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PubMed2005

Qualitative differences between naïve and scientific theories of evolution.

Philosophers of biology have long argued that Darwin's theory of evolution was qualitatively different from all earlier theories of evolution. Whereas Darwin's predecessors and contemporaries explained adaptation as the transformation of a species' "essence," Darwin explained adaptation as the selective propagation of randomly occurring mutations within a population. The present study explored the possibility of a parallel between early "transformational" theories of evolution and modern naïve theories. Forty-two high school and college students and three evolutionary biologists were tested on their understanding of six evolutionary phenomena: variation, inheritance, adaptation, domestication, speciation, and extinction. As predicted, a plurality of participants demonstrated transformational reasoning inconsistent with natural selection. Correlational analyses revealed that participants who demonstrated transformational reasoning were as internally consistent as participants who demonstrated an understanding of natural selection, with the exception of one group of participants who appeared to have assimilated two heuristics--"survival of the fittest" and "acquired traits are not inherited"--into an otherwise transformational framework. These findings suggest that the widespread and early-developing tendency to essentialize biological kinds precludes students from conceptualizing species as populations of individuals differentially affected by the environment.

Adaptation, Physiological↗

PubMed2005

The evolution of the neocortex in mammals: how is phenotypic diversity generated?

Evolution of the mammalian neocortex is difficult to examine directly. For this reason, comparative studies and developmental studies are the best way of gaining insight into the evolutionary process. Comparative studies indicate that neocortical evolution is constrained, and that the types of systems-level modifications made to the neocortex are limited. Developmental studies of gene expression suggest that genetic contingencies set up aspects of cortical organization and connectivity, and that the complex spatial and temporal interactions of genes constrain development and evolution. Although genes obviously contribute to phenotypic variability, variability can also be achieved through alterations in the sensory receptor arrays, or changes in sensory driven activity. The intracellular mechanisms that enable phenotypic variability might evolve, but often the phenotypic characteristic in question is context-dependent.

Animals↗

PubMed2005

Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design.

Many research groups successfully rely on whole-gene random mutagenesis and recombination approaches for the directed evolution of enzymes. Recent advances in enzyme engineering have used a combination of these random methods of directed evolution with elements of rational enzyme modification to successfully by-pass certain limitations of both directed evolution and rational design. Semi-rational approaches that target multiple, specific residues to mutate on the basis of prior structural or functional knowledge create 'smart' libraries that are more likely to yield positive results. Efficient sampling of mutations likely to affect enzyme function has been conducted both experimentally and, on a much greater scale, computationally, with remarkable improvements in substrate selectivity and specificity and in the de novo design of enzyme activities within scaffolds of known structure.

Combinatorial Chemistry Techniques↗

PubMed2005

Social cognitive evolution in captive foxes is a correlated by-product of experimental domestication.

Dogs have an unusual ability for reading human communicative gestures (e.g., pointing) in comparison to either nonhuman primates (including chimpanzees) or wolves . Although this unusual communicative ability seems to have evolved during domestication , it is unclear whether this evolution occurred as a result of direct selection for this ability, as previously hypothesized , or as a correlated by-product of selection against fear and aggression toward humans--as is the case with a number of morphological and physiological changes associated with domestication . We show here that fox kits from an experimental population selectively bred over 45 years to approach humans fearlessly and nonaggressively (i.e., experimentally domesticated) are not only as skillful as dog puppies in using human gestures but are also more skilled than fox kits from a second, control population not bred for tame behavior (critically, neither population of foxes was ever bred or tested for their ability to use human gestures) . These results suggest that sociocognitive evolution has occurred in the experimental foxes, and possibly domestic dogs, as a correlated by-product of selection on systems mediating fear and aggression, and it is likely the observed social cognitive evolution did not require direct selection for improved social cognitive ability.

Animals↗

PubMed2006

Experimental evolution of mating discrimination in budding yeast.

Assortative mating, when individuals of similar phenotypes mate, likely plays a key role in preventing gene flow during speciation. Reinforcement occurs when two previously geographically separated (allopatric) groups meet after having evolved partial postzygotic isolation; they are selected to evolve or enhance assortative mating to prevent costly intergroup matings that produce only maladaptive or sterile hybrids. Studies in Drosophila have shown that the genetic architectures of mating discrimination could differ significantly with or without reinforcement, suggesting that the evolution of assortative mating may be more complicated than expected. To study the evolution of assortative mating, we evolved mating discrimination in populations of the budding yeast, Saccharomyces cerevisiae. After 36 cycles of selection, these cells are five times more likely to mate with each other than to their ancestors, despite detectable one-way gene flow between the selected and reference populations. Several individual cultures evolved mating discrimination by changing their mating kinetics, with some mating more rapidly and others more slowly than the ancestral population. Genetic analysis indicates that multiple mutations have accumulated to produce the altered mating preference. Our results show that subtle details of mating behavior can play an important role in the evolution of reproductive isolation.

Biological Evolution↗

PubMed2006

Convergent evolution of receptors for protein import into mitochondria.

BACKGROUND: Mitochondria evolved from intracellular bacterial symbionts. Establishing mitochondria as organelles required a molecular machine to import proteins across the mitochondrial outer membrane. This machinery, the TOM complex, is composed of at least seven component parts, and its creation and evolution represented a sizeable challenge. Although there is good evidence that a core TOM complex, composed of three subunits, was established in the protomitochondria, we suggest that the receptor component of the TOM complex arose later in the evolution of this machine. RESULTS: We have solved by nuclear magnetic resonance the structure of the presequence binding receptor from the TOM complex of the plant Arabidopsis thaliana. The protein fold suggests that this protein, AtTom20, belongs to the tetratricopeptide repeat (TPR) superfamily, but it is unusual in that it contains insertions lengthening the helices of each TPR motif. Peptide titrations map the presequence binding site to a groove of the concave surface of the receptor. In vitro functional assays and peptide titrations suggest that the plant Tom20 is functionally equivalent to fungal and animal Tom20s. CONCLUSIONS: Comparison of the sequence and structure of Tom20 from plants and animals suggests that these two presequence binding receptors evolved from two distinct ancestral genes following the split of the animal and plant lineages. The need to bind equivalent mitochondrial targeting sequences and to make similar interactions within an equivalent protein translocation machine has driven the convergent evolution of two distinct proteins to a common structure and function.

Amino Acid Sequence↗

PubMed2005

Using models of nucleotide evolution to build phylogenetic trees.

Molecular phylogenetics and its applications are popular and useful tools for making comparative investigations in genetics; however, estimating phylogenetic trees is not always straightforward. Some phylogenetic estimators use an explicit model of nucleotide evolution to estimate evolutionary parameters such as branch lengths and tree topology. There are many models to choose from, and use of the optimal model for a particular data set is important to avoid a loss of power and accuracy in phylogenetic estimations. Here, we review some molecular evolutionary forces and the parameters included in some common models of evolution used to interpret resulting patterns of molecular variation. We present some statistical methods of selecting a particular model of nucleotide evolution, and provide an empirical example of model selection. Statistical model selection strikes a balance between the bias introduced by some models and the increased variance of parameter estimates that results from using other models.

Animals↗

PubMed2004

Evolution of the serine beta-lactamases: past, present and future.

We present a protein structure-based phylogeny of Classes A, C and D of the serine beta-lactamases, and a new, detailed, sequence-based phylogeny of the Class A beta-lactamases. In addition, we discuss the historical evolution of Classes C and D. The evolutionary histories of all three classes indicate that the serine beta-lactamases are ancient enzymes, originating over two billion years ago, and that some have been on plasmids for millions of years. We also discuss the recent, antibiotic-era, evolution of the serine beta-lactamases in response to the clinical use of beta-lactam antibiotics. We also discuss a method that is being used to predict the future evolution of beta-lactamases in response to selection with new drugs.

Anti-Bacterial Agents↗

PubMed2004

Evolution of cyanobacterial and plant phytochromes.

Phytochromes are broadly distributed photochromic photoreceptors that are most sensitive in the red and far-red region of the visible spectrum. Three different bilins can be used as chromophores: plant phytochromes incorporate phytochromobilin, while phycocyanobilin serves as a chromophore of some cyanobacterial phytochromes, whereas all other phytochromes, including cyanobacterial orthologs incorporate biliverdin. During the evolution of plant and cyanobacterial phytochromes, the chromophore binding site has changed from a cysteine close to the N-terminus of the protein, the biliverdin attachment site, to a cysteine which lies within the so-called GAF domain and serves as phytochromobilin or phycocyanobilin attachment site. Since phylogenetic analyses imply that plant phytochromes are not direct successors of cyanobacterial phytochromes, chromophore exchange and the switch of the chromophore binding site has probably occurred at least twice in evolution. This may be regarded as an example for convergent evolution at the molecular level.

Cyanobacteria↗

PubMed2003

Adaptive evolution of genes and gene families.

The huge influx of genomic sequence and new statistical methods is making the discovery of genes subjected to adaptive evolution increasingly common. The use of comparative genomics to identify adaptive evolution is resulting in predictions of functionally important genes and gene regions. However, the selective pressure driving the adaptive evolution of most genes remains mysterious.

Adaptation, Physiological↗

PubMed2005

A 21st century view of evolution: genome system architecture, repetitive DNA, and natural genetic engineering.

The last 50 years of molecular genetics have produced an abundance of new discoveries and data that make it useful to revisit some basic concepts and assumptions in our thinking about genomes and evolution. Chief among these observations are the complex modularity of genome organization, the biological ubiquity of mobile and repetitive DNA sequences, and the fundamental importance of DNA rearrangements in the evolution of sequenced genomes. This review will take a broad overview of these developments and suggest some new ways of thinking about genomes as sophisticated informatic storage systems and about evolution as a systems engineering process.

Animals↗

PubMed2005

MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants.

MIKC-type proteins represent a class of MADS-domain transcription factors and are defined by a unique domain structure: in addition to the highly conserved DNA-binding MADS-domain, they have three other domains ('I', 'K' and 'C'), with the keratin-like K-domain being the most highly conserved and characteristic one. The number and functional diversity of MIKC-type proteins increased considerably during land plant evolution, culminating in higher flowering plants, where they dominate the control of reproductive development from early to late stages. We wonder how one special class of proteins became important in the control of essentially all stages of a morphogenetic process. All MADS-domain proteins appear to bind to DNA as homo- or heterodimers and may function as part of ternary transcription factor complexes involving non-MADS-domain proteins. Only MIKC-type proteins, however, generate complex intrafamily interaction networks. These are based on the special potential of MIKC-type proteins to form complexes involving more than two homologous proteins constituting transcriptional regulators. We speculate that the potential to form heteromultimers of homologous proteins was achieved by the acquisition of the K-domain during evolution. There is emerging evidence that organismal complexity arises from progressively more elaborate regulation of gene expression. We hypothesize that combinatorial multimer formation of MIKC-type MADS-domain proteins facilitated an unusually efficient and rapid functional diversification based on gene duplication, sequence divergence and fixation. This 'networking' may have enabled a more sophisticated transcriptional control of target genes which was recruited for controlling increasingly complex and diverse developmental pathways during the rapid origin and diversification of plant reproductive structures. Therefore, MIKC-type proteins may owe their evolutionary 'success' and present-day developmental importance in part to their modular domain structure. Investigating the evolution of MIKC-type genes may thus help to better understand origin and diversification of gene regulatory networks.

Amino Acid Sequence↗

PubMed2005

The roles of positive and negative selection in the molecular evolution of insect endosymbionts.

The evolutionary rate acceleration observed in most endosymbiotic bacteria may be explained by higher mutation rates, changes in selective pressure, and increased fixation of deleterious mutations by genetic drift. Here, we explore the forces influencing molecular evolution in Blochmannia, an obligate endosymbiont of Camponotus and related ant genera. Our goals were to compare rates of sequence evolution in Blochmannia with related bacteria, to explore variation in the strength and efficacy of negative (purifying) selection, and to evaluate the effect of positive selection. For six Blochmannia pairs, plus Buchnera and related enterobacteria, estimates of sequence divergence at four genes confirm faster rates of synonymous evolution in the ant mutualist. This conclusion is based on higher dS between Blochmannia lineages despite their more recent divergence. Likewise, generally higher dN in Blochmannia indicates faster rates of nonsynonymous substitution in this group. One exception is the groEL gene, for which lower dN and dN/dS compared to Buchnera indicate exceptionally strong negative selection in Blochmannia. In addition, we explored evidence for positive selection in Blochmannia using both site-and lineage-based maximum likelihood models. These approaches confirmed heterogeneity of dN/dS among codon sites and revealed significant variation in dN/dS across Blochmannia lineages for three genes. Lineage variation affected genes independently, with no evidence of parallel changes in dN/dS across genes along a given branch. Our data also reveal instances of dN/dS greater than one; however, we do not interpret these large dN/dS ratios as evidence for positive selection. In sum, while drift may contribute to an overall rate acceleration at nonsynonymous sites in Blochmannia, variable selective pressures best explain the apparent gene-specific changes in dN/dS across lineages of this ant mutualist. In the course of this study, we reanalyzed variation at Buchnera groEL and found no evidence of positive selection that was previously reported.

Animals↗

PubMed2005

Evolution of metabolic networks by gain and loss of enzymatic reaction in eukaryotes.

The metabolic network is composed of enzymatic reactions (ERs) in which one or more enzymes catalyze the reaction of pertinent substrates. Since metabolism is a basal system for maintaining life of all organisms, any change in the metabolic networks must greatly affect organismic evolution. The aim of this study is to examine how often gains and losses of ER have occurred during the evolution of metabolic networks in eukaryotes and how these evolutionary events have affected phenotypic traits of organisms. In this study, we conducted comparative studies of 751 ERs in the metabolic networks of 6 eukaryotic species whose complete genome sequences were determined. As a result, we found that a total of 804 gains and losses of ERs had occurred in the evolutionary diversification of metabolic networks in different lineages. Moreover, the vertebrate lineage, after the separation from Drosophila melanogaster, showed a remarkable increase in the number of ER gains compared with ER losses. In particular, 41% of the ER gains were predominantly involved with lipids and complex lipid metabolism. Because some products of these two metabolisms function as hormones, we concluded that the ER gain of these two metabolisms accelerated the development of hormonal signal transduction for the elaborate regulation of physiological systems during vertebrate evolution.

Amino Acid Sequence↗

PubMed2006

Molecular evolution of the brain size regulator genes CDK5RAP2 and CENPJ.

Primary microcephaly is a developmental defect of the brain characterized by severely reduced brain size but an absence of other overt abnormalities. Mutations in several loci have been linked to primary microcephaly. The underlying genes for two of these were recently identified as CDK5RAP2 and CENPJ. Here, we focus on CDK5RAP2 and show that the protein evolutionary rate of this gene is significantly higher in primates than rodents or carnivores. We further show that the evolutionary rate within primates is particularly high in the human and chimpanzee terminal branches. Thus, the pattern of molecular evolution seen in CDK5RAP2 appears to parallel, at least approximately, that seen in two other previously identified primary microcephaly genes, microcephalin and ASPM. We also briefly discuss CENPJ, which similarly exhibits higher rate of protein evolution in primates as compared to rodents and carnivores. Together, the evolutionary patterns of all four presently known primary microcephaly genes are consistent with the hypothesis that genes regulating brain size during development might also play a role in brain evolution in primates and especially humans.

Animals↗

PubMed2006

Does lack of recombination enhance asymmetric evolution among duplicate genes? Insights from the Drosophila melanogaster genome.

Gene duplication has different outcomes: pseudogenization (death of one of the two copies), gene amplification (both copies remain the same), sub-functionalization (both copies are required to perform the ancestral function) and neo-functionalization (one copy acquires a new function). Asymmetric evolution (one copy evolves faster than the other) is usually seen as a signature of neo-functionalization. However, it has been proposed that sub-functionalization could also generate asymmetric evolution among duplicate genes when they experience different local recombination rates. Indeed, the low recombination copy is expected to evolve faster because of Hill-Robertson effects. Here we tested this idea with about 100 pairs of young duplicates from the Drosophila melanogaster genome. Looking only at young duplicates allowed us to compare recombination rates and evolutionary rates on a similar time-scale contrary to previous work. We found that dispersed pairs tend to evolve more asymmetrically than tandem ones. Among dispersed copies, the low recombination copy tends to be the fast-evolving one. We also tested the possibility that all this was explained by a confounding factor (expression level) but found no evidence for it. In conclusion, our results do support the idea that asymmetric evolution among duplicates is enhanced by restricted recombination. However, further work is needed to clearly distinguish between sub-functionalization and neo-functionalization for the asymmetrically-evolving duplicate pairs that we found.

Animals↗

PubMed2006

Radical amino acid change versus positive selection in the evolution of viral envelope proteins.

To detect positive selection in protein-coding sequence evolution, the ratio of the nonsynonymous to synonymous substitution rate (K(A)/K(S)) is commonly used. When this ratio is higher than 1, positive selection on nonsynonymous changes is considered to have occurred. However, the question of what kinds of amino acid change are likely to be involved in positive selection has not been well studied, though intuitively it seems that radical changes frequently occur in positively selected changes. To address this question, we examined chemically radical and conservative replacements in the evolution of hepatitis C virus (HCV) protein sequences. In the envelope region, 34 positively and 440 negatively selected sites were identified by the K(A)/K(S) ratio. Radical and conservative changes were compared between the two types of selected sites using two methods. First, the numbers of radical and conservative replacements were counted at the positively and negatively selected sites according to three kinds of chemical classifications. In all three classifications, the resulting ratios of the two numbers were not statistically different for the two types of selected sites (P>0.05). Second, the distribution of chemical changes was compared between the two types of selected sites using two kinds of chemical distances. The distributions of the two chemical distances were not statistically different for the two types of selected sites (P>0.05). These results indicate that the ratio of chemically radical and conservative changes is similar for positively and negatively selected sites in the envelope protein of HCV or, in other words, there is no correlation between radical change and positive selection in the evolution of this protein.

Amino Acid Substitution↗

PubMed2006

The evolution of retrotransposon regulatory regions and its consequences on the Drosophila melanogaster and Homo sapiens host genomes.

It has now been established that transposable elements (TEs) make up a variable, but significant proportion of the genomes of all organisms, from Bacteria to Vertebrates. However, in addition to their quantitative importance, there is increasing evidence that TEs also play a functional role within the genome. In particular, TE regulatory regions can be viewed as a large pool of potential promoter sequences for host genes. Studying the evolution of regulatory region of TEs in different genomic contexts is therefore a fundamental aspect of understanding how a genome works. In this paper, we first briefly describe what is currently known about the regulation of TE copy number and activity in genomes, and then focus on TE regulatory regions and their evolution. We restrict ourselves to retrotransposons, which are the most abundant class of eukaryotic TEs, and analyze their evolution and the subsequent consequences for host genomes. Particular attention is paid to much-studied representatives of the Vertebrates and Invertebrates, Homo sapiens and Drosophila melanogaster, respectively, for which high quality sequenced genomes are available.

Animals↗