Detecting excess radical replacements in phylogenetic trees

Molecular evolution and genetic diversity of defective chorion 1 in Anastrepha fraterculus and Anastrepha obliqua (Diptera, Tephritidae)

The family Tephritidae comprises numerous fruit fly species, some of which are economically significant, such as several in the genus Anastrepha. Most pest species in this genus belong to the fraterculus group, characterized by closely related species that are difficult to differentiate due to recent divergence and gene flow. Identifying genetic markers for their study is paramount for understanding the group's evolution and eventual phytosanitary control. Because there is variation in eggshell morphology among species in the genus, the study of the rapidly evolving defective chorion 1 (dec-1) gene, which is crucial for chorion formation and reproduction, could provide relevant information for Anastrepha differentiation. We compared transcriptome sequences of dec-1 from two of the most important pest species in the genus, Anastrepha fraterculus and Anastrepha obliqua to dec-1 sequences from Anastrepha ludens, which was used for structure prediction. Furthermore, we amplified a conserved exon across populations of these species. These data revealed three alternative transcripts in A. fraterculus and A. obliqua, consistent with patterns found in other Tephritidae; we obtained orthologous sequences for these other tephritids from NCBI to investigate patterns of selection affecting this gene at different hierarchical levels using different methods. These analyses show a general pattern of purifying selection across the whole gene and throughout its history at different hierarchical levels, from populations to more distantly related species. That notwithstanding, we still found evidence of positive and episodic diversifying selection at different levels. Different parts of the gene have shown distinct evolutionary rates, which were associated with the diverse proproteins produced by posttranslational changes of DEC-1, with proproteins that are incorporated in the chorion earlier in egg formation being in general more conserved than others that are incorporated later. This correlation appears more evident in certain lineages, including the branch that separates Anastrepha, as well as other internal branches that differentiate species within the genus. Our data showed that this gene shows remarkable variation across its different exons, which has proven to be informative at different evolutionary levels. These changes hold promise not only for studying differentiation in Anastrepha but also for the eventual management of selected pest species.

Evidence for the Selective Basis of Transition-to-Transversion Substitution Bias in Two RNA Viruses

The substitution rates of transitions are higher than expected by chance relative to those of transversions. Many have argued that selection disfavors transversions, as nonsynonymous transversions are less likely to conserve biochemical properties of the original amino acid. Only recently has it become feasible to directly test this selective hypothesis by comparing the fitness effects of a large number of transition and transversion mutations. For example, a recent study of six viruses and one beta-lactamase gene did not find evidence supporting the selective hypothesis. Here, we analyze the relative fitness effects of transition and transversion mutations from our recently published genome-wide study of mutational fitness effects in influenza virus. In contrast to prior work, we find that transversions are significantly more detrimental than transitions. Using what we believe to be an improved statistical framework, we also identify a similar trend in two HIV data sets. We further demonstrate a fitness difference in transition and transversion mutations using four deep mutational scanning data sets of influenza virus and HIV, which provided adequate statistical power. We find that three of the most commonly cited radical/conservative amino acid categories are predictive of fitness, supporting their utility in studies of positive selection and codon usage bias. We conclude that selection is a major contributor to the transition:transversion substitution bias in viruses and that this effect is only partially explained by the greater likelihood of transversion mutations to cause radical as opposed to conservative amino acid changes.

Adaptive evolution of the chrysanthemyl diphosphate synthase gene involved in irregular monoterpene metabolism

BACKGROUND

Chrysanthemyl diphosphate synthase (CDS) is a key enzyme in biosynthetic pathways producing pyrethrins and irregular monoterpenes. These compounds are confined to plants of the tribe Anthemideae of the Asteraceae, and play an important role in defending the plants against herbivorous insects. It has been proposed that the CDS genes arose from duplication of the farnesyl diphosphate synthase (FDS) gene and have different function from FDSs. However, the duplication time toward the origin of CDS and the evolutionary force behind the functional divergence of the CDS gene are still unknown.

RESULTS

Two duplication events were detected in the evolutionary history of the FDS gene family in the Asteraceae, and the second duplication led to the origin of CDS. CDS occurred after the divergence of the tribe Mutisieae from other tribes of Asteraceae but before the birth of the Anthemideae tribe. After its origin, CDS accumulated four mutations in sites homologous to the substrate-binding and catalysis sites of FDS. Of these, two sites were involved in the binding of the nucleophilic substrate isopentenyl diphosphate in FDS. Maximum likelihood analyses showed that some sites in CDS were under positive selection and were scattered throughout primary sequences, whereas in the three-dimensional structure model they clustered in the large central cavity.

CONCLUSION

Positive selection associated with gene duplication played a major role in the evolution of CDS.

Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping

Genes and genomes do not evolve similarly in all branches of the tree of life. Detecting and characterizing the heterogeneity in time, and between lineages, of the nucleotide (or amino acid) substitution process is an important goal of current molecular evolutionary research. This task is typically achieved through the use of non-homogeneous models of sequence evolution, which being highly parametrized and computationally-demanding are not appropriate for large-scale analyses. Here we investigate an alternative methodological option based on probabilistic substitution mapping. The idea is to first reconstruct the substitutional history of each site of an alignment under a homogeneous model of sequence evolution, then to characterize variations in the substitution process across lineages based on substitution counts. Using simulated and published datasets, we demonstrate that probabilistic substitution mapping is robust in that it typically provides accurate reconstruction of sequence ancestry even when the true process is heterogeneous, but a homogeneous model is adopted. Consequently, we show that the new approach is essentially as efficient as and extremely faster than (up to 25 000 times) existing methods, thus paving the way for a systematic survey of substitution process heterogeneity across genes and lineages.

Reduced selective constraint in endosymbionts: elevation in radical amino acid replacements occurs genome-wide

As predicted by the nearly neutral model of evolution, numerous studies have shown that reduced N(e) accelerates the accumulation of slightly deleterious changes under genetic drift. While such studies have mostly focused on eukaryotes, bacteria also offer excellent models to explore the effects of N(e). Most notably, the genomes of host-dependent bacteria with small N(e) show signatures of genetic drift, including elevated K(a)/K(s). Here, I explore the utility of an alternative measure of selective constraint: the per-site rate of radical and conservative amino acid substitutions (D(r)/D(c)). I test the hypothesis that purifying selection against radical amino acid changes is less effective in two insect endosymbiont groups (Blochmannia of ants and Buchnera of aphids), compared to related gamma-Proteobacteria. Genome comparisons demonstrate a significant elevation in D(r)/D(c) in endosymbionts that affects the majority (66-79%) of shared orthologs examined. The elevation of D(r)/D(c) in endosymbionts affects all functional categories examined. Simulations indicate that D(r)/D(c) estimates are sensitive to codon frequencies and mutational parameters; however, estimation biases occur in the opposite direction as the patterns observed in genome comparisons, thereby making the inference of elevated D(r)/D(c) more conservative. Increased D(r)/D(c) and other signatures of genome degradation in endosymbionts are consistent with strong effects of genetic drift in their small populations, as well as linkage to selected sites in these asexual bacteria. While relaxed selection against radical substitutions may contribute, genome-wide processes such as genetic drift and linkage best explain the pervasive elevation in D(r)/D(c) across diverse functional categories that include basic cellular processes. Although the current study focuses on a few bacterial lineages, it suggests D(r)/D(c) is a useful gauge of selective constraint and may provide a valuable alternative to K(a)/K(s) when high sequence divergences preclude estimates of K(s). Broader application of D(r)/D(c) will benefit from approaches less prone to estimation biases.

Evolutionary patterns of amino acid substitutions in 12 Drosophila genomes

BACKGROUND

Harnessing vast amounts of genomic data in phylogenetic context stemming from massive sequencing of multiple closely related genomes requires new tools and approaches. We present a tool for the genome-wide analysis of frequencies and patterns of amino acid substitutions in multiple alignments of genes' coding regions, and a database of amino acid substitutions in the phylogeny of 12 Drosophila genomes. We illustrate the use of these resources to address three types of evolutionary genomics questions: about fluxes in amino acid composition in proteins, about asymmetries in amino acid substitutions and about patterns of molecular evolution in duplicated genes.

RESULTS

We demonstrate that amino acid composition of Drosophila proteins underwent a significant shift over the last 70 million years encompassed by the studied phylogeny, with less common amino acids (Cys, Met, His) increasing in frequency and more common ones (Ala, Leu, Glu) becoming less frequent. These fluxes are strongly correlated with polarity of source and destination amino acids, resulting in overall systematic decrease of mean polarity of amino acids found in Drosophila proteins. Frequency and radicality of amino acid substitutions are higher in paralogs than in orthologous single-copy genes and are higher in gene families with paralogs than in gene families without surviving duplications. Rate and radicality of substitutions, as expected, are negatively correlated with overall level and uniformity of gene expression. However, these correlations are not observed for substitutions occurring in duplicated genes, indicating a different selective constraint on the evolution of paralogous sequences. Clades resulting from duplications show a marked asymmetry in rate and radicality of amino acid substitutions, possibly a signal of widespread neofunctionalization. These patterns differ among protein families of different functionality, with genes coding for RNA-binding proteins differing from most other functional groups in terms of amino acid substitution patterns in duplicated and single-copy genes.

CONCLUSIONS

We demonstrate that deep phylogenetic analysis of amino acid substitutions can reveal interesting genome-wide patterns. Amino acid composition of drosophilid proteins is shaped by fluxes similar to those previously observed in prokaryotic, yeast and mammalian genomes, indicating globally present patterns. Increased frequency and radicality of amino acid substitutions in duplicated genes and the presence of asymmetry of these parameters between paralogous clades indicate widespread neofunctionalization among paralogs as the mechanism of duplication retention.

Characterizing molecular adaptation: a hierarchical approach to assess the selective influence of amino acid properties

MOTIVATION

A number of methods for detecting positive selection in protein coding DNA sequences are based on whether each site/region has a non-synonymous to synonymous substitution rates ratio ω greater than one. However, a site/region may show a relatively large number of non-synonymous mutations that conserve a particular property. Recent methods have proposed to consider as evidence for molecular adaptations how conserving, or radically different, non-synonymous mutations are with respect to some key amino acid properties. While such methods have been useful in providing a qualitative assessment of molecular adaptation, they rely on independent statistical analyses for each amino acid property and typically do not properly adjust for multiple comparisons when selection needs to be assessed at several sites.

RESULTS

We consider a Bayesian hierarchical model that allows us to jointly determine if a set of amino acid properties are being conserved or radically changed while simultaneously adjusting for multiple comparisons at the codon level. We illustrate how this model can be used to characterize molecular adaptation in two datasets: an alignment from six class I alleles of the human major histocompatibility complex and a sperm lysin alignment from 25 abalone species. We compare the results obtained with the proposed hierarchical models to those obtained with alternative methods. Our analyses indicate that a more complete quantitative and qualitative characterization of molecular adaptation is achieved by taking into account changes in amino acid properties.

AVAILABILITY

The R code for implementing the hierarchical models is freely available at http://www.ams.ucsc.edu/∼raquel/software/.

Evolution of BK virus based on complete genome data

The human polyomavirus BK virus (BKV) is ubiquitous in humans, infecting children asymptomatically. BKV is the only primate polyomavirus that has subtypes (I-IV) distinguishable by immunological reactivity. Nucleotide (nt) variations in a major capsid protein (VP1) gene region (designated the epitope region), probably responsible for antigenic diversity, have been used to classify BKV isolates into subtypes. Here, with all the protein-encoding gene sequences, we attempted to elucidate the evolutionary relationships among 28 BKV isolates belonging to subtypes I, III, and IV (no isolate belonging to subtype II, a minor one, was included). First, using the GTR + Gamma + I model, maximum likelihood trees were reconstructed for individual viral genes as well as for concatenated viral genes. On the resultant trees, the 28 BKV isolates were consistently divided into three clades corresponding to subtypes I, III, and IV, although bootstrap probabilities are not always high. Then we used more sophisticated likelihood models, one of which takes account of codon structure, to elucidate the phylogenetic relationships among BKV subtypes, but the phylogeny of the deep branchings remained ambiguous. Furthermore, the possibility of positive selection in the evolution of BKV was examined using the nonsynonymous/synonymous rate ratio as a measure of selection. An analysis based on entire genes could not detect any strong evidence for positive selection, but that based on the epitope region identified a few sites potentially under positive selection (these sites were among those showing subtype linked polymorphisms).

Molecular evolution of animal antimicrobial peptides: widespread moderate positive selection

An increasing number of studies in both vertebrates and invertebrates show that the evolution of antimicrobial peptides is driven by positive selection. Because these diverse molecules show potential for therapeutic applications, they are currently the targets of much structural and functional research, providing extensive background data for evolutionary studies. In this paper, patterns of molecular evolution in antimicrobial peptide genes are reviewed. Evidence for positive selection on antimicrobial peptides includes an excess of nonsynonymous nucleotide substitutions, an excess of charge-changing amino acid substitutions, nonneutral patterns of allelic variation, and functional assays in vivo and in vitro that show improved antimicrobial effects for derived sequence variants. Positive selection on antimicrobial peptides may be as common as, but perhaps weaker than, selection on the best-known example of adaptively evolving immunity genes, the major histocompatibility complex. Thus, antimicrobial peptides present a useful and underutilized model for the study of adaptive molecular evolution.

Enhanced Synonymous Site Divergence in Positively Selected VertebrateAntimicrobial Peptide Genes

Nonrandom patterns associated with adaptively evolving genes can shed light on how selection and mutation produce rapid changes in sequences. I examine such patterns in two independent families of antimicrobial peptide genes: those in frogs, which are known to have evolved under positive selection, and those in flatfishes, which I show have also evolved under positive selection. I address two recently proposed hypotheses about the molecular evolution of antimicrobial peptide genes. The first is that the mature peptide region is replicated by an error-prone polymerase that increases the mutation rate and the transversion/transition ratio compared to the signal sequence of the same genes. The second is that mature peptides evolve in a coordinated fashion with their propieces, such that a change in net charge in one molecular region prompts an opposite change in charge in the other region. I test these hypotheses using alternative methods that minimize alignment errors, correct for phylogenetic nonindependence, reduce sequence saturation, and account for differing selection pressures on different regions of the gene. In both gene families I show that divergence at both synonymous and nonsynonymous sites within the mature peptide region is enhanced. However, in neither gene family is there evidence of an increased mutational transversion/transition ratio or coordinated evolution. My observations are consistent with either an elevated mutation rate in an adaptively evolving gene region or widespread selection on "silent" sites. These hypotheses challenge the assumption that mutations are random and can be measured by the synonymous substitution rate.

The exchangeability of amino acids in proteins

The comparative analysis of protein sequences depends crucially on measures of amino acid similarity or distance. Many such measures exist, yet it is not known how well these measures reflect the operational exchangeability of amino acids in proteins, since most are derived by methods that confound a variety of effects, including effects of mutation. In pursuit of a pure measure of exchangeability, we present (1) a compilation of data on the effects of 9671 amino acid exchanges engineered and assayed in a set of 12 proteins; (2) a statistical procedure to combine results from diverse assays of exchange effects; (3) a matrix of "experimental exchangeability" values EX(ij) derived from applying this procedure to the compiled data; and (4) a set of three tests designed to evaluate the power of an exchangeability measure to (i) predict the effects of amino acid exchanges in the laboratory, (ii) account for the disease-causing potential of missense mutations in the human population, and (iii) model the probability of fixation of missense mutations in evolution. EX not only captures useful information on exchangeability while remaining free of other effects, but also outperforms all measures tested except for the best-performing alignment scoring matrix, which is comparable in performance.

A Model-Based Approach for Detecting Coevolving Positions in a Molecule

We present a new method for detecting coevolving sites in molecules. The method relies on a set of aligned sequences (nucleic acid or protein) and uses Markov models of evolution to map the substitutions that occurred at each site onto the branches of the underlying phylogenetic tree. This mapping takes into account the uncertainty over ancestral states and among-site rate variation. We then build, for each site, a "substitution vector" containing the posterior estimates of the number of substitutions in each branch. The amount of coevolution for a pair of sites is then measured as the Pearson correlation coefficient between the two corresponding substitution vectors and compared to the expectation under the null hypothesis of independence. We applied the method to a 79-species bacterial ribosomal RNA data set, for which extensive structural characterization has been done over the last 30 years. More than 95% of the intramolecular predicted pairs of sites correspond to known interacting site pairs.