Comparative analyses for adaptive radiations

Biologists generally agree that most morphological variation between closely related species is adaptive. The most common method of comparative analysis to test for co-evolved character variation is based on a Brownian-motion model of character evolution. If we are to test for the evolution of character-covariation, and we believe that characters have evolved adaptively to fill niches during an adaptive radiation, then it is appropriate to employ appropriate models for character evolution. We show here that under several models of adaptive character evolution and coevolution during an adaptive radiation, which result in closely related species being more similar to each other than to more distantly related species, cross-species analyses are statistically more appropriate than contrast analyses. If the evolution of some traits fits the Brownian-motion model, while others evolve to fill niches during an adaptive radiation, it might be necessary to identify the number of relevant niche dimensions and the modes of character evolution before deciding on appropriate statistical procedures. Alternatively, maximum-likelihood procedures might be used to determine appropriate transformations of phylogenetic branch lengths that accord with particular models of character evolution.     

SINEs, evolution and genome structure in the opossum

Short INterspersed Elements (SINEs) are non-autonomous retrotransposons, usually between 100 and 500 base pairs (bp) in length, which are ubiquitous components of eukaryotic genomes. Their activity, distribution, and evolution can be highly informative on genomic structure and evolutionary processes. To determine recent activity, we amplified more than one hundred SINE1 loci in a panel of 43 M. domestica individuals derived from five diverse geographic locations. The SINE1 family has expanded recently enough that many loci were polymorphic, and the SINE1 insertion-based genetic distances among populations reflected geographic distance. Genome-wide comparisons of SINE1 densities and GC content revealed that high SINE1 density is associated with high GC content in a few long and many short spans. Young SINE1s, whether fixed or polymorphic, showed an unbiased GC content preference for insertion, indicating that the GC preference accumulates over long time periods, possibly in periodic bursts. SINE1 evolution is thus broadly similar to human Alu evolution, although it has an independent origin. High GC content adjacent to SINE1s is strongly correlated with bias towards higher AT to GC substitutions and lower GC to AT substitutions. This is consistent with biased gene conversion, and also indicates that like chickens, but unlike eutherian mammals, GC content heterogeneity (isochore structure) is reinforced by substitution processes in the M. domestica genome. Nevertheless, both high and low GC content regions are apparently headed towards lower GC content equilibria, possibly due to a relative shift to lower recombination rates in the recent Monodelphis ancestral lineage. Like eutherians, metatherian (marsupial) mammals have evolved high CpG substitution rates, but this is apparently a convergence in process rather than a shared ancestral state.     

A putative insect intracellular endosymbiont stem clade, within the Enterobacteriaceae, infered from phylogenetic analysis based on a heterogeneous model of DNA evolution.

Insect intracellular symbiotic bacteria (intracellular endosymbionts, or endocytobionts) were positioned within the gamma 3-Proteobacteria using a non-homogeneous model of DNA evolution, allowing for rate variability among sites, for GC content heterogeneity among sequences, and applied to a maximum likelihood framework. Most of them were found to be closely related within the Enterobacteriaceae family, located between Proteus and Yersinia. These results suggest that such a bacterial group might possess several traits allowing for insect infection and the stable establishment of symbiotic relationships and that this could represent a stem clade for numerous insect endocytobionts. Based on the estimations of the equilibrium GC content and branch lengths in the phylogenetic tree, we have made comparisons of the relative ages of these different symbioses.     

Mutation Exposed: A Neutral Explanation for Extreme Base Composition of an Endosymbiont Genome

The influence of neutral mutation pressure versus selection on base composition evolution is a subject of considerable controversy. Yet the present study represents the first explicit population genetic analysis of this issue in prokaryotes, the group in which base composition variation is most dramatic. Here, we explore the impact of mutation and selection on the dynamics of synonymous changes in Buchnera aphidicola, the AT-rich bacterial endosymbiont of aphids. Specifically, we evaluated three forms of evidence. (i) We compared the frequencies of directional base changes (ATGC vs. GCAT) at synonymous sites within and between Buchnera species, to test for selective preference versus effective neutrality of these mutational categories. Reconstructed mutational changes across a robust intraspecific phylogeny showed a nearly 1:1 ATGC:GCAT ratio. Likewise, stationarity of base composition among Buchnera species indicated equal rates of ATGC and GCAT substitutions. The similarity of these patterns within and between species supported the neutral model. (ii) We observed an equivalence of relative per-site AT mutation rate and current AT content at synonymous sites, indicating that base composition is at mutational equilibrium. (iii) We demonstrated statistically greater equality in the frequency of mutational categories in Buchnera than in parallel mammalian studies that documented selection on synonymous sites. Our results indicate that effectively neutral mutational pressure, rather than selection, represents the major force driving base composition evolution in Buchnera. Thus they further corroborate recent evidence for the critical role of reduced N_e in the molecular evolution of bacterial endosymbionts.Reviewing Editor: Dr. J. William Ballard     

Across bacterial phyla, distantly-related genomes with similar genomic GC content have similar patterns of amino acid usage

The GC content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic GC content are observed within many bacterial phyla, including both gram negative and gram positive phyla. Thus, divergent genomic GC content has evolved repeatedly in widely separated bacterial taxa. Since genomic GC content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic GC content within eight different phyla or classes of bacteria. We found that similar patterns of codon usage and protein amino acid content have evolved independently in all eight groups of bacteria. For example, in each group, use of amino acids encoded by GC-rich codons increased by approximately 1% for each 10% increase in genomic GC content, while the use of amino acids encoded by AT-rich codons decreased by a similar amount. This consistency within every phylum and class studied led us to conclude that GC content appears to be the primary determinant of the codon and amino acid usage patterns observed in bacterial genomes. These results also indicate that selection for translational efficiency of highly expressed genes is constrained by the genomic parameters associated with the GC content of the host genome.     

Horizontal gene transfer depends on gene content of the host

Horizontal gene transfer is a major contributor to the evolution of bacterial genomes. We examine this process through a combination of comparative genomics and in silico analysis of the Escherichia coli metabolic network. We validate our horizontal transfer estimates by confirming the predicted gradual amelioration of GC content over time. We find that the chance of acquiring a gene by horizontal transfer is up to six times higher if an enzyme that catalyses a coupled metabolite flux is already encoded in the host genome.     

Single Cell Analysis of a Bacterial Sender-Receiver System

Monitoring gene expression dynamics on the single cell level provides important information on cellular heterogeneity and stochasticity, and potentially allows for more accurate quantitation of gene expression processes. We here study bacterial senders and receivers genetically engineered with components of the quorum sensing system derived from Aliivibrio fischeri on the single cell level using microfluidics-based bacterial chemostats and fluorescence video microscopy. We track large numbers of bacteria over extended periods of time, which allows us to determine bacterial lineages and filter out subpopulations within a heterogeneous population. We quantitatively determine the dynamic gene expression response of receiver bacteria to varying amounts of the quorum sensing inducer N-3-oxo-C6-homoserine lactone (AHL). From this we construct AHL response curves and characterize gene expression dynamics of whole bacterial populations by investigating the statistical distribution of gene expression activity over time. The bacteria are found to display heterogeneous induction behavior within the population. We therefore also characterize gene expression in a homogeneous bacterial subpopulation by focusing on single cell trajectories derived only from bacteria with similar induction behavior. The response at the single cell level is found to be more cooperative than that obtained for the heterogeneous total population. For the analysis of systems containing both AHL senders and receiver cells, we utilize the receiver cells as ‘bacterial sensors’ for AHL. Based on a simple gene expression model and the response curves obtained in receiver-only experiments, the effective AHL concentration established by the senders and their ‘sending power’ is determined.     

Role of premature stop codons in bacterial evolution

When the stop codons TGA, TAA, and TAG are found in the second and third reading frames of a protein-encoding gene, they are considered premature stop codons (PSC). Deinococcus radiodurans disproportionately favored TGA more than the other two triplets as a PSC. The TGA triplet was also found more often in noncoding regions and as a stop codon, though the bias was less pronounced. We investigated this phenomenon in 72 bacterial species with widely differing chromosomal GC contents. Although TGA and TAG were compositionally similar, we found a great variation in use of TGA but a very limited range of use of TAG. The frequency of use of TGA in the gene sequences generally increased with the GC content of the chromosome, while the frequency of use of TAG, like that of TAA, was inversely proportional to the GC content of the chromosome. The patterns of use of TAA, TGA and TAG as real stop codons were less biased and less influenced by the GC content of the chromosome. Bacteria with higher chromosomal GC contents often contained fewer PSC trimers in their genes. Phylogenetically related bacteria often exhibited similar PSC ratios. In addition, metabolically versatile bacteria have significantly fewer PSC trimers in their genes. The bias toward TGA but against TAG as a PSC could not be explained either by the preferential usage of specific codons or by the GC contents of individual chromosomes. We proposed that the quantity and the quality of the PSC in the genome might be important in bacterial evolution.     

Rapid determination of nucleotide content and its application to the study of genome structure.

We have developed a sensitive, reliable and accurate procedure for estimating the base composition of small samples of DNAs. This method has been applied to the analysis of genomic DNAs from several sources including large regions of human DNA cloned as yeast artificial chromosomes. To determine whether the human genome is compartmentalized into large segments of homogeneous base composition, we examined the GC content of a 1.2 megabase contig spanning the cystic fibrosis gene.     

A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents.

We present a new likelihood method for detecting constrained evolution at synonymous sites and other forms of nonneutral evolution in putative pseudogenes. The model is applicable whenever the DNA sequence is available from a protein-coding functional gene, a pseudogene derived from the protein-coding gene, and an orthologous functional copy of the gene. Two nested likelihood ratio tests are developed to test the hypotheses that (1) the putative pseudogene has equal rates of silent and replacement substitutions; and (2) the rate of synonymous substitution in the functional gene equals the rate of substitution in the pseudogene. The method is applied to a data set containing 74 human processed-pseudogene loci, 25 mouse processed-pseudogene loci, and 22 rat processed-pseudogene loci. Using the informatics resources of the Human Genome Project, we localized 67 of the human-pseudogene pairs in the genome and estimated the GC content of a large surrounding genomic region for each. We find that, for pseudogenes deposited in GC regions similar to those of their paralogs, the assumption of equal rates of silent and replacement site evolution in the pseudogene is upheld; in these cases, the rate of silent site evolution in the functional genes is approximately 70% the rate of evolution in the pseudogene. On the other hand, for pseudogenes located in genomic regions of much lower GC than their functional gene, we see a sharp increase in the rate of silent site substitutions, leading to a large rate of rejection for the pseudogene equality likelihood ratio test.     

FROM METABOLISM TO POLYMORPHISM IN BACTERIAL POPULATIONS: A THEORETICAL STUDY

Abstract Stable polymorphisms are commonly observed in experimental bacterial populations grown in homogeneous media. Evidence is accumulating that metabolic interactions might be the main mechanism underlying the emergence and maintenance of such polymorphisms. To date, however, attempts to model the evolution of bacterial polymorphism have not considered metabolism as a possible component of polymorphism maintenance. Here, we propose a simulation approach to model the evolution of selected polymorphisms in a bacterial population. Using recent knowledge of the relationship between bacterial fitness and metabolism, we build a simple metabolic model and test the effect of resource competition on polymorphism. Without making an a priori hypothesis on fitness functions, we show that stable polymorphic situations could be observed under high nutrient competition, and we propose a functional, metabolism‐based explanation to the debated issue of polymorphism maintenance.     

Integrating genomics,bioinformatics, and classical genetics to study the effects of recombination on genome evolution

This study presents compelling evidence that recombination significantly increases the silent GC content of a genome in a selectively neutral manner, resulting in a highly significant positive correlation between recombination and "GC3s" in the yeast Saccharomyces cerevisiae. Neither selection nor mutation can explain this relationship. A highly significant GC-biased mismatch repair system is documented for the first time in any member of the Kingdom Fungi. Much of the variation in the GC3s within yeast appears to result from GC-biased gene conversion. Evidence suggests that GC-biased mismatch repair exists in numerous organisms spanning six kingdoms. This transkingdom GC mismatch repair bias may have evolved in response to a ubiquitous AT mutational bias. A significant positive correlation between recombination and GC content is found in many of these same organisms, suggesting that the processes influencing the evolution of the yeast genome may be a general phenomenon. Nonrecombining regions of the genome and nonrecombining genomes would not be subject to this type of molecular drive. It is suggested that the low GC content characteristic of many nonrecombining genomes may be the result of three processes (1) a prevailing AT mutational bias, (2) random fixation of the most common types of mutation, and (3) the absence of the GC-biased gene conversion which, in recombining organisms, permits the reversal of the most common types of mutation. A model is proposed to explain the observation that introns, intergenic regions, and pseudogenes typically have lower GC content than the silent sites of corresponding open reading frames. This model is based on the observation that the greater the heterology between two sequences, the less likely it is that recombination will occur between them. According to this "Constraint" hypothesis, the formation and propagation of heteroduplex DNA is expected to occur, on average, more frequently within conserved coding and regulatory regions of the genome. In organisms possessing GC-biased mismatch repair, this would enhance the GC content of these regions through biased gene conversion. These findings have a number of important implications for the way we view genome evolution and suggest a new model for the evolution of sex.     

Birth-and-death evolution of the internalin multigene family in Listeria

The birth-and-death model of multigene family evolution describes patterns of gene origination, diversification and loss within multigene families. Since it was first developed in the 1990s, the model has been found to characterize a large number of eukaryotic multigene families. In this paper, we report for the first time a bacterial multigene family that undergoes birth-and-death evolution. By analyzing the evolutionary relationships among internalins, a relatively large and diverse family of genes associated with key virulence functions in Listeria, we demonstrate the importance of birth-and-death evolution in the diversification of this important bacterial pathogen. We also detected two instances of lateral gene transfer within the internalins, but the estimated frequency would have been much higher had it not been analyzed within the context of birth-and-death evolutionary dynamics and a phenomenon that we term "paralog-sorting", which involves the unequal transmittal of gene duplicates during or subsequent to the speciation process. As such, in addition to providing the first demonstration of birth-and-death evolution within a bacterial multigene family, our results indicate that the extent of lateral transfer in bacterial multigene families should be re-examined in the light of birth-and-death evolution.     

Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles

We review and further develop an analytical model that describes how thermodynamic constraints on the stability of the native state influence protein evolution in a site-specific manner. To this end, we represent both protein sequences and protein structures as vectors: structures are represented by the principal eigenvector (PE) of the protein contact matrix, a quantity that resembles closely the effective connectivity of each site; sequences are represented through the "interactivity" of each amino acid type, using novel parameters that are correlated with hydropathy scales. These interactivity parameters are more strongly correlated than the other hydropathy scales that we examine with: (1) the change upon mutations of the unfolding free energy of proteins with two-states thermodynamics; (2) genomic properties as the genome-size and the genome-wide GC content; (3) the main eigenvectors of the substitution matrices. The evolutionary average of the interactivity vector correlates very strongly with the PE of a protein structure. Using this result, we derive an analytic expression for site-specific distributions of amino acids across protein families in the form of Boltzmann distributions whose "inverse temperature" is a function of the PE component. We show that our predictions are in agreement with site-specific amino acid distributions obtained from the Protein Data Bank, and we determine the mutational model that best fits the observed site-specific amino acid distributions. Interestingly, the optimal model almost minimizes the rate at which deleterious mutations are eliminated by natural selection.     

A test of the null model for 5' UTR evolution based on GC content

Eukaryotic mRNAs are headed by a stretch of noncoding sequence,the 5' untranslated region (UTR). It has been proposed thatthe length of 5' UTRs is selectively neutral and evolves undera process of stochastic destruction and recruitment of corepromoter elements, combined with selection against the prematureinitiation of translation. We test this null model by investigatingwhether 5' UTR length varies with genomic GC content, an implicitprediction of the model. Using simulations, we show that thenull model predicts a positive relationship between GC contentand UTR length for genes regulated by a TATA box. Although thisprediction is borne out qualitatively in genomic data from yeast,fruit flies, and humans, we find marked quantitative discrepancies.We conclude that UTR length may be shaped to some degree bythe forces considered in the null model but that the model failsto provide a complete explanation for UTR length evolution.