A role for selection in regulating the evolutionary emergence of disease-causing and other coding CAG repeats in humans and mice

The evolutionary expansion of CAG repeats in human triplet expansion disease genes is intriguing because of their deleterious phenotype. In the past, this expansion has been suggested to reflect a broad genomewide expansion of repeats, which would imply that mutational and evolutionary processes acting on repeats differ between species. Here, we tested this hypothesis by analyzing repeat- and flanking-sequence evolution in 28 repeat-containing genes that had been sequenced in humans and mice and by considering overall lengths and distributions of CAG repeats in the two species. We found no evidence that these repeats were longer in humans than in mice. We also found no evidence for preferential accumulation of CAG repeats in the human genome relative to mice from an analysis of the lengths of repeats identified in sequence databases. We then investigated whether sequence properties, such as base and amino acid composition and base substitution rates, showed any relationship to repeat evolution. We found that repeat-containing genes were enriched in certain amino acids, presumably as the result of selection, but that this did not reflect underlying biases in base composition. We also found that regions near repeats showed higher nonsynonymous substitution rates than the remainder of the gene and lower nonsynonymous rates in genes that contained a repeat in both the human and the mouse. Higher rates of nonsynonymous mutation in the neighborhood of repeats presumably reflect weaker purifying selection acting in these regions of the proteins, while the very low rate of nonsynonymous mutation in proteins containing a CAG repeat in both species presumably reflects a high level of purifying selection. Based on these observations, we propose that the mutational processes giving rise to polyglutamine repeats in human and murine proteins do not differ. Instead, we propose that the evolution of polyglutamine repeats in proteins results from an interplay between mutational processes and selection.     

Positive directional selection in the proline-rich antigen (PRA) gene among the human pathogenic fungi Coccidioides immitis, C. posadasii and their closest relatives

In this study, we investigate the possibility of selection acting on the proline-rich antigen (PRA) gene in natural populations of the two human pathogens, Coccidioides immitis and Coccidioides posadasii, and three of their close relatives, Chrysosporium lucknowense, Chrysosporium queenslandicum, and Uncinocarpus reesii. We addressed the following questions: Is diversifying selection acting on PRA in the pathogenic species as a result of avoidance of the host's immune system, and has adaptation to a pathogenic life style lead to positive directional selection and increased rate of evolution in PRA between the species? For these purposes, we amplified and sequenced from 40 individuals belonging to the five species, the entire coding region of the PRA gene, as well as partial sequences from the coding region of each of the three housekeeping genes glyderaldehyde-3-phosphate dehydrogenase, glutamine synthetase A, and hexokinase A. We used likelihood-based methods to compare models of different types of selective pressure among codons to analyze the mode of evolution of the genes and found that the PRA gene evolves under positive selection, but the investigated parts of the housekeeping genes evolve primarily under purifying selection. We found a very low level of intraspecific variability and no evidence of diversifying selection, suggesting that the increased rate of evolution in the PRA gene is not a result of avoidance of the host's immune system. Neither did likelihood-based analyses suggest that selection was stronger on the branch separating pathogenic and nonpathogenic species. Instead, we suggest that positive selection act on PRA as a consequence of spore cell-wall morphogenesis unique to each species.     

Behavioral genomics and the study of speciation at a porous species boundary

Porous species boundaries are characterized by differential gene flow, where some regions of the genome experience divergent evolution while others experience the homogenizing effects of gene flow. If species can arise or remain distinct despite gene flow between them, speciation can only be understood on a gene by gene level. To understand the genetics of speciation, we therefore must identify the targets of selection that cause divergent evolution and identify the genetic architecture underlying such “speciation phenotypes”. This will enable characterization of genomic regions that are “free to flow” between species, and those that diverge in the face of gene flow. We discuss this problem in the genus Laupala, a morphologically cryptic, flightless group of crickets that has radiated in Hawaii. Because songs are used in courtship and always distinguish close relatives of Laupala as well as species in sympatry, we argue that songs in Laupala are speciation phenotypes. Here, we present our approaches to identify the underlying genomic regions and song genes that differentiate closely related species. We discuss what is known about the genetic basis of this species difference derived from classic quantitative genetics and quantitative trait locus mapping experiments. We also present a model of the molecular expression of cricket song to assist in our goal to identify the genes involved in song variation. As most species are sympatric and exchange genes with congeners, we discuss the importance of understanding the genetic and genomic architecture of song as a speciation phenotype that must be characterized to identify differential patterns of gene flow at porous species boundaries.     

Do essential genes evolve slowly?

Approximately two thirds of all knockouts of individual mouse genes give rise to viable fertile mice. These genes have thus been termed 'non-essential' in contrast to 'essential' genes, the knockouts of which result in death or infertility. Although non-essential genes are likely to be under selection that favours sequence conservation [1], it is predicted that they are less subject to such stabilising selection than essential genes, and hence evolve faster [2]. We have addressed this issue by analysing the molecular evolution of 108 non-essential and 67 essential genes that have been sequenced in both mouse and rat. On preliminary analysis, the non-essential genes appeared to be faster evolving than the essential ones. We found, however, that the non-essential class contains a disproportionate number of immune-system genes that may be under directional selection (that is, selection favouring change) because of host-parasite coevolution. After correction for this bias, we found that the rate at which genes evolve does not correlate with the severity of the knockout phenotype. This was corroborated by the finding that, whereas neuron-specific genes have significantly lower rates of change than other genes, essential and non-essential neuronal genes have comparable rates of evolution. Our findings most probably reflect strong selection acting against even very subtle deleterious phenotypes, and indicate that the putative involvement of directional selection in host-parasite coevolution and gene expression within the nervous system explains much more of the variance in rates of gene evolution than does the knockout phenotype.     

Interspecific Comparison in the Frequency of Concerted Evolution at the Polyubiquitin Gene Locus

The polyubiquitin gene, encoding tandemly repeated multiple ubiquitins, constitutes a uniquitin gene subfamily. It has been demonstrated that polyubiquitin genes are subject to concerted evolution; namely, the individual ubiquitin coding units contained within a polyubiquitin gene are more similar to one another than they are to the ubiquitin coding units in the orthologous gene from other species. However there has been no comprehensive study on the concerted evolution of polyubiquitin genes in a wide range of species, because the relationships (orthologous or paralogous) among multiple polyubiquitin genes from different species have not been extensively analyzed yet. In this report, we present the results of analyzing the nucleotide sequence of polyubiquitin genes of mammals, available in the DDBJ/EMBL/GenBank nucleotide sequence databases, in which we found that there are two groups of polyubiquitin genes in an orthologous relationship. Based on this result, we analyzed the concerted evolution of the polyubiquitin gene in various species and compared the frequency of concerted evolutionary events interspecifically by taking into consideration that the rate of synonymous substitution at the polyubiquitin gene locus may vary depending on species. We found that the concerted evolutionary events in polyubiquitin genes have been more frequent in rats and Chinese hamsters than those in humans, cows, and sheep. The guinea pig polyubiquitin gene was an intermediate example. The frequency of concerted evolution in the mouse gene was unexpectedly low compared to that of other rodent genes. Received: 18 January 2000 / Accepted: 26 April 2000     

G+C3 structuring along the genome: a common feature in prokaryotes

The heterogeneity of gene nucleotide content in prokaryotic genomes is commonly interpreted as the result of three main phenomena: (1) genes undergo different selection pressures both during and after translation (affecting codon and amino acid choice); (2) genes undergo different mutational pressure whether they are on the leading or lagging strand; and (3) genes may have different phylogenetic origins as a result of lateral transfers. However, this view neglects the necessity of organizing genetic information on a chromosome that needs to be replicated and folded, which may add constraints to single gene evolution. As a consequence, genes are potentially subjected to different mutation and selection pressures, depending on their position in the genome. In this paper, we analyze the structuring of different codon usage measures along completely sequenced bacterial genomes. We show that most of them are highly structured, suggesting that genes have different base content, depending on their location on the chromosome. A peculiar pattern of genome structure, with a tendency toward an A+T-enrichment near the replication terminus, is found in most bacterial phyla and may reflect common chromosome constraints. Several species may have lost this pattern, probably because of genome rearrangements or integration of foreign DNA. We show that in several species, this enrichment is associated with an increase of evolutionary rate and we discuss the evolutionary implications of these results. We argue that structural constraints acting on the circular chromosome are not negligible and that this natural structuring of bacterial genomes may be a cause of overestimation in lateral gene transfer predictions using codon composition indices.     

The consequence of natural selection on genetic variation in the mouse

Laboratory mouse strains are known to have emerged from recent interbreeding between individuals of Mus musculus isolated populations. As a result of this breeding history, the collection of polymorphisms observed between laboratory mouse strains is likely to harbor the effects of natural selection between reproductively isolated populations. Until now no study has systematically investigated the consequences of this breeding history on gene evolution. Here we have used a novel, unbiased evolutionary approach to predict the founder origin of laboratory mouse strains and to assess the balance between ancient and newly emerged mutations in the founder subspecies. Our results confirm a contribution from at least four distinct subspecies. Additionally, our method allowed us to identify regions of relaxed selective constraint among laboratory mouse strains. This unique structure of variation is likely to have significant consequences on the use of mouse to find genes underlying phenotypic variation.     

The Relationship between Gene Network Structure and Expression Variation among Individuals and Species

Variation among individuals is a prerequisite of evolution by natural selection. As such, identifying the origins of variation is a fundamental goal of biology. We investigated the link between gene interactions and variation in gene expression among individuals and species using the mammalian limb as a model system. We first built interaction networks for key genes regulating early (outgrowth; E9.5–11) and late (expansion and elongation; E11-13) limb development in mouse. This resulted in an Early (ESN) and Late (LSN) Stage Network. Computational perturbations of these networks suggest that the ESN is more robust. We then quantified levels of the same key genes among mouse individuals and found that they vary less at earlier limb stages and that variation in gene expression is heritable. Finally, we quantified variation in gene expression levels among four mammals with divergent limbs (bat, opossum, mouse and pig) and found that levels vary less among species at earlier limb stages. We also found that variation in gene expression levels among individuals and species are correlated for earlier and later limb development. In conclusion, results are consistent with the robustness of the ESN buffering among-individual variation in gene expression levels early in mammalian limb development, and constraining the evolution of early limb development among mammalian species.     

The emergence and fate of horizontally acquired genes in Escherichia coli

Bacterial species, and even strains within species, can vary greatly in their gene contents and metabolic capabilities. We examine the evolution of this diversity by assessing the distribution and ancestry of each gene in 13 sequenced isolates of Escherichia coli and Shigella. We focus on the emergence and demise of two specific classes of genes, ORFans (genes with no homologs in present databases) and HOPs (genes with distant homologs), since these genes, in contrast to most conserved ancestral sequences, are known to be a major source of the novel features in each strain. We find that the rates of gain and loss of these genes vary greatly among strains as well as through time, and that ORFans and HOPs show very different behavior with respect to their emergence and demise. Although HOPs, which mostly represent gene acquisitions from other bacteria, originate more frequently, ORFans are much more likely to persist. This difference suggests that many adaptive traits are conferred by completely novel genes that do not originate in other bacterial genomes. With respect to the demise of these acquired genes, we find that strains of Shigella lose genes, both by disruption events and by complete removal, at accelerated rates.     

Numbers of genes in the NBS and RLK families vary by more than four-fold within a plant species and are regulated by multiple factors

Many genes exist in the form of families; however, little is known about their size variation, evolution and biology. Here, we present the size variation and evolution of the nucleotide-binding site (NBS)-encoding gene family and receptor-like kinase (RLK) gene family in Oryza, Glycine and Gossypium. The sizes of both families vary by numeral fold, not only among species, surprisingly, also within a species. The size variations of the gene families are shown to correlate with each other, indicating their interactions, and driven by natural selection, artificial selection and genome size variation, but likely not by polyploidization. The numbers of genes in the families in a polyploid species are similar to those of one of its diploid donors, suggesting that polyploidization plays little roles in the expansion of the gene families and that organisms tend not to maintain their ‘surplus’ genes in the course of evolution. Furthermore, it is found that the size variations of both gene families are associated with organisms’ phylogeny, suggesting their roles in speciation and evolution. Since both selection and speciation act on organism’s morphological, physiological and biological variation, our results indicate that the variation of gene family size provides a source of genetic variation and evolution.     

30株大肠杆菌的泛基因组学特征分析

泛基因组(Pan-genome)是某一物种全部基因的总称,其中包括核心基因组(该物种所有个体中都存在的基因)和非必须基因组(只在部分个体中存在的基因,以及某个体特有的基因)。文章从泛基因组学角度比较分析了30株已经完成测序的大肠杆菌的基因、基因组成及其进化特征,结果表明核心基因只占据每株大肠杆菌全部基因数目的 50%左右,而平均每个菌株有146个特有基因,结果表明随着更多大肠杆菌菌株的基因组被测序,将会不断有新基因被发现。通过比较分析大肠杆菌不同菌株之间基因的保守性与基因的GC含量以及选择压力之间的关系,发现越保守的基因其GC含量变化范围越窄,同时在进化中受到的选择压力也越大。这些结果将有助于深入了解大肠杆菌基因组的进化特征及其基因组成的动态变化,并为预防和控制由致病性大肠杆菌引发的流行疾病提供理论依据,同时也为大规模病原菌基因组数据的分析方法提供借鉴。     

Why mice have lost genes for COL21A1, STK17A, GPR145 and AHRI: evidence for gene deletion at evolutionary breakpoints in the rodent lineage

The mouse genome has undergone extensive chromosome rearrangement relative to the human genome since these species last shared a common ancestor. One possible consequence of these rearrangements is the deletion of genes that are located within evolutionary breakpoint regions. In this article, we present evidence of four human genes (COL21A1, STK17A, GPR145 and ARHI) that are located in regions corresponding to evolutionary breakpoints in rodents and lack mouse and rat orthologues. We propose that "evolutionary breakpoint-associated gene deletion" is an unexpected consequence of evolutionary chromosome rearrangement, and we describe a novel mechanism through which genes can be lost during evolution.     

Human and mouse protein-noncoding snoRNA host genes with dissimilar nucleotide sequences show chromosomal synteny

snoRNAs are small protein-noncoding RNAs essential for pre-rRNA processing and ribosome biogenesis, and are encoded intronically in host genes (HGs) that are either protein coding or noncoding. mRNAs of protein-noncoding HGs differ in their nucleotide sequences among species. Although the reason for such sequential divergence has not been well explained, we present evidence here that such structurally different HGs have evolved from a common ancestral gene. We first identified two novel protein-noncoding HGs (mU50HG-a and mU50HG-b) that intronically encode a mouse ortholog of a human snoRNA, hU50. The sequences of mU50HG mRNA differed from that of hU50HG. However, a chromosome mapping study revealed that mU50HG is located at 9E3-1, the murine segment syntenic to human 6q15, where hU50HG is located. Synteny is a phenomenon whereby gene orthologs are arranged in the same order at equivalent chromosomal loci in different species; synteny between two species means it is highly likely that the genes have evolved from a common ancestral gene. We then extended this mapping study to other protein-noncoding snoRNA-HGs, and found again that they are syntenic, implying that they have evolved from genes of common ancestral species. Furthermore, on these syntenic segments, exons of adjacent protein-coding genes were found to be far better conserved than those of noncoding HGs, suggesting that the exons of protein-noncoding snoRNA-HGs have been much more fragile during evolution.     

Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny

Although the possibility of gene evolution by domain rearrangements has long been appreciated, current methods for reconstructing and systematically analyzing gene family evolution are limited to events such as duplication, loss, and sometimes, horizontal transfer. However, within the Drosophila clade, we find domain rearrangements occur in 35.9% of gene families, and thus, any comprehensive study of gene evolution in these species will need to account for such events. Here, we present a new computational model and algorithm for reconstructing gene evolution at the domain level. We develop a method for detecting homologous domains between genes and present a phylogenetic algorithm for reconstructing maximum parsimony evolutionary histories that include domain generation, duplication, loss, merge (fusion), and split (fission) events. Using this method, we find that genes involved in fusion and fission are enriched in signaling and development, suggesting that domain rearrangements and reuse may be crucial in these processes. We also find that fusion is more abundant than fission, and that fusion and fission events occur predominantly alongside duplication, with 92.5% and 34.3% of fusion and fission events retaining ancestral architectures in the duplicated copies. We provide a catalog of ～9,000 genes that undergo domain rearrangement across nine sequenced species, along with possible mechanisms for their formation. These results dramatically expand on evolution at the subgene level and offer several insights into how new genes and functions arise between species.     

Evolution of a membrane protein regulon in Saccharomyces

Expression variation is widespread between species. The ability to distinguish regulatory change driven by natural selection from the consequences of neutral drift remains a major challenge in comparative genomics. In this work, we used observations of mRNA expression and promoter sequence to analyze signatures of selection on groups of functionally related genes in Saccharomycete yeasts. In a survey of gene regulons with expression divergence between Saccharomyces cerevisiae and S. paradoxus, we found that most were subject to variation in trans-regulatory factors that provided no evidence against a neutral model. However, we identified one regulon of membrane protein genes controlled by unlinked cis- and trans-acting determinants with coherent effects on gene expression, consistent with a history of directional, nonneutral evolution. For this membrane protein group, S. paradoxus alleles at regulatory loci were associated with elevated expression and altered stress responsiveness relative to other yeasts. In a phylogenetic comparison of promoter sequences of the membrane protein genes between species, the S. paradoxus lineage was distinguished by a short branch length, indicative of strong selective constraint. Likewise, sequence variants within the S. paradoxus population, but not across strains of other yeasts, were skewed toward low frequencies in promoters of genes in the membrane protein regulon, again reflecting strong purifying selection. Our results support a model in which a distinct expression program for the membrane protein genes in S. paradoxus has been preferentially maintained by negative selection as the result of an increased importance to organismal fitness. These findings illustrate the power of integrating expression- and sequence-based tests of natural selection in the study of evolutionary forces that underlie regulatory change.     

Gene regulation divergence is a major contributor to the evolution of Dobzhansky-Muller incompatibilities between species of Drosophila

The Dobzhansky-Muller model denotes incompatible gene interactions between diverging populations/species and is recognized as the basis of postzygotic reproductive isolation. Little is known about the molecular nature of such gene interactions. We have carried out comparative gene expression analyses in the testes of 3 closely related species of the Drosophila melanogaster subgroup and their hybrids (all of which are sterile). We show that in hybrids 1) a higher proportion of male-biased genes (i.e., genes with a higher level of expression in males) are underexpressed (or not expressed) compared with non-sex-biased genes, 2) the majority of the underexpressed genes appear to be under stabilizing selection by virtue of showing similar levels of expression in the parental species, and only a small proportion of genes show signs of directional selection, 3) very few of the misexpressed genes are shared between species pairs, suggesting that there may not be a "common" set of "speciation genes," and 4) expression of non-testes-specific genes is observed in the testes of interspecific hybrids, and the number of such genes is positively correlated with divergence time. These results suggest that gene regulation divergence of sex- and reproduction-related genes is a major contributor to the evolution of Dobzhansky-Muller incompatibilities between species of Drosophila.