artificial gene regulatory network model. From this model, different interaction networks can be extracted, based on an activation threshold. By using an evolutionary computation approach, the model is allowed to evolve, in order to reach specific network statistical measures. The results obtained show that, when the model uses a duplication and divergence initialisation, such as seen in nature, the resulting regulation networks not only are closer in topology to scale-free networks, but also require only a few evolutionary cycles to achieve a satisfactory error value.     

The evolutionary potential of the Drosophila sex determination gene network

The evolution of sex determination mechanisms is known to be relatively rapid, though recent evidence indicates that certain parts of the mechanism may be more highly conserved. These characteristics establish the sex determination mechanism as a good candidate for the theoretical study of gene network evolution, particularly of networks involved in development. We investigate the short-term evolutionary potential of the sex determination mechanism in Drosophila melanogaster with the aid of a synchronous logical model. We introduce general theoretical concepts such as a network-specific form of mutation, and a notion of functional equivalence between networks. We apply this theoretical framework to the sex determination mechanism and compare it to a population of random networks, enabling us to find features both general to sex determination networks, and particular to the Drosophila network. In general, sex determination networks exist within large sets of functionally equivalent networks all of which satisfy the sex determination task. These large sets are in turn composed of subsets which are mutationally related, suggesting a high degree of flexibility is available without compromising the core functionality. Two particular characteristics of the Drosophila network are found: (a) a parsimonious use of gene interactions, and (b) the network structure can produce a relatively large number of dynamical pattern variations through single network mutations.     

Expression diversity and evolutionary dynamics of rice duplicate genes

Duplicate genes are believed to be a major source of new gene functions over evolutionary time. In order to evaluate the evolutionary dynamics of rice duplicate genes, formed principally by paleoployploidization prior to the speciation of the Poaceae family, we have employed a public microarray dataset including 155 gene expression omnibus sample plates and bioinformatics tools. At least 57.4% of old ~70 million years ago (MYA) duplicate gene pairs exhibit divergences in expression over the given experimental set, whereas at least 50.9% of young ~7.7-MYA duplicate gene pairs were shown to be divergent. When grouping the rice duplicate genes according to functional categories, we noted a striking and significant enrichment of divergent duplicate metabolism-associated genes, as compared to that observed in non-divergent duplicate genes. While both non-synonymous substitution (Ka) and synonymous substitution (Ks) values between non- and divergent duplicate gene pairs evidenced significant differences, the Ka/Ks values between them exhibited no significant differences. Interestingly, the average numbers of conserved motifs of the duplicate gene pairs revealed a pattern of decline along with an increase in expression diversity, partially supporting the subfunctionalization model with degenerative complementation in regulatory motifs. Duplicate gene pairs with high local similarity (HLS) segments, which might be formed via conversion between rice paleologs, evidenced higher expression correlations than were observed in the gene pairs without the HLS segments; this probably resulted in an increased likelihood of gene conversion in promoters of the gene pairs harboring HLS segments. More than 60% of the rice gene families exhibited similar high expression diversity between members as compared to that of randomly selected gene pairs. These findings are likely reflective of the evolutionary dynamics of rice duplicate genes for gene retention. An erratum to this article can be found at     

Evolutionary dynamics of duplicated genes in plants

Gene duplication, arising from region-specific duplication or genome-wide polyploidization, is a prominent feature in plant genome evolution. Understanding the mechanisms generating duplicate gene copies and the subsequent dynamics among gene duplicates is vital because these investigations shed light on regional and genome-wide aspects of evolutionary forces shaping intra- and interspecific genome contents, evolutionary relationships, and interactions. This review discusses recent gene duplication analyses in plants, focusing on the molecular and evolutionary dynamics occurring at three different timescales following duplication: (1). initial establishment and persistence of cytotypes, (2). interactions among duplicate gene copies, and (3). longer term differentiation between duplicated genes. These relative time points are presented in terms of their potential adaptive significance and impact on plant evolutionary genomics research.     

Comparative analysis of essential genes and nonessential genes in Escherichia coli K12

Genes can be classified as essential or nonessential based on their indispensability for a living organism. Previous researches have suggested that essential genes evolve more slowly than nonessential genes and the impact of gene dispensability on a gene’s evolutionary rate is not as strong as expected. However, findings have not been consistent and evidence is controversial regarding the relationship between the gene indispensability and the rate of gene evolution. Understanding how different classes of genes evolve is essential for a full understanding of evolutionary biology, and may have medical relevance in the design of new antibacterial agents. We therefore performed an investigation into the properties of essential and nonessential genes. Analysis of evolutionary conservation, protein length distribution and amino acid usage between essential and nonessential genes in Escherichia coli K12 demonstrated that essential genes are relatively preserved throughout the bacterial kingdom when compared to nonessential genes. Furthermore, results show that essential genes, compared to nonessential genes, have a significantly higher proportion of large (>534 amino acids) and small proteins (<139 amino acids) relative to medium-sized proteins. The pattern of amino acids usage shows a similar trend for essential and nonessential genes, although some notable exceptions are observed. These findings help to clarify our understanding of the evolutionary mechanisms of essential and nonessential genes, relevant to the study of mutagenesis and possibly allowing prediction of gene properties in other poorly understood organisms.     

When does gene flow facilitate evolutionary rescue?

Experimental and theoretical studies have highlighted the impact of gene flow on the probability of evolutionary rescue in structured habitats. Mathematical modeling and simulations of evolutionary rescue in spatially or otherwise structured populations showed that intermediate migration rates can often maximize the probability of rescue in gradually or abruptly deteriorating habitats. These theoretical results corroborate the positive effect of gene flow on evolutionary rescue that has been identified in experimental yeast populations. The observations that gene flow can facilitate adaptation are in seeming conflict with traditional population genetics results that show that gene flow usually hampers (local) adaptation. Identifying conditions for when gene flow facilitates survival chances of populations rather than reducing them remains a key unresolved theoretical question. We here present a simple analytically tractable model for evolutionary rescue in a two-deme model with gene flow. Our main result is a simple condition for when migration facilitates evolutionary rescue, as opposed as no migration. We further investigate the roles of asymmetries in gene flow and/or carrying capacities, and the effects of density regulation and local growth rates on evolutionary rescue.     

An ancient frame-shifting event in the highly conserved KPNA gene family has undergone extensive compensation by natural selection in vertebrates

One of the prevailing arguments in evolutionary theory is that the duplicates of genes can acquire novel functionality. This is because only one of the paralogs need maintain the ancestral function, leaving room for natural experimentation due to a respite in purifying selection. Although many duplicates can subsequently become disabled by nullifying mutations, a few may also go on to diverge along a novel evolutionary trajectory. Here, evidence is provided that demonstrates how this scenario may not always be true. Rather, in the case of the highly conserved KPNA importin family, an initial relaxation in selection induced a frameshift that was later suppressed and heavily compensated for as part of a reparative and optimizing process. Despite a resulting divergence, there remains a distinct preservation of both sequence and functionality among the paralogs. This would indicate that duplicates can be retained by selection for reasons related to their redundant functionality. It also shows that, even when positive selection is inferred in duplicate genes, this may be of a compensatory nature rather than one representing any biochemical innovation. Generally, this development would perhaps be a more common outcome for gene duplication than is currently maintained.     

Accelerated Evolutionary Rate May Be Responsible for the Emergence of Lineage-Specific Genes in Ascomycota

The evolutionary origin of “orphan” genes, genes that lack sequence similarity to any known gene, remains a mystery. One suggestion has been that most orphan genes evolve rapidly so that similarity to other genes cannot be traced after a certain evolutionary distance. This can be tested by examining the divergence rates of genes with different degrees of lineage specificity. Here the lineage specificity (LS) of a gene describes the phylogenetic distribution of that gene’s orthologues in related species. Highly lineage-specific genes will be distributed in fewer species in a phylogeny. In this study, we have used the complete genomes of seven ascomycotan fungi and two animals to define several levels of LS, such as Eukaryotes-core, Ascomycota-core, Euascomycetes-specific, Hemiascomycetes-specific, Aspergillus-specific, and Saccharomyces-specific. We compare the rates of gene evolution in groups of higher LS to those in groups with lower LS. Molecular evolutionary analyses indicate an increase in nonsynonymous nucleotide substitution rates in genes with higher LS. Several analyses suggest that LS is correlated with the evolutionary rate of the gene. This correlation is stronger than those of a number of other factors that have been proposed as predictors of a gene’s evolutionary rate, including the expression level of genes, gene essentiality or dispensability, and the number of protein-protein interactions. The accelerated evolutionary rates of genes with higher LS may reflect the influence of selection and adaptive divergence during the emergence of orphan genes. These analyses suggest that accelerated rates of gene evolution may be responsible for the emergence of apparently orphan genes. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Martin Kreitman]