The evolution of mimicry under constraints

The resemblance between mimetic organisms and their models varies from near perfect to very crude. One possible explanation, which has received surprisingly little attention, is that evolution can improve mimicry only at some cost to the mimetic organism. In this article, an evolutionary game theory model of mimicry is presented that incorporates such constraints. The model generates novel and testable predictions. First, Batesian mimics that are very common and/or mimic very weakly defended models should evolve either inaccurate mimicry (by stabilizing selection) or mimetic polymorphism. Second, Batesian mimics that are very common and/or mimic very weakly defended models are more likely to evolve mimetic polymorphism if they encounter predators at high rates and/or are bad at evading predator attacks. The model also examines how cognitive constraints acting on signal receivers may help determine evolutionarily stable levels of mimicry. Surprisingly, improved discrimination abilities among signal receivers may sometimes select for less accurate mimicry.     

Structural constraints and emergence of sequence patterns in protein evolution

The aim of this work was to study the relationship between structure conservation and sequence divergence in protein evolution. To this end, we developed a model of structurally constrained protein evolution (SCPE) in which trial sequences, generated by random mutations at gene level, are selected against departure from a reference three-dimensional structure. Since at the mutational level SCPE is completely unbiased, any emergent sequence pattern will be due exclusively to structural constraints. In this first report, it is shown that SCPE correctly predicts the characteristic hexapeptide motif of the left-handed parallel beta helix (LbetaH) domain of UDP-N-acetylglucosamine acyltransferases (LpxA).     

MatrixPlot: visualizing sequence constraints.

SUMMARY: MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information about the sequences (e.g. a sequence logo profile) along the edges of the plot, as well as zoom in on any region in the plot. AVAILABILITY: MatrixPlot can be obtained on request, and can also be accessed online at http://www. cbs.dtu.dk/services/MatrixPlot. CONTACT: gorodkin@cbs.dtu.dk     

RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods

We test models for the evolution of helical regions of RNA sequences, where the base pairing constraint leads to correlated compensatory substitutions occurring on either side of the pair. These models are of three types: 6-state models include only the four Watson-Crick pairs plus GU and UG; 7-state models include a single mismatch state that combines all of the 10 possible mismatches; 16-state models treat all mismatch states separately. We analyzed a set of eubacterial ribosomal RNA sequences with a well-established phylogenetic tree structure. For each model, the maximum-likelihood values of the parameters were obtained. The models were compared using the Akaike information criterion, the likelihood-ratio test, and Cox's test. With a high significance level, models that permit a nonzero rate of double substitutions performed better than those that assume zero double substitution rate. Some models assume symmetry between GC and CG, between AU and UA, and between GU and UG. Models that relaxed this symmetry assumption performed slightly better, but the tests did not all agree on the significance level. The most general time-reversible model significantly outperformed any of the simplifications. We consider the relative merits of all these models for molecular phylogenetics.     

Genetic constraints on the evolution of mate recognition under natural selection

Field populations of Drosophila serrata display reproductive character displacement in cuticular hydrocarbons (CHCs) when sympatric with Drosophila birchii. We have previously shown that the naturally occurring pattern of reproductive character displacement can be experimentally replicated by exposing field allopatric populations of D. serrata to experimental sympatry with D. birchii. Here, we tested whether the repeated evolution of reproductive character displacement in natural and experimental populations was a consequence of genetic constraints on the evolution of CHCs. The genetic variance-covariance (G) matrices for CHCs were determined for populations of D. serrata that had evolved in either the presence or absence of D. birchii under field and experimental conditions. Natural selection on mate recognition under both field and experimental sympatric conditions increased the genetic variance in CHCs consistent with a response to selection based on rare alleles. A close association between G eigenstructure and the eigenstructure of the phenotypic divergence (D) matrix in natural and experimental populations suggested that G matrix eigenstructure may have determined the direction in which reproductive character displacement evolved during the reinforcement of mate recognition.     

Structural constraints on the evolution of the collagen fibril: convergence on a 1014-residue COL domain

Type I collagen is the fundamental component of the extracellular matrix. Its α1 gene is the direct descendant of ancestral fibrillar collagen and contains 57 exons encoding the rod-like triple-helical COL domain. We trace the evolution of the COL domain from a primordial collagen 18 residues in length to its present 1014 residues, the limit of its possible length. In order to maintain and improve the essential structural features of collagen during evolution, exons can be added or extended only in permitted, non-random increments that preserve the position of spatially sensitive cross-linkage sites. Such sites cannot be maintained unless the twist of the triple helix is close to 30 amino acids per turn. Inspection of the gene structure of other long structural proteins, fibronectin and titin, suggests that their evolution might have been subject to similar constraints.     

Innovation from reduction: gene loss, domain loss and sequence divergence in genome evolution

Analyses of genome sequences have revealed a surprisingly variable distribution of genes, reflecting the generation of novel genes, lateral gene transfer and gene loss. The impact of gene loss on organisms has been difficult to examine, but the loss of protein coding genes, the loss of domains within proteins and the divergence of genes have made surprising contributions to the differences among organisms. This paper reviews surveys of gene loss and divergence in fungal and archaeal genomes that indicate suites of functionally related genes tend to undergo loss and divergence. Instances of fungal gene loss highlighted here suggest that specific cellular systems have changed, such as Ca 2+ biology in Saccharomyces cerevisiae and peroxisome function in Schizosaccharomyces pombe. Analyses of loss and divergence can provide specific predictions regarding protein-protein interactions, and the relationship between networks of protein interactions and loss may form a part of a parametric model of genome evolution.     

A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution

Variations of nucleotidic composition affect phylogenetic inference conducted under stationary models of evolution. In particular, they may cause unrelated taxa sharing similar base composition to be grouped together in the resulting phylogeny. To address this problem, we developed a nonstationary and nonhomogeneous model accounting for compositional biases. Unlike previous nonstationary models, which are branchwise, that is, assume that base composition only changes at the nodes of the tree, in our model, the process of compositional drift is totally uncoupled from the speciation events. In addition, the total number of events of compositional drift distributed across the tree is directly inferred from the data. We implemented the method in a Bayesian framework, relying on Markov Chain Monte Carlo algorithms, and applied it to several nucleotidic data sets. In most cases, the stationarity assumption was rejected in favor of our nonstationary model. In addition, we show that our method is able to resolve a well-known artifact. By Bayes factor evaluation, we compared our model with 2 previously developed nonstationary models. We show that the coupling between speciations and compositional shifts inherent to branchwise models may lead to an overparameterization, resulting in a lesser fit. In some cases, this leads to incorrect conclusions, concerning the nature of the compositional biases. In contrast, our compound model more flexibly adapts its effective number of parameters to the data sets under investigation. Altogether, our results show that accounting for nonstationary sequence evolution may require more elaborate and more flexible models than those currently used.     

The evolution of life histories under pleiotropic constraints and r-selection

A way of generating simple derivatives from H. Caswell's (1978, Theor. Pop. Biol.14, 215–230) population growth rate sensitivity measure is described that allows the analysis of pleiotropism involving modifications of an arbitrary number of life history parameters. Some cases are investigated that show that the precise nature of the pleiotropic constraints is critical in determining whether or not a new life history trait will be favored, thereby making it difficult to identify a single optimal life history. Caswell's measure is then generalized to cases in which the stable age distribution does not hold, a situation more applicable to many r-selected species.     

Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution

Background  

Proteins show a broad range of evolutionary rates. Understanding the factors that are responsible for the characteristic rate of evolution of a given protein arguably is one of the major goals of evolutionary biology. A long-standing general assumption used to be that the evolution rate is, primarily, determined by the specific functional constraints that affect the given protein. These constrains were traditionally thought to depend both on the specific features of the protein's structure and its biological role. The advent of systems biology brought about new types of data, such as expression level and protein-protein interactions, and unexpectedly, a variety of correlations between protein evolution rate and these variables have been observed. The strongest connections by far were repeatedly seen between protein sequence evolution rate and the expression level of the respective gene. It has been hypothesized that this link is due to the selection for the robustness of the protein structure to mistranslation-induced misfolding that is particularly important for highly expressed proteins and is the dominant determinant of the sequence evolution rate.     

Genetic constraints on protein evolution

Evolution requires the generation and optimization of new traits ("adaptation") and involves the selection of mutations that improve cellular function. These mutations were assumed to arise by selection of neutral mutations present at all times in the population. Here we review recent evidence that indicates that deleterious mutations are more frequent in the population than previously recognized and that these mutations play a significant role in protein evolution through continuous positive selection. Positively selected mutations include adaptive mutations, i.e. mutations that directly affect enzymatic function, and compensatory mutations, which suppress the pleiotropic effects of adaptive mutations. Compensatory mutations are by far the most frequent of the two and would allow potentially adaptive but deleterious mutations to persist long enough in the population to be positively selected during episodes of adaptation. Compensatory mutations are, by definition, context-dependent and thus constrain the paths available for evolution. This provides a mechanistic basis for the examples of highly constrained evolutionary landscapes and parallel evolution reported in natural and experimental populations. The present review article describes these recent advances in the field of protein evolution and discusses their implications for understanding the genetic basis of disease and for protein engineering in vitro.     

The domain model for eukaryotic DNA organization. 2: A molecular basis for constraints on development and evolution

A model for eukaryotic DNA organization has been proposed in which DNA regulatory processes depend on multiple site-specific DNA-nuclear matrix interactions throughout a DNA domain. In this model gene regulation depends on combinations of a few control factors in a cell to activate cell type-specific genes. This model suggests simple molecular mechanisms for organismal development which can account for sequential activation of appropriate groups of genes throughout development and for specific constraints on developmental pathways. Additionally, these suggested developmental pathways are consistent with mechanisms of evolution in which gradualism and punctuated equilibrium are not exclusive of one another and are interrelated mechanisms of evolution that are both induced by specific chromosomal mutations.     

Genome size evolution in vertebrates: trends and constraints

1. Studies on the genomic evolution in vertebrates have highlighted the differences existing between anamniotes and amniotes, both in quantitative and compositional terms. 2. These differences do not seem to depend on a different tendency to genic amplification, but rather on the existence of more strict and efficient constraints in amniotes. 3. Some constraints, that may be defined as "intrinsic", would act directly on the genome; among these particularly important is the chiasma frequency during meiosis. 4. Other, "extrinsic", constraints, would act indirectly through genic products or through cell morphometric parameters. 5. The genome size increase seems to depend on various mechanisms. The most wide-spread one seems to be the amplification of interspersed repetitive and non-repetitive sequences.     

Selective constraints on P-element evolution.

P elements, like mariners, inhabit eukaryotic genomes and transpose via a DNA intermediate. Mutant and wild-type elements in the same genome should be transposed with equal probability by trans-acting transposase, and so no selection should counteract the accumulation of inactivating mutations in transposase genes. Thus, copies of mariner elements diverge within a host species under no selection (Robertson and Lampe 1995). It is unknown whether or not this pattern holds for P elements, which are unrelated to mariner elements but share the same life history. Publicly available P-element sequences were analyzed for evidence of conservative selection for the function of P-element-encoded proteins. Results were compared to predictions derived from several hypotheses that could explain selection, or the lack of it. P-element protein-coding sequences do evolve under conservative selection but apparently because of more than one selective force. Of the four exons in the P-element transposase, the first three (exons 0, 1, and 2) can be translated alone into a repressor of transposition, while the last (exon 3) is only expressed as part of the full-length transposase and probably serves a transposition-specific role. As full-length P-element copies diverge from each other within a host population, selection maintains exons 0-2 but apparently not exon 3. The selection acting on exons 0-2 may act at the host level for repression of transposition (since host level selection does act on orthologous truncated elements that contain only exons 0-2). Evidence of selection on exon 3 is only found in comparisons of more diverged elements from different species, suggesting that selection for transposition acts primarily at horizontal transfer events. Thus, horizontal transfer events may be the sole source of the selection that is crucial to the maintenance of autonomous P elements in the face of mutation (as suggested by Robertson and Lampe 1995). The predictions derived here suggest a strategy for collecting sequence data that could definitively answer these questions.     

Recurrent intragenomic recombination leading to sequence homogenization during the evolution of the lipoyl-binding domain

The lipoyl-binding domain is often present, in one or several copies, in the E2 subunit and, less often, in the E1 and E3 subunits of 2-oxo acid dehydrogenase complexes. Phylogenetic analysis shows evidence of multiple, independent intragenomic recombination events between different versions of the lipoyl-binding domain in various bacteria and eukaryotic mitochondria, leading to homogenization of the sequences of the lipoyl-binding domain within the same enzymatic complex in several bacterial lineages. This appears to be the first case of sequence homogenization at the level of an individual domain in prokaryotes.     

Tissue strategies as developmental constraints: Implications for animal evolution

A consideration of developmental constraints at the tissue level brings into focus the relationship between genes, cell behavior and morphological evolution. This common framework provides a rationale for phenomena as seemingly divergent as the lack of homeotic appendages in humans and the Cambrian explosion.