A Test of Amino Acid Reversibility

In studies of molecular evolution, the assumption that protein evolution is reversible has often been made, but rarely tested. Here we use a large set of orthologous murid protein coding sequences to perform a simple test of reversibility, and find no evidence to reject the assumption of reversibility in protein evolution. Received: 10 October 2000 / Accepted: 18 January 2001     

Cultural evolution: implications for understanding the human language faculty and its evolution

Human language is unique among the communication systems of the natural world: it is socially learned and, as a consequence of its recursively compositional structure, offers open-ended communicative potential. The structure of this communication system can be explained as a consequence of the evolution of the human biological capacity for language or the cultural evolution of language itself. We argue, supported by a formal model, that an explanatory account that involves some role for cultural evolution has profound implications for our understanding of the biological evolution of the language faculty: under a number of reasonable scenarios, cultural evolution can shield the language faculty from selection, such that strongly constraining language-specific learning biases are unlikely to evolve. We therefore argue that language is best seen as a consequence of cultural evolution in populations with a weak and/or domain-general language faculty.     

Adaptive gene expression divergence inferred from population genomics

Detailed studies of individual genes have shown that gene expression divergence often results from adaptive evolution of regulatory sequence. Genome-wide analyses, however, have yet to unite patterns of gene expression with polymorphism and divergence to infer population genetic mechanisms underlying expression evolution. Here, we combined genomic expression data—analyzed in a phylogenetic context—with whole genome light-shotgun sequence data from six Drosophila simulans lines and reference sequences from D. melanogaster and D. yakuba. These data allowed us to use molecular population genetics to test for neutral versus adaptive gene expression divergence on a genomic scale. We identified recent and recurrent adaptive evolution along the D. simulans lineage by contrasting sequence polymorphism within D. simulans to divergence from D. melanogaster and D. yakuba. Genes that evolved higher levels of expression in D. simulans have experienced adaptive evolution of the associated 3′ flanking and amino acid sequence. Concomitantly, these genes are also decelerating in their rates of protein evolution, which is in agreement with the finding that highly expressed genes evolve slowly. Interestingly, adaptive evolution in 5′ cis-regulatory regions did not correspond strongly with expression evolution. Our results provide a genomic view of the intimate link between selection acting on a phenotype and associated genic evolution.     

Losing Sight of Regressive Evolution

When we teach evolution to our students, we tend to focus on “constructive” evolution, the processes which lead to the development of novel or modified structures. Most biology students are familiar with the subjects of finches’ beaks, giraffes’ necks, and hair in mammals. Of course, there is nothing inherently wrong with a constructivist approach to teaching evolution, but if it is our only focus, we may overlook the flip side of the coin. By the flip side of the coin, of course, we are referring to regressive evolution: the loss or degeneration of a trait. Regressive evolution does not often make its way into biology textbooks, but it is of great relevance nonetheless. In all likelihood, when a new trait evolves or an existing one is modified, something is sacrificed in return. In order to develop a flipper, a marine mammal must sacrifice individual digits. You may be familiar with one or more of the following familiar characters lost through regressive evolution: teeth in birds, scales in mammals, and tails in higher primates. For aficionados of cave biology like us, one of the most interesting examples of regressive evolution concerns cave fish: Why do cave fish lose their eyes?     

Next-generation sequencing and genome evolution in allopolyploids

?Premise of the study: Hybridization and polyploidization (allopolyploidy) are ubiquitous in the evolution of plants, but tracing the origins and subsequent evolution of the constituent genomes of allopolyploids has been challenging. Genome doubling greatly complicates genetic analyses, and this has long hindered investigation in that most allopolyploid species are "nonmodel" organisms. However, recent advances in sequencing and genomics technologies now provide unprecedented opportunities to analyze numerous genetic markers in multiple individuals in any organism. ?Methods: Here we review the application of next-generation sequencing technologies to the study of three aspects of allopolyploid genome evolution: duplicated gene loss and expression in two recently formed Tragopogon allopolyploids, intergenomic interactions and chromosomal evolution in Tragopogon miscellus, and repetitive DNA evolution in Nicotiana allopolyploids. ?Key results: For the first time, we can explore on a genomic scale the evolutionary processes that are ongoing in natural allopolyploids and not be restricted to well-studied crops and genetic models. ?Conclusions: These approaches can be easily and inexpensively applied to many other plant species-making any evolutionarily provocative system a new "model" system.     

Surfactant-Induced hydrogen production in cyanobacteria

Addition of Tween 85 to aqueous suspensions of Anabaena variabilis induced photosynthetic evolution of hydrogen over a time span of several weeks: As much as 148 nmol H(2)/h . mg dry weight was produced in the first week by a suspension containing 4.2 mg dry weight of cells and 77 mM Tween 85. The chemical structure of Tween 85 was a necessary prerequisite for inducing hydrogen production, as compounds such as Tween 20, 60, and 80 had a quite different effect. There was a coupling between photosynthetic oxygen evolution and hydrogen evolution: Hydrogen evolution started to be effective only when oxygen evolution subdued. The presence of heterocysts in A. variabilis was also required for the Tween-induced hydrogen production. Based on these observations, possible mechanisms for the photosynthetic effect of Tween 85 are advanced and discussed. (c) 1993 John Wiley & Sons, Inc.     

ProtTest: selection of best-fit models of protein evolution

SUMMARY: Using an appropriate model of amino acid replacement is very important for the study of protein evolution and phylogenetic inference. We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment. AVAILABILITY: ProtTest is available under the GNU license from http://darwin.uvigo.es     

人14-3-3蛋白家族的生物信息学分析

目的:分析人14-3-3蛋白家族的同源性及分子进化关系。方法:利用已公布的人基因组数据库,采用BLASTN程序检索人14-3-3蛋白家族各成员的编码基因和假基因,并利用DNAMAN软件进行序列联配,绘制其分子进化树。结果:该家族半数成员具有多个假基因序列,为返转座类型假基因。进化分析表明该家族有共同的祖先,可归为3个亚类。结论:人14-3-3蛋白家族每个成员长期进化所形成的多样性提示其功能具有独特性。     

Why Did a Female Penis Evolve in a Small Group of Cave Insects?

The evolution of a female penis is an extremely rare event and is only known to have occurred in a tribe of small cave insects, Sensitibillini (Psocodea: Trogiomorpha: Prionoglarididae). The female penis, which is protrudable and inserted into the male vagina‐like cavity during copulation to receive semen, is thought to have evolved independently twice in this tribe, in the Brazilian Neotrogla and the African Afrotrogla. These findings strongly suggest that there are some factors unique to Sensitibillini that have facilitated female penis evolution. Here, several hypothetical factors are presented that may have enabled the evolution of the female penis in Sensitibillini. The female–female competition for nutritious semen, the oligotrophic environment, and the twin insemination slots with switching valve are considered to be the driving factors for female penis evolution. Additionally, the following factors are considered responsible for relaxing the constraint against female penis evolution: preexistence of the female‐above mating position, the elongated duct connecting the female pre‐penis with the sperm storage organ, and the small male genital cavity accepting the female genital tubercle bearing the opening of this duct. Understanding the factors enabling female penis evolution may also shed light on the evolution of the male penis.     

Tempo, mode and phylogenetic associations of relative embryo size evolution in angiosperms

Relative embryo size (E : S, the ratio of embryo to seed) is a key trait related to germination ecology and seed plant evolution. A small, underdeveloped embryo is a primitive feature of angiosperms, which has led to the hypothesis that an evolutionary trend towards increasing E : S has occurred. Here, I examine first the tempo and mode of E : S evolution in angiosperms; then I test for phylogenetic associations of E : S with traits hypothetically related to anagenetic (germination time) and cladogenetic (number of species per family and differential speciation) change, and finally I test the existence of a directional increasing trend in E : S. The analysis of the evolutionary tempo suggests that E : S changed very fast early in evolutionary time and remained stable later, which is consistent with early radiations and fits well with the history of angiosperms consisting of rapid spread associated with great diversification rates soon after their origin. E : S evolution in angiosperms has not followed a punctuational mode of evolution but a scaled-gradualism evolution in which stasis has occurred in longer branches of the phylogeny. An evolutionary trend towards increasing E : S has not been actively driven by anagenesis nor cladogenesis, although large E : S is associated with high levels of diversification (i.e. number of species per family). This rapid ecological diversification occurring in the early radiation probably produced an increasing phenotypic variance in the E : S. Because the ancestral embryo was so small, an increase in variance might have produced a passive trend towards the only direction allowed for the ancestral embryo to evolve. Thus, a passive diffusion away from a lower bound may explain the average increase in E : S.     

Is the "small world" effect relevant to evolution?

Mutations and selection are the driving forces of biological evolution. We model here the simplest case: an evolving population of asexual organisms. We consider two kinds of mutations: point mutations, corresponding to local displacements in the genotypic space, and all the other genotypic rearrangements, equivalent to long-range jumps. We show that a small-world effect is present in evolution: even a small fraction of quenched long-range jumps makes the results indistinguishable from those obtained by assuming all mutations equiprobable. We apply this result to the evolution of a population on a smooth fitness landscape, showing that the equilibrium distribution is a Boltzmann one, in which the fitness plays the role of an energy, and mutations that of a temperature.     

Large-scale analysis of microRNA evolution

ABSTRACT: BACKGROUND: In animals, microRNAs (miRNA) are important genetic regulators. Animal miRNAs appear to have expanded in conjunction with an escalation in complexity during early bilaterian evolution. Their small size and high-degree of similarity makes them challenging for phylogenetic approaches. Furthermore, genomic locations encoding miRNAs are not clearly defined in many species. A number of studies have looked at the evolution of individual miRNA families. However, we currently lack resources for large-scale analysis of miRNA evolution. RESULTS: We addressed some of these issues in order to analyse the evolution of miRNAs. We perform syntenic and phylogenetic analysis for miRNAs from 80 animal species. We present synteny maps, phylogenies and functional data for miRNAs across these species. These data represent the basis of our analyses and also act as a resource for the community. CONCLUSIONS: We use these data to explore the distribution of miRNAs across phylogenetic space, characterise their birth and death, and examine functional relationships between miRNAs and other genes. These data confirm a number of previously reported findings on a larger scale and also offer novel insights into the evolution of the miRNA repertoire in animals, and it's genomic organization.     

Mutation-biased adaptation in a protein NK model

Evolutionary trends responsible for systematic differences in genome and proteome composition have been attributed to GC:AT mutation bias in the context of neutral evolution or to selection acting on genome composition. A possibility that has been ignored, presumably because it is part of neither the Modern Synthesis nor the Neutral Theory, is that mutation may impose a directional bias on adaptation. This possibility is explored here with simulations of the effect of a GC:AT bias on amino acid composition during adaptive walks on an abstract protein fitness landscape called an "NK" model. The results indicate that adaptation does not preclude mutation-biased evolution. In the complete absence of neutral evolution, a modest GC:AT bias of realistic magnitude can displace the trajectory of adaptation in a mutationally favored direction, to such a degree that amino acid composition is biased substantially and persistently. Thus, mutational explanations for evolved patterns need not presuppose neutral evolution.     

We Know in Part: James McCosh on Evolution and Christian Faith

James McCosh (1811–1894), president of Princeton College from 1868 to 1888, played a significant role in the American reception of evolution in the late 1800s – he was one of the more prominent clergyman to assuage the public’s fears of evolution while incorporating evolution into a conservative Christian worldview. McCosh was a prolific writer, whose books document his intellectual journey from hostility to acceptance of evolution. Three things will stand out in this overview that have not been emphasized in detail in other works: (1) James McCosh’s perspective on evolution dramatically changed over time; (2) McCosh’s motivations for engaging in the evolution-religion debate serve to clear up confusion regarding McCosh’s final position on evolution; and (3) the theological and philosophical basis for McCosh’s acceptance of evolution was established while McCosh was still hostile to evolution. His theological background therefore ‘pre-adapted’ him for evolution, and he was able to preach theology and evolution without substantially altering his theology.     

Effect of temperature on h(2) evolution and acetylene reduction in pea nodules and in isolated bacteroids

Nitrogenase (EC 1.7.99.2) activity in pea (Pisum savitum) nodules formed after infection with Rhizobium leguminosarum (lacking uptake hydrogenase) was measured as acetylene reduction, H₂ evolution in air and H₂ evolution in Ar:O₂. With detached roots the relative efficiency, calculated from acetylene reduction, showed a decrease (from 55 to below 0%) with increasing temperature. With excised nodules and isolated bacteroids similar results were obtained. However, the relative efficiency calculated from H₂ evolution in Ar:O₂ was unaffected by temperature. Measurements on both excised nodules and isolated bacteroids showed a marked difference between acetylene reduction and H₂ evolution in Ar:O₂ with increased temperature, indicating that either acetylene reduction or H₂ evolution in Ar:O₂ are inadequate measures of nitrogenase activity at higher temperature.     

Cognitive Apartheid: On the Manner in Which High School Students Understand Evolution without Believing in Evolution

High school science students are often unwilling to learn about evolution due to a perceived conflict with their religious beliefs. Other students are able to understand evolution despite the fact that they do not believe in evolution. According to Cobern (Sci Educ 80:579?C610, 1996), students can wall off that which is believed from that which is not believed in a process he called cognitive apartheid. A mixed-methods study was conducted to determine the extent to which understanding of evolution differed among high school Advanced Placement science students who did and did not believe in evolution. Two students who demonstrate a sophisticated understanding of evolution despite their admonition that they do not believe in evolution were then interviewed. Eight themes emerged from the interview that provide insight into the views of students learning of evolution despite the fact that they do not believe in evolution. Based on these themes, several implications for the teaching of evolution are presented.     

CORRELATED EVOLUTION OF MIGRATION AND SEXUAL DICHROMATISM IN THE NEW WORLD ORIOLES (ICTERUS)

The evolution of sexual dimorphism has long been attributed to sexual selection, specifically as it would drive repeated gains of elaborate male traits. In contrast to this pattern, New World oriole species all exhibit elaborate male plumage, and the repeated gains of sexual dichromatism observed in the genus are due to losses of female elaboration. Interestingly, most sexually dichromatic orioles belong to migratory or temperate‐breeding clades. Using character scoring and ancestral state reconstructions from two recent studies in Icterus, we tested a hypothesis of correlated evolution between migration and sexual dichromatism. We employed two discrete phylogenetic comparative approaches: the concentrated changes test and Pagel's discrete likelihood test. Our results show that the evolution of these traits is significantly correlated (CCT: uncorrected P < 0.05; ML: LRT = 12.470, P < 0.005). Indeed, our best model of character evolution suggests that gains of sexual dichromatism are 23 times more likely to occur in migratory taxa. This study demonstrates that a life‐history trait with no direct relationship with sexual selection has a strong influence on the evolution of sexual dichromatism. We recommend that researchers further investigate the role of selection on elaborate female traits in the evolution of sexual dimorphism.     

Evolutionary Medicine: A Key to Introducing Evolution

Science teachers can use examples and concepts from evolutionary medicine to teach the three concepts central to evolution: common descent, the processes or mechanisms of evolution, and the patterns produced by descent with modification. To integrate medicine into common ancestry, consider how the evolutionary past of our (or any) species affects disease susceptibility. That humans are bipedal has produced substantial changes in our musculoskeletal system, as well as causing problems for childbirth. Mechanisms such as natural selection are well exemplified in evolutionary medicine, as both disease-causing organism and their targets adapt to one another. Teachers often use examples such as antibiotic resistance to teach natural selection: it takes little alteration of the lesson plan to make explicit that evolution is key to understanding the principles involved. Finally, the pattern of evolution can be illustrated through evolutionary medicine because organisms sharing closer ancestry also share greater susceptibility to the same disease-causing organisms. Teaching evolution using examples from evolutionary medicine can make evolution more interesting and relevant to students, and quite probably, more acceptable as a valid science.