Replicated evolution of integrated plastic responses during early adaptive divergence

Colonization of a novel environment is expected to result in adaptive divergence from the ancestral population when selection favors a new phenotypic optimum. Local adaptation in the new environment occurs through the accumulation and integration of character states that positively affect fitness. The role played by plastic traits in adaptation to a novel environment has generally been ignored, except for variable environments. We propose that if conditions in a relatively stable but novel environment induce phenotypically plastic responses in many traits, and if genetic variation exists in the form of those responses, then selection may initially favor the accumulation and integration of functionally useful plastic responses. Early divergence between ancestral and colonist forms will then occur with respect to their plastic responses across the gradient bounded by ancestral and novel environmental conditions. To test this, we compared the magnitude, integration, and pattern of plastic character responses in external body form induced by shallow versus open water conditions between two sunfish ecomorphs that coexist in four postglacial lakes. The novel sunfish ecomorph is present in the deeper open water habitat, whereas the ancestral ecomorph inhabits the shallow waters along the lake margin. Plastic responses by open water ecomorphs were more correlated than those of their local shallow water ecomorph in two of the populations, whereas equal levels of correlated plastic character responses occurred between ecomorphs in the other two populations. Small but persistent differences occurred between ecomorph pairs in the pattern of their character responses, suggesting a recent divergence. Open water ecomorphs shared some similarities in the covariance among plastic responses to rearing environment. Replication in the form of correlated plastic responses among populations of open water ecomorphs suggests that plastic character states may evolve under selection. Variation between ecomorphs and among lake populations in the covariance of plastic responses suggests the presence of genetic variation in plastic character responses. In three populations, open water ecomorphs also exhibited larger plastic responses to the environmental gradient than the local shallow water ecomorph. This could account for the greater integration of plastic responses in open water ecomorphs in two of the populations. This suggests that the plastic responses of local sunfish ecomorphs can diverge through changes in the magnitude and coordination of plastic responses. Although these results require further investigation, they suggest that early adaptive evolution in a novel environment can include changes to plastic character states. The genetic assimilation of coordinated plastic responses could result in the further, and possibly rapid, divergence of such populations and could also account for the evolution of genes of major effect that contribute to suites of phenotypic differences between divergent populations.     

The evolution of adaptive immune systems

A clonally diverse anticipatory repertoire in which each lymphocyte bears a unique antigen receptor is the central feature of the adaptive immune system that evolved in our vertebrate ancestors. The survival advantage gained through adding this type of adaptive immune system to a pre-existing innate immune system led to the evolution of alternative ways for lymphocytes to generate diverse antigen receptors for use in recognizing and repelling pathogen invaders. All jawed vertebrates assemble their antigen-receptor genes through recombinatorial rearrangement of different immunoglobulin or T cell receptor gene segments. The surviving jawless vertebrates, lampreys and hagfish, instead solved the receptor diversification problem by the recombinatorial assembly of leucine-rich-repeat genetic modules to encode variable lymphocyte receptors. The convergent evolution of these remarkably different adaptive immune systems involved innovative genetic modification of innate-immune-system components.     

The genomic rate of adaptive evolution

The role of positive darwinian selection in evolution at the molecular level has been keenly debated for many years, with little resolution. However, a recent increase in DNA sequence data and the development of new methods of analysis have finally made this question tractable. Here, I review the current state-of-play of the field. Initial estimates in Drosophila suggest that approximately 50% of all amino acid substitutions, and a substantial fraction of substitutions in non-coding DNA, have been fixed as a consequence of adaptive evolution. Estimates in microorganisms are even higher. By contrast, there is little evidence of widespread adaptive evolution in our own species.     

Molecular evolution of the calmodulin gene

On the basis of the intron/exon organization and the intramolecular homology of DNA sequences, I propose a novel model for genesis of the calmodulin gene. A primordial calmodulin gene consisting of 51 base pairs (17 amino acids) was subjected to three-fold duplication to create modern calmodulin with four calcium-binding subdomains. The model elucidates the seemingly enigmatic positions of splice junctions observed in calmodulin genes.     

The stochastic edge in adaptive evolution

In a recent article, Desai and Fisher proposed that the speed of adaptation in an asexual population is determined by the dynamics of the stochastic edge of the population, that is, by the emergence and subsequent establishment of rare mutants that exceed the fitness of all sequences currently present in the population. Desai and Fisher perform an elaborate stochastic calculation of the mean time tau until a new class of mutants has been established and interpret 1/tau as the speed of adaptation. As they note, however, their calculations are valid only for moderate speeds. This limitation arises from their method to determine tau: Desai and Fisher back extrapolate the value of tau from the best-fit class's exponential growth at infinite time. This approach is not valid when the population adapts rapidly, because in this case the best-fit class grows nonexponentially during the relevant time interval. Here, we substantially extend Desai and Fisher's analysis of the stochastic edge. We show that we can apply Desai and Fisher's method to high speeds by either exponentially back extrapolating from finite time or using a nonexponential back extrapolation. Our results are compatible with predictions made using a different analytical approach (Rouzine et al.) and agree well with numerical simulations.     

The evolution and adaptive significance of heterostyly

The origin and adaptive significance of heterostylous breeding systems have fascinated evolutionary biologists since Darwin's early work on the subject. Models of the evolution of heterostyly differ in the emphasis given to different selective forces and in the sequence in which the physiological and morphological components of the polymorphism are thought to arise. Recent field studies of the population biology of heterostylous plants provide support for Darwin's hypothesis that the style-stamen polymorphism promotes disassortative pollination among the floral morphs.     

Microbial adaptive evolution

Bacterial species can adapt to significant changes in their environment by mutation followed by selection, a phenomenon known as “adaptive evolution.” With the development of bioinformatics and genetic engineering, research on adaptive evolution has progressed rapidly, as have applications of the process. In this review, we summarize various mechanisms of bacterial adaptive evolution, the technologies used for studying it, and successful applications of the method in research and industry. We particularly highlight the contributions of Dr. L. O. Ingram. Microbial adaptive evolution has significant impact on our society not only from its industrial applications, but also in the evolution, emergence, and control of various pathogens.     

Predicting adaptive evolution

Phylogenetic trees reconstruct past evolution and can provide evidence of past evolutionary pressure on genes and on individual codons. In addition to tracing past evolutionary events, molecular phylogenetics might also be used to predict future evolution. Our ability to verify adaptive hypotheses using phylogenetics has broad implications for vaccine design, genomics and structural biology.     

The adaptive evolution database (TAED)

Background

The Master Catalog is a collection of evolutionary families, including multiple sequence alignments, phylogenetic trees and reconstructed ancestral sequences, for all protein-sequence modules encoded by genes in GenBank. It can therefore support large-scale genomic surveys, of which we present here The Adaptive Evolution Database (TAED). In TAED, potential examples of positive adaptation are identified by high values for the normalized ratio of nonsynonymous to synonymous nucleotide substitution rates (K_A/K_S values) on branches of an evolutionary tree between nodes representing reconstructed ancestral sequences.

Results

Evolutionary trees and reconstructed ancestral sequences were extracted from the Master Catalog for every subtree containing proteins from the Chordata only or the Embryophyta only. Branches with high K_A/K_S values were identified. These represent candidate episodes in the history of the protein family when the protein may have undergone positive selection, where the mutant form conferred more fitness than the ancestral form. Such episodes are frequently associated with change in function. An unexpectedly large number of families (between 10% and 20% of those families examined) were found to have at least one branch with high K_A/K_S values above arbitrarily chosen cut-offs (1 and 0.6). Most of these survived a robustness test and were collected into TAED.

Conclusions

TAED is a raw resource for bioinformaticists interested in data mining and for experimental evolutionists seeking candidate examples of adaptive evolution for further experimental study. It can be expanded to include other evolutionary information (for example changes in gene regulation or splicing) placed in a phylogenetic perspective.     

蝎对干旱环境的适应进化

蝎类是荒漠环境中占优势的无脊椎动物捕食者,在长期的适应进化过程中,发展出了一系列适应性特征。从形态结构、生理学、生物学和行为学等几个方面初步阐述了荒漠蝎类对干旱环境的适应进化问题。     

The rate of adaptive evolution in enteric bacteria

Here we estimate the rate of adaptive substitution in a set of 410 genes that are present in 6 Escherichia coli and 6 Salmonella enterica genomes. We estimate that more than 50% of amino acid substitutions in this set of genes have been fixed by positive selection between the E. coli and S. enterica lineages. We also show that the proportion of adaptive substitutions is uncorrelated with the rate of amino acid substitution or gene function but that it may be correlated with levels of synonymous codon usage bias.     

The evolution of early vertebrate photoreceptors

Meeting the challenge of sampling an ancient aquatic landscape by the early vertebrates was crucial to their survival and would establish a retinal bauplan to be used by all subsequent vertebrate descendents. Image-forming eyes were under tremendous selection pressure and the ability to identify suitable prey and detect potential predators was thought to be one of the major drivers of speciation in the Early Cambrian. Based on the fossil record, we know that hagfishes, lampreys, holocephalans, elasmobranchs and lungfishes occupy critical stages in vertebrate evolution, having remained relatively unchanged over hundreds of millions of years. Now using extant representatives of these ‘living fossils’, we are able to piece together the evolution of vertebrate photoreception. While photoreception in hagfishes appears to be based on light detection and controlling circadian rhythms, rather than image formation, the photoreceptors of lampreys fall into five distinct classes and represent a critical stage in the dichotomy of rods and cones. At least four types of retinal cones sample the visual environment in lampreys mediating photopic (and potentially colour) vision, a sampling strategy retained by lungfishes, some modern teleosts, reptiles and birds. Trichromacy is retained in cartilaginous fishes (at least in batoids and holocephalans), where it is predicted that true scotopic (dim light) vision evolved in the common ancestor of all living gnathostomes. The capacity to discriminate colour and balance the tradeoff between resolution and sensitivity in the early vertebrates was an important driver of eye evolution, where many of the ocular features evolved were retained as vertebrates progressed on to land.     

The early evolution of cellular life

Recent progress in data collection and analysis has changed the study of origin of life from an area dominated by speculation into a field abundant with testable hypotheses. This review discusses advances in the following areas: the fossil recordsd; the 'retrodiction' of biochemical pathways; and contradictions between different molecular phylogenies. The latter indicates a limited number of horizontal gene transfers during the early evolution. However, these cases of horizontal gene transfer are so infrequent that they can be detected as exceptions in an otherwise coherent picture. Cases of horizontal gene transfer can be recognized within the background of the majority consensus of molecular markers. The fusion of separate lineages to form new species is revealed by the simultaneous horizontal transfer of several independent genes.     

The molecular basis of adaptive evolution of squirrelfish rhodopsins

The wavelengths of maximal absorption (lambdamax) of the rhodopsins of nine squirrelfishes (N. sammara, N. argenteus, S. punctatissimum, S. microstoma, S. diadema, S. xantherythrum, S. spiniferum, N. aurolineatus, and S. tiere) and two soldierfishes (M. violacea and M. berndti) vary between 481 and 502 nm. Phylogenetic and mutagenesis analyses suggest that the common ancestor of these pigments had a lambdamax value of approximately 493 nm, and the contemporary lambdamax values were generated mostly by amino acid replacements E122M, F261Y, and A292S. The probability of observing all these amino acid replacements at specific branches of the phylogenetic tree is only 2.5 x 10(-9); it is highly unlikely that these changes have occurred by neutral evolution. Because of a close association between the lambdamax values of these pigments and the wavelengths of light available to the corresponding species, the excess number of amino acid changes at specific branches in the phylogenetic tree strongly suggests that the rhodopsins have undergone adaptive changes at various stages of the holocentrid evolution.     

无颌类脊椎动物适应性免疫系统的进化

适应性免疫系统的起源与进化问题一直是人们研究的热点, 以七鳃鳗为代表的无颌类脊椎动物, 被普遍认为处在进化出适应性免疫系统的边缘。因此, 研究无颌类脊椎动物适应性免疫的机制, 对揭示适应性免疫系统的起源与进化具有重要意义。研究表明, 无颌类在一定范围内具有高等脊椎动物特有的适应性免疫特征, 并发现了一些在结构或功能上与高等脊椎动物免疫相关基因同源的免疫因子。文章就近年来对无颌类脊椎动物适应性免疫系统机制的研究进展作一概述, 为进一步深入研究脊椎动物适应性免疫系统的起源与进化提供有益的参考。     

The problem of adaptive individual choice in cultural evolution

This paper tries to explain how individuals manage adaptive individual choice (i.e., the decision to acquire a fitter than average behavior or idea rapidly and tractably) in cultural evolution, despite the fact that acquiring fitness information is very difficult. I argue that the means of solving this problem suggested in the cultural evolution literature largely are various types of decision rules employing representations of fitness correlated properties or states of affairs. I argue that the problem of adaptive individual choice is best solved where some of these learning rule representations are socially transmitted and some are biologically transmitted.

The structural organization of the ascidian, Halocynthia roretzi, calmodulin genes. The vicissitude of introns during the evolution of calmodulin genes

Two distinct calmodulin (CaM) genes are isolated from the ascidian, Halocynthia roretzi, (Hr-CaM A and Hr-CaM B) and those structures are determined. There are three nucleotide substitutions, producing two amino acid differences between Hr-CaM A and Hr-CaM B, and those are corresponding to two of the known eight variable residues among metazoan CaMs. Both Hr-CaM A and Hr-CaM B are constructed from six exons and five introns, and the positions of introns are identical. The positions of introns of Hr-CaMs are also identical with those of vertebrate CaMs, except third introns. The third introns of Hr-CaMs are inserted at 28bp upstream when compared with vertebrate CaMs. Thus, sliding of the third intron might have occurred in only the ascidian lineage prior to the gene duplication that also occurred only in that lineage. In addition, with the comparison of the intron positions, we attempt to investigate the vicissitude of introns during the evolution of metazoan CaMs.